To In: Instrumentation Life Sciences

Introduction to
Instrumentation
in Life Sciences
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Prakash S. Bisen
Anjana Sharma
Introduction to
Instrumentation
in Life Sciences
Introduction to
Instrumentation
in Life Sciences
Prakash S. Bisen
Anjana Sharma
Boca Raton London New York
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Contents
Preface.............................................................................................................................................. xv
About the Book...............................................................................................................................xvii
Acknowledgments............................................................................................................................xix
Chapter 1 Microscopy.................................................................................................................... 1
1.1 Introduction........................................................................................................ 1
1.2 Magnification, Resolution, and Contrast............................................................1
1.3 Light (Bright Field) Microscopy........................................................................3
1.3.1 Resolution..............................................................................................5
1.3.2 Contrast of a Microscope...................................................................... 7
1.3.3 Uses of the Light (Bright Field) Microscope........................................ 9
1.3.4 Care of the Microscope.........................................................................9
1.4 Dark Field Microscope..................................................................................... 11
1.5 Phase Contrast Microscope.............................................................................. 12
1.6 Interference Microscope................................................................................... 13
1.7 UV and Fluorescence Microscopes.................................................................. 13
1.7.1 Uses of UV and Fluorescence Microscopes........................................ 15
1.8 Electron Microscopy........................................................................................ 15
1.8.1 Operation of TEM............................................................................... 16
1.8.1.1 Parts..................................................................................... 16
1.8.1.2 Sample Preparation.............................................................. 16
1.8.1.3 Operational Problems.......................................................... 18
1.8.2 Disadvantages of TEM........................................................................ 19
1.8.3 Operation of the SEM......................................................................... 19
1.8.3.1 Principle............................................................................... 19
1.8.3.2 Parts..................................................................................... 19
1.8.3.3 Sample Preparation..............................................................20
1.8.4 Advantages and Disadvantages of SEM over TEM............................20
1.9 Tunneling Electron Microscopy.......................................................................20
1.10 Confocal Microscopy....................................................................................... 21
1.10.1 Modern Confocal Microscopes........................................................... 22
1.11 Techniques in Microscopy................................................................................24
1.11.1 Hanging Drop Technique....................................................................24
1.11.2 Use of the Hemocytometer..................................................................24
1.11.3 Ocular Meter and Stage Micrometer for Micrometry.........................25
1.12 Electron Microscopy........................................................................................26
1.12.1 Freeze Etching and Metal Shadowing................................................26
Suggested Reading...................................................................................................... 36
Important Links........................................................................................................... 36
Chapter 2 Micrometry ................................................................................................................ 37

2.1 Introduction...................................................................................................... 37
2.2 Structure of an Ocular Micrometer.................................................................. 37
2.3 Conjugate Image-Forming Focal Planes.......................................................... 37
v
vi Contents
2.4 Eyepiece Designs.............................................................................................. 39

2.4.1 Types of Eyepieces.............................................................................. 39
2.5 Stage Micrometer.............................................................................................40
2.5.1 Counting Chambers Stage Micrometer...............................................40
2.6 Filar Eyepiece Micrometer............................................................................... 41
2.7 Principle of Filar Eyepiece Micrometer........................................................... 42
2.8 Working............................................................................................................ 42
2.8.1 Components of the Ocular Micrometer.............................................. 42
Suggested Reading......................................................................................................44
Important Links...........................................................................................................44
Chapter 3 Electrochemical Techniques....................................................................................... 45

3.1 Introduction...................................................................................................... 45
3.2 Structure of a pH Meter.................................................................................... 45
3.2.1 Glass Membrane Electrodes................................................................ 45
3.2.2 Reference Electrode............................................................................46
3.3 Principles.......................................................................................................... 47
3.4 Factors Limiting the Accuracy of pH Measurements...................................... 48
3.5 Measurement of pH.......................................................................................... 49
3.6 Working............................................................................................................ 50
3.6.1 Potentiometric Method of pH Measurement....................................... 50
3.6.2 Reagents Used in the Potentiometric Method of
pH Measurement................................................................................. 50
3.6.2.1 Calibration of the Electrode System against
Standard Buffer Solutions of Known pH............................. 50
3.6.2.2 pH 4 Buffer Solution............................................................ 50
3.6.2.3 pH 7 Buffer Solution............................................................ 50
3.6.2.4 pH 9.2 Buffer Solution......................................................... 50
3.7 Procedure for Measuring pH Using a pH Meter.............................................. 50
3.7.1 Modified Glass and Solid-State Membrane Electrodes...................... 51
3.7.2 Solid-State Membrane Electrodes....................................................... 51
3.7.3 Storage Conditions for Glass Probes................................................... 51
3.8 Cleaning and Troubleshooting of Glass Probes............................................... 52
3.9 Application of pH Measurements..................................................................... 53
3.10 Oxygen Electrode............................................................................................. 53
3.10.1 Calibration of the Oxygen Electrode................................................... 55
3.10.2 Applications of the Oxygen Electrode................................................ 56
Suggested Reading...................................................................................................... 59
Important Links........................................................................................................... 59
Chapter 4 Chromatography.......................................................................................................... 61
4.1 Introduction...................................................................................................... 61
4.2 General Principles............................................................................................ 61
4.3 Column Chromatography................................................................................. 62
4.3.1 Chromatography Columns.................................................................. 62
4.3.2 Stationary Phases................................................................................ 62
4.3.3 Packing of Columns............................................................................64
4.3.4 Application of Sample.........................................................................64
4.3.5 Column Development.......................................................................... 65
4.3.6 Fraction Collection and Analysis........................................................66
Contents vii
4.4 Paper Chromatography and Thin-Layer

Chromatography............................................................................................... 67
4.4.1 Principles............................................................................................. 67
4.4.2 Types of Paper..................................................................................... 68
4.4.3 Thin Layer........................................................................................... 68
4.4.4 Sample Application............................................................................. 68
4.4.5 Development........................................................................................ 68
4.4.6 Component Detection.......................................................................... 70
4.4.7 High-Performance Thin-Layer Chromatography............................... 70
4.4.8 Advantages of Thin-Layer Chromatography
over Paper Chromatography................................................................ 70
4.5 Sample Collection, Preservation, and Preparation........................................... 71
4.6 Adsorption Chromatography............................................................................ 71
4.6.1 Principle.............................................................................................. 71
4.6.2 Adsorbents........................................................................................... 72
4.6.3 Solvents............................................................................................... 73
4.7 Partition Chromatography................................................................................ 73
4.7.1 Principles............................................................................................. 73
4.7.2 Countercurrent Chromatography........................................................ 74
4.8 High-Performance Liquid Chromatography.................................................... 74
4.8.1 Principles............................................................................................. 74
4.8.2 Column................................................................................................ 74
4.8.3 Column Packing.................................................................................. 76
4.8.4 Column-Packing Procedure................................................................ 76
4.8.5 Chromatographic Solvent (Mobile Phase).......................................... 76
4.8.6 Pumping Systems................................................................................ 76
4.8.7 Detector Systems................................................................................. 77
4.8.8 Practical Procedure............................................................................. 77
4.9 Fast Protein Liquid Chromatography............................................................... 78
4.9.1 Principles............................................................................................. 78
4.9.2 Apparatus and Materials..................................................................... 78
4.9.3 Calibrations......................................................................................... 81
4.9.4 Maintenance........................................................................................ 81
4.9.5 Troubleshooting................................................................................... 82
4.9.6 Advantages.......................................................................................... 82
4.9.7 Applications......................................................................................... 82
4.10 Gas–Liquid Chromatography........................................................................... 85
4.10.1 Principle.............................................................................................. 85
4.10.2 Solid Support and Stationary Phase.................................................... 86
4.10.2.1 Column Packing.................................................................. 87
4.10.3 Sample Preparation and Application................................................... 87
4.10.4 Carrier Gas.......................................................................................... 88
4.10.5 Detectors............................................................................................. 88
4.10.6 Amplifiers and Recorders.................................................................... 89
4.11 Ion-Exchange Chromatography........................................................................ 89
4.11.1 Principle..............................................................................................90
4.11.2 Ion-Exchange Materials......................................................................90
4.12 Exclusion Chromatography.............................................................................. 91
4.12.1 Principle.............................................................................................. 91
4.12.2 Materials and Methods........................................................................92
4.12.3 Applications.........................................................................................94
viii Contents
4.13 Affinity Chromatography.................................................................................94

4.13.1 Principle..............................................................................................94
4.13.2 Materials and Methods........................................................................ 95
Suggested Reading.................................................................................................... 111
Important Links......................................................................................................... 113
Chapter 5 Spectroscopy............................................................................................................. 115

5.1 Introduction.................................................................................................... 115
5.1.1 Definition and General Principles..................................................... 115
5.1.2 Beer–Lambert’s Law......................................................................... 117
5.1.3 Mechanics of Measurement.............................................................. 120
5.2 UV–Visible Spectroscopy............................................................................... 121
5.2.1 Definition........................................................................................... 121
5.2.2 Principle............................................................................................ 121
5.2.3 Instrumentation................................................................................. 122
5.2.3.1 Colorimeter........................................................................ 122
5.2.3.2 Spectronic 20 Spectrocolorimeter..................................... 123
5.2.3.3 Choice of Instruments for Colorimetry............................. 123
5.2.3.4 UV–Visible Spectrophotometer......................................... 123
5.2.4 Applications....................................................................................... 125
5.2.4.1 Concentration Measurement.............................................. 125
5.2.4.2 Growth Kinetics................................................................ 126
5.2.4.3 Structural Studies.............................................................. 126
5.2.4.4 Enzyme Kinetics and Assays............................................. 127
5.2.4.5 Difference Spectra............................................................. 127
5.2.4.6 Purity and Homogeneity.................................................... 127
5.3 IR (Vibrational) Spectroscopy........................................................................ 129
5.3.1 Principle............................................................................................ 129
5.3.3 Applications....................................................................................... 130
5.4 Flame/Atomic Absorption Spectroscopy....................................................... 131
5.4.1 Principle............................................................................................ 131
5.4.2 Instrumentation for Emission Flame Spectroscopy.......................... 132
5.4.3 Instrumentation for Atomic Absorption Spectroscopy..................... 132
5.4.4 Applications....................................................................................... 133
5.5 Fluorescence Spectroscopy............................................................................ 133
5.5.1 Principle............................................................................................ 133
5.5.3 Pre- and Postfilter Effects................................................................. 135
5.5.4 Applications....................................................................................... 135
5.5.4.1 Concentration Measurement.............................................. 135
5.5.4.2 Compound Identification/Excitation Spectrum................. 136
5.5.4.3 Kinetic and Structural Studies........................................... 136
5.6 ESR Spectroscopy.......................................................................................... 137
5.6.1 Principles........................................................................................... 137
5.6.3 Applications....................................................................................... 140
5.7 NMR Spectroscopy........................................................................................ 140
5.7.1 Principle............................................................................................ 140
Contents ix
5.7.3 Chemical Shifts................................................................................. 141

5.7.4 Applications....................................................................................... 142
5.7.5 Comparison of ESR and NMR......................................................... 142
5.8 MALDI-TOF Mass Spectrometry.................................................................. 143
5.8.1 Introduction....................................................................................... 143
5.8.2 MALDI-Mass Spectrometry in Chemical
Identification...................................................................................... 143
5.8.3 Synthetic Polymer Analysis.............................................................. 147
5.8.4 Impurity in Oligocarbons.................................................................. 149
5.8.5 Side Reaction in Oligocarbons.......................................................... 150
5.9 Circular Dichroism (CD) Spectroscopy......................................................... 150
5.9.1 Principle............................................................................................ 150
5.9.3 Applications....................................................................................... 152
5.9.3.1 Protein Conformation........................................................ 152
5.9.3.2 Nucleic Acid Structure....................................................... 152
5.9.3.3 Secondary Structures of Proteins...................................... 152
Important Links......................................................................................................... 162
Chapter 6 Centrifugation........................................................................................................... 163

6.1 Introduction.................................................................................................... 163
6.1.1 Increasing the Effect of Gravity: The Centrifuge............................. 163
6.2 Principle of Centrifugation............................................................................. 163
6.3 Types of Centrifuges...................................................................................... 163
6.4 Types of Centrifugal Separations................................................................... 168
6.4.1 Differential Centrifugation................................................................ 168
6.4.2 Density Gradient Centrifugation....................................................... 169
6.5 Rotor Categories............................................................................................. 170
6.6 Selection of Centrifuge Tubes........................................................................ 172
6.7 Common Centrifugation Vocabulary and Formulas...................................... 173
6.8 Analytical Ultracentrifuge............................................................................. 174
6.8.1 Theory of Ultracentrifugation........................................................... 174
6.8.2 Analytical Ultracentrifugation.......................................................... 175
6.8.3 Examination of SV............................................................................ 178
6.8.4 Examination of Sample Purity.......................................................... 178
6.8.5 Determination of Molecular Weight................................................. 179
6.8.6 Detection of Conformational Changes.............................................. 180
6.8.7 Analysis of Associating Systems...................................................... 181
6.8.8 Ligand Binding.................................................................................. 181
6.8.9 Cell Fractionation and Metabolic Studies......................................... 181
Important Links......................................................................................................... 184
Chapter 7 Electrophoresis.......................................................................................................... 185

7.1 Introduction.................................................................................................... 185
7.1.1 Structure of the Agarose GE Instrument.......................................... 185
7.1.1.1 Components of the Agarose GE Instrument...................... 185
7.2 Principles of GE............................................................................................. 188
x Contents
7.3 Working with the Electrophoresis Apparatus................................................ 189

7.3.1 Applications of GE............................................................................ 189
7.4 Denaturing Gradient GE................................................................................ 190
7.4.1 Structure of the DGGE Instrument................................................... 190
7.4.2 Principle of DGGE............................................................................ 190
7.4.3 Working with the DGGE Instrument................................................ 191
7.4.4 Applications of DGGE...................................................................... 191
7.5 Temperature Gradient GE.............................................................................. 192
7.5.1 Structure of the TGGE Instrument................................................... 192
7.5.1.1 Components of the TGGE Instrument............................... 192
7.5.1.2 Electrophoresis Unit.......................................................... 192
7.5.1.3 Controller Unit................................................................... 192
7.5.2 Principles........................................................................................... 193
7.5.3 Working with the TGGE Instrument................................................ 193
7.5.4 Applications of TGGE....................................................................... 194
7.6 Pulsed-Field GE.............................................................................................. 194
7.6.1 Structure............................................................................................ 194
7.6.2 Principles........................................................................................... 194
7.6.3 Working with the PFGE Instrument................................................. 196
7.6.3.1 Gel Box.............................................................................. 196
7.6.3.2 High-Voltage Power Supply............................................... 196
7.6.3.3 Switch Unit........................................................................ 196
7.6.3.4 Computer Program............................................................ 196
7.6.3.5 Cooler................................................................................ 196
7.6.4 Applications....................................................................................... 196
7.7 Capillary Electrophoresis............................................................................... 197
7.7.1 Principles........................................................................................... 197
7.7.2 Structure of the CE Instrument......................................................... 197
7.7.2.1 Capillaries.......................................................................... 198
7.7.2.2 Buffer................................................................................. 198
7.7.2.3 Injection System................................................................ 198
7.7.2.4 Detectors............................................................................ 198
7.7.3 Working with the CE Instrument...................................................... 198
7.7.4 Applications....................................................................................... 199
Suggested Reading....................................................................................................205
Important Links.........................................................................................................207
Chapter 8 X-Ray Microanalysis.................................................................................................209

8.1 Introduction....................................................................................................209
8.2 Principles........................................................................................................209
8.3 Instrumentation.............................................................................................. 210
8.4 Applications of X-Ray Microanalysis............................................................ 212
8.5 Techniques for the Analysis of Secondary, Tertiary, and
Quaternary Proteins by X-Ray Crystallography............................................ 213
8.5.1 Introduction....................................................................................... 213
8.5.2 Principles of X-Ray Crystallography................................................ 213
8.5.3 Some Results of X-Ray Crystallography........................................... 217
8.5.4 Investigation of Protein Structure in Solution................................... 220
Important Link...........................................................................................................224
Contents xi
Chapter 9 Techniques with Radioisotopes................................................................................. 225

9.1 Introduction.................................................................................................... 225
9.2 Isotopes and Radioactivity............................................................................. 225
9.3 Ionization Effects........................................................................................... 227
9.4 Measurement Units......................................................................................... 228
9.5 Measurement Techniques............................................................................... 228
9.5.1 Scintillation Counting Systems......................................................... 229
9.5.2 Geiger–Mueller Counter.................................................................... 232
9.6 Autoradiography............................................................................................. 234
9.7 Counting Statistics.......................................................................................... 235
9.8 Biological Uses of Radioisotopes................................................................... 236
9.9 Tracer Dilution Technique.............................................................................. 236
9.10 Radioimmunoassay........................................................................................ 237
9.11 Miscellaneous Uses of Radioisotopes............................................................ 238
9.11.1 A Short Guide to Isotopes................................................................. 238
9.11.2 Using Radioisotopes.......................................................................... 238
9.11.3 Food and Agriculture........................................................................ 239
9.11.3.1 Insect Eradication.............................................................. 239
9.11.3.2 Food Preservation.............................................................. 239
9.11.3.3 Fertilizer Labeling............................................................. 239
9.11.3.4 Genetic Alteration.............................................................. 239
9.11.3.5 Sterilization........................................................................ 239
9.11.4 Industry............................................................................................. 239
9.11.4.1 Nuclear Gauging................................................................ 239
9.11.4.2 Gamma Radiography......................................................... 239
9.11.4.3 Tracing...............................................................................240
9.11.5 Medicine............................................................................................240
9.11.5.1 Sterilization........................................................................ 241
9.11.5.2 Medical Diagnostics.......................................................... 241
9.11.5.3 Medical Treatments........................................................... 241
9.12 Radioisotope Production................................................................................ 241
9.12.1 Nuclear Reactors............................................................................... 241
9.12.2 Research Reactors............................................................................. 242
9.12.3 Cyclotrons and Linear Accelerators.................................................. 242
9.13 Most Widely Used Radioisotopes................................................................... 242
Important Links.........................................................................................................248
Chapter 10 Fermentation.............................................................................................................. 249

10.1 Introduction.................................................................................................... 249
10.2 History............................................................................................................ 249
10.3 Principles of Fermentation............................................................................. 250
10.4 Introduction to Microorganisms..................................................................... 251
10.4.1 Prokaryotes........................................................................................ 251
10.4.2 Eukaryotes......................................................................................... 252
10.5 Types of Fermentation Metabolism................................................................ 253
10.5.1 Aerobic Fermentation........................................................................ 253
10.5.1.1 Acetyl Co-A: The Transition Reaction.............................. 253
10.5.1.2 Kreb’s Cycle (the Citric Acid Cycle).................................. 254
10.5.1.3 Electron Transport Phosphorylation.................................. 254
xii Contents
10.5.2 Anaerobic Fermentation.................................................................... 255

10.5.2.1 Anaerobic Fermentation and Glycolysis............................ 256
10.5.3 Pathways/Fermentation..................................................................... 257
10.5.3.1 Fatty Acid and Hydrocarbon Pathway............................... 257
10.5.3.2 Oxidation of Methane and Methanol................................. 257
10.5.3.3 Oxidation of Amino Acids................................................ 257
10.5.3.4 Oxidation of Polymers....................................................... 257
10.6 Fermentation Process..................................................................................... 257
10.6.1 Selection of Substrates in a Culture Medium.................................... 257
10.6.1.1 Carbon Sources.................................................................. 258
10.6.1.2 Carbohydrates.................................................................... 258
10.6.1.3 Oils and Fats...................................................................... 259
10.6.1.4 Hydrocarbons..................................................................... 259
10.6.1.5 Nitrogen Sources............................................................... 259
10.6.1.6 Minerals............................................................................. 259
10.6.1.7 Growth Factors.................................................................. 259
10.6.1.8 Chelating Agents............................................................... 259
10.6.2 Controlling pH.................................................................................. 259
10.6.3 Antifoaming Agents..........................................................................260
10.6.4 Air.....................................................................................................260
10.6.5 Steam.................................................................................................260
10.6.6 Fermentation Vessels......................................................................... 261
10.6.7 Shaker Flasks.................................................................................... 261
10.7 Types of Fermentation.................................................................................... 262
10.7.1 Solid-State Fermentation................................................................... 262
10.7.2 Semicontinuous Fermentation........................................................... 262
10.7.3 Continuous Fermentation.................................................................. 263
10.8 Types of Fermentors.......................................................................................264
10.8.1 Stirred-Tank Fermentors...................................................................264
10.8.1.1 Fermentation Vessel Additional Equipment...................... 265
10.8.2 ALF................................................................................................... 270
10.8.3 Fixed-Bed Fermentors....................................................................... 271
10.8.4 Tower Fermentors.............................................................................. 271
10.8.5 Batch Culture Fermentation.............................................................. 271
10.8.6 Fed-Batch Culture............................................................................. 272
10.8.6.1 Fixed-Volume Fed-Batch................................................... 272
10.8.6.2 Variable-Volume Fed-Batch............................................... 272
10.8.6.3 Advantages and Disadvantages of
Fed-Batch Reactors............................................................ 273
10.8.6.4 Equipment.......................................................................... 273
10.8.6.5 Control Techniques for Fed-Batch Fermentations............. 274
10.8.7 Continuous Culture Fermentation..................................................... 277
10.8.7.1 Chemostat.......................................................................... 277
10.8.7.2 Turbidostat......................................................................... 278
10.9 Sterilization in Fermentation.......................................................................... 278
10.9.1 Moist Heat Sterilization.................................................................... 279
10.9.1.1 Moist Heat Sterilization at Temperatures below 100°C........ 280
10.9.1.2 Moist Heat Sterilization at 100°C...................................... 281
10.9.1.3 Moist Heat Sterilization at Temperatures above 100°C........ 281
10.9.2 Dry Heat Sterilization....................................................................... 282
10.9.3 Incineration....................................................................................... 282
Contents xiii
10.9.4 Chemicals........................................................................................... 283

10.9.4.1 Alcohols............................................................................284
10.9.4.2 Aldehydes..........................................................................284
10.9.4.3 Phenol................................................................................284
10.9.4.4 Halogens............................................................................ 285
10.9.4.5 Heavy Metals..................................................................... 285
10.9.4.6 Surface Active Agents....................................................... 286
10.9.4.7 Dyes................................................................................... 286
10.9.4.8 Hydrogen Peroxide............................................................ 286
10.9.4.9 Ethylene Oxide.................................................................. 286
10.9.4.10 β-Propiolactone................................................................. 287
10.9.5 Sterilization Using Filtration.............................................................. 287
10.9.6 Sterilization Using Radiation............................................................. 288
10.10 Product Recovery............................................................................................ 289
10.10.1 Precipitation....................................................................................... 290
10.10.2 Product Recovery by Solvent Extraction........................................... 290
10.10.2.1 Distribution Coefficient..................................................... 291
10.10.2.2 Solvent Selection............................................................... 293
10.10.2.3 Acid–Base Extraction........................................................ 295
10.10.3 Ion Exchange...................................................................................... 295
10.10.3.1 Resin Types....................................................................... 297
Important Links.........................................................................................................306
Chapter 11 Conductivity Meters..................................................................................................307

11.1 Introduction.....................................................................................................307
11.2 Principles.........................................................................................................307
11.2.1 Strong Electrolytes.............................................................................307
11.2.2 Weak Electrolytes..............................................................................307
11.3 Common Definitions.......................................................................................307
11.3.1 Resistance...........................................................................................307
11.3.2 Conductance.......................................................................................308
11.4 Conductivity Meter..........................................................................................309
11.4.1 Cell Constant...................................................................................... 310
11.5 Conductivity Cells........................................................................................... 311
11.5.1 Two-Pole Cell..................................................................................... 311
11.5.2 Three-Pole Cell.................................................................................. 311
11.5.3 Four-Pole Cell.................................................................................... 311
11.5.4 Platinized Cells.................................................................................. 312
11.5.5 Flow-Through Cell............................................................................. 312
11.5.6 Advantages and Disadvantages of Two-Pole and
Four-Pole Cells................................................................................... 312
11.5.7 Conductivity Cells and Measurement Ranges................................... 312
11.5.8 Calibration.......................................................................................... 313
11.5.9 Standard Solution............................................................................... 313
11.5.10 Reference Temperature...................................................................... 313
11.5.11 Automatic Temperature Correction................................................... 314
11.6 Factors Influencing the Measurement............................................................. 314
11.6.1 Polarization........................................................................................ 314
11.6.1.1 Preventing Polarization..................................................... 314
xiv Contents
11.6.2
Contamination of Electrode Surfaces................................................ 315
11.6.3
Geometry-Related Errors: Field Effects............................................ 315
11.6.4
Cable Resistance................................................................................ 315
11.6.5
Cable Capacitance.............................................................................. 316
11.6.6
Frequency Change.............................................................................. 316
11.6.7
Temperature Effect............................................................................. 316
11.6.7.1 Linear Temperature Correction......................................... 317
11.6.7.2 Determination of the Temperature Coefficient (θ)............ 317
11.6.7.3 Nonlinear Temperature Correction................................... 318
11.7 Measuring Techniques.................................................................................... 318
11.7.1 Determination of the Cell Constant................................................... 318
11.7.2 Conductivity Measurements............................................................... 319
11.7.2.1 Low-Conductivity Measurements (Pure Water)................ 319
11.7.2.2 Principle of Pure Water Measurements............................. 319
11.7.2.3 High-Conductivity Measurements..................................... 319
11.7.3 Contacting Conductivity.................................................................... 319
11.7.4 Toroidal “Inductive” Conductivity..................................................... 320
11.8 Reliable Measurements................................................................................... 320
11.8.1 Calibrate Frequently........................................................................... 320
11.8.2 Temperature and Stirring Conditions................................................ 320
11.8.3 Position of Conductivity Cell............................................................. 320
11.8.4 Low-Conductivity Measurements...................................................... 321
11.8.5 High-Conductivity Measurements..................................................... 321
11.8.6 Traceability........................................................................................ 321
11.9 Maintenance and Storage................................................................................ 321
11.9.1 Make Sure That Your Cell Is Clean................................................... 321
11.9.2 Store the Conductivity Cell Carefully................................................ 321
11.9.3 Handle Platinized Cells Carefully..................................................... 321
11.10 Applications..................................................................................................... 321
11.10.1 Conductivity Measurements............................................................... 321
11.10.2 Resistivity Measurements.................................................................. 322
11.10.3 TDS Measurements............................................................................ 322
11.10.3.1 What Is TDS and How Is It Measured?............................. 322
11.10.3.2 Determination of the TDS Factor...................................... 322
11.10.4 Concentration Measurements............................................................. 323
11.10.4.1 Necessary Conditions........................................................ 323
11.10.4.2 Determination of Concentration Coefficients.................... 324
11.10.4.3 Determination of the Sample Concentration..................... 324
11.10.4.4 Limitations of the Concentration Method......................... 324
11.10.4.5 Recommendations............................................................. 325
11.10.5 Salinity Measurements....................................................................... 325
11.10.5.1 Determination of the Sample Salinity............................... 326
11.10.5.2 Demal Solution.................................................................. 326
Important Links......................................................................................................... 331
Glossary......................................................................................................................................... 333
Preface
The current technological boom has put forth a variety of techniques being used in life science
teaching and research. There is now more than ever a great deal of interaction between the physical
and biological sciences. The biologist today depends on instrumentation to study the physiology and
genetics of living organisms, particularly at the molecular level. A series of technologies have been
developed over the years to address the challenges of different disciplines of biology. There is
therefore a need for a thorough understanding of the physical principals involved in the operation of
instruments and parameters of study required in using such instruments. This book is an endeavor
toward that end.
This book on instrumentation includes 11 chapters that amalgamate basic techniques along with
advanced instrumentation that hold the modern impetus in research and development. The book
deals with the principles, concepts, techniques, and applications of optical and electron microscopy;
the concepts and applications of micrometry, especially in microbial taxonomy; the principles and
uses of pH meters and oxygen electrodes; the basic theoretical and practical details of chromatogra-
phy to separate and purify a product from complex mixtures; the methods based on quantum prin-
ciples and important spectroscopic and spectrophotometric techniques to determine the structure
and underlying function of different biomolecules; various centrifugation techniques for the separa-
tion of mixtures for both preparative and analytical purposes; electrophoretic techniques and their
applications for deciphering the molecular nature of cell components and also in gene technology;
the principles involved in x-ray microanalysis and applications of radioactivity in biology; and the
principles of fermentation and applications of fermentation technology and downstream processing
to identifying the different techniques, their methodologies, and their applications regarding separa-
tion of the products of interest.
All 11 chapters have been organized from the basic to the practical with appropriate illustrations
to make them comprehensive. The book will be useful for undergraduate and graduate students
of life sciences, pharmacy, biotechnology, and microbiology as an introduction to the tools and
techniques currently in practice. The book fine-tunes the principle behind the modus operandi of
various instruments that illustrate the seed of prospective rationale in undergraduate students. All
11 chapters encompass a well-defined methodology that describes the instruments and their cor-
responding applications in different fields of life science, illuminating the young minds of graduate
students knocking on the door of innovative research.
A unique facet of this book is its broad subject coverage that incorporates fundamental concepts
like microscopy, micrometry, and electrochemical techniques and also advocates the important
applications of modern molecular and proteomic tools that lay the basis for state-of-the-art research
in the present era of metagenomics, metaproteomics, and metabolomics. This book devotes a chap-
ter to fermentation, which emphasizes the principles, designs, and types of different bioreactors
and the various separation techniques that help in purifying the products of interest for further
studies. The present aspects of industrial microbiology and biotechnology will provide readers with
comprehensive insight into the dynamics of the core commercial application industry, a sanguine
component that has been missing in contemporary books related to biological science. The book can
also help researchers by laying down the inventory of methods and their principles that could be put
to practice to further their study.
xv
About the Book
Introduction to Instrumentation in Life Sciences addresses different aspects of instrumentation
that hold the keys to cutting-edge research and innovative applications. The book has been designed
to serve a wide multitude of students and researchers diversified in the field of life sciences: phar-
macy, biotechnology, microbiology, biochemistry, and environmental sciences. Graduate students
are introduced to different aspects of basic experimental methods and instrumentation used in prac-
tical life sciences. Due emphasis has been given to techniques encountered both in practical classes
and also in high-throughput technique involved in the modern era of commercialization and prod-
uct inventories. As a further aid to students, well-illustrated diagrams are presented to explain the
principles and theories behind these instruments.
This is essential reading for all life science, undergraduate, graduate, and medical students for
whom practical molecular biology, proteomics, biochemistry, microbiology, and immunology are
part of the syllabus. We hope that the book will be able to respond to the requirements of students
and researchers involved in life science teaching and research.
xvii
Acknowledgments
We wish to express our gratitude to Dr. M. P. Kaushik, Dr. R. Vijayaraghavan, and Dr. S. J. S. Flora,
Director, Former Director and Scientist G, respectively, of the Defense Research and Development
Establishment (DRDE), Defense Research and Development Organization (DRDO), Ministry
of Defense, Government of India, Gwalior; Professor G. P. Agarwal, Senior Microbiologist,
Department of Postgraduate Studies and Research in Biological Sciences, R. D. University,
Jabalpur; Prof. G. B. K. S. Prasad, Head, School of Studies in Biochemistry, Jiwaji University,
Gwalior; R. S. Rathore, Vikrant Group of Institutions, Gwalior; and Puneet Davar, Tropilite Foods
Pvt. Ltd., Gwalior, India, for providing necessary facilities and extending help in various ways.
Sincere thanks to Devendra Singh and Avinash Dubey for their computational work preparing the
book in a presentable form.
We express our sincere thanks to our research students, Dr. Ruchika Singh Raghuwanshi, Gulab
Singh Thakur, Bhagwan Singh Sanodiya, Rakesh Kumar Baghel, Rohit Sharma, Dr. Abhishek
Bhattacharya, Rani Verma, Chandan R. Bora, Varsha Shukla, Padmini Ramteke, Poonam Kumar,
Ankita Shrivastava, Arunima Sharma, Shraddha Trivedi, Pankaj Parihar, and Islam Husain for
extending scientific inputs and technical support.
Finally, we would like to express thanks to the Council of Scientific and Industrial Research,
New Delhi, for the award of Scientist Emeritus to Professor Prakash S. Bisen.
Prakash S. Bisen
Gwalior, India
Anjana Sharma
Jabalpur, India
xix
1 Microscopy
1.1 INTRODUCTION
A microscope is defined as an instrument that magnifies objects by means of lenses to reveal details
that are invisible to the naked eye. It was only after the discovery of the first microscope around
1590 by a Dutch spectacle maker, Zacharias Jensen, that it was realized there were certain living
organisms so small in size that they were invisible to the naked eye and hence never believed to
be in existence. The microscope opened new doors into the living world, bringing forth a realm
of microorganisms. This gave concrete evidence to Louis Pasteur’s germ theory of disease. Thus
began the science of microbiology.
Through the microscope, the different shapes, sizes, and even colors of microorganisms can
be seen. The degree of magnification needed to see a microorganism depends on the size of the
microbe. Protozoa, fungi, algae, and bacteria whose sizes range from 1–200 μm can be viewed with
a light microscope, that is, a microscope that uses visible light to illuminate a specimen. It gives
a magnification of about 1500×. Viewing smaller microorganisms like viruses, whose size varies
from 0.015 to 2.0 µm, as well as the internal structure of bacterial cells or eukaryotic cell organ-
elles, requires the use of a more specialized electron microscope, which has a higher magnification,
that is, 200,000× (Table 1.1). It may be noted here that the extent of magnification is limited by the
capacity of resolution, which we shall discuss in Section 1.2. Without resolution, magnification is
called empty magnification and it is of practically no use whatsoever.
Today, microbiologists have a variety of microscopes at their disposal (Table 1.1). Together with
the different techniques available for exploration, they can choose and use these microscopes for
study. The choice of a particular microscope depends on the size of the object, degree of detail to be
viewed, and purpose of microscopic observation.
In this chapter, we examine different type of microscopes, their advantages and disadvantages,
and also different analytical techniques using microscopes. In order to understand the indispens-
able role played by the microscope in the study of microorganisms, it is necessary to appreciate the
intrinsic limitation of the eye as a magnifying instrument. The image formed by the eye lens, L, in
Figure 1.1 must appear on the retina, R, in order to be clearly seen. The ciliary muscles attached to
the lens surfaces can alter the focal length of the lens. This enables the eye to focus different dis-
tances on the retina; this is a property of the eye known as its power of accommodation. However,
the eye cannot accommodate objects closer than approximately 25 cm due to muscular orientation.
1.2 MAGNIFICATION, RESOLUTION, AND CONTRAST

In order to view an object closer to the eye than 25 cm, a converging lens is placed between the
object (at less than 25 cm from the eye) and the eye. This produces an enlarged virtual image 25 cm
from the eye (Figure 1.2). The apparent size of an object as viewed by the unaided eye is directly
related to the angle subtended by the object at the eye. Magnification is achieved by increasing the
angle subtended by the image at the eye so that the size of the object apparently increases from h to
hʹ (Figure 1.2). Magnification is therefore defined as M = θ /θ, where
M = Magnification
θʹ = Angle subtended at the eye by an image at 25 cm
θ = Angle subtended at the unaided eye by the object at 25 cm
1
2 Introduction to Instrumentation in Life Sciences
TABLE 1.1
Microscopes, Magnification, and Applications
Type of Maximum Useful
Microscope Magnification Resolution Useful Application
Bright field 1500× 100–200 nm Extensively used for visualization of microorganisms and
their gross morphological features; usually staining is
necessary to view specimens.
Dark field 1500× 100–200 nm Used for viewing live microorganisms particularly those with
characteristic morphology, for example, spirochetes. Staining
is not required, and the specimen appears bright on a dark
background.
Phase contrast 1500× 100–200 nm Used to examine cellular structures of living cells of yeast,
algae, protozoa, and some bacteria; does not require staining.
Interference 1500× 100–200 nm Used to examine structure of microorganisms; produces sharp,
multicolored image with 3D appearance.
UV 2500× 100 nm Useful for obtaining improved resolution; largely replaced by
an electron microscope.
Fluorescence 1500× 100–200 nm Used for fluorescence staining. Useful in many diagnostic
procedures for identifying microorganisms.
TEM 500,000×– 1 nm Used to view ultrastructure of microorganisms including
100,000× viruses; much greater resolving power and useful
magnification achieved than with light microscope.
SEM 10,000×– 1–10 nm Used for viewing surface structures in detail; produces a 3D
1,000,000× image.
L R
25 cm
FIGURE 1.1 Image formation on the retina of the eye.
h´ F = Focal length of lens

h I = Image
F O = Object
I
FIGURE 1.2 Use of a converging lens to view an object closer than 25 cm to the eye.
In Figure 1.2,
F = Focal length of lens

I = Image
O = Object
Microscopy 3
The principle of a compound microscope involves the use of an eyepiece to magnify an already
enlarged real image produced by a first lens called an objective. In a compound microscope, mag-
nification is brought about by a system of lenses.
Two other factors, contrast and resolution, are of great importance in microscopy. In order to be
perceived through a microscope an object must possess a certain degree of contrast with its sur-
rounding medium, and in order to produce useful magnification the microscope must have resolu-
tion, that is, the ability to discern two closely adjacent points as separate points.
1.3 LIGHT (BRIGHT FIELD) MICROSCOPY

The use of a microscope in which the final image of an object, which is illuminated by visible light
(400–700 μm), is seen through glass lenses is called light microscopy. The light microscope con-
sists of three separate but coordinated lens systems (Figure 1.3): (1) condenser, (2) objective, and
(3) eyepiece. The total useful magnification produced is about 1500× and is equal to the product of
the magnifications of the objective and eyepiece. The lens systems are defined as follows:
Condenser: The condenser collimates the light beam, regulates the passage of light, and elimi-
nates peripheral rays from a source. Occasionally, there is a substage condenser, which con-
centrates the light beam on an object. This effectively increases the numerical aperture (NA),
which, as will become clear in Section 1.3.1, increases the resolving power of the microscope.
Objective: The objective lens system magnifies an object by about 90× to 100× and produces
a real image inside the microscope.
Eyepiece: The eyepiece magnifies the real image to form a virtual image on the retina of
the eye, producing a total magnification of 1500×. In a compound light microscope, light
rays from below the condenser are refracted through the condenser and emerge from the
top surface of the slide, at the plane of the object as a cone of light with the apex pointing
downward (Figures 1.4 and 1.5).
Single lenses have two inherent defects:
1. Spherical aberration
2. Chromatic aberration
Eyepiece
Analytical
Objective system
Microscope stage
Reference plane
(housing the object
plane)
Substage condensers
Aperture iris Illumination

Field iris system
Field condenser
Light source
FIGURE 1.3 The student microscope.

FIGURE 1.4 (See color insert.) Microscopic view under a compound microscope of the cyanobacterium
Anabaena variabilis, showing cell differentiation.
Virtual image on
retina of the eye
Lens of the eye
Eyepiece
Real image formed by

the objective inside
the microscope
Objective
Specimen
Working platform
Condenser
Hole
Light source
FIGURE 1.5 Schematic representation of the optical system of a compound microscope.

Microscopy 5
µ1 µ2
Fp Fc
Spherical aberration
F
Iris
diaphragm correction
(a)
f1+f2
d=
F 2
d
f1 f2
Violet red
Chromatic aberration
µ2 µ1
Correction
(b)
FIGURE 1.6 Defects of the lens and their correction: (a) spherical aberration and (b) chromatic aberration.
Spherical aberration is the inequalities of refraction and focus by the peripheral portions of the
lens. This is due to the curved surface characteristics of the lens element. Rays at the outermost
margins of the lens are refracted to a greater degree, which causes the image to be formed at a point
closer to the emergent side of the lens. This can be corrected either by combining with the lens
another lens of opposite diverging power or by using an iris diaphragm, which eliminates peripheral
rays (Figures 1.6 and 1.7).
Chromatic aberration is the inequality of refraction and focus of all the different wavelengths of
white light producing multiple colored images. This is corrected by combining two lenses that have
different refractive indices.
1.3.1 Resolution
The ability to distinguish between two closely spaced objects is called resolution. It is the property
of the microscope by which magnification is rendered useful and more detail can be observed
(Figure 1.8).
FIGURE 1.7 (See color insert.) Microscopic observation of a mutant A. variabilis under high resolution.
Unresolved Partially resolved Resolved
FIGURE 1.8 Resolution of two points: At low resolution, structures blur together. The greater the resolution
the more detail that can be observed.
The distance between two points that can just be distinguished is called the resolving limit (d).
The resolving limit is dependent on the wavelength of light (λ) and the NA:
d = 0.5λ / NA
The NA is the property of a lens that describes the amount of light that can enter it:
NA = sinθ
where
μ = Refractive index of the medium between the specimen and lens
θ = Half the angular aperture
The angular aperture is the angle between the most divergent rays of the inverted cone of
light emerging from the condenser that enters the objective (Figure 1.9). Resolving power can be
increased by using a shorter wavelength and increasing the refractive index of the medium that fills
the space between the specimen and the front of the objective.
Due to the physiological restriction of the human retina to perceive light between 400 and 700
nm, the resolving limit, d, in a light microscope is approximately 200 nm. Ultraviolet (UV) light,
which still has a shorter wavelength than visible light, is preferable for increasing resolution, but
because UV light does not penetrate glass lenses well and directly viewing UV light results in
eye damage, it is normally not possible to depend on the improved resolving power that could be
achieved using this shorter-wavelength light. Also, the advent of the electron microscope, which
utilizes the wave motion of electrons (electrons have a much shorter wavelength than UV light), has
made such UV microscopes obsolete.
Microscopy 7
Aq
Aq
θ
θ
Objective
Working distance
Air
Glass slide
Condenser
Dry objective Oil immersion
FIGURE 1.9 The NA is improved by the use of immersion oil to replace the air between the specimen on
the glass slide and the objective as shown by the wider angular aperture (Aa) obtained using an oil immersion
lens. It is noted that θ is the angle between the most divergent rays entering the objective and the optical axis,
and it is equal to half Aa. The working distance is also reduced in an oil immersion.
The refractive index of the medium filling the space between the specimen and objective can be
increased by using immersion oil, which has a refractive index of 1–5, similar to that of glass. Many
of the divergent peripheral rays lost by reflection and refraction at the surface of the condenser,
slide, and objective lens are refracted within the angular aperture, thereby increasing the NA and
consequently the resolution. Recall that the use of a substage condenser concentrates peripheral
light waves on the object, thereby effectively increasing the NA and decreasing the resolving limit,
which means increasing the resolution.
The use of immersion oil also effectively decreases the focal length of the lens so that the speci-
men has to be very close to the objective in order to be focused. Therefore, there is a short working
distance between the lens and objective. A short focal length also reduces the depth of field so that
only very thin sections can be focused.
The observation of algae, fungi, and protozoa can be achieved with dry objectives, that is, air that
occupies the space between the specimen and objective. The viewing of bacteria, which are smaller
in size, normally requires the use of an oil immersion lens. Such lenses are specially designed for
use with immersion oil and should never be used without it.
1.3.2 Contrast of a Microscope

A microbial cell largely comprises water; it is the medium in which the cell is normally suspended.
In order to be seen through a microscope, the cell should have some degree of contrast with the
surrounding medium. The contrast arises because less light is transmitted through the cell than
through the medium. This is because some light is absorbed by the cell and some is refracted out
of the optical path of the microscope by the difference in the refractive index between the cell and
the surrounding medium.
Contrast can be enhanced by either staining or the use of dark field or phase contrast microscopy.
In the process of staining, the specimen is treated with dyes that bind selectively either to the whole
cell or to certain cell components, thus producing a much greater absorption of incidental light.
Specific types of microorganisms and/or particular structures of microorganisms exhibit different
staining reactions that can be readily distinguished (Figures 1.10 through 1.12).
(a) (b)
FIGURE 1.10 (See color insert.) Photomicrograph of A. cylindrica showing the position of heterocysts in
between the vegetative cells: (a) bright field and (b) fluorescent photomicrographs.
Cover glass
Glass slide
Oblique rays Reflected rays
Condenser Immersion oil
Light stop
The star diaphragm allows only peripheral A cardioid condenser provides greater light
light rays to pass through the condenser. concentration for oblique illumination than
This method requires maximum illumination. the star diaphragm.
(a) (b)
FIGURE 1.11 Figure showing (a) dark field microscopy and (b) phase contrast microscopy.
Wave A
λ Wave B
4
Wave C
λ
2
FIGURE 1.12 Figure showing retardation of phases of light waves as they pass through a transparent liv-
ing cell mounted in saline. Compared to the waves that do not pass through the cell (Wave A), waves passing
through the full thickness of the cytoplasm (Wave B) are retarded by λ/4 and those passing through a more
refractile inclusion (Wave C) are retarded by λ/2.
Microscopy 9
1.3.3 Uses of the Light (Bright Field) Microscope

With a magnification of 1500× and a resolution of 100–200 nm, the light (bright field) microscope
is a very useful tool for the gross morphological observation of microorganisms ranging 1–200 μm.
This range includes bacteria, yeasts, molds, algae, and protozoa among the microorganisms and
cells of tissues of several bacterial and zoological specimens.
The morphological examination of microorganisms can be put to a variety of uses. For exam-
ple, the viewing of bacteria (except cyanobacteria) requires the use of special staining techniques
that not only help in visualizing the bacteria but also often form the basis of their classification.
This is the case of gram staining, which stains blue for gram-positive and pink for gram-negative
cells. This gives information about the chemical nature of the cell wall and forms the basis of clas-
sification. It is also possible to see the characteristic sizes, shapes, and arrangements of chains,
clusters, or individual unicells.
The occurrence of fission presence of endospores and other such features help to elaborate the life
cycles of bacteria. The purity of bacterial cultures is established by observing a drop of bacterial sus-
pension under a light microscope. Contamination is detected either as morphologically different bacte-
ria or as bacteria that stain differently from what is expected of the particular culture being examined.
A hemocytometer, which is explained in Section 1.11.2, can estimate the number of bacteria in a sample.
Again, by using an ocularmeter and a stage micrometer, the size of bacterium can be found.
Using the hanging drop technique, the mode of motility of bacteria can be observed, for example,
the vibratory movement of Oscillatoria, a cyanobacterium, or the twisting movement of spirochetes.
Using nuclear stain, the chromatin material of a cell becomes visible. In a prokaryote, this shows the
location of the nucleus or its dividing condition during fission. In a eukaryote, the different stages of
mitosis in a cell of a young dividing tissue can be seen.
The morphological observation of fungi, algae, and protozoa is likewise used for classification
and elaborating lifecycles, identifying modes of motility, finding the number and size of spores, and
so on. As an example, the presence or absence of septa in a fungal mycelium separates Phycomycetes
from higher fungi (Figure 1.13a and b).
The anatomy of plant and animal tissue specimens is also studied principally under the light
microscope. By simple observation of a blood smear on a slide, the heterogeneous nature of blood
tissue can be understood. Treatment with antisera and subsequent observation under the microscope
shows whether or not coagulation has occurred, which aids the process of blood grouping.
The light microscope is by far the most widely used microscope due to its low cost, easy work-
ability, and immense versatility. However, due to its low magnification and resolution as com-
pared to the electron microscope (Table 1.2), the detailed examination of microorganisms or, for
that matter, examination of small microorganisms like mycoplasmas and viruses is not possible
(Figure 1.13c). Until the advent of the electron microscope, the great complexity of a eukaryotic cell
was concealed because structures like endoplasmic reticulum, Golgi bodies, mitochondria, and the
internal structure of chloroplasts cannot be seen through a light microscope. Also, because it has
no system for enhancing the contrast, the light microscope relies on either staining or the intrinsic
contrast of the specimen. A structure with a low refractive index is difficult to stain, so, for example,
slime sheaths around bacteria often go unnoticed. Under such circumstances, one resorts to either
dark field microscopy (Figure 1.14a) or phase contrast microscopy (Figure 1.15).
1.3.4 Care of the Microscope

Since the light microscope has so much to offer, we should take good care of it as follows:
• The lens surface of the eyepiece and objective should be wiped clean using either a lint-free
soft cloth or lens-cleaning paper before and after use.
• The lens covers should be duly replaced after use.
(a)
(b)
(c)
FIGURE 1.13 (See color insert.) Figure showing (a) sporangium and sporangiospore in a slime mold
viewed under a compound microscope, (b) fungal conidia of Fusarium and Alternaria under oil immersion,
and (c) electron micrograph of phycovirus attached to cyanobacteria and different types of phycoviruses.
TABLE 1.2
Depiction of Relative Sizes of Microbes, Molecules, and Atoms Together
with an Indication of the Useful Range of Different Types of Microscopes
Size Object Microscope
0.1 mm 100 µm Protozoa
Light microscope
10 µm Blood cells
1000 mm 1 µm Bacteria
100 mm Viruses
microscope
Electron
UV
10 mm Macromolecules
1 mm 10 Å Molecules
1Å Atoms
Microscopy 11
Resultant wave
(a)
Resultant wave
(b)
Resultant wave
Wave 2
Wave 1
Amplitude (intensity)
Just in phase
(c)
Wave 1
Resultant wave
Wave 2
180° out of phase

(d)
FIGURE 1.14 Additive and destructive interference of light waves: (a) amplitude objects, (b) phase objects,
(c) direct and diffracted rays, and (d) coincidence and interference.
• If fungal growth occurs on the lens, it should never be scratched with nails or a sharp
instrument. It should be given to specialists who will clean it by dipping it in special
solutions.
• The 100× objective lens should never be used without oil.
• The microscope should be kept covered when not in use.
1.4 DARK FIELD MICROSCOPE

Contrast can be enhanced not only by staining but also by using several alternative microscope
designs that do not require staining, thereby permitting the visualization of living specimens. The
simplest of these microscopes is the dark field microscope. Many objects appear invisible against a
bright background due to a lack of contrast, but they are visible against a dark background. In order
to obtain a dark background, direct light that illuminates the objective must not enter the objective.
This is accomplished by the use of a special condenser that transmits a hollow cone of light apex
down and through the specimen. The diverging rays do not enter the objective. Only light scattered
Image plane
Phase-shifting element
Objective lens
Diffracted rays
Undiffracted rays
Specimen
Condenser lens
Annular diaphragm
FIGURE 1.15 Schematic representation of a phase microscope.
by the specimen enters the objective. Thus, the specimen appears as a bright speck in a dark field.
The special dark field condenser can be either paraboloid or cardioid. It could also be the bright field
condenser used with a dark field stop (Figure 1.15).
1.5 PHASE CONTRAST MICROSCOPE

The contrast between a specimen and a surrounding medium can be increased by using a spe-
cialized microscope called a phase contrast microscope, in which the optical system is modified.
The phase contrast microscope optically converts differences in the speed with which light passes
through a specimen into differences in contrast that can be seen. Similar to the dark field micro-
scope, it is useful for visualizing living microorganisms and eliminates the necessity of staining to
view microbial structures.
This type of microscope relies on the fact that light passing through a cell of a higher refrac-
tive index (with a greater ability to change the direction of a ray of light) than the surrounding
medium slows down relative to the light passing directly through the less dense background
medium. The greater the refractive index of the cell the greater the retardation of a light wave.
Thus when light passes through a microorganism, there is a slight alteration in the phase of the
light wave, that is, the point of advancement within the light wave cycle. The conversion of dif-
ferences in the phase of the light wave is based on interference between light waves reaching the
image plane. When two waves that are out of phase with each other by a phase difference of λ/2
reach the image plane, they destructively interfere, cancel each other out, and produce darkness.
On the contrary, two light waves that are in phase combine and reinforce each other on reaching
the image plane to produce a wave of twice the amplitude and higher intensity, which results in
brightness (Figure 1.14).
Microscopy 13
The phase contrast microscope is designed to separate direct, undiffracted background light
from light passing through an object and getting diffracted, causing these two different waves to
be approximately 90° out of phase with each other so that they destructively interfere at the image
plane and cause changes in light intensity. To achieve this phenomenon, an annular diaphragm on
the substage condenser allows a ring of light to pass through the condenser and the objective and
fall on a corresponding ring-shaped area on a phase-shifting plate placed on the back focal plane
of the objective.
The ring-shaped area of the phase-shifting plate is thinner than the rest of the plate so that rays
passing through it are altered in phase by 90° or λ/4. Rays that pass through the specimen directly,
undiffracted, fall on this thin ring-shaped area and are advanced by 90°, while those diffracted
by the specimen pass through the thicker portion and are retarded by 90°. When these two waves
recombine on the image plane, they interfere destructively, which greatly increases the contrast of
the cells or intracellular structures that differ slightly in the refractive index from their surround-
ings. The difference in phase increases contrast, hence the design of a phase contrast microscope.
1.6 INTERFERENCE MICROSCOPE

Similar to a phase contrast microscope, an interference microscope is used for enhancing contrast.
Both phase contrast and interference microscopes utilize the fact that light travels as waves and the
addition of light waves that are out of phase with each other produces interference that alters the
amplitude of light waves. Whereas phase contrast microscopes use one beam of light passing through
the specimen, interference microscopes have two beams of plane-polarized light that are combined
after passing through the specimen. These microscopes have higher NAs and better contrast, and
they can produce colored pictures with vivid topographic relief. However, because of its expense, the
phase contrast microscope is the preferred device for observing wet specimens of bacteria.
1.7 UV AND FLUORESCENCE MICROSCOPES

The resolving power of the light microscope is directly related to the wavelength of the light used:
d = 0.5λ/NA

A slight improvement in resolution (about twofold) can be achieved by the use of a UV light source;
UV light has a shorter wavelength than visible light. This is called UV microscopy, and the micro-
scope is modified as glass lenses are replaced by quartz lenses since glass is opaque to UV light.
Also, a camera is used to record the image because the eye cannot perceive UV light; in fact, UV
light causes blindness. However, its complexity and high cost have limited the use of UV micros-
copy. A modification called fluorescence microscopy, which has the same resolving power as UV
microscopy, has recently come into the limelight.
Microscopy that involves staining with fluorescent dyes is known as fluorescence microscopy.
When a fluorescent dye is illuminated by light of one wavelength, the excitation wavelength, it gives
off light of another wavelength, the emission wavelength, which is always shorter than the excitation
wavelength. The wavelength of light used to excite the dye may be in the UV range, but the emitted
light that is to be viewed must be in the visible range (Figures 1.16 through 1.18).
Excitation light may be transmitted either from below the specimen, in which case it is called
transmitted fluorescence, or to the specimen through the objective lens, in which case the system
is referred to as epifluorescence (Figure 1.16a and b). Fluorescence microscopes are equipped with
various excitation filters that permit the selection of the wavelength used to illuminate the specimen
and barrier filters that prevent all but the emission wavelength from reaching the ocular lens.
Control S1P S1P+Et-OH
Lyso-tracker
Auramine
Merged
FIGURE 1.16 (See color insert.) Figure showing (a) fluorescence in situ hybridization of Betaproteobacteria
and (b) immunofluorescence detection of sphingosine 1-phosphate (S1P) in tuberculosis. (Courtesy of Pernthaler
et al., 2008, Proceedings of the National Academy of Sciences 105, 7052–7057 10.1073/pnas.0711303105.)
Eye
Ocular lens
Barrier filter
Removes any exciter wavelength that
gets past the condenser without absorbing
Barrier filter longer wavelengths of fluorescing objects.
Light source Reflector
Fluorochrome
Excitation light Emits fluorescence due to activation
Exciter by exciting wavelength of light.
wavelength
filter Dark field condenser
Provides high contrast for
Mercury vapor fluorescence.
arc lamp
Objective
Light from specimen
Heat filter Exciter filter
at different wavelength Removes infrared rays. Allows only high-energy short
than excitation light wavelengths to pass through.
Specimen
(a)
Transmission
BG12 OG1
Exciter Barrier
filter filter
350 400 450 500 550

Wavelength (nm)
(b)
FIGURE 1.17 Figure showing (a) a diagram of an epifluorescence microscope showing the light path and
(b) the spectral transmissions of Bg12 and OG1 filters.
Microscopy 15
+ =
Bacterial cell Fluorescent dye coated Bacterial cell combined with

on antibody flourescent dye–coated antibody
FIGURE 1.18 Fluorescence staining technique and microscopy.
1.7.1 Uses of UV and Fluorescence Microscopes

An example of direct staining of bacteria with fluorescent dye/antibodies is shown in Figures 1.16
and 1.18. One of the reasons fluorescence microscopy has become important in microbiology is that
fluorescent dyes can be conjugated (linked) with antibodies (specific proteins produced against anti-
gens as part of the immune response), providing great specificity in staining procedures. Antibodies
to which a fluorescent dye is attached are referred to as labeled antibodies. These are mixed with
a suspension of bacteria (antigen) and then the preparation can be examined by fluorescence
microscopy. The bacterial cells that have been combined with the labeled antibody will be visible.
This phenomenon is called immunofluorescence, and it is widely used in diagnostic procedures
(Figures 1.16 and 1.18).
1.8 ELECTRON MICROSCOPY

Electron microscopy is based on the discovery that a circular electromagnetic field acts on a beam
of electrons in a way that is analogous to the action of a glass lens on a beam of photons. The cir-
cular electromagnetic field acting as a lens is a lens coil formed by several thousand turns of wire
in a soft iron casing. When a current passes through the coil, a magnetic field is developed, which
directs the movement of electrons. An electron beam has the properties of an electromagnetic wave
of a very short wavelength. When accelerated through an electric field, its wavelength (λ) has the
following relation with the accelerating voltage:
λ α 1√ accelerating voltage
With an accelerating voltage of 100 KV, a wavelength of 0.04 nm (10,000× shorter than visible
light) is obtained. Consequently, the resolving power increases and high useful magnification can
be achieved.
There are two types of electron microscopy:
1. Transmission electron microscopy (TEM), in which electrons are transmitted through the
specimen. TEM is similar in many respects to light microscopy (Figure 1.19). Both require
the electron beam to pass through a vacuum. If this is not done, molecules in the air deflect
the electron beam and a sharp image cannot be obtained. Extremely thin specimens must
be used for TEM studies. These may be prepared in a number of different ways. The dif-
ferential scattering of electrons by a specimen is viewed on a fluorescent screen or captured
on a photographic plate. This was first constructed by Borries and Ruska in Berlin and
Hillier and Vance in the United States in 1938.
2. Scanning electron microscopy (SEM), in which electrons are made to impinge the speci-
men from above. The secondary electrons ejected are collected by a positively charged
plate (anode), amplified, and viewed on a cathode ray tube (CRT).
The number of secondary electrons ejected depends on the surface topography of the specimen.
Hence, a three-dimensional (3D) specimen is possible.
Light source Electron beam
Field condenser Condenser magnet
Substage condenser Condenser magnet

Object-plane Object plane
Objective Objective magnet
Eyepiece Project lens

magnet
Final image Final image on
screen
FIGURE 1.19 Comparison between a light microscope and a transmission electron microscope.
1.8.1 Operation of TEM

1.8.1.1 Parts
Source: The source of electrons is a hot tungsten filament at 30–150 KV potential. Electrons are
drawn from the filament and accelerated as a fine beam past an anode by a high voltage established
between the filament and the anode.
Lens system and viewing: Analogous to the glass lens system in a light microscope, there is a
magnetic lens coil system in a transmission electron microscope, comprising
a. Condenser lens coil system

b. Objective lens coil system
c. Intermediate projector
The condenser lens collimates the electron beam on a specimen by varying the current to the
lens. After transmission through the specimen, the objective lens coil focuses the electron beam
into a first (real) image of the object enlarged about 2000×. The projector, like the eyepiece of the
light microscope, magnifies a portion of the first image to about 250,000× total magnification and
projects the image onto a fluorescent screen or film plate, which is necessary because the electron
beam cannot be viewed directly. The operator can look into the main tube by means of portholes
or magnifying binocular glasses, and can scan the images on the fluorescent screen, manipulate the
objects, and adjust the alignment and field strength of the focusing magnets.
Vacuum system: Air is removed from the path of the electron beam to prevent collisions with gas
molecules, which scatter the electron beam, and to reduce heat associated with the electron beam,
which would otherwise destroy the biological specimen and also reduce the life of the filament. This
necessitates introduction of air locks for insertion and removal of photographic plates and specimens.
1.8.1.2 Sample Preparation

The vacuum system of the microscope, lack of sufficient contrast in biological specimens, and
extra thickness of microorganisms necessitate the preparation of a sample prior to microscopic
examination.
Fixing and dehydration: Biological specimens containing water cannot be placed under a high
vacuum because the water will boil, destroying the integrity of the specimen. Fixing and dehydra-
tion is carried out carefully in several stages (Figure 1.20). Fixation is achieved either by rapid
freezing or treatment with chemicals to stabilize and cross-link the protein and lipid components
of membranes. Osmium tetra oxide is a common fixative for electron microscopy. Fixed tissue is
Microscopy 17
Dry sections are

stained and viewed
Specimen is dehydrated
by placing it in increasing
concentrations of acetone Knife blade
or alcohol
Ribbon of
sections
Sections are
Specimen is placed collected and
in a dilute solution of placed on a
plastic embedding copper grid
media
Water trough
Plastic is polymerized The hard plastic Sections are cut on an

by heating in an oven block is trimmed ultramicrotome
(a)
Copper grid covered with

carbon and/or plastic film
Specimen in ribbon
Ribbon
of thin sections
Copper
grid
3 mm
(b)
FIGURE 1.20 (a) Preparation of a specimen for viewing by TEM. (b) Inset dry section which goes for stain-
ing and viewing.
then dehydrated by passing through increasing concentrations of ethanol. A more recent technique
is critical point drying, where after treatment with ethanol the specimen is immersed in pressur-
ized liquid CO2 and the temperature is raised to 32 °C, when liquid CO2 vaporizes, leaving a dry,
undistorted specimen.
Ultramicrotomy: Even microorganisms are too thick to be viewed under TEM; therefore, it is
necessary to slice them into thin sections by a process called microtomy. In this process, the speci-
men after being dehydrated and fixed is embedded in a plastic material for easy handling under a
microtome, which is a mechanical slicing instrument that moves a specimen across a knife that has a
diamond or glass edge. The plastic material is removed with solvents. The specimen is subsequently
stained.
Staining: In TEM, contrast is produced by differential scattering of electrons by a specimen.
Electron images are “shadows” produced mainly by the scattering of electrons. Scattering is produced
when electrons encounter atoms. Heavy atoms like Au, Pb207, U237, and OSl92 produce more scattering
than light atoms such as C12, N14, and O16. Since biological specimens comprise mainly light atoms
such as C, N, and O, electron scattering and therefore contrast is very slight. Contrast can be greatly
enhanced by “positive” staining, that is, a combination of the organic matter in a cell with metals
of high molecular weights, such as Pb, U, Os, and Au. Since they have different weights and com-
bine differently with different organic compounds, their use permits a helpful degree of differential
staining. In “negative” staining, the background is stained with an electron-opaque material, which
scatters electrons, commonly phosphotungstic acid. This does not penetrate the cell but darkens the
background.
Mounting: Instead of placing the specimen on a glass slide as is done in light microscopy, it
is placed on a copper mesh grid within the evacuated column of the electron microscope. The
specimen is sprayed onto a very thin film of electron-transparent organic material such as collodion,
which is then supported on the copper mesh grid.
1.8.1.3 Operational Problems

Magnetic lenses suffer from problems similar to those found in glass lenses, although they are of
electrical rather than refractive origin, for example, spherical and chromatic aberration caused by
differences in electron velocities and energies.
A common problem is the appearance of artifacts that are not true representations of the speci-
men being viewed. This is a problem common to all microscopes, but it is particularly true for
electron microscopes due to the use of high magnifications, improper dehydration of specimens,
and improper adjustment of the electron beam (Figure 1.21).
Cathode filament
Electron gun
Anode
First condenser lens
Second condenser lens
Specimen on grid
Objective lens
Intermediate projector lens
Final projector lens
Fluorescent screen
Photographic plate
FIGURE 1.21 A transmission electron microscope allowing visualization of fine detail of a microbial cell.
Microscopy 19
1.8.2 Disadvantages of TEM

The most outstanding disadvantage for biological specimens is that they cannot be viewed live. The
high-energy electron beam falling on them and the necessary process of sample preparation kill the
specimen cell. Also, with the sophistication required for such a high magnification, the cost of an
electron microscope becomes prohibitively expensive.
1.8.3 Operation of the SEM

1.8.3.1 Principle
The operational principle and design of an SEM are quite different from those of a TEM. The
principle combines the mechanisms of electron microscopy and television. It involves the electronic
amplification of signals generated by irradiating the surface of a specimen with a very narrow
beam of electrons (probe). Such primary irradiation knocks off electrons from the specimen. These
secondary electrons are collected on a positively charged plate called a detector and amplified and
viewed on a CRT. Magnification is the ratio of the size of the image on the CRT to the diameter of
the area scanned by the probe. Resolution depends on the size of the phosphorescent dots that are
used to illuminate the CRT screen and on the size of the primary electron beam.
1.8.3.2 Parts
Source: An anode accelerates electrons generated on lanthanum hexabromide cathode at 30–150 KV
potential (Figure 1.22).
Condenser lens coil system: The condenser lens coil system sharply focuses a fine beam of elec-
trons on the specimen. Instead of forming an inverted cone of rays illuminating a wide field as in
a light microscope/TEM, electrons are made to form a needle-sharp probe. The primary beam or
probe acts as an exciter of image-forming secondary electrons that are ejected from the surface of
the specimen. The number of electrons ejected depends on topography of the specimen. The probe
scans the specimen in a raster pattern, similar to that on a blank TV screen.
Detector: The secondary electrons are magnetically deflected to a collector or detector, which is
a positively charged plate.
Cathode
filament
Electron gun
Anode
Beam deflector coils
Condenser
lenses
Scan generator
Secondary
electrons CRT display
Amplifier
Detector
Specimen
FIGURE 1.22 Use of SEM for viewing surface structures and their 3D spatial relationships.
Cytosol
Nuclear
pore
Nucleus
50 nm
FIGURE 1.23 A nuclear pore and frozen nuclear envelopes as seen in a high-resolution SEM, which is
equipped with an emission gun as the source of electrons.
Amplifier: The successive signals from the detector are amplified and transmitted to a CRT.
The CRT beam and scanning beam are synchronized so that the image on the CRT is an accurate
reproduction of the scanning image.
ACRT display: The final image is actually a series of pictures of different points on the specimen
seen in such rapid succession as to provide the eye with a unified view of the entire surface of the
specimen.
1.8.3.3 Sample Preparation

Fixing and dehydration: As in TEM, the electron fixing and dehydration beam in SEM must be
transmitted through a vacuum, and therefore biological specimens must be fixed and dehydrated.
The process is similar to the one followed in TEM (Figure 1.23).
Coating with metal: Once the specimen is dehydrated, it is covered by a thin film of metal, like gold
or gold palladium, by vaporizing the metal under vacuum and depositing it on the specimen. Coating
with metal produces a conductive surface that permits dissipation of secondary electrons, which oth-
erwise create a surface charge on the nonconducting biological specimen. This distorts the image.
Mounting: After coating, specimens are mounted and viewed. Unlike TEM, thin sectioning of the
specimen is unnecessary because only the surface structure of the specimen is viewed (Figure 1.24).
1.8.4 Advantages and Disadvantages of SEM over TEM

Since the intensity of the secondary electron beam depends on the topography of a specimen, the
CRT screen gives a 3D appearance of the specimen. This is not possible in TEM. However, TEM has
a better resolution (l nm) as compared to SEM (10 nm); also, TEM allows examination of internal
structures of cells, whereas SEM does not, because the electron beam is not transmitted through the
specimen. However, it is possible to expose and then view subsurface layers by a technique called
cryofracturing. In this technique, the specimen is frozen at very low temperatures, usually in liquid
N2 (–198°C), and then fractured with a sharp blade. The specimen fractures along planes that cor-
respond to the internal surfaces of the organism, which can then be coated with metal and viewed.
1.9 TUNNELING ELECTRON MICROSCOPY

Tunneling electron microscopy is a relatively recent technique. In this technique, magnets are
used to draw electrons from the specimen rather than an electron beam. A scanning needle tip
is used to explore the surface of the specimen. The intensity of the electron cloud decreases with
an increase in the distance from the specimen surface. As the tip is swept across the surface,
the flow of electrons establishes a current called the tunneling current, which is used to hold the
tip at a uniform height above the surface of the specimen. The movement of the tip is detected
Microscopy 21
Specimen
Support
1. Heavy metal evaporated from a filament

shadows the specimen
2. A strengthening film of carbon evaporated

from above
3. The replica is floated on the surface of

a powerful solvent to dissolve
4. The replica is washed and picked up on

a copper grid for examination
FIGURE 1.24 Preparation of a metal-shadowed replica of the surface of a specimen for SEM.
and computer processed to produce an image on the screen with high resolution and 3D view.
This technique is used to view surface structures of viruses and deoxyribonucleic acid (DNA)
macromolecules.
1.10 CONFOCAL MICROSCOPY

A confocal microscope creates sharp images of a specimen that would appear blurred when viewed
through a conventional microscope. This is achieved by excluding most of the light from the speci-
men that is not from the microscope’s focal plane. This image has less haze and better contrast
than the image of a conventional microscope and represents a thin cross section of the specimen.
Thus, apart from allowing better observation of fine details, it is possible to build 3D reconstruc-
tions of a volume of the specimen by assembling a series of thin slices taken along the vertical axis
Confocal microscopy was pioneered by Marvin Minsky in 1955 while he was a junior fellow at
Harvard University (Minsky 1988). Minsky’s invention performed a point-by-point image construc-
tion by focusing a point of light sequentially across a specimen and then collecting some of the return-
ing rays. By illuminating a single point at a time, Minsky avoided most of the unwanted scattered
light that obscures an image when the entire specimen is illuminated at the same time. Additionally,
the light returning from the specimen passed through a second pinhole aperture that rejected rays
that were not directly from the focal point. The remaining “desirable” light rays were then collected
by a photomultiplier and the image was gradually reconstructed using a long-persistence screen. To
build the image, Minsky scanned the specimen by moving the stage rather than the light rays. This
was to avoid the challenge of trying to maintain the sensitive alignment of moving optics. Minsky
managed to obtain a frame rate of approximately 1 image every 10 seconds by using a 60-Hz solenoid
to move the platform vertically and a lower-frequency solenoid to move the platform horizontally.
Detector
Pinhole
Focusing lens
Laser Beam splitter
Scanning optics
Objective lens
Tissue sample
FIGURE 1.25 A modern confocal microscope.
FIGURE 1.26 Point-by-point illuminations and imaging onto specimens.
1.10.1 Modern Confocal Microscopes

Modern confocal microscopes retain the key elements of Minsky’s design, that is, the pinhole aper-
tures and point-by-point illumination of a specimen. Advancements in optics and electronics have
been incorporated into current designs to provide improvements in speed, image quality, and stor-
age of generated images. Although there are a number of different confocal microscope designs,
we discuss the general type here; note that the other designs are not markedly different from the
general design.
The confocal microscope incorporates the ideas of point-by-point illumination of a specimen and
rejection of out-of-focus light. One drawback of imaging a point onto the specimen is that there are
fewer emitted photons to collect at any given instant. Thus, to avoid building a noisy image each
point must be illuminated for a long time to collect enough light to make an accurate measurement.
This increases the length of time needed to create a point-by-point image. The solution is to use
a light source of very high intensity, which Minsky did using a zirconium arc lamp. The modern
choice is a laser light source, which has the additional benefit of being available in a wide range of
wavelengths.
A laser provides intense blue excitation light. The light is reflected by a dichroic mirror, which
directs it to an assembly of vertically and horizontally scanning mirrors. These motor-driven mir-
rors scan the laser across the specimen. Recall that Minsky’s invention kept the optics stationary
Microscopy 23
and instead scanned the specimen by moving the stage back and forth in vertical and horizontal
directions. As awkward (and slow) as the method seems to be, it does have, among others, the fol-
lowing two major advantages (Sheppard 1997):
1. The specimen is illuminated axially everywhere rather than at different angles as in the
case of the scanning-mirror configuration, thereby avoiding optical aberrations. Thus, the
entire field of view is illuminated uniformly.
2. The field of view can be made larger than that of the static objective by controlling the
amplitude of stage movements.
In confocal microscopy, there is never a complete image of the specimen because at any instant
only one point is observed. Thus, for visualization the detector is attached to a computer, which
builds up the image one pixel at a time. For a 512-pixel image, this is typically done at a frame rate
of 0.1–30 Hz. The image created by the confocal microscope is of a thin planar region of the speci-
men, an effect referred to as “optical sectioning.” Out-of-plane unfocused light is rejected, resulting
in a sharp, better-resolved image. The ability of a confocal microscope to create sharp optical sec-
tions makes it possible to build 3D renditions of a specimen. Data gathered from a series of optical
sections imaged at short and regular intervals along the optical axis are used for the 3D reconstruc-
tion. Software can combine two-dimensional (2D) images to create a 3D rendition. Representing
3D information in a meaningful way out of 2D data is nontrivial, and a number of different schemes
have been developed for this purpose.
Figure 1.27 shows a 3D reconstruction from slices of a suspension of 2-mm-diameter colloidal
particles using “alpha blending,” a technique that combines images by first making each of their
individual pixels less or more transparent according to a computed weight called the alpha value
(Porter 1984). The result is a 3D-like structure.
A confocal microscope provides significant imaging improvement over a conventional micro-
scope. It creates sharper, more detailed 2D images and allows for the collection of data in three
dimensions. In biological applications, it is particularly useful in measuring dynamic processes.
A number of designs have been developed to achieve video-rate confocal microscopy, which enables
the capture of short-timescale dynamics.
100
90
80
Alexa 555 BV (550 nm)
F1
70
Quantum efficiency (%)
VP
Alexa 488 TIL
60 CFP
YFP
RFP
50
40
LAEDANS
30 Cy3
Cy5
TRITC
20 CC2-DMPE
DISBAC4(3)
10
FITC Texas red
0
200 300 400 500 600 700 800 900 1000 1100
Wavelength (nm)
FIGURE 1.27 The 3D reconstruction of a series of 2D images of poly(methyl methacrylate) spheres sus-
pended in a cyclohexylbromide and decalin solution. The image was created using alpha blending.
1.11 TECHNIQUES IN MICROSCOPY

1.11.1 Hanging Drop Technique
The hanging drop technique enables the viewing of the size, shape, arrangement, and motility of
live microorganisms in fluid media. It requires the use of special ground slides (Figure 1.28).
In this technique, a loopful of bacterial suspension is placed in the center of a cover slip.
At the four corners, tiny droplets of mineral oil are placed. The hollow ground slide is placed
over the cover slip with the depression side down and the slide is inverted quickly so that water
cannot run off to one side. However, the lack of contrast yields limited, although valuable,
information.
1.11.2 Use of the Hemocytometer

The hemocytometer, which was originally devised for counting hemocytes, can be used for
counting the number of bacteria, fungal spores, and so on, in a given volume of a sample. The
hemocytometer is a glass slide with a central area partitioned off by ridges into regular cubicle
chambers of exactly known volume (Figure 1.29). By counting the individual cells in each cham-
ber under a microscope and adding them, the number of living and dead organisms may be
computed.
1. A small amount of mineral oil is placed near each corner of the

cover glass with a toothpick.
2. Two loopfuls of organisms are placed at the center of the cover glass.
3. Depression slide is pressed against vaseline on cover glass and

quickly inverted.
Cover glass
Vaseline
Organisms
4. The complete preparation can be examined under oil immersion.
FIGURE 1.28 Hanging drop preparation.

Microscopy 25
Cover glass
Platform with rulings fluid in which bacteria

are suspended occupies space between
platform and cover glass
(a) (b)
(c)
FIGURE 1.29 A hemocytometer adapted for counting bacteria and other microorganisms: (a) plan view
showing a central dark square covered by ruled chambers, which is enlarged in the figure at the bottom (c),
and (b) vertical section with cover glass in place.
Clear glass area Scale (of definite

Glass slide length)
Scale of arbitrary length (sometimes
blackened)
Eyepiece micrometer/ocular meter Stage micrometer
FIGURE 1.30 An ocular meter and a stage micrometer.
1.11.3 Ocular Meter and Stage Micrometer for Micrometry

This is a technique in which the microscope is calibrated so that the size of the objects being viewed
can be found. It involves the use of an ocular meter or eyepiece micrometer, and a stage micrometer
or an object micrometer (Figure 1.30).
The following operations are performed in sequence:
1. The eyepiece is removed from the microscope and the ocular meter is inserted between the
lens and the diaphragm.
2. The stage micrometer is viewed through this eyepiece.
3. The number of divisions of the eyepiece and the stage micrometer is noted, say, x divisions
of the stage micrometer = y divisions of the ocular meter and x/y division of the stage
micrometer = one division of the ocular meter; x/y is called the least count.
4. The stage micrometer is then replaced by the slide with the specimen.
5. The number of divisions of the ocular meter equal to the length of object to be measured is
observed.
6. This value is then multiplied with the least count to give the size of the object.
1.12 ELECTRON MICROSCOPY

1.12.1 Freeze Etching and Metal Shadowing
Freeze etching is used to reveal the detailed structures of microorganisms. In this procedure, a specimen
frozen in liquid N2 is fractured by striking it with a knife blade; the fractured specimen is then etched, that
is, some of the ice is allowed to evaporate, which raises the surface layer of the specimen (Figure 1.31).
The specimen is then exposed to vapors of a heavy metal while being held at a 45° angle to produce a
shadow effect, after which it is rotated and exposed to vaporized carbon at a 90° angle to produce a rep-
lica of the surface. Any adhering biological specimen is removed, and the carbon replica is then viewed.
This method reveals much detail of both internal and external surface structures and also eliminates
some problems with artifacts that arise from chemical fixation and sectioning of biological specimens.
Experiment: Microscopic Examination of Microorganisms

Principle
Microorganisms are difficult to observe in a broth or when wet because there is very little contrast
between them and the liquid in which they are suspended. In studying their properties and differentiat-
ing microorganisms into specific groups for diagnostic purposes, biological stains and staining proce-
dures in conjunction with light microscopy have become major tools in microbiology.
Chemically, a stain may be defined as an organic compound containing a benzene ring plus a chro-
mophore and auxochrome group. Numerous staining techniques are available for the visualization,
Specimen Specimen
Bell jar
Liquid freon
Cold knife
Liquid N2
Specimen
at 196ºC
Specimen
support
Specimen table
(1) (2) (3)
Kn
ife
(4) (5)
Fracturing Etching
Heavy
metal
vapors
(7)
Replica viewed in
electron microscope
(6)
Shadowing and replicating
FIGURE 1.31 Diagrammatic view for the procedure for the formation of freeze-fracture replicas used for
visualizing surface structure in conjunction with TEM.
Microscopy 27
differentiation, and separation of microorganisms. Different types of stains are used to differentiate
between different groups of microorganisms. Two major types of staining techniques are as follows:
1. Simple staining or use of a single stain
2. Differential staining or use of two contrasting strains
A. Fungi
Place the material to be examined on a clean glass microscopic slide. Add a drop of lactophenol to the
material and mix. Place a cover glass over the preparation and observe it under the appropriate microscope.
B. Algae and Cyanobacteria

Place the material to be examined on a clean glass microscopic slide. Place a cover slip over the smear
preparation in simple water or 10% glycerol, and observe it under the appropriate microscope.
C. Bacteria
The success of a staining procedure depends on the preparation of a suitable smear of organisms. A
good smear is one that when dried appears as a thin, whitish layer or film. A properly prepared smear
withstands one or more washings during staining without any loss of organisms. The first step in pre-
paring a bacterial smear differs according to the source of the organisms; those made from broth cul-
tures or cultures from a solid medium require variations in technique.
Procedure
A. From Liquid Media (Figure 1.32)
1. Apply one or two loopfuls of suspended cells to a clean glass slide.
2. Spread it evenly over a small area on the slide.
From liquid media From solid media

Target circle on bottom of the slide.
Two loopfuls
of water are placed
Two loopfuls of liquid containing
in the center of the
organisms are placed in the center
target circle.
of the “target circle.”
Organisms are dispersed over A very small amount of organisms

entire area of the “target circle.” is dispersed with an inoculating
needle in water over entire area of
“target circle.”
The smear is allowed to dry at

room temperature.
Slide is passed several times through

a flame to heat-kill and fix organisms
to the slide.
FIGURE 1.32 Procedure for preparing bacteria smear from liquid media and from solid media.
3. Allow the slide to dry by normal evaporation of water. Do not apply heat.
4. After the smear is completely dry, pass the slide over a Bunsen burner flame to heat-kill and
fix the organisms to the slide.
B. From Solid Media (Figure 1.32)

1. Place a loopful of water on the slide.
2. Flame an inoculating needle and let it cool; pick up a very small amount of the organism, and
mix it with the water on the slide.
3. Disperse the mixture over a small area at the center of the slide.
4. Allow the slide to dry by normal evaporation of the water.
5. Once the smear is completely dry, pass the slide over the flame of a Bunsen burner to heat fix
the organism to the slide.
D. Simple Staining
Principle
In simple staining, the bacterial smear is stained with a single reagent (Figure 1.33). Basic stains with a
positively charged chromogen are preferred, since bacterial nucleic acids and certain cell wall compo-
nents carry a negative charge that strongly attracts and binds to the cationic chromogen. The purpose
of simple staining is to elucidate the morphology and arrangement of bacterial cells. Commonly used
basic stains are methylene blue, crystal blue, and carbolfuchsin.
Procedure
1. Prepare a bacterial smear as described in the smear preparation section.
2. Place the slide on the staining tray and flood with a required simple stain using the appropri-
ate exposure time (carbolfuschin requires 15–30 seconds, crystal violet 20–60 seconds, and
methylene blue 1–2 minutes).
3. Wash the smear with tap water to remove excess stain. During this step, hold the slide parallel
to the stream of water to reduce the loss of cells.
4. Blot dry the slide and observe it under a light microscope.
E. Negative Staining
Principle
Negative staining requires the use of an acidic stain such as eosin or nigrosine (Figure 1.34). The acidic
stain, with its negatively charged chromogen, will not penetrate the cells because of the negative charge
on the surface. Therefore, unstained cells are easily visible against the colored background.
Procedure
1. Place a small drop of nigrosin close to one end of a clean slide.
2. Using a sterile technique, place a loopful of inoculums from the culture in the drop of nigro-
sin and mix.
1. A bacterial smear is stained with 2. Stain is briefly washed off the slide 3. Water drops are carefully blotted
methylene blue for 1 minute. with water. off the slide with bibulous paper.
FIGURE 1.33 Simple staining.

Microscopy 29
1. Organisms are dispersed into a small drop 2. Spreader slide is moved toward drop of
of nigrosine or India ink. Drop should not suspension until it contacts the drop
exceed 1/8-inch diameter and should be causing the liquid to be spread along
near one end of the slide. its spreading edge.
3. Once the spreader slide contacts the drop 4. Spreader slide is pushed to the left, dragging
on the bottom slide, the suspension will the suspension over the bottom slide. After
spread out along the spreading edge the slide is air dried, it may be examined
as shown. under oil immersion.
FIGURE 1.34 Negative staining of bacteria smear.
3. With the edge of a second slide held at a 30° angle and placed in front of the bacterial suspen-
sion, push the mixture to form a thin smear.
4. Air dry. Do not heat-fix the smear.
5. Examine the slide under oil immersion.
F. Gram Staining
The most important differential stain used in bacteriology is the Gram stain, which is named after
Dr. Christian Gram. A Gram stain divides bacterial cells into two major groups, gram-positive
and gram-negative, which make it an essential tool for the classification and differentiation of
microorganisms.
Principle
In Gram staining, a bacterial smear is dried and then heat-fixed. It is then stained with crystal violet
(primary stain), which is rinsed off and replaced with an iodine solution. The iodine acts as a mordant,
that is, it binds the dye to the cell. The smear is then decolorized with alcohol and counterstained with
safranin. In gram-positive organisms, the purple crystal violet dye, complexed with the iodine solution,
is not removed by alcohol, and thus the organisms remain purple. On the other hand, the purple stain is
removed from gram-negative organisms by alcohol and the colorless cells take up the red color of the
safranin counterstain (Figure 1.35).
Procedure
1. Prepare a smear and heat-fix it.
2. Cover the smear with crystal violet; leave it for 20 seconds.
3. Briefly wash off the stain using a wash bottle of distilled water. Drain off excess water.
4. Flood the slide with Gram’s iodine for about 30–60 seconds, and wash with water.
5. Flood the smear with 95% ethyl alcohol for 10–20 seconds or until no more purple dye
runs off.
6. Immediately wash the slide with tap water.
7. Flood the smear with safranin and leave it for 20 seconds. Wash with tap water.
8. Immediately examine the slide using an optical microscope under oil immersion.
1. Crystal (20 seconds) 2. Wash (2 seconds) 3. Gram’s (1 minute)

violet iodine
4. Decolorize (10−20 seconds 5. Wash (2 seconds) 6. Safranin (20 seconds)

with or until solvent
alcohol flows colorlessly)
7. Wash (2 seconds) 8. Blot dry
Reagent Gram positive Gram negative
None
(heat-fixed cells)
Crystal violet
(20 seconds)
Gram’s iodine
(1 minute)
Ethyl alcohol
(10−20 seconds)
Safranin
(20 seconds)
FIGURE 1.35 Steps in Gram staining.
Note
1. Preferably use a fresh culture for making smear.
2. Old cultures of gram-positive organisms lose their ability to retain the crystal violet.
3. Do not excessively decolorize with alcohol. The gram-positive organisms may also appear
gram negative.
4. Use thin smears. It is difficult for the dyes to penetrate properly if thick smears are used.
Microscopy 31
1. Two loopfuls of the organism are 2. The ink suspension of bacteria is 3. The slide is gently heat-dried
mixed in a small drop of India ink. spread over a slide and air dried. to fix the organisms to the slide.
4. Smear is stained with crystal 5. Crystal violet is gently washed 6. Slide is blotted dry with bibulous
violet for 1 minute. off with water. paper, and examined with oil
immersion objective.
FIGURE 1.36 Capsular staining.
G. Capsular Staining
Principle
Some bacterial cells are surrounded by a pronounced gelatinous or slimy layer called a capsule.
Capsules appear to be made up of glycoprotein or polypeptides. They can be observed by differential
staining (Figure 1.36).
Procedure
1. Make a suspension of the organism in a drop of water on a clean slide.
2. Put a small drop of India ink next to it.
3. Spread the ink suspension of bacteria over the slide and air dry it. Caution: Do not heat-fix.
4. Stain the smear with crystal violet for 1 minute.
5. Wash off the crystal violet gently with water.
6. Gently blot dry and immediately examine the slide using an optical microscope under oil
immersion.
H. Spore Staining
Species of bacteria belonging principally to the genera Bacillus and Clostridium produce extremely
heat-resistant structures called endospores. Besides heat, endospores are resistant to many chemicals
and starvation. The endospore is resistant to most stains, so special staining procedures are needed.
There are two different methods that are mainly used for spore staining: (1) Schaeffer–Fulton and (2)
Dorner.
I. Schaffer–Fulton Method
This method utilizes malachite green to stain an endospore and safranin to stain the vegetative por-
tion of the cell. A properly formed spore will have a green endospore contained in a pink sporangium
(Figure 1.37).
Procedure
1. Prepare a smear on a clean slide and heat-fix it.
2. Take a beaker with about an inch of water and bring it to boil.
3. Place the slide on the beaker.
1. Cover smear with a small piece of paper towel 2. After the slide has cooled sufficiently, remove
and saturate it with malachite green. Steam over the paper towel and rinse with water for
boiling water for 5 minutes. Add additional stain 30 seconds.
if stain boils off.
3. Counterstain with safranin for 4. Rinse briefly with water to 5. Hot dry with bibulous paper and
about 20 seconds remove safranin. examine slide under oil immersion.
FIGURE 1.37 Steps in the Schaffer–Fulton method of endospore staining.
4. Flood the slide with malachite green. Steam the slide over a boiling water bath for 5 minutes.
Add additional stain if stain comes off.
5. After the slide has cooled sufficiently, rinse it with water for 30 seconds.
6. Counterstain with safranin for about 30 seconds and then wash with tap water for
30 seconds.
7. Blot dry and microscopically examine the slide under oil immersion.
J. Dorner Method
The Dorner method for staining endospores produces a red spore within a colorless sporangium.
Nigrosine is used to provide a dark background for contrast (Figure 1.38).
Procedure
1. Make a heavy suspension of bacteria by dispersing several loopfuls of bacteria in five drops
of sterile water.
2. Add five drops of carbolfuchsin to the bacterial suspension.
3. Heat the carbolfuschin suspension of bacteria in a beaker of boiling water for 10 minutes.
4. Mix several loopfuls of bacteria in a drop of nigrosine on the slide.
5. Spread the nigrosine–bacteria mixture on the slide.
6. Allow the smear to air dry. Examine the slide under oil immersion.
K. Acid Fast Staining

Principle
Acid fast staining is useful for identifying bacteria that has a waxy lipid cell wall. Most of these organ-
isms are members of a group of the genus Mycobacterium. These organisms have a gram-positive cell
wall, but the lipid in the cell wall prevents staining with Gram-stain dyes (Figure 1.39). In the Ziel–
Neelsen method, three different reagents are used:
Microscopy 33
1. Make a heavy suspension of bacteria by 2. Add five drops of carbol fuchsin

dispersing several loopfuls of bacteria in to the bacterial suspension.
five drops of sterile water.
3. Heat the carbol fuchsin suspension of bacteria 4. Mix several loopfuls of bacteria in a drop
in beaker of boiling water for 10 minutes. of nigrosine on the slide.
6. Allow the smear to air dry. Examine the

5. Spread the nigrosine-bacteria mixture slide under oil immersion.
on the slide.
FIGURE 1.38 Steps in the Dorner method of endospore staining.
A: Mycobacterium
tuberculosis
B: Streptococci Methylene
C: Staphylococci blue stain
D: Macrophages
FIGURE 1.39 Various forms of acid fast stain bacteria.
1. Primary stain: Carbolfuschin, a phenolic stain, is driven into the waxy cell wall with steam.
2. Decolorizing agent: Acid alcohol (3% HCl + 9.5% ethanol) is used as the decolorizing agent.
The mycobacterial cells are acid fast and not decolorized, and thus they retain the primary
stain. Nonmycobacteria are, however, decolorized by acid alcohol.
3. Counterstain: Methylene blue is used as the final reagent to stain previously decolorized cells.
The colorless nonmycobacteria take up the blue color; so, they contrast with the pink acid-fast
bacteria that are not decolorized.
Procedure
1. Prepare a smear of the material and heat-fix it.
2. Place the slide over a beaker of boiling water and cover the slide with carbolfuschin. Cover it
with a paper towel to prevent the dye from flowing out.
3. Keep the slide covered with the stain and steam for 5 minutes.
4. Remove the paper and wash off the carbolfuschin using tap water.
5. Flush all freely removable stain with acid alcohol.
6. Flood the entire slide with acid alcohol and allow it to stand for 1–2 minutes.
7. Wash with water for 5 seconds.
8. Counterstain for about 30–45 seconds with methylene blue.
9. Wash with water.
10. Blot dry carefully and microscopically examine the slide under the oil immersion lens.
L. Flagella Staining
Some bacteria have flagella for motility. As their width is below the resolving power of the microscope,
they cannot be seen in a light microscope. Flagella can be viewed if they are dyed with a special stain
that precipitates on them, making them appear thicker. Leifson’s method accomplishes this by using a
single staining reagent that utilizes pararosaniline as a staining reagent and tannic acid as a mordant.
The arrangement of flagella on bacteria is usually characteristic of the organism and can aid in its iden-
tification (Figure 1.40).
Procedure
A. Culture preparation
1. Inoculate nutrient broth with the organism and incubate at room temperature for 18–20 hours.
2. Add 0.25 mL of formalin to the culture, mix by shaking, and let it stand for 15 minutes.
3. Fill the tube to within 1 cm of its top with distilled water, and mix and centrifuge for 3 minutes.
4. Pour away the supernatant fluid without disturbing the pellet.
5. Resuspend the pellet in about 2 mL of distilled water.
6. Dilute the suspension with additional distilled water until the suspension is barely turbid.
B. Staining procedure
1. Heat a clean slide in a Bunsen burner flame.
2. While the slide is still hot, mark an oval outline on the slide with pencil.
3. Place several loopfuls of the organism at the right end of the cooled slide.
4. Tilt the slide to allow the organism to flow down over the surface of the slide.
5. Allow the smear to completely air-dry. Do not apply any heat.
6. Cover the smear with Leifson’s stain and leave it on the slide until all the alcohol evaporates.
7. Wash gently to remove the stain from the slide.
8. Allow the stained organisms to air-dry. Microscopically examine the slide under oil immersion.
Experiment: Scanning Electron Microscopy

To perform an experiment for preparing sample for SEM, Anabaena cylindrica cells growing in log
phase, are harvested by centrifugation and prefix in a culture medium by the addition of an equal
volume of 1% glutaraldehyde in phosphate buffer. Cells are allowed to stand for 30 minutes on ice,
pelletized, suspended in phosphate buffer with 2% glutaraldehyde, and incubate for 1 hour at room
temperature. Samples are then washed with phosphate buffer, post-fix in 1% osmium tetraoxide in the
same buffer, and wash once in distilled water. After that the samples are kept on carbon stubs and gold
coating is done with fine coat ion sputter JFC 1100. Samples are observed under an electron microscope
(JEOL JSM-840; Figure 1.41).
Microscopy 35
1. Heat a clean slide in blue portion 2. While the slide is still hot, mark with
of Bunsen burner flame. a China marking pencil as shown.
3. Place several loopfuls of organisms at 4. Tilt slide to allow organisms to flow

the right end of cooled slide as shown. down over the surface of the slide.
5. Allow the smear to completely air dry. 6. Cover the smear with Leifson’s stain and
Do not apply any heat. leave it on the slide until all the alcohol
has evaporated.
7. Wash gently to remove the stain from 8. Allow the stained organisms to air dry.
the slide. Examine under oil immersion.
FIGURE 1.40 Steps in flagella staining and an electron microscope view of bacterial flagella.
H - Heterocyst
V - Vegetative cell
(a) (b)
FIGURE 1.41 Scanning electron micrograph image of Anabaena sp.: (a) cell arrangement and
(b) differentiation.
SUGGESTED READING
Benson, H. J. 1998. Microbiological Applications Laboratory Manual in General Microbiology, 7th ed.
New York: WCB/McGraw-Hill.
Boatman, E. S., M. W. Berns, R. J. Walter, and J. S. Foster. 1987. Today’s microscopy. BioScience 37: 384–394.
Bradbury, S. 1997. Introduction to Light Microscopy, 2nd ed. New York: Springer-Verlag.
Clark, G. L. 1961. The Encyclopedia of Microscopy. New York: Van Nostrand Reinhold.
Cosslett, V. E. 1966. Modern Microscopy or Seeing the Very Small. Ithaca, NY: Cornell University Press.
Gerhard, P., R. G. E. Murray, W. A. Wood, and N. R. Krieg, eds. 1994. Methods for General and Molecular
Bacteriology. Washington, DC: American Society for Microbiology.
Hawker, L. E., and A. H. Linton. 1974. Micro-Organisms Function Form and Environment. London: Edward
Arnold Ltd.
Minsky, M. 1988. “Memoir on Inventing the Confocal Scanning Microscope.” Scanning 10: 128–138.
Perkins, G. A., and T. G. Frey. 2000. Microscopy, Optical. In Encyclopedia of Microbiology, 2nd ed., vol. 3,
edited by J. Lederberg, 288–306. San Diego: Academic Press.
Pernthaler, A., A. E. Dekas, C. T. Brown, S. K. Goffredi, T. Embaye, and V. J. Orphan. 2008. “Diverse Syntrophic
Partnerships from Deep-Sea Methane Vents Revealed by Direct Cell Capture and Metagenomics.”
Proceedings of the National Academy of Sciences 105: 7052–7057.
Porter, T. 1984. “Compositing Digital Images.” Computer Graphics 18: 253–259.
Rawlins, D. J. 1992. Light Microscopy. Philadelphia: Coronet Books.
Rochow, T. G. 1994. Introduction to Microscopy by Means of Light, Electrons, X-rays, or Acoustics. New York:
Plenum.
Sheppard, C. J. R. 1997. “Confocal Microscopy.” XVI Meeting of the Brazilian Society for Electron
Microscopy. Caxambu, Brazil, keynote.
Slayter, E. M. 1992. Light and Electron Microscopy. New York: Cambridge University Press.
IMPORTANT LINKS
1. Light microscope: http://www.sigmainstruments.org/laboratory-instruments.html#microscope
2. Dark field microscope: http://www.olympusmicro.com/primer/techniques/darkfieldindex.html
3. Phase contrast microscope: http://www.olympusmicro.com/primer/techniques/phasecontrast/phaseindex
.html
4. Fluorescence microscope: http://microscopeinternational.com/Fluorescence-Microscopes
5. Transmission electron microscope: http://www.jeol.com/PRODUCTS/ElectronOptics/TransmissionElectron
MicroscopesTEM/300kV/J EM3100F/tabid/128/Default.aspx
6. Scanning electron microscope: http://www.jeol.com/PRODUCTS/ElectronOptics/ScanningElectron
MicroscopesSEM/tabid/92/Default.aspx
7. Confocal microscope: http://www.zeiss.de/c12567be0045acf1/ContentsFrame/731dfc84f15572fac125
74310056687c
2 Micrometry
2.1 INTRODUCTION
Micrometry is the measurement of microorganisms. Since microorganisms can only be seen under
a microscope, a suitable scale for their measurements should be located somewhere in the micro-
scope itself. For this, an ocular micrometer serves as a scale or rule. An ocular micrometer consists
of disks of glass upon which lines are etched. There are in general use two practical methods of
measuring microscopic objects: (1) by means of the ocular micrometer and (2) by means of camera
lucida sketches. The latter method is the best one for measuring spores and bacterial size in tax-
onomy (Figure 2.1a and b).
A stage micrometer and an ocular micrometer are necessary for measuring microscopic objects.
A stage micrometer should be ruled in tenths and one-hundredths of a millimeter. It does not matter
what the spacing is in an ocular micrometer, except that the lines must be at equal distances from
one another. As a matter of fact, the ocular micrometer is generally ruled in tenths of a millimeter,
but this ruling is more or less magnified by the lens of the ocular.
2.2 STRUCTURE OF AN OCULAR MICROMETER

Illustrated in Figure 2.2 is a modern microscope eyepiece (often termed an ocular) equipped with
an internal reticle scale. Also presented in the figure is a stage micrometer, which contains a small,
metalized millimeter ruler that is subdivided into increments of 10 and 100 μm. Juxtaposing gradu-
ations on the eyepiece reticle with those on the stage micrometer enables the microscopist to cali-
brate the reticle gauge and perform linear measurements on specimens.
2.3 CONJUGATE IMAGE-FORMING FOCAL PLANES

The principle of a transfer scale has been in use since the earliest days of humankind, and it can be
applied to specimens studied under a microscope even though they may not be accessible for direct
measurement with a standardized scale. There are various approaches for using a transfer scale in
microscopy, including placing the scale on a transparent material for use with a drawing tube or con-
ducting measurements directly on a projected image. An alternative method is to photograph or engrave
the scale onto a glass element, which can be placed in the optical path at one of the image-forming con-
jugate planes of the microscope, so that it can be observed in sharp focus superimposed on the specimen
image. Before a quantitative measurement is done, the arbitrary divisions of the transfer scale must be
calibrated by comparison with the absolute graduations of a master scale, such as a stage micrometer.
The critical requirement for superimposing a graduated scale onto a specimen in such a manner
that it can be imaged together with the specimen is to place the scale in a suitable conjugate plane
of the microscope. Two primary sets of principle conjugate focal planes occur along the optical axis
of a properly focused and aligned compound microscope. One set of planes consists of four image-
forming or field planes (Figure 2.3), whereas the other set consists of four illumination or aperture
planes. Each plane within a set is termed conjugate with the other planes in the set because the
planes are simultaneously in focus and can be viewed superimposed on one another when observ-
ing specimens through the microscope. An object placed in one plane of a conjugate set appears in
sharp focus at all the other conjugate planes of the same set. Obviously, if a scale must be visible
and in focus while observing the image of a specimen, then the scale must be placed in one of the
image-forming sets of planes.
37
Macroconidium
Germinating
Micro conidium
conidia
Conidia Wall (Peridium) Conidia
Conidiophore
Host tissue
Setae
Oil
C globule
Conidiophore Conidiophore Germ

Conidia tube
(a) (b) (c) (d)
FIGURE 2.1 Camera lucida sketches of (a) the pycnidium of a fungus, (b) Fusarium sp. macro and micro-
conidium, (c) acervulus, setae, and conidia of Colletotrichum gloeosporoides, and (d) the conidial structure
and conidial germination of Colletotrichum gloeosporoides.
Overlapping reticles and

micrometer scales
Eyepiece Slide
(Ocular) 0 0.0
1
0.1
2
3 0.2
0 0.0
1 4
2 0.1
3 5 0.3 0.2
4
5 6 0.3
6
7 0.4 0.4
7
8 8 0.5
0.5 Stage micrometer
FIGURE 2.2 Eyepiece reticles and stage micrometers.
Potential
Retina
measuring reticle
image
locations
plane Camera
Eyepiece
image
Eyepiece fixed
plane
fixed diaphragm
diaphragm Field diaphragm
Objective
Specimen
plane
Specimen
plane
Condenser
aperture
Field
diaphragm
Partially coherent light
source
Field diaphragm
FIGURE 2.3 Image-forming conjugate planes in the optical microscope.

Micrometry 39
2.4 EYEPIECE DESIGNS

The image-forming conjugate in a set has an alternative location, that is, an intermediate image
plane, at which a measuring scale can be inserted. This plane coincides with the diaphragm fixed
to the eyepiece, which is generally easily accessible (Figure 2.4). Nearly any eyepiece can be fitted
with a scale in the focal plane, converting the eyepiece into a measuring device for specimen fea-
tures observed through the microscope. Eyepiece scales are often referred to as reticles, although
the terms reticules or graticules are commonly used in the same sense and are frequently encoun-
tered in literature. The most common conventional eyepieces differ with respect to the physical
location of the fixed diaphragm. Some eyepiece designs position the diaphragm at the center of
the unit (between the lenses), whereas other models have a fixed diaphragm at the base of the
eyepiece, beneath and external to the lens assembly. In both eyepiece styles the field diaphragm is
located at the intermediate image focal plane, but the external diaphragm design is preferred for
measurement because any reticle, pointer, or other scale will be outside the optical system of the
eyepiece.
2.4.1 Types of Eyepieces

One of the simplest eyepiece designs, known as the Huygenian (or Huygens) eyepiece, consists of
two plano-convex lenses mounted with their convex faces oriented toward the objective (Figure 2.4).
The lens nearest to the eye is referred to as the eye lens, and the one closest to the objective is termed
the field lens. Eyepieces of this type are uncorrected for optical aberrations and have the disadvan-
tage of the image plane being located between the two lenses (internal diaphragm). Therefore, reticle
accuracy is affected by aberrations of the eye lens alone, whereas the specimen image suffers from
any optical defects arising in the field lens as well.
The Ramsden eyepiece has a construction motif similar to that of the Huygenian eyepiece except
that the field lens is oriented with the plane surface facing the objective (Figure 2.4). In addition,
the focal plane and diaphragm are located outside the optical system (external diaphragm design),
just beneath the field lens. A reticle or similar scale placed in the diaphragm experiences less
distortion than with the Huygenian design, and any optical aberrations of the eyepiece affect the
specimen and reticle images equally. One of the primary applications of the Ramsden eyepiece is
in micrometry.
For the introduction of infinity-corrected optical systems, compensating eyepieces are utilized
to assist in the correction of chromatic aberration. These eyepieces are generally constructed with
two separate lenses, one or both of which are doublets or triplets (Figure 2.4, widefield eyepiece).
Compensating eyepieces can be identified by the color fringe appearing around the inside edge of
the fixed diaphragm when the eyepiece is viewed in front of a bright light source (ordinary eyepieces
display a blue fringe, whereas compensating eyepieces exhibit a yellow, orange, or blue fringe).
Eye lens Eye lens

Widefield Eyecup
Eye Internal
lens lens
Reticle
elements
Reticle
Reticle Field
Field lens
lens
Huygenian Ramsden Compensating
FIGURE 2.4 Microscopy eyepiece anatomy and reticle location.

Chromatic difference of magnification, an aberration common to all high-power objectives, can be

corrected by coupling the optical system to a compensating eyepiece. In addition, compensating
eyepieces are designed to correct image curvature to a limited extent.
2.5 STAGE MICROMETER

Linear measurement requires the comparison of the object to be measured with a standardized
scale, such as a ruler. In utilizing eyepiece reticles or micrometer eyepieces for measurements in a
microscope, the arbitrary units of the transfer scale (reticle), which is superimposed on the speci-
men image, must be converted to absolute units such as millimeters or micrometers. The calibration
of reticle scale graduations is commonly performed by imaging a stage micrometer with the same
objective used for specimen measurements (Figure 2.5). Proper calibration involves determining
an absolute distance on the stage micrometer, imaged in place of a specimen, which corresponds
to one division of the scale in the eyepiece reticle. This value is often referred to as the micrometer
value or calibration factor for that particular objective. Once the value is determined, the size of any
specimen feature may be calculated by multiplying the number of eyepiece reticle divisions spanned
by the feature with the calibration factor for the objective in use.
Stage micrometers designed for applications using transmitted-light microscopes consist of stan-
dard-sized microscope slides (1 × 3 in.) that have scales of defined length attached directly to the
surface or, preferably, sandwiched beneath a cover glass of known thickness. Micrometers com-
monly have a graduated scale, either 1 or 2 mm in length, subdivided into units that are one-tenth of
a millimeter in length (100-μm units). Each 100-μm unit is further divided into 10 equal sections,
and the smallest graduation represents 10 μm.
2.5.1 Counting Chambers Stage Micrometer

Included in the broad category of stage micrometers are calibration scales, finder reticles, and count-
ing chambers (Figure 2.6). Finder reticles are utilized for locating a region of interest on a specimen,
whereas counting chambers are designed to enable particle and cell counts in a specific volume of
liquid. Counting chambers are widely used for counting blood cells and spermatozoa and consist
of a thick glass slide (Figure 2.6) that has a central polished and ruled platform. The platform is
positioned a short distance (typically 0.1 mm) beneath twin polished coverslip supports to create
a chamber that can be filled with a precise quantity of fluid. In practice, a clean glass coverslip is
placed over the chamber and centrally positioned on the polished supports. The gap between the
ruled counting platform and the coverslip equals 100 μm, and the ruled (engraved) face is divided
into squares of exact dimensions. As a result, the volume of the liquid placed in the chamber can
be easily calculated to yield an accurate analysis of the number of particles (cells) present per unit
volume in a suspension.
30
20 30
0 1 2 3 4 5 6 7 8 0 1 2 3 4 5 6 7 8 0 1 2 3 4 5 6 7 8
20
0 1 2 3 4 5 6 7 8 0 1 2 3 4 5 6 7 8 0 1 2 3 4 5 6 7 8
(a) (b) (c)
FIGURE 2.5 (a) Stage micrometer overlapping with ocular, (b) synchronization of division of stage and
ocular micrometer, and (c) with object.
Micrometry 41
Counting Hemocytometer
chamber
Coverslip
Thick glass slide
Polished coverslip
mounted support Specimen insertion
FIGURE 2.6 Counting chamber stage micrometer.
2.6 FILAR EYEPIECE MICROMETER

The standard eyepiece reticle, when combined with a precision stage micrometer, provides a rapid,
convenient, and accurate means of conducting measurements in the microscope. However, for
easier and more precise measurements (with greater objectivity), a specialized vernier micrometer
eyepiece known as the filar eyepiece micrometer is often considered essential. This specialized
eyepiece micrometer utilizes the same principle as a standard eyepiece and reticle combination
but features a moveable line rule (or line rule group) in addition to a fixed or mobile graduated
scale positioned in the focal plane. A filar micrometer avoids the necessity of estimating frac-
tions of a division on a stage micrometer (a difficult and subjective maneuver), which can lead to
considerable error.
The mobile line rule group in a filar micrometer is designed to translate across the field of
view, traversing a fixed vernier scale, by means of a precision screw mechanism that is oper-
ated by rotating an external drum. In general applications, a single rule or other reference point
(depending on the particular design) is aligned with one end of the specimen feature to be mea-
sured and a reading of the calibrated drum is noted. The drum is then rotated to move the ref-
erence line across the specimen feature, and a second reading is taken on the drum scale. The
difference between the two readings yields an apparent linear dimension of the specimen feature
measured and, when calibrated with a stage micrometer, enables an absolute determination of the
feature size.
Some filar micrometer design variations incorporate an additional movement of the reticle scale
by the external drum, which allows zeroing of the drum scale after the reference line is positioned
at the first edge of the object to be measured. This feature enables each measurement to begin with
the drum scale set at zero and avoids the necessity of determining the difference between the two
drum readings. For most filar micrometers, the primary reticle scale has a travel distance of 10 mm.
The scale is also divided into 100 graduations with each division representing 0.1 mm. The drum
of the micrometer screw is also divided into 100 intervals, so that one interval of the drum division
corresponds to a 0.1 interval of the eyepiece scale. One full rotation of the drum translates the mea-
suring rule (line) across one interval of the eyepiece scale.
Several modern filar eyepiece micrometer styles contain an internal zoom lens system that eases
calibration of the micrometer with different objectives. The lower portion of the eyepiece contains
Eye lens
Diopter adjustment
Graduate scale
Ruled line
Graduated recticle Micrometer shift knob

Eyepiece barrel
Eye tube clamping screw
FIGURE 2.7 Filar eyepiece micrometer anatomy.
a graduated ring that can be rotated to optically alter the effective tube length in order to super-
impose graduations of the stage micrometer directly on the internal scale of the filar micrometer
(Figure 2.7).
2.7 PRINCIPLE OF FILAR EYEPIECE MICROMETER

The basic principle is applicable to the measurement of specimens observed under the microscope,
but in practice it is often not possible with a compound microscope to place a ruler in direct contact
with a specimen (although this is often done in low-magnification stereomicroscopy). Alternative
mechanisms for performing measurements at high magnifications in compound optical microscopy
must be used, and the most common of these is the application of eyepiece reticles in combina-
tion with stage micrometers. A majority of the measurements made with compound microscopes
fall into the size range of 0.2 μm to 25 mm (the average field diameter of widefield eyepieces).
Horizontal distances below 0.2 μm are beneath the resolving power of compound microscopes, and
lengths larger than the field of view of a widefield eyepiece are usually (and far more conveniently)
measured with a stereomicroscope (Benson 2001).
A method has been presented that uses a longitudinal mode splitting laser to sense microdis-
placements and measure air refractivity with very simple construction, large measurement ranges,
high sensitivity, and precision. The phase differences of two power curves of the split modes can be
used to judge the movement direction, and the number of lamb dips and mode-change dips can be
used to measure micrometer displacement. Because of anomalous dispersion, the relative variation
of beat frequency is the function of the change of cavity length, which is the basis of measuring
nanometer displacement (Zhang and Tang 1994).
2.8 WORKING
2.8.1 Components of the Ocular Micrometer
1. If eyepieces that contain ocular micrometers are available, replace the eyepiece in the
microscope with one of them. If it is necessary to insert an ocular micrometer in your
eyepiece, find out from your instructor whether it is to be inserted below the bottom lens
or placed between the two lenses within the eyepiece. In either case, great care must be
Micrometry 43
(a) (b) (c) (d)
FIGURE 2.8 (a), (b), (c), and (d) show the various steps involved with the standardization of the ocular micro-
meter in measuring microbial cells (1µ = 1 × 10−6 m).
taken to avoid dropping the eyepiece or reassembling the lenses incorrectly. Eyepieces
should be disassembled only with your instructor’s prior approval. During the place-
ment of the eyepiece, the graduation should be on the upper surface of the glass disk
(Figure 2.8).
2. Place the stage micrometer on the stage and center it exactly over the light source.
3. With the low-power (10 µm) objective in position, bring the graduations of the stage
micrometer into focus by using the coarse adjustment knob. Reduce the lighting.
4. Rotate the eyepiece until the graduations of the ocular micrometer lie parallel to the lines
of the stage micrometer.
5. If a low-power objective is the objective to be calibrated, proceed to step 8.
6. If a high-dry objective is to be calibrated, swing it into position and proceed to step 8.
7. If an oil immersion lens is to be calibrated, place a drop of immersion oil on the stage
micrometer, swing the oil immersion lens into position, and bring the lines into focus; then,
proceed to the next step.
8. Move the stage micrometer laterally until the lines at one end coincide. Then look for
another line on the ocular micrometer that coincides exactly with a line on the stage
micrometer. Occasionally one stage micrometer division includes an even number of ocu-
lar divisions, as shown in the following example. In most instances, however, several stage
graduations are involved. In this case, divide the number of stage micrometer divisions by
the number of ocular divisions that coincide. The figure you get will be that part of a stage
micrometer division that is seen in an ocular division. This value must then be multiplied
by 0.01 mm to get the amount of each ocular division.
Example: Note that 3 divisions of the stage micrometer line up with 20 divisions of the
ocular micrometer:
Each ocular division = 3 / 20 × 0.01

= 0.0015 μm
= 1.5 μm
9. Replace the stage micrometer with the slides of organisms to be measured.
The micrometric technique can be used for measuring the size of protozoa, algae, fungi, and bacteria.
Experiment: Calibration of Ocular Micrometer

The measurement of minute objects seen under a microscope is called micrometry. The unit of such
measurement is called a micron (µ or micrometer). 1 μm equals 1/1000 of a mm. The ocular or eyepiece
micrometer consists of a diaphragm with a graduated scale unit. The ruled lines superimpose certain
distance markers on the microscopic field, on which parallel lines that are approximately 0.01 mm apart
are etched. By determining how many units of the ocular micrometer superimpose a known distance
on the stage micrometer, the exact distance measured by each division on the microscopic field can be
calculated. Once calibrated, the micrometer can be used to determine the size of various microscopic
objects.
Procedure
1. Carefully, place the calibrated ocular micrometer inside the eyepiece and put it back inside
the tube of microscope.
2. Put a drop of oil immersion in the centre of the prepared slide of object to be measured and
focus properly.
3. Count the number of ocular divisions that occupies a single cell/object. Measure size of 5–10
cells/object and take average of it.
4. Find out the accurate size of the cell/object by multiplying with calibration value of ocular
micrometer.
Results
For example, if the cell/object occupies 5 divisions of ocular micrometer and the calibration value of the
ocular micrometer is 2.5 µm, the size will be 5 × 2.5 µm = 12.5 µm.
SUGGESTED READING
Beach, C. B., and F. M. McMurry et al. 1911. The New Student’s Reference Work, Vol. 3. Chicago: F. E.
Compton and Company.
Benson. 2001. Microbiological Application: Laboratory Manual in General Microbiology, 8th ed. New York:
McGraw−Hill Companies.
Zhang, S., and M. Tang. 1994. Principle for measurement of micrometer and nanometer displacement and air
refractivity based on laser mode split technology and lasing action. Optical Engineering 33: 3381–87.
IMPORTANT LINKS
1. Stage micrometer: http://www.opticsplanet.net/nikon-stage-micrometer-a-1mm-in-mbm11100.html
2. Filar eyepiece micrometer: http://www.lomoplc.com/Micrometer%20Eyepieces.htm
3 Electrochemical Techniques
3.1 INTRODUCTION
Ordinary laboratory voltmeters cannot be used for the measurement of electron motive force (emf)
of glass electrode cells because of the high electrical resistance of glass electrodes (typically,
10–200 MΩ). Special high-impedance voltmeter circuits are required, which draw 10–12 A or less
from the circuit. The pH meter is a voltmeter but with several critical additional functions. It mea-
sures potential across the pH-sensing and reference electrode system, converts the potential differ-
ence measurement at a given temperature into pH terms, and provides (pH-metry) mechanisms to
correct for the nonideal behavior of the electrode system. An operational amplifier not only serves
as a high-impedance voltmeter but provides stability and automatic operation through the use of
a feedback loop. The operational controls on a pH meter are best understood by referring to the
operational manual provided by the manufacturer for an individual instrument. Modern electronic
techniques permit the production of a simplified pH meter that measures pH with an accuracy
of +0.1 pH unit. The microprocessor-equipped pH meters include a temperature probe to display
temperature compensation, a memory to store pH values of standard buffers, a waiting period to
allow draft before taking pH readings, and built-in diagnostics to alert for electronic malfunctions
or defective electrodes. Along with a pH meter, we also require a reference electrode and a glass
membrane electrode, which act as indicator electrodes in pH measurement.
3.2 STRUCTURE OF A pH METER

3.2.1 Glass Membrane Electrodes
The pH glass electrode, although it is somewhat mechanically fragile, resists a variety of sample media
and, with the exception of hydroxide, is largely free from interferences. Moreover, pH-sensitive glass
electrodes form the basis of many successful sensors for environmentally sensitive gases. Thus, glass
membranes represent an important class of solid-membrane ion-selective electrodes (ISEs).
As illustrated in Figure 3.1a, these electrodes have a thin glass membrane fused to the end of a
hard glass or, sometimes, epoxy body. The main body of the electrode contains an internal reference
electrode, typically Ag/AgCl, and is filled with a solution that is usually aqueous HCl of concentra-
tion around 0.1 M. The selectivity coefficient of glass membrane is such that excellent dissemination
is achieved against common cationic species.
A pH electrode responds to hydrogen ions as a result of the thin ion-exchange sites existing on
the surface of a hydrated glass membrane. The electrode consists of a thin layer of glass, typically
about 50 μm thick. Charge is transported across the membrane by sodium or lithium ions within the
glass. The membranes are primarily made from lithia (lithium oxide) or sodium oxide, SiO2, and
some amount of Al2O3 and B2O3 or multicomponent glasses whose sensitivity pattern depends on
the composition of the glass. The surface layer of the glass consists of silicate group associated with
sodium ion (−SiO−Na+), as shown in Figure 3.1b. When this electrode is dipped in water, sodium
ions are exchanged with the protons in water.
Determination of pH using glass electrodes is a very accurate and widely used method despite
there being a few disadvantages. For example, the glass membrane is very fragile, so it requires great
care while using. Therefore, the varying potential of a glass electrode can be compared to an external
reference electrode, such as a calomel electrode, producing steady potential by joining internal and
45
Electrode
beads
Interfacial region
AgCl covered
silver wire
Solution
Glass
H+ Na+O+ Si
Internal solution
HCl
Glass membrane
(a) (b)
FIGURE 3.1 A glass electrode: (a) typical glass electrode consisting of both an indicator glass electrode and
a silver/silver chloride reference electrode, and (b) illustration showing ion exchange.
external reference electrodes. An ordinary potentiometer cannot be used for measuring the potential
of the glass electrode. Therefore, electronic potentiometers must be used; they need frequent stan-
dardization, and they cannot be used in pure ethyl alcohol, acetic acid, and gelatin. The following fea-
tures of a glass electrode make it more versatile for use as an indicator electrode for pH measurement:
• A glass electrode can be used in the presence of strong oxidizing and reducing solutions
in viscous media and even in the presence of proteins that interfere with the operation of
other electrodes.
• It can be used for solutions with pH values of 2–10; using some special glass electrodes,
measurements can be extended to pH values greater than 10.
• It is simple to operate and immune to poisoning.
• Equilibrium can be reached quickly.
3.2.2 Reference Electrode

The two most popular types of reference electrodes are saturated calomel and silver/silver chloride
systems. Both types of reference electrodes exhibit many ideal characteristics, including maintain-
ing fixed potential over time and temperature, having long-term stability, and returning to the initial
potential after being subject to small currents. It may be either a separate probe (Figure 3.2a) or built
around the glass electrode giving a combination electrode (Figure 3.2b):
1. A saturated calomel electrode (SCE) is composed of metallic Hg, solid mercurous chloride
(Hg2Cl2), and a saturated solution of KCl for maintaining an equilibrium. Consequently,
the potential of the SCE (+0.241/2 V versus the potential of the standard hydrogen elec-
trode) remains constant even if some of the liquid evaporates over time. The SCE is more
popular with a constant temperature bath, which gives the SCE the capacity to eliminate
error caused by fluctuating temperature. The SCE can be used as a reference electrode in a
sample that does not exceed 80°C.
2. The Ag/AgCl electrode includes a silver wire, which is coated on one end with the insol-
uble AgCl salt. When the electrode is immersed in saturated KCl solution, its potential
Electrochemical Techniques 47
pH meter
pH meter
Inlet for
KCl
Pt wire Mercury and

Glass mercurous
Calomel electrode
electrode chloride paste
Hg2Cl2 and Hg
Ag
Saturated
KCl KCL solution
KCl
Solid KCI
Membrane of
special glass Porous plug
(a) (b)
FIGURE 3.2 Reference electrodes: (a) a calomel reference electrode, and (b) a combination electrode.
at 25°C depends only on the Cl− concentration and is +0.192 V versus the potential of
the standard hydrogen electrode. The Ag/AgCl electrode should not be used in solutions
in cases of experiments containing bacterial species that may precipitate or complex
with silver.
If a combination electrode is in use, the level of test solution should be kept high enough to
cover the liquid junction, but it should not be above the salt bridge solution in the external electrode
because it is essential for KCl to diffuse slowly in the test solution. The reference electrode should
be prepared and maintained so that the level of the internal liquid is kept above that of the sample
solution to avoid infusion of the sample into the reference electrode. This is a commonly used pre-
cautionary measure to avoid any contamination of the sample by Cl−, Ag+, or Hg2+ ions.
3.3 PRINCIPLES
pH is a measure of the hydrogen ion activity of a solution, which defines the degree of acidity or
alkalinity of the solution. Therefore, pH is the unit of measurement for acidity, as pounds are for
weight. Acidity is a chemical parameter; it is a concentration. But due to the wide measurement
range and unwieldy nature of chemical notations, R. L. Sorensen, a Danish chemist who developed
the pH scale in 1909, defined pH as the negative logarithm of hydrogen ion concentration, which he
later changed to hydrogen ion activity:
pH = − log10 [H + ]
This gives a concentration of about 0.0000001 M hydrogen ions as pH 7.

The pH electrode depends on ion exchange in the hydrated layers formed on the glass electrode
surface. Glass consists of a silicate network through which metal ions are coordinated to oxygen
atoms, which causes the exchange of metal ions with H+. Measuring the pH of a solution with a
potentiometric cell requires the use of a pH-sensitive glass electrode, a reference electrode, and a
high-input-impedance voltmeter. The output of the cell is temperature sensitive in accordance with
the Nernst equation, so a temperature electrode is also included in most systems. Walther Nernst first
elucidated the theory of galvanic cells in 1889, which relates the voltage of a cell to its physical and
chemical properties. For pH, the equation is as follows:
E = E ^ sub 0 ^ 2.3 RT / F log a^ sub H

At 25ο C, this becomes
E = E* + 0.059 pH
Here, E is the voltage of the cell; E^sub 0^ is the standard voltage of the cell; E* includes the stan-
dard electrode potential of glass electrode, potential of the reference electrode, and liquid-junction
potentials between the reference electrode and the solution; R is the universal gas constant; F is
the Faraday constant; and T is the temperature in degrees Kelvin. The term 2.3RT/F is the Nernst
number or slope.
3.4 FACTORS LIMITING THE ACCURACY OF pH MEASUREMENTS

The factors limiting the accuracy of pH measurements are as follows:
Alkaline error: It has been noted that in a high pH range (above 9 or 10 pH units), the ordinary
glass electrode becomes sensitive to alkali ions and gives a low reading. The reason for this
error is that, although the glass membrane is selective to hydrogen ions, it also responds to
other ions. This error becomes more significant when the activity of other ions is greater
than the activity of the hydrogen ions.
Note: Alkaline error is relatively more frequent in the case of sodium ions because of
the higher selective coefficient of sodium ions. This occurs because sodium ions can be
reduced by the use of Li2O glass in place of Na2O glass.
Acid error: At a low pH range (pH less than 0.5), the values determined by the glass
electrode tend to be somewhat higher. This error is the result of ignoring the activity
of water while writing the Nernst equation for the indicator electrode. It is assumed
that the activity of water may be taken as unity, as it is in excess in the solution and
behaves as a pure substance. However, in highly acidic solutions, the activity of water
becomes less than unity because a good amount of water is used in hydrating the pro-
tons. Similar effects are also observed upon addition of large amounts of any dissolved
salt and addition of a miscible nonaqueous solvent such as ethanol. This results in an
increased pH value.
Variation in junction potential: In most cases, the compositions of the standard buffer solu-
tion and the test solution are different. In such situations, the liquid-junction potential will
be different and the standard uncertainty will be ±0.015.
Error in the pH of the standard buffer: This may result from inaccurate composition of a
buffer solution during preparation or storage will cause an error in subsequent pH mea-
surements and a standard uncertainty of up to ±0.01 (Table 3.1).
Temperature: A change in temperature may affect pH measurement with an uncertainty error
of ± 0.005 because the change in temperature affects the activities of ions as well as the
liquid-junction potentials. Therefore, it is advised to calibrate the electrode at the tempera-
ture of the test solution.
Calibration procedures: Buffer solutions cannot be prepared with more accuracy than ±0.01
pH units. Therefore, we cannot calibrate the electrode with a better accuracy than this value.
Equipment-related errors: These errors may result from power fluctuations, parallax errors in
reading analog scales, and so on.
3.5 MEASUREMENT OF pH
pH measurements are used to check and control many aspects of our day-to-day life, such as in
determining potable water quality, soil usability for different plants, and water quality in aquaris-
tics; they are performed to control industrial processes, in wine making and beer making, to check
milk quality, and to check the quality of cosmetics. There is no need to mention all the laboratories
throughout the world where pH measurements are performed many times a day to control reactions
and analysis conditions.
There are several ways in which pH can be measured; of them, two methods are widely used.
First, one of the simple, and often precise, methods is the use of colorimetric indicator methods,
that is, use of pH strips (pH papers). Second, a more costly and demanding method in terms of
procedure, but giving much more precise results, is the potentiometric method, which uses glass
electrodes and pH meters (Figure 3.3). Colorimetric (spectroscopic) methods have never gained
much popularity, although they are occasionally used in places where glass electrodes are in use.
TABLE 3.1
High-Purity Salts as Primary pH Standard
pH at Stated Temperature
Concentration
High-Purity Salts (g/L) 15°C 20°C 25°C 30°C
Potassium tetraoxolate 12.61 1.67 1.68 1.68 1.68
Potassium hydrogen phthalate 10.13 4.00 4.00 4.01 4.02
Potassium dihydrogen phosphate 3.39 6.90 6.88 6.87 6.85
Disodium hydrogen phosphate 3.53 6.90 6.88 6.87 6.85
Sodium tetraborate decahydrate 3.80 9.28 9.23 9.18 9.14
Sodium hydrogen carbonate 2.09
Sodium carbonate 2.64 10.12 10.06 10.01 9.97
Note: The uncertainty of the tabulated pH values is estimated to be ±0.01.
FIGURE 3.3 Analog pH meter.

3.6 WORKING
3.6.1 Potentiometric Method of pH Measurement
The pH is determined by measuring the emf of a cell comprising an indicator electrode (an elec-
trode responsive to hydrogen ions such as a glass electrode) immersed in the test solution and a
reference electrode (usually an SCE); contact between the test solution and the reference electrode
is achieved by means of liquid junction, which forms the part of a reference electrode. The emf of
this cell is measured with pH.
3.6.2 Reagents Used in the Potentiometric Method of pH Measurement

3.6.2.1 C alibration of the Electrode System against Standard
Buffer Solutions of Known pH
Buffer tablets having pH values 4.0, 7.0, and 9.2 are commercially available. Because buffer
solutions may deteriorate as a result of mold growth or contamination, prepare fresh solution as
needed. Alternatively, buffer solutions can be prepared by the methods discussed in Sections 3.6.2.2
through 3.6.2.4.
3.6.2.2 pH 4 Buffer Solution

Dissolve 10.2 g of anhydrous potassium biphthalate (KHC8H4) in boiled and cooled distilled water.
Dilute to 1 dm3.
3.6.2.3 pH 7 Buffer Solution

Dissolve 1.361 g of anhydrous potassium dihydrogen phosphate (KH2PO4) and 1.42 g of anhydrous
disodium hydrogen phosphate (Na2HPO4), both of which have been dried at 110°C to 130°C, in
distilled water. Use distilled water that has been boiled and cooled. Dilute to 1 dm3.
3.6.2.4 pH 9.2 Buffer Solution

Dissolve 3.81 g of borax (Na2B4O7 10H2O) in distilled water and dilute to 1 dm3.
3.7 PROCEDURE FOR MEASURING pH USING A pH METER

Numerous pH meters of various designs are marketed by instrument manufacturers. General-
purpose pH meters are either line-operated instruments that are readable to 0.05 pH unit or battery-
operated instruments suitable for field jobs. Nowadays, digital pH meters readable to 0.01 pH unit
are more popular compared to scale-needle instruments. The pH of a solution can be measured with
the instrument (analog meter) shown in Figure 3.3, following the procedure given here in a stepwise
manner:
1. Keep the selector switch at the zero position and adjust the zero position with a screwdriver
if the pointer does not indicate zero.
2. Before using the pH meter, remove electrodes from storage solutions (recommended by
manufacturers) and rinse with distilled water. Electrodes should be dried by gently blotting
with a soft tissue paper.
3. Mount the electrodes in the clip on the stand.
4. Connect the power cable to a 220 V alternating current (AC) supply. Switch on the instru-
ment and wait for a few minutes until the instrument warms up.
5. Adjust the temperature/solution temperature value.
6. Put the standard buffer solution of desired range (e.g., buffer of pH 4 for acidic solutions) in
a beaker. The electrode assembly is immersed in the pH reference buffer, and the solution
is agitated gently by swirling the solution in the region of the glass electrode surface so as
to bring it into pH equilibrium. Ascertain that the glass electrode membrane is completely
immersed in the solution. The electrodes should not touch each other, or the sides or bottom
of the beaker.
7. Put the selector switch to a suitable pH range (0–7 for acidic or 7–14 for basic solutions),
and adjust the buffer knob so that the pointer reads the pH of the standard buffer solution
(placed in the beaker).
8. Put the selector switch back to the zero position. Remove the electrodes from the buffer
solution, wash the electrodes with distilled water, and wipe them gently with tissue paper.
9. Immerse the electrodes in a second buffer with pH below 10, approximately 3 pH units
different from the first one; the reading should be within 0.1 units for the pH of the sec-
ond buffer. (If the meter response shows a difference greater than 0.1 pH units from the
expected value, the electrodes or the pH meter may be at fault.)
10. Transfer the standard buffers back to the storage bottle and wash the beaker well with
distilled water.
11. Take the sample solution in the beaker. Introduce the electrodes to the solution and swirl it
gently.
12. Set the selector switch in the suitable range position and read the pH on the scale.
13. Put the selector switch back to the zero position. Remove the electrodes from the solution,
wash them with distilled water, and keep the electrodes in distilled water when not in use.
3.7.1 Modified Glass and Solid-State Membrane Electrodes

Glass electrodes can be made selective for ions other than hydrogen ions with some modifications.
These modifications achieved by changing the composition of the glass and the internal solution of
the glass electrode. By adding aluminum oxide to sodium oxide and silicon oxide glass, and changing
the internal filling solution from hydrochloric acid to sodium chloride, the glass electrode becomes
selective to Na+ ions. There is another types of glass electrode made up of Li2O, Al2O3, and SiO2,
which can be also be used as sodium electrode. Sodium electrodes have many applications in the
measurement of sodium in water analysis and in biological fluid analysis. For measuring potassium
and ammonium ions, modified glass containing 27% Na2O, 4% Al2O3, and 69% SiO2 is used. These
days, potassium/ammonium electrodes are replaced by other ISEs using more selective membranes.
3.7.2 Solid-State Membrane Electrodes

In solid-state membrane electrodes, we use a doped single-crystal membrane in place of a glass
membrane. This change enables us to design electrodes which respond to a number of different
anions and cations, such as F−, Cl+, and Ag+ (Figure 3.4).
In this electrode system, similar to a glass electrode system, the internal solution and electrode
form the internal reference. For example, fluoride ISE consists of LaF3 membrane and an internal
Ag, AgCl reference electrode immersed in an internal solution of KF and KCl. The LaF3 membrane
is highly selective and responds to fluoride ions only.
3.7.3 Storage Conditions for Glass Probes

The following conditions must be met for storing glass probes:
1. When not in use, the glass probe tip must be kept wet at all times to avoid dehydration of
the pH-sensing membrane and subsequent dysfunction of the electrode.
2. A glass electrode by itself (i.e., without a combined reference electrode) is typically stored
immersed in an acidic solution with a pH of around 3.0. In an emergency, acidified tap
Coaxial cable
Electrode
Epoxy resin
cover
Electrode
Solid electric
internal contact
Selective
membrane:
Epoxy resin Ag2S CdS
(a) (b)
FIGURE 3.4 Typical solid state electrode with its (a) outer and (b) inner view.
water can be used, but distilled or deionized water must never be used for long-term probe
storage as the relatively ionless water “sucks” ions out of the probe membrane through dif-
fusion, which degrades it.
3. Combined electrodes (glass membrane + reference electrode) are better stored immersed
in the bridge electrolyte (often 3 M KCl) to avoid diffusion of the electrolyte (KCl) out of
the liquid junction.
3.8 CLEANING AND TROUBLESHOOTING OF GLASS PROBES

Cleaning and troubleshooting of glass probes must be performed at regular intervals to ensure they
work properly:
1. Occasionally (about once a month), the probe may be cleaned using the pH-electrode
cleaning solution; generally, 0.1 M solution of hydrochloric acid (HCl) is used, which has
a pH of about 1.
2. In the case of strong degradation of glass membrane performance due to membrane
poisoning, diluted hydrofluoric acid (HF < 2%) can be used to quickly etch (<1 min-
ute) a thin damaged film of glass. Alternatively, a dilute solution of ammonium fluoride
(NH4F) can be used. To avoid unexpected problems, however, the best practice is to
always refer to electrode manufacturer recommendations or a classical textbook on ana-
lytical chemistry.
3.9 APPLICATION OF pH MEASUREMENTS

pH measurements have many applications, some of which are summarized in the following list:
• pH-metric or electrometric methods help in detecting the end point of acid–base titration
more accurately and precisely as compared to indicator methods.
• pH-metry is an important analytical tool in studying the acid–base equilibrium, which
is controlled by the carbon dioxide–bicarbonate–carbonate equilibrium system in most
natural waters.
• The estimation of alkalinity and acidity based on pH-metry serves to provide useful infor-
mation regarding the buffering capacity of water.
• In water and wastewater treatment, pH measurement gives an estimate of the alkalinity
required to react with the coagulant, that is, alum, ferrous sulfate, and so on, or otherwise
to be supplemented with lime.
• pH measurements are used in industrial process control, especially in batch or flow-through
configurations, through online pH-monitoring and chemical-dosing systems.
• In neutralization of wastewaters, pH is measured to evaluate the doses of acid or alkali to
be added.
• pH measurements are useful in the development of biosensors-based pH-sensitive immobi-
lized enzymes and in other academic studies.
Further, the flexibility in available configurations allows the ions to be monitored in a single sample
solution (batch mode) or continuously in a flow-through apparatus (flow-injection analysis).
3.10 OXYGEN ELECTRODE

The Clark-type electrode is the most used oxygen sensor for measuring oxygen dissolved in a liq-
uid. The basic principle is that there is a cathode and an anode submersed in an electrolyte. Oxygen
enters the sensor through a permeable membrane by diffusion and is reduced at the cathode, creat-
ing a measurable electrical current. There is a linear relationship between the concentration of oxy-
gen and the electrical current produced. With a two-point calibration (0% and 100% air saturation),
it is possible to measure oxygen in the sample.
There are several types of oxygen electrodes, which differ in design, but the most common one is
the Clark-type electrode. It utilizes an annular silver reference electrode (anode) and a glass-coated
platinum electrode (cathode) connected to a small external voltage source that charges the circuit
with a potential difference of 500–700 mV. This is called polarizing voltage. Oxygen gets reduced
at the cathode giving rise to a current, which is proportional to the concentration of oxygen in the
solution provided that the polarizing voltage remains constant at approximately 700 mV. Oxygen
from the solution diffuses in through a thin semipermeable membrane, which separates the elec-
trodes from the test solution (Figure 3.5). Both electrodes are immersed in the same solution at
saturated KCl.
One drawback to this approach is that oxygen is consumed during pH measurement with a rate
equal to diffusion in the sensor. This means that the sensor must be stirred in order to get the cor-
rect measurement and avoid stagnant water. Oxygen consumption increases with increasing sensor
size, and so does stirring sensitivity. In large sensors, there also tends to be a drift in the signal
over time due to consumption of the electrolyte. However, Clark-type sensors can be made very
small, with a tip size of 10 µm. The oxygen consumption of such a microsensor is so small that it
is practically insensitive to stirring and can be used in stagnant media such as sediments or inside
plant tissue.
Rubber O ring
Constant temperature Stopper
jacket
Water out
Magnetic follower
Reaction vessel
Teflon
Locking ring membrane
KCI solution
in lens tissue
Rubber O ring
+ve
Annular silver –ve
anode Leads to polarising
unit
Platinum
cathode
FIGURE 3.5 Diagram of the oxygen electrode.
The electroreduction of oxygen at the cathode, which gives rise to electrical current, occurs
according to the following equations:
O 2 + 2H 2 O + 2e − → H 2 O 2 + 2e − → 2OH −
OH − + KCl → KOH + Cl −
The electrons required for this electroreduction reaction are produced at the reference electrode
(anode) as follows:
4Ago + 4Cl − → 4AgCl + 4e −
The whole unit is mounted on a magnetic stirrer and a magnetic follower (flea) placed inside
the reaction vessel. This ensures that the test solution is constantly stirred so as to obtain correct
values of change in dissolved oxygen levels. Since the rate of dissolution of oxygen is temperature
dependent, it is important to maintain constant temperature. This is achieved by circulating water
in a water jacket around the reaction vessel. Both the water jacket and the reaction vessel are made
of a special type of transparent plastic so that photosynthetic studies requiring the use of light can
be carried out.
The unit is connected to a control box, which takes electrical signals from the electrode and
conveys them to a chart recorder. The semipermeable membrane used is generally made of Teflon.
This is highly permeable, leading to quick establishment of equilibrium, but it responds differently
for the same values of dissolved oxygen in gas and liquid. Less permeable membranes include
polypropylene and polyethylene membranes, which show little difference in their response to liquid
and gas.
3.10.1 Calibration of the Oxygen Electrode

An oxygen electrode is calibrated in the following manner:
1. Calibration is done with a liquid standard or a gas standard that has been equilibrated with
water vapor. Either standard must be equilibrated to the measuring temperature.
2. The proper scale is selected; certain instruments have more than one scale to accommo-
date the wide ranges sometimes encountered during analysis.
3. A standard, usually distilled water, is added to the reaction vessel; the magnetic follower
is introduced and the instrument is switched on for 30 minutes warm-up time. During this
time, the lid of the reaction vessel is kept open. The pen recorder stabilizes at a particular
point. This is taken as the dissolved oxygen concentration of the standard whose value can
be obtained from Table 3.2.
4. Now, if a few crystals of sodium dithionite (Na2S2O4) are added, all the oxygen is used up
in accordance with the following reaction:
Na 2 S2 O 4 + O 2 + H 2 O → NaHSO4 + NaHSO3
The pen recorder moves a certain distance and stabilizes at a particular point on the chart.
This is the zero point of dissolved oxygen concentration. This point is adjusted with the
zero calibration control of the recorder.
5. This process is repeated several times until the zero concentration and standard concentra-
tion need no further adjustment.
6. The number of divisions between the zero and standard concentrations correspond to the
standard oxygen concentration. Hence, one division represents a certain dissolved oxygen
concentration:
If 10 divisions = x mol 1−1 oxygen
1 division = 0.x mol 11 oxygen
7. The instrument is thus calibrated and ready to determine unknowns.
TABLE 3.2
Standard Value of Dissolved Oxygen
Concentration
Temperature (°C) O2 (ppm) O2 (μmole/mL)
0 14.16 0.442
5 12.37 0.386
10 10.92 0.341
15 9.76 0.305
20 8.84 0.276
25 8.11 0.253
30 7.52 0.30
35 7.02 0.219
3.10.2 Applications of the Oxygen Electrode

The oxygen electrode is being put to increasingly wide uses because of the ease of portability of the
instrument, which is also inexpensive and does not require much expertise in handling.
Clinical uses: The oxygen content of blood requires assessment during oxygen therapy.
Oxygen electrodes have been designed to be small enough to be inserted into a blood ves-
sel; however, this involves the danger of infection or blood clot formation. Hence, a trans-
cutaneous electrode system has been devised to measure oxygen levels in the blood without
having to pierce the skin. In this method, a small area on the skin, say, an earlobe or a
fingertip, is heated externally to 43°C, and the electrode is held tightly to the depilated skin
surface by an airtight bond. A polypropylene membrane separates the heated skin surface
from the electrode assembly, which consists of a polarized platinum cathode surrounded
by a silver ring-type anode held at a constant temperature, usually 43°C. Oxygen in the
blood diffuses from the blood capillary through the skin and the electrode membrane, and
actuates the Clark-type electrode to produce the reading.
Chloroplast and mitochondrial studies: Oxygen evolution in cyanobacteria, algae, and
chloroplasts, that is, those containing photosystem II, can be studied using a sufficiently
illuminated Clark oxygen electrode. The oxygen content of the suspension medium is nor-
mally reduced below 100% oxygen by bubbling nitrogen through it, so that the oxygen
produced stays in the solution and is recorded. In marine biology or limnology, oxygen
measurements are usually carried out in order to measure respiration of a community or
an organism, but they have also been used to measure primary production of algae. There
are, however, commercially available oxygen sensors that measure oxygen concentration
in liquids with great accuracy. Two types of oxygen sensors are available: (1) electrodes
(electrochemical sensors) and (2) optodes (optical sensors). Respiratory control studies and
the effect of various inhibitors on mitochondrial respiration can also be studied using the
oxygen electrode. Inhibitors of respiration slow down the rate of respiration.
Enzyme assays: The activity of enzymes that require oxygen for reaction ego, such as glucose
oxidase and catalase, can be studied using the Clark-type oxygen electrode.
Microorganism studies: Bacteria that use oxygen as a terminal electron acceptor can be stud-
ied using an oxygen electrode, and the effect of electron inhibitors can be determined. The
efficiency of different carbohydrates as respiratory substrates can be studied by comparing
their rates of oxygen uptake. In soil respiration studies, oxygen sensors can be used in con-
junction with carbon dioxide sensors to help improve the characterization of soil respiration.
Typically, soil oxygen sensors use a galvanic cell to produce a current flow that is propor-
tional to the oxygen concentration being measured. These sensors are buried at various
depths to monitor oxygen depletion over time, which is then used to predict soil respiration
rates. Generally, these soil sensors are equipped with a built-in heater to prevent condensa-
tion from forming on the permeable membrane, as relative humidity can reach 100% in soil.
Experiment: Determination of pH of the Given Water/Soil Sample

Principle
pH is the measure of the relative acidity or alkalinity of a solution and is represented as the negative
logarithm of the concentration of free hydrogen ions in a solution. The “p” of pH denotes the power of
hydrogen ion activity in moles per liter:
pH = − log10 ( H + ) = log10 × 1/( H + )
When two electrodes are dipped in two solutions of different pH levels and connected with each
other, a potential difference is set up between the two electrodes, which is measured using a potentiom-
eter. This is directly related to the pH of the solution.
The pH is measured of H+ ion concentration in an aqueous medium. Chemically, pure water at

25°C is dissociated equally into H+ and OH– ions with 10 –7 H+ per litre. If the number of free H+ ions
is greater than the number of OH– ions, the water is acidic; otherwise, the water is alkaline. The term
pH is expressed as the negative logarithm of H+ concentration. Thus, pH 7 indicates neutral water, pH
below 7 indicates acidic solution, and pH values 7–14 indicate alkaline solution.
Requirements
pH meter, standard pH buffers, and tissue paper.
Method
The pH can be measured by two different methods:
1. Colorimetric method (using indicators): Commercially available pH papers are used in this
method. A color change of the paper strip on application of a drop of the test sample indicates
the pH, which is matched with the provided standard color chart.
2. Electrometric method (using pH meter): A pH meter with a combined glass electrode is gener-
ally used.
a. Wash electrode with distilled water.
b. Standardize electrode with standard buffers in the range of pH 4–9.2.
c. Adjust temperature knob setting according to that of the sample.
d. Wash the electrode again with distilled water and wipe with tissue paper.
e. Dip the electrode in the test sample and note the pH.
Precautions to be taken when performing the electrometric method are as follows:
a. Soak a new or dried glass electrode for several hours in 0.01 M HCl.
b. There should be no air bubbles either at the ends of the electrode or in the salt bridge.
c. Temperature correction should be performed before starting.
d. After each use, the electrode should be washed with distilled water and wiped clean with
tissue paper.
Experiment: Determination of the pH of Fruit Juice

Principle
The acidity and alkalinity of fruit juice is measured as a pH value.
Procedure
The pH of fruit juice can be determined colorimetrically by the use of various indicators, which are as
follows:
1. pH paper: The color of the pH paper corresponds to a definite pH. A drop of fruit juice is put
on the pH paper and the color of the pH paper is matched with the pH color key provided by
the pH paper manufacturing company.
2. Lovibond comparator: This comparator consists of a Bakelite case with two holes at the top
for tubes of standard bore and of colorless glass. Tube A contains water. The hinged door of
the case holds a rotatable disk containing a series of standard colored glasses corresponding
to various pH values; each glass can be brought in front of tube A in turn and viewed through
aperture A. A solution of the indicator phenol red is added to tube B, which contains fruit
juice, and the pH disk is rotated until a match is obtained. The pH is then read in the aperture
at the bottom of the apparatus.
3. pH meter: This instrument gives an accurate pH reading. Adjust the instrument with a
standard buffer solution of known pH after setting its knob at room temperature. The elec-
trode is then washed with distilled water. Thereafter, the fruit juice is filled in a beaker
and the pH reading is recorded. The electrodes should be washed with distilled water after
every use. When the instrument is not in use, the electrodes should always be immersed in
distilled water.
Experiment: Measurement of the pH of a Soil Sample

Principle
The pH of soil affects plant nutrient availability, microbial and fungal activity, and plant growth. It is
a measurement of hydrogen ion activity in a soil/water solution. Soil pH has many primary determin-
ing factors, such as decomposition of organic material, parent material, rainfall, and anthropogenic
alteration. A neutral solution has a pH of 7, whereas an acidic solution has a pH less than 7. Note that a
basic solution always has a pH greater than 7, but an alkaline solution does not. This is due to the acid-
neutralizing capacity of soil or buffering of a soil by strong bases.
Altering soil pH is a common practice in many fields of plant production, cultivation, and growth.
Methods include addition of organic matter, hydrogen/aluminum sulfate, sulfur, fertilizers containing
ammonium or urea, and liming agents. In this experiment, we will be measuring soil pH.
Reagents
Prepare all the solutions in previously boiled and cooled distilled water.
Standard buffer solutions are as follows:
1. Potassium tetraoxalate (KH3C4O82.H2O): Dissolve 3.175 g KH3C4O82.H2O in water and make
up the solution to 250 mL (pH = 1.68).
2. Potassium tartarate (KHC4H4O6): To 250 mL water in a glass stopper bottle, add excess
KHC4O4O6; shake the bottle vigorously for about 10 minutes to obtain a saturated solution.
Filter and preserve the solution by adding 0.1 g of thymol (pH = 3.55).
3. Potassium phthalate (KHC8H4O6): Dissolve 2.552 g of KHC8H4O6 in water and make up the
solution to 250 mL (pH = 4.0).
4. Potassium dihydrogen phosphate (KH2PO4): Dissolve 0.30 g of KH2PO4, 0.8875 g of Na2PO4,
and 0.8875 g of Na2HPO4 in water and make up the solution to 250 mL (pH = 6.86).
5. Borax (Na2B4O7): Dissolve 0.9502 g of Na2B4O7 in water and make up the solution to 250 mL
(pH = 9.18).
Procedure
1. Warm up the instrument for 15 minutes.
2. Calibrate the instrument with the known buffer solutions. (Calibration is done with a buffer
solution whose pH is close to that of the sample.)
3. Immerse the electrode in the unknown sample, stir for 3 minutes, and note the pH.
Note
Instead of preparing standard buffer solutions, commercially available buffer tablets can be used for
calibrating the pH meter.
Experiment: Measurement of Oxygen Evolution during Photosynthesis

Principle
Oxygen enters the sensor through a permeable membrane by diffusion and is reduced at the cathode,
creating a measurable electrical current. There is a linear relationship between the concentration of
oxygen and the electrical current produced. With a two-point calibration (0% and 100% air saturation),
it is possible to measure oxygen in the sample.
Clark-type electrodes utilize an annular silver reference electrode (anode) and a glass-coated plati-
num electrode (cathode) connected to a small external voltage source, which charges the circuit with a
potential difference of 500–700 mV. This is called polarizing voltage. Oxygen is reduced at the cathode,
giving rise to a current, which is proportional to the concentration of oxygen in the solution provided
that the polarizing voltage remains constant at approximately 700 mV. Oxygen from the solution dif-
fuses in through a thin semipermeable membrane, which separates the electrodes from the test solution.
Both electrodes are immersed in the same solution of saturated KCl.
Requirements
Clark-type oxygen electrode, exponentially growing cyanobacterial culture, 0.05 M phosphate buffer
with a pH of 7.8, 0.1 M KCl, magnetic stirrer.
Procedure
Estimation of photosynthetic O2 evolution: Photosynthetic O2 evolution was measured with a Clark-
type oxygen electrode (Hansatech Instruments, Ltd., United Kingdom). Exponentially growing mea-
sured cyanobacterial cells are placed on a flat platinum cathode that is polarized at 0.6 V with reference
to a large Ag/AgCl electrode. The electrodes are immersed in an electrolyte (consisting of 0.05 M
phosphate buffer with pH 7.8; 0.1 M KCl). The electrodes are separated from the magnetically stirred
assay medium by a Teflon membrane. The difference between the output of the electrode in water in
equilibrium with air and in water in equilibrium with pure N2 was considered to represent 0.235 mol
m–3 in the assay medium. After injection of the same into the assay medium, the medium is illuminated
from the opposite side with a projector lamp. The rate of O2 evolution is determined from the initial
slope of the electrode output as a function of time.
SUGGESTED READING
Akhtar, M. 2007. Method of Analysis and Assay: Potentiometry. Pharmaceutical Analysis.
Cavins, T. J., J. L. Gibson, B. E. Whipker, and W. C. Fonteno. 2000. pH and EC meters—Tools for Substrate
Analysis (Florex. 001). Raleigh: N.C. State University.
Rupert, S. 2005. Principles and guidelines of pH measurement. InTech. North Carolina: Instrument Society of
America NC.
Vytras, K. 1995. Potentiometry. In Encyclopedia of Pharmaceutical Technology, v. 12, edited by. J. Swarbric
and J. C. Boylan. New York: Marcel Dekker.
Walker, D. 1990. The Use of the Oxygen Electrode and Fluorescence Probes in Simple Measurements of
Photosynthesis. Sheffield, UK: Robert Hill Institute, University of Sheffield.
Wilson, K., and J. Walker. 2003. Practical Biochemistry: Principles and Techniques, 5th ed. Cambridge:
Cambridge University Press.
Wilson, K., and J. Walker. 2007. Principles and Techniques of Biochemistry and Molecular Biology. Cambridge,
UK: Cambridge University Press.
IMPORTANT LINKS
1. Membrane electrode: http://www.horiba.com/in/application/material-property-characterization/water-
analysis/water-quality-electrochemistry-instrumentation/ph-guide/1/details/thick-membrane-electrode-
9611-10d-9451/
2. Oxygen electrode:
http://www.enotec.com/en/products-services/products/oxitec/oxitec-5000.Html#c9 35
http://www.hansatech-instruments.com/
http://www.ysilifesciences.com/index.php?page=special-methods-and-applications
4 Chromatography
4.1 INTRODUCTION
What may be called chromatographic effects today were already in use some 2000 years ago. Dyers
were accustomed to judge the quality of their dyes and, in particular, to detect the presence of adul-
terants by letting a drop of solution spread out on a piece of cloth or paper (papyrus). The fringe of
colors formed at the boundary of the spot was a useful diagnostic. This could be the root of paper
chromatography (PC). Around the same time, column chromatography was born in the oil industry,
where crude oils were purified by allowing them to percolate through beds of carbon. However,
as with many great discoveries the exact origin of the process could not be pointed out, although
a few can be appreciated for giving due importance to the process by using it for the separation,
purification, and identification of compounds. The first to give convincing evidence of the power
and versatility of the process was M. S. Tswett, a botanist, who in 1906 isolated the principal
plant pigments by passing them in a solution of petroleum ether through a column of powdered
chalk. Chromatography based on the differential partition between two immiscible solvents was
first described, in 1941, by A. J. P. Martin and R. L. M. Synge. In this process, water was fixed
within silica gel, the mobile phase used was chloroform, and the amino acids of a protein were ana-
lyzed. Subsequently, other classes of compounds, for example, antibiotics, were analyzed. Today,
the technique has developed in all dimensions as perhaps the single most powerful analytical and
preparative method available in the laboratory.
4.2 GENERAL PRINCIPLES

The basis of all forms of chromatography is the differential partition of a compound between two
immiscible phases, one of which is stationary and the other, mobile. The way in which a compound
is partitioned or distributed between two immiscible phases is given by the partition coefficient (Kd):
Concentration in phase A
Kd =
Concentration in phase B
The value of Kd is constant at a given temperature. Depending on the different types of phases
involved, there are different forms of chromatography (Table 4.1). Depending on the mode by which
separation is achieved, there are three types of chromatography:
1. Column chromatography, in which the stationary phase is packed into glass or metal col-
umns and the mobile phase percolates through the column.
2. PC, in which the stationary phase is supported by cellulose fibers of paper and the mobile
phase moves through the interstitial spaces by capillary action. Sometimes, the cellulose
fibers of the paper act as the solid stationary phase.
3. Thin-layer chromatography (TLC), in which the stationary phase is thinly coated onto
glass plates and the mobile phase moves along the stationary phase.
61
TABLE 4.1
Types of Chromatography
Form Phase Mobile Phase Stationary Phase Principle of Separation
1. Adsorption or solid–liquid Liquid Solid Adsorption equilibrium between
chromatography stationary solid and mobile liquid phases
2. Liquid–liquid or partition Liquid Liquid Partition equilibrium between stationary
chromatography liquid and mobile liquid phases
3. Gas–liquid Gas Liquid Partition equilibrium between stationary
chromatography liquid and mobile gaseous phases
4. Ion-exchange Electrolyte Ion exchange Ion-exchange equilibrium between ion
chromatography exchangers in resin stationary phase and
mobile electrolyte phase
5. Exclusion chromatography/ Liquid Liquid Molecular sieve action of pores of gel
gel filtration or particles
permeation
chromatography
6. Affinity chromatography Liquid containing Ligand Biological specificity and reversibility of
macromolecule binding between macromolecules and
ligands
4.3 COLUMN CHROMATOGRAPHY

In the column chromatography technique, the components of a mixture are separated in a column
as distinct zones and each zone is eventually displaced from the column as a series of fractions
(Figure 4.1). The apparatus and general techniques used for column adsorption partition, ion
exchange, exclusion, and affinity chromatography have much in common and are discussed in
Section 4.3.1. Gas–liquid chromatography (GLC) and high-performance liquid chromatography
(HPLC) have their own unique apparatus and procedures and are discussed separately.
4.3.1 Chromatography Columns

Chromatography columns are usually made up of glass and in general long columns give good
resolution of components, although wide columns are better for the separation of large quantities
of material. The essential features of a chromatography column are shown in Figure 4.1. The glass
column should have a means of supporting the stationary phase as near to the base of the column as
possible to minimize dead space below the column support in which post-column mixing of sepa-
rated compounds can occur. Commercial columns possess either a porous glass plate fused onto the
base of the column or a suitable device for supporting a replaceable nylon net, which in turn sup-
ports the stationary phase over it. Glass wool plugs are often used.
4.3.2 Stationary Phases

Depending on the particular form of chromatography to be carried out, there are different types of
stationary phases, such as solids (alumina, silica, etc.) for adsorption chromatography, liquids for
partition chromatography, gels for exclusion chromatography, and resins for ion-exchange chroma-
tography. All materials must be equilibrated with the mobile liquid phase, called a solvent, before
preparing the column. During equilibration, the solid support material is allowed to settle and fine
particles remaining in the suspension are removed by decantation (Figures 4.1 and 4.2). If this is
not carried out, the flow rate of the mobile phase is clogged by these fine particles. In addition,
some form of pretreatment of the stationary phase is often required, for example, some gel filtration
Chromatography 63
Mariotte flask with eluant, attached to

constant-pressure device
Elution solvent/eluant
Filter paper disk to avoid disturbing
the surface
Separated component zones
Nylon grid or glass wool plug

for support
Effluent to detector or fraction

collector
Fractions
FIGURE 4.1 Column chromatography.
Measuring cylinder with

suspension allowed to settle Slurry
Glass rod to avoid trapping of

air bubbles
Fine particles removed by Dilute suspension

decantation or in solvent
aspiration
Trap gently for even
packing and to release
air bubbles
Packed material
Packed column material
later resuspended
in 1.5x the volume
for pouring Nylon support or glass wool
Tap kept slightly open to

encourage packing
FIGURE 4.2 Preparation of a chromatography column.

materials need to swell, adsorbents need to be activated by heating or an acid treatment, or ion-
exchange resins have to be obtained in the required ionized form by washing.
4.3.3 Packing of Columns

A chromatography column is packed with a stationary phase (adsorbent, resin, or gel) by pouring
a slurry from the stationary phase to the mobile phase into the column with the help of a glass rod
(Figure 4.2b). This prevents the trapping of air bubbles. Gentle tapping or stirring in the upper part
of the slurry also ensures that no air bubbles are trapped and helps in evenly packing the column.
Poor column packing gives rise to uneven flow (channeling) and reduced resolution. The slurry
is added until the required height is obtained. The suspension is then allowed to settle and excess
mobile phase is allowed to run off by opening the outlet. The column is then washed with the
mobile phase and the level of the liquid is kept just above the surface of the material. To prevent the
column from being disturbed either by the addition of the mobile phase or during the application of
the sample to the column, a filter paper disk or nylon or rayon gauze is placed on the surface of the
column. Some commercial columns have an adaptor or a plunger, which serves the dual purpose
of protecting the surface and providing an inlet (often capillary tubing) to carry the solvent to the
column surface. Once a column has been prepared, no part of it should be allowed to run dry, that
is, a layer of mobile liquid should always be maintained above the column surface (Figure 4.3). The
total volume of solid and liquid in the column is referred to as the bed volume, and the volume of
liquid phase outside the solid is called the void volume (Vo).
4.3.4 Application of Sample

Several methods are available for applying a sample to the top of the prepared column. A simple
method is to remove most of the solvent from above by suction and to just drain the remainder into the
column bed. The sample is then carefully applied using a pipette and allowed to run into the column.
A small volume of solvent is then applied in a similar manner to wash final traces of the sample into
the bed. More solvent is then carefully added to the column to a height of 5–10 cm. The column is
then connected to a suitable reservoir, which contains more solvent, so that the height of the solvent
Pump Eluant
reservoir
Flask containing
eluant
Eluant
Adjustable plunger
Glass
column Nylon disk
Column
packing Adjustable plunger
Glass wool
Eluant to
detector
and/or fraction
(a) collector (b)
FIGURE 4.3 Columns for column chromatography: (a) simple and (b) sophisticated versions of columns.
Chromatography 65
in the column can be maintained at 5–10 cm. An alternative procedure that avoids the necessity
of draining the column to the surface of the bed is to increase the density of the sample by adding
sucrose to a concentration of about 1%. When this solution is layered onto the solvent above the col-
umn bed, it will automatically sink to the surface of the column and hence be quickly passed into the
column. This method, however, can be used only if sucrose does not interfere with the separation and
subsequent analysis of the sample. A third method involves the use of capillary tubing, a syringe, or
a peristaltic pump to pass the sample directly to the column surface.
In all cases, care must be taken to avoid overloading the column with the sample; otherwise,
irregular separation occurs. It is also advantageous to apply the sample in as minimal a volume as
possible, as this ensures the presence of an initial tight band of material when the separation com-
mences. In addition, to prevent anomalous adsorption effects the sample should be desalted before
application to the column.
4.3.5 Column Development

Once components of the mixture have separated into zones in the column, the next step is to remove
these components from the zones and collect them as separate fractions. This is carried out by con-
tinuously passing the mobile phase (eluant/solvent) through the column. This process is called col-
umn development. In displacement column development, the mobile phase interacts more strongly
with the stationary phase than the component of the mixture bound to it, thereby displacing the
bound molecules. However, for better resolution, elution column development is preferred. In this
process, the mobile phase interacts weakly with the stationary phase than the bound molecules and
overrides the bound molecules, gradually eluting them from the column. Different components can
be removed from the column by changing the strength or pH of the eluting mobile phase in a step-
wise fashion (gradient elution).
In order to produce a suitable gradient, two solvents should be mixed using either commercially
available gradient mixers or a more simple method as follows: The two solutions are placed in sepa-
rate chambers (Figure 4.4). The recipient chamber is linked to the column and the donor chamber
is linked to the recipient chamber by a siphon. As the eluant enters the column from the recipient
chamber, the solution in the donor replaces it and is mixed by a stirrer. The diameter of the two
chambers determines whether the gradient varies with time in a linear, convex, or concave manner.
Gradient elution achieves better resolution as compared to isocratic elution, which uses a single sol-
vent as the eluant. The volume of eluant required to elute a particular solute is known as the elution
volume (Ve), whereas the corresponding time for elution is known as retention time (tr).
During elution, it is essential that the flow rate is maintained constant. The flow rate may be
regulated by adjusting the operating pressure, which corresponds to the difference between the level
of the solvent in a reservoir situated above the column and the level at the outlet side of the column.
An ordinary open reservoir is not satisfactory because the operating pressure drops as the solvent
Donor Recepient
chamber chamber
Magnetic
bar
To column
Adjustable Magnetic
pinchcock stirrer
FIGURE 4.4 Gradient maker.

level drops while it runs through the column. A Mariotte flask (Figure 4.1) can keep the pressure
constant. Alternatively, a peristaltic pump can pump the eluant at a predetermined rate onto the
column. Care must be taken to see that the column structure does not change due to excessive pres-
sure from the pump.
4.3.6 Fraction Collection and Analysis

As components of a mixture emerge from the column as effluent, it is necessary to detect their
presence in order to enable them to be isolated for further study. This can be done in two ways. In
the first method the effluent can be continuously monitored, and in the other it can be collected as
separate fractions that are subsequently analyzed.
In continuous monitoring, the effluent is passed through a flow cell (8 mm3) located in the detec-
tor. Detection may be based on UV or visible light absorption by components of characteristic wave-
lengths, fluorescence, changes in the refractive index of the effluent, the presence of a radioactive
label, or the ease of oxidation or reduction as measured by an electrochemical detector. The signal
generated by the detector is recorded on a chart recorder with each emerging compound giving a
characteristic peak from which it is possible to calculate the retention time and/or the elution volume
(Figure 4.5a–c).
Separate fractions can be collected either manually or by using an automatic fraction collector.
The amount of effluent in each fraction can be determined in one of several ways. There may be a
siphoning system to deliver a predetermined volume into each tube or there may be an electronic
means of allowing a predetermined number of drops to enter each tube. This has the disadvantage
that if the composition of the effluent changes during gradient elution, its surface tension and there-
fore the size of the drops may also change so that the volume of collected liquid changes. In another
method, the effluent is allowed to enter a tube for a fixed interval of time, but if the flow rate of the
column varies, the volume of the fraction collected also varies. However, once the fractions have
been collected they can be detected by spectrophotometer, fluorimeter, scintillation counting, and
radioimmunoassay.
Quantitative estimations of fractions collected can also be made using peak area. The area of the
peak is the product of the height of the peak (hp) and its width at half height (Wha). The peak area
can be shown to be proportional to the amount of the sample component present. Alternatively, the
peak may be cut out, weighed, and the assumption made that area and weight are linearly related.
The amount of a specific component can be found by a standard curve made by chromatographing
the known sample under identical conditions and weighing the peak cutout (Figure 4.6).
Injection (a) (b) (c)
tRB
Recorder signal
tRB
hρ ωhA σ ωhB
1/2 0.607 hρ
hρ
Baseline
ωA ωB
Time
FIGURE 4.5 Figure showing (a) chromatogram of two compounds showing complete resolution and the
calculation of retention times, (b) two compounds giving incomplete resolution and the production of fused
peaks, and (c) a compound showing excessive tailing.
Chromatography 67
4.5 10
4 9
3.5 8
7
3
Optical density at 350 nm
Absorbance at 280 nm
2.5
5
2
4
1.5
3
1 2
0.5 1
0
0 10 15 21 27 34
1 4 7 10 13 16 19 22 25 28 31 34 37 40 43 46 49 52 55 58 61 64 67 70
Sample number
70 kDa 18 kDa
(a) Elution volume
(b)
FIGURE 4.6 Figure showing (a) purification of bioactive compounds by using sepharose CL-6B column and
(b) graphical presentation of fractionation of metabolic proteins of Aspergillus fumigates by size-exclusion
chromatography.
4.4 PAPER CHROMATOGRAPHY AND THIN-LAYER CHROMATOGRAPHY

4.4.1 Principles
Unlike column chromatography, the components of a mixture after separation remain on the chro-
matogram in PC and TLC. On spraying the appropriate detecting agent, they appear as a series of
spots. The position of the spots is recorded in terms of the Rf value (Figure 4.7). This is defined as
the following ratio:
distance moved by component

Rf =
distance moved by mobilee liquid phase/solvent
The Rf values are constant for a particular component under particular conditions.
In PC, the stationary phase is supported by cellulose fibers of paper and the mobile phase moves
through the interstitial spaces by capillary action. If paper merely acted as an inert support, the
separation of the components of a mixture would be exclusively due to continuous partition between
mobile phase flowing along the paper and water held in the paper; filter paper contains l5% of its
weight in water and this may be the case in some circumstances. Usually the paper affects separa-
tion in a number of ways; it acts as an adsorbent, especially for polar molecules for which it has great
affinity. They are held by hydrogen bonding and the van der Waals force; the paper also functions
as an ion-exchange material due to the carboxyl groups it contains.
In TLC, a slurry of the stationary phase, generally in water, is applied to a glass, plastic, or foil
plate as a uniform thin layer, by a plate spreader starting from one end and moving to the other.
A variety of materials can be used as the stationary phase and, similar to PC separation, TLC is
achieved in multifarious ways. On heat-activated layers of silica gel and similar substances, when
nonaqueous solvent systems are used, adsorption is the predominant process, and this is useful
for separating hydrophobic substances such as lipids. When aqueous solvents are used on layers
of crystalline material that have a large surface area and fine particle size, a situation between
these two extremes exists and the magnitude of influence of individual components is difficult
to assess.
Solvent
front
Rf = x
y
y
Origin x
FIGURE 4.7 Finding the Rf value.
4.4.2 Types of Paper

Whatman no. 1 is the paper most frequently used for analytical purposes. Whatman no. 3 is a thick
paper and is best used for separating large quantities of material. However, its resolution is inferior
to that of Whatman no. 1. For rapid separation Whatman no. 4 and no. 5 are convenient, although
spots are less well defined. In all cases, flow rate is faster in the machine direction, which is nor-
mally noted on the box containing the papers. The paper may be impregnated with materials like
silica for adsorption, liquid for partition chromatography, and so on. Silica-impregnated papers are
commercially available and used for separating lipids and hydrophobic molecules.
4.4.3 Thin Layer

Slurry of the stationary phase in water is applied evenly onto a plate. Calcium sulfate is often incor-
porated into the slurry to facilitate adhesion of the thin layer on the plate. For analytical purposes,
a layer 0.25 mm thick is desired. For preparative separations, 5-mm-thick plates are used. With
the exception of thin-layer exclusion chromatography, the plates are dried to leave a coating of the
stationary phase. In the case of adsorbents, drying is carried out in an oven at 100°C–120°C. This
also activates the adsorbent.
4.4.4 Sample Application

A drop of the solution containing the mixture of compounds to be separated is placed near one end
of the strip by means of a syringe, capillary, or micropipette. It is allowed to dry at room tempera-
ture. The strip is then placed so that the end with the spot dips into the solvent, which is the mobile
liquid phase and moves by capillary action. The mobile liquid phase is usually a mixture of solvents.
It is essential that the spot is not immersed in the solvent as it would dissolve and become lost.
4.4.5 Development
It is essential to make sure that prior to development the atmosphere of the separation chamber is
fully saturated with the solvent; otherwise, Rf values will vary from chamber to chamber. The pro-
cess is called equilibration and is carried out as follows: About 1.5 cm of mobile phase/solvent is
added to the chamber and covered with a lid for at least half an hour. Unless this is done, irregular
running of the solvent will occur as it ascends the plate, resulting in poor separations. After equili-
bration, the lid is removed and the strip is placed inside the spot slightly over the solvent. Whenever
the solvent reaches the far end of the strip or after a convenient time period, the sheet is removed
Chromatography 69
and rapidly dried and spots are detected by spraying a suitable locating agent on it. When a mixture
contains many components, complete separations on a strip of finite length may not be possible. In
order to overcome this difficulty, a number of different solvents with different properties are used so
that components running together in one solvent will probably separate in another solvent. Although
many one-way chromatograms each in a different solvent can be compared, a lot more information
is obtained if two solvents are used in conjunction to prepare a two-way chromatogram than if the
two are used to prepare two one-way separations (Figure 4.8).
A two-way chromatogram is prepared by placing a drop of the mixture near a corner of a square
or rectangular sheet of paper or layer. The solvent is then allowed to flow through the sheet with the
result that a one-way separation is obtained. After drying completely, the sheet is turned at right
angles and run in a second solvent, which performs a further separation and causes the components
to be distributed on the sheet in two dimensions instead of the previous one dimension. This tech-
nique is called 2D chromatography.
There are two techniques that can be used for the development of paper chromatograms:
(1) ascending and (2) descending (Figure 4.9). In both cases, the solvent is placed at the base of a
sealed tank or glass jar to allow the chamber to become saturated with solvent vapor. In the ascend-
ing method, the end of the paper with the spot is dipped in the solvent at the base of the tank and
as the solvent rises up, or ascends, by capillary action, separation is achieved. In the descending
technique, the end of the paper with the spot is held in a trough at the top of the tank and the rest
of the paper is allowed to hang vertically but not in contact with the solvent at the base of the tank.
The solvent moves down from the trough, or descends, under the force of gravity, and separation is
achieved. Although the descending technique achieves faster flow rates, it is not preferred because
it is far more cumbersome to set up than the ascending technique.
Direction of
first development Direction of
second development
Origin Origin
FIGURE 4.8 A 2D chromatogram.
Cover
Supporting rod
Clip
Paper
Glass tank
Sample position
Solvent
(a) (b)
FIGURE 4.9 Methods of PC: (a) ascending and (b) descending methods.
4.4.6 Component Detection

Relatively few compounds are naturally colored or fluoresce or absorb UV light, and so after separation
the majority of compounds are detected with a chemical location reagent. The term location reagent is
defined as the total material applied to the dry chromatogram after chromatography in order to locate
or reveal the positions of the separated substances so that a color is produced that is different from the
color produced when the reagent is applied to a blank sheet that has been run in the solvent. Thus the
reagent includes the chemicals (active constituents) that react to produce the color, the solvent in which
they are dissolved, and any subsidiary substance added to strengthen or stabilize the colors so produced.
Chemical reagents of this type suffer from the disadvantage that when compared to physical location
methods (fluorescence, radioactivity, UV light, etc.), they destroy the compounds being located.
4.4.7 High-Performance Thin-Layer Chromatography

High-performance TLC (HPTLC) is an enhanced form of TLC. A number of enhancements can be
made to the basic method of TLC to automate the different steps, increase the resolution achieved,
and ensure more accurate quantitative measurements.
Automation is useful to overcome the uncertainty in droplet size and position when the sample is
applied to the TLC plate by hand. One recent approach to automation has been the use of piezoelec-
tric devices and ink-jet printers for applying the sample (Figure 4.10). Spot capacity (analogous to
peak capacity in HPLC) can be increased by developing the plate with two different solvents. After
the plate is exposed to the first solvent, the solvent is removed, the plate is rotated through 90°, and the
plate is developed with the second solvent. If the two solvents show different selectivity, then the spots
may be spread over the entire surface of the plate. This is obviously a form of 2D chromatography.
4.4.8 Advantages of Thin-Layer Chromatography over Paper Chromatography

A variety of supporting media can be used in TLC so that separation can be achieved in several ways,
such as adsorption, partition, exclusion, or ion exchange, depending on the type of stationary phase
applied to the plate. TLC is rapid, taking as little as 1 hour as compared to 7–8 hours for PC. Compounds
can be detected in a much lower concentration as the spots are very compact. Separated compounds
can be detected by corrosive sprays and elevated temperature, for example, spraying with 50% sulfuric
acid or 25% sulfuric acid in ethanol and heating will result in most compounds becoming charred and
showing up as brown spots. This is not possible with paper, which will burn and disintegrate.
KJ KJ
900 900
800 800
700 700
600 600
500 500
400 400
300 300
200 200
100 100
0.14 0.34 0.54 0.74 0.94 1.14 1.34 0.14 0.34 0.54 0.74 0.94 1.14 1.34
(a) (b)
FIGURE 4.10 (a) HPTLC equipment and (b) demonstration of separation and reading of intensity of sepa-
rated compounds in chromatograms.
Chromatography 71
4.5 SAMPLE COLLECTION, PRESERVATION, AND PREPARATION

These are identical for all chromatographic methods as for any other biochemical investigation
of biological fluids or tissues. The complex mixtures of substances present in biological fluids
often result in their mutual interference when chromatography of a particular group of compounds
is attempted. Either the interferences must be removed or the substances of interest selectively
extracted. Care must be taken at this stage to prevent or at least minimize losses. Sometimes sub-
stances are converted to more satisfactory derivatives, which are subsequently chromatographed,
for example, labile keto acids are converted to stable dinitrophenyl hydrazones or amino acids,
which may be separated by TLC or PC.
4.6 ADSORPTION CHROMATOGRAPHY

4.6.1 Principle
The separation of components of a mixture depends on differences in both their degree of adsorp-
tion and their solubility in the solvent used for separation. This can be carried out in column,
thin-layer, and paper modes. Compounds are adsorbed onto the stationary phase to the extent deter-
mined by the charge, van der Waal forces, dipole interactions, hydrogen bonding, and steric factors.
Adsorption chromatography depends on the structure of the components due to which they have
greater or lesser affinity for the stationary and mobile phases.
The mass of solute adsorbed per unit weight of adsorbent (m) depends on the concentration of the
solute (c); Langmuir derived an equation on the basis that only a monolayer is adsorbed and only a
proportion of the molecules in collision are adsorbed. This is known as the Langmuir adsorption
isotherm:
k1 k2 c
m=
1 + k2c
In the aforementioned equation, k1 is a measure of the number of active adsorption sites per unit
weight of adsorbent and depends on the nature of the adsorbent. The term k2 is a measure of the
affinity of the solute for the adsorbent and is affected by all the components of the system.
Langmuir assumed only one binding site, although in practice there are a number of binding
sites on the surface of the adsorbent, each with a different affinity, thus giving a series of Langmuir-
type isotherms. Hinshelwood therefore suggested that the following equation gives a more accurate
picture:
k1 k2 c
m=
1 + k2c
This approximates to Freundlich adsorption isotherm, which is found in practice:
m = Kc x
In this equation, K and cx are constants depending on the particular system used.
The difference between these two isotherms is illustrated in the graph shown in Figure 4.11a. The
mixture of binding sites of different affinities is the cause of tailing observed in the elution profile in
column chromatography (Figure 4.11b). This tailing can be overcome by eluting with a suitable gra-
dient of pH, ionic strength, or polarity so that the more strongly adsorbed molecules meet a higher
concentration of displacing compound than the more weakly bound molecules.
Freundlich
Mass of solute
absorbed (m)
Langmuir
Concentration of solute (c)

(a)
Amount of
compound
Weakest Binding sites Strongest binding sites release

release molecules molecules reluctantly, producing
first a tail
Volume of effluent
(b)
FIGURE 4.11 Figure showing (a) absorption isotherms of Freundlich and Langmuir, and (b) tailing observed
in the elution of a compound from an absorption column.
4.6.2 Adsorbents
Compounds such as silicic acid (silica gel), aluminum oxide, CaCO3, MgCO3, ZnCO3, MgO, and
cellulose may be used as the stationary phase. The choice of adsorbent and solvent depends on
the separation to be achieved. Hydroxyapatite (CaPO4) is widely used for the separation of pro-
teins, nucleic acids, and viruses. Unlike most other adsorbents, it has some ion-exchange properties
that aid separation. In addition, in nucleic acid separation it has the advantage that it can bind to
double-stranded DNA but not single-stranded DNA. Adsorbents of TLC are often impregnated with
AgNO3 to enhance the separation of compounds differing in the number of double bonds. This is
called argentation TLC. Some adsorbents have a tendency to take up water from the atmosphere
during storage and this may adversely affect their adsorption properties. In such cases, the adsor-
bents are activated by heating at 110°C for some time to remove any water.
Poly-E-caprolactam TLC sheets do not require activation and are semitransparent, which allows
the unknown compounds and their standard to run on opposite sides to be compared. They can
be reused if they are immediately cleared with ammonia-acetone and are widely used in pro-
tein sequencing. In general, the adsorption affinity of compounds increases with the polarity of
Chromatography 73
molecules, the number of double bonds in alkenes, and the introduction of functional groups. In
order of increasing affinity, some functional groups are as follows:
− O – R , − NO 2 – COR , − OCOR , − NH 2 , − OH, – CONH 2 , − COOH
4.6.3 Solvents
The choice of solvents depends on the polarity of the compounds to be resolved and their dis-
tribution coefficients. Commonly used low-polarity solvents are hexane, heptane, acetonitrile,
toluene, diethyl ether, and chloroform. Intermediate-polarity solvents include ethanoic acid,
dichloromethane, and pyridine, whereas polar solvents are propanol, ethanol, methanol, acetone,
and water.
4.7 PARTITION CHROMATOGRAPHY

4.7.1 Principles
The separation of components of a mixture depends on differences in their solubility in two immis-
cible liquids, one of which is kept stationary by keeping it supported by an inert matrix. The other
is mobile (Figure 4.12). The component distributes itself between the two immiscible liquid phases
as described by the partition coefficient Kd at equilibrium. As already mentioned,
Concentration in solvent 1
Kd =
Concentration in solvent 2
In normal-phase partition chromatography, the stationary phase is usually water, whereas the
mobile phase is an organic, nonpolar liquid that is immiscible in water and flows past the stationary
phase. Thus, compounds that are soluble in both water and nonpolar organic solvents are readily
separated by partition methods, as compared to adsorption chromatography, in which compounds
sparingly soluble in water but insoluble in organic liquids are separated.
In the case of column chromatography, the matrix may be cellulose, starch, or silicic acid. For
TLC it is most commonly cellulose, whereas for paper partition chromatography sufficient water is
naturally present in paper to act as the stationary phase.
Solid phase
(inert support)
Mobile liquid phase
(hydrophobic solvent)
Solute
(molecules partitioned
between two liquid
phases)
Stationary
liquid phase
(absorbed layer
of hydrophilic solvent)
FIGURE 4.12 The principles of liquid–liquid partition chromatography.

In reverse-phase partition chromatography, the stationary phase is a nonpolar liquid, for example,
liquid paraffin supported by an inert matrix as in normal phase. This phase is prepared by treating
the supporting matrix with a solution of the mobile phase in a suitable nonpolar and volatile solvent;
the solvent is subsequently removed by evaporation.
4.7.2 Countercurrent Chromatography

Countercurrent chromatography (CCC) is a separation process based on the distribution of a com-
pound between two immiscible liquid phases, but neither phase is supported on an inert matrix and
it differs from conventional liquid–liquid partition chromatography. The mixture components are
partitioned between two immiscible liquid phases, which move relative to one another. The usual
form of the required apparatus comprises a series of extraction tubes through which the less dense
of the two phases moves. Each extraction is performed by shaking the tubes and, after waiting for
the phases to separate, the transfer of the upper phase is effected. The components of the mixture
progress through the tubes as a result of the movement of phases but at different rates. These rates
depend on the K of the components in the two phases; when these coefficients are different, separa-
tion is achieved.
4.8 HIGH-PERFORMANCE LIQUID CHROMATOGRAPHY

4.8.1 Principles
HPLC is a form of chromatography in the column mode, using a small particle-size stationary phase
and high-pressure eluant pumping systems to give a high performance; hence, it is named high-
performance liquid chromatography.
All forms of column chromatography rely on gravity or low-pressure pumping systems for the
supply of eluant to the column. The flow rates are therefore low and cannot be increased by merely
increasing the pressure of the eluant supply, as this would create back pressure, which would eventu-
ally damage the column structure. The use of small particle-size stationary phases makes it possible
to withstand these high pressures and, at the same time, give better resolutions. In recent years, how-
ever, special pumping systems have been designed that can give higher flow rates. These, together
with the use of small particle-size stationary phases, result in quick, efficient, and better resolution
in adsorption, partition ion-exchange, exclusion, and affinity column chromatography. The princi-
pal components of an HPLC system are shown in Figure 4.13a and b.
4.8.2 Column
Since glass tubing cannot withstand pressures in excess of 70 atm, stainless steel, precision-
bored columns with an internal mirror finish for efficient packing are normally used. These
straight columns of 15–50 cm length and 1–4 mm diameter can withstand very high pressures
of up to 5.5 × 107 Pa (8000 psi) and are relatively corrosion resistant. At the end of the column,
homogenously porous plugs of stainless steel or Teflon are used to retain the packing material
and to ensure uniform flow of the solvent through the column. At times, the repeated application
of impure samples such as urine, blood, or crude cell extracts results in clogging and the loss
of the resolving power of the column. To prevent this, a short column of 1–2 cm in length and
an internal diameter equal to that of the analytical column is generally introduced between the
injector and the analytical column. This short column is called the guard column and it is packed
with the same material with which the analytical column is packed. The guard column retains the
solid particles in the sample before the sample enters the main column. Guard columns can be
replaced at regular intervals. In some separations, it is required to maintain constant temperature
thermostatically.
Chromatography 75
(a)
Sample injection loop
Detector
Column
Solvent High-pressure Sample collector

reservoir pump at all
occurrences
Recorder and
data system
Sample
injection port
Reservoirs Flow
Solvent 1 Solvent 2 splitter
Pressure
Precolumn gauge
Degasser 1 Degasser 2
Mixing vessel
Analytical
column
High pressure pump

Differential detector
To waste
To waste or
fraction collector
(b)
FIGURE 4.13 Figure showing (a) HPLC and (b) the diagrammatic representation of the components of an
isocratic HPLC system and an HPLC column with its associated pumps, detector, and recording instruments.
4.8.3 Column Packing

Three forms of column packing material are available:
1. Microporous supports where micropores ramify through the particles, which are 5–10
μnanometers in diameter
2. Pellicular supports where porous particles are coated onto an inert solid core such as a
glass bead of about 40 nm in diameter
3. Bonded phase where the stationary phase is chemically bonded onto an inert support
For adsorption chromatography, adsorbents such as silica or alumina are available in micropo-
rous or pellicular forms in a range of particle sizes. Pellicular forms have high efficiency but low
sample capacity and, therefore, microporous supports are preferred where applicable. All HPLC
packing materials are regular and spherical in shape, giving good packing and flow properties.
In liquid–liquid partition systems, the stationary phase may be coated onto an inert support. Both
microporous and pellicular supports are used, but in these the stationary solvent gradually gets washed
out with the mobile solvent. To overcome this problem, bonded phases have been developed in which
the stationary liquid is covalently bonded to the supporting material (silica or a silicone polymer).
Many different types of covalently bonded phase ion exchangers are available of which the cross-
linked microporous polystyrene resins (silicone network) are widely used. Pellicular resin forms are also
available. These are called hard gels, and they readily withstand the pressures required during analysis.
The stationary phases for exclusion chromatography in the HPLC mode are porous silica, glass,
polystyrene, or polyvinylacetate beads. These are generally used with organic eluting solvents;
semirigid gels such as sephadex and nonrigid gels such as sepharose are of limited use in HPLC
since they can withstand only low pressures. The supports for affinity separations are the same as
those for exclusion apparatus. The spacer arm and ligand are chemically bound to the support.
4.8.4 Column-Packing Procedure

The most widely used column-packing procedure is the high-pressure slurrying technique. A sus-
pension of the packing is made in a solvent of equal density to the packing material. The slurry is
then rapidly pumped at a high pressure into a column with a porous plug at its outlet. The resulting
bed of packing material can then be prepared for use by running the mobile phase through the col-
umn when hard gels are packed. It is necessary to allow them to swell first in the solvent to be used
in the chromatographic separation before packing under pressure. Soft gels cannot be packed under
pressure, and they are allowed to pack from a slurry in the column under gravitational sedimenta-
tion only as in conventional column chromatography.
4.8.5 Chromatographic Solvent (Mobile Phase)

The choice of mobile phase depends on the type of separation to be achieved. Isocratic separations
may be made using a single solvent, two solvents, or more solvents mixed in fixed proportions.
Alternatively, a gradient elution system may be used. For this system, two pumps are required to
pump the two solvents to produce a gradient. In all cases, the solvent should be free from even traces
of impurities as this would hamper the development and interfere in the detection of compounds.
To this end, 1–5 nm microfilters are used to filter the solvent before it enters the pump, even though
extra-pure HPLC solvents are commercially available.
4.8.6 Pumping Systems

The main features of a good pumping system are that it should be capable of outputs of at least
3.4 × 107 Pa (5000 psi) and there should be no pulses of flow through the system. There must be
a flow delivery of at least 10 cm·min−1 for normal analysis and up to 30 cm·min−1 for preparative
Chromatography 77
analysis. Several pumping systems are available that operate on the principle of constant pressure
or constant displacement. Constant-pressure pumps produce a pulseless flow through the column,
but any decrease in the permeability of the column will result in lower flow rates for which the
pump will not compensate. These pumps operate by the introduction of high-pressure gas into the
pump, and the gas in turn forces the solvent from the pump chamber into the column. The use of an
intermediate solvent between the gas and the eluting solvent reduces the chances of dissolved gas
directly entering the eluting solvent and causing problems during analysis.
Constant-displacement pumps maintain a constant flow rate through the column irrespective of
changing conditions within the column. One form of the constant displacement pump is a motor-
driven syringe type; it is a pump in which a fixed volume of solvent is forced from the pump to the
column by a piston driven by a motor. Such pumps provide uniform solvent flow rates and also yield
a pulseless solvent flow, which is important because certain detectors are sensitive to changes in
solvent flow rate.
4.8.7 Detector Systems

Most commonly, the detector is a variable-wavelength UV spectrophotometer, fluorimeter, refrac-
tive index monitor, or electrochemical detector. A recent development is the interfacing of HPLC to
a mass spectrometer. In all cases, the detector should be very sensitive since the quantity of material
is very small.
4.8.8 Practical Procedure

The correct application of a sample onto an HPLC column is important in achieving success-
ful separations. Ideally, the sample should be introduced as an infinitely narrow band into the
column. Two methods are generally used. (1) The first method makes use of a microsyringe
designed to withstand high pressure. The sample is injected through a system in an injection
port, either directly onto the column packing or onto a small plug of inert material immediately
above the column packing. (2) The second method involves the use of a loop injector. It consists
of a metal loop of a small volume that can be filled with the sample by means of an appropriate
valve; the eluant from the pump is channeled through the loop, the outlet of which leads to the
column. The sample is thus flushed onto the column by the eluant without the interruption of
solvent flow to the column. Automatic versions of the loop injector are commercially available
(Figure 4.14).
25.3 (β-car)
30.2 (Myza)
Wild (+)
30.9 (β-car)
Wild (–)
29.3 (Zea)
26.8 (Myza)
27.1 (Zea)
Relative fluorescence
10.2 (Chl o)
10.6 (Ech)
7.2 (Chl o)
2.4 (Ech)
0 5 10 15 20 25 30 0 5 10 15 20 25 30
Retention time Retention time
(a) (b)
FIGURE 4.14 HPLC analysis of acetone extract of pigments of wild type (a and b) and Het- Fix- mutant
strain (c and d) of Anabaena variabilis.
Mutant (–) Mutant (+)
35.1 (Ech)
35.4 (Ech)
15.8 (Chl o)
12.5 (Myza)
10.6 (β-car)
9.4 (Myza)
10.9 (Zea)
13.6 (Zea)
5.2 (β-car)
2.9 (Chl o)
7.5
9.3
4.7
5.8
0 5 10 15 20 25 30 0 5 10 15 20 25 30
(c) (d)
FIGURE 4.14 (Continued) HPLC analysis of acetone extract of pigments of wild type (a and b) and Het- Fix-
mutant strain (c and d) of Anabaena variabilis.
4.9 FAST PROTEIN LIQUID CHROMATOGRAPHY

4.9.1 Principles
Fast protein liquid chromatography (FPLC) is also known as fast performance liquid chromatog-
raphy. It is used to separate or purify proteins, biomolecules, and other polymers from complex
mixtures.
In FPLC, the constant flow rate of solvents is controlled by a pump. The solvents (buffers) enter
through tubing from an outside reservoir; the pump pushes the buffer or sample through the tub-
ing into the injector, which is then carried into the column by the flowing solvent. As the solvent
is forced into the chromatographic bed, the sample separates into various zones (bands). These
fractions are collected using a fraction collector. FPLC uses tubing that has inert fluid surfaces
(i.e., Teflon, titanium, and glass), which can operate at pressures up to 700 psi.
4.9.2 Apparatus and Materials

The FPLC system consists of a program controller, two high-precision pumps (one each for buf-
fers/solvents A and B), a mixer for gradient formation, an inline filter, an automatic motor valve for
injection of samples, a column, a sensitive UV monitor (fitted with a flow cell and a filter), and a
fraction collector.
The FPLC system is controlled by a software program that allows automatic control of separa-
tion procedures and also systematic recording and documentation of profile generated for an applied
sample with the help of a recorder. The principal components of an FPLC system are shown in
Figures 4.15 and 4.16 and described as follows:
Column: Various columns are used in liquid chromatography depending on the type of sepa-
ration under study. The column contains a microporous, high-resolving packing material
with a small diameter (stationary phase). The stationary phase typically consists of resins
comprising cross-linked agarose beads or gel beads. Different FPLC columns are used
to separate macromolecules based on size, charge distribution, hydrophobicity, desalting,
reverse phase, and affinity chromatography (Table 4.2).
Pumps: Pumps allow the analyte to flow through the column in a controlled manner at a con-
stant flow rate. High-precision, laboratory-grade, peristaltic, or some other type of pump is
Chromatography 79
In-line
filter
Filter wavelength
Injection UV detector
1 7
valve (VI)
6
2
3 4
5 Cond. Conductivity
System Mixer monitor
pumps
pH pH detector
(electrode optional)
A B
Column
Fraction
collector
(Frac-950)
FIGURE 4.15 Schematic representation of working of an FPLC system.
Monitor for UV,

conductivity, and Mixer Filter
pH Gate
Pump A Pump B Injector UV flow cell Flow restrictor
FIGURE 4.16 Typical FPLC system.
required in the FPLC system, which can generate moderate back pressures of 50–600 psi.
A twin pump system provides the highest degree of accuracy, precision, and reproducibil-
ity in gradient formation. One pump delivers the binding buffer, whereas the other delivers
the elution buffer. The pump controls the flow rate from a few milliliters per minute to
liters per minute and substantiates the requirements for industrial scale purification.
Monitor: A monitor consists of a control unit, an optical unit with lamp assembly (Zn or Hg
lamp), and conductivity and pH flow cells with a pH electrode. These monitoring modules
measure traces of the analyte with the help of software interfaces.
UV and conductivity flow cells: The types of UV flow cells are selected depending on the
amount of sample applied and the size of the column. The continuous recording of the
absorbance of the analyte mixed with elution flow is achieved by pumping the elute through
a flow-through cell placed in the UV monitor operated at 254, 280, or 405 nm. The choice
of wavelength depends on the spectral properties of both the eluant and the substances to
TABLE 4.2
Different FPLC Columns and Their Applications
Columns Type Applications
Mono Q HR 5/5 Hi trap Q Anion exchange Frequently used chromatographic technique for the
separation of proteins
Mono SH R 5/5 Cation exchange Polypeptides, nucleic acids, polynucleotides, and other
charged molecules
Superdex 200 HiLoad 16/60 Size exclusion (gel Include fractionation and determination of molecular
Superdex 200 HR 10/30 filtration) weight of proteins, nucleic acid separation, plasmid
Superose 6 HR 10/30 purification, and polysaccharide fractionation
HiPrep 16/60 (Phenyl high Hydrophobic interaction For protein, peptides, and other biomolecules with
sub), Phenyl Superose HR 5/5 hydrophobic ligands
HiTrapChelating 1 mL Chelating Allow purification of proteins with exposed histidine
HiTrapChelating 5 mL groups via formation of metal ion complex
HiTrap Protein A 1 mL Affinity Used for purification of immunoglobulins and tagged
HiTrap Protein G 5 mL proteins
HiTrap Desalting Buffer Used for removing free low-molecular-weight labels or
Fast Desalting HR 10/10 Exchange/desalting contaminants from proteins/peptides, substrates, and
HiPrep 26/10 Desalting inhibitors or cofactors from enzymes; and for preparing
samples for concentration, freeze drying, and storage
Polystyrene/divinyl benzene Reverse phase Used for high-resolution analysis and purification of
peptides, proteins, and oligonucleotides, especially when
high pH is needed, and use in liquid chromatography–
mass spectrometry (LC-MS) applications
be detected. The FPLC system is delivered with a 5-mm cell and it also contains a 2-mm
cell that is available as an accessory, which allows the desired sensitivity detection.
Mixer: The mixer is a chamber where the buffer/solvents are mixed properly. It is powered
and controlled by a pump. All the eluants commonly used in ion exchange, hydrophobic
interaction, and affinity and reverse-phase chromatography can be mixed in the mixer
with a high degree of accuracy and reproducibility. Mixing is important when gradients
between two buffers are formed.
Injection valve: A motorized valve is associated in the FPLC system for loading the sample.
Different operating positions (load, inject, and purge positions) are used for loading the
sample in the sample loop via an injection valve. Depending on the sample volume, sample
loops of varying sizes are available (25 μL, 50 μL, 100 μL, 200 μL, 500 μL, 8 mL, etc.).
Fraction collector: Fraction collectors are made up of glass and polypropylene. They allow
for efficient sample collection and prevent sample loss. There are two types of fraction
collectors:
1. Fixed-volume fractionation allows for the collection of a fixed volume before elution
starts.
2. Eluate fractionation or automatic peak fractionation allows for the collection of fixed
volumes during elution within a set interval. It also minimizes peak dilution and cross
contamination.
The choice of collection mode varies from microtiter plates to large vessels or funnels
according to the fractions to be collected.
Flow restrictor: The flow restrictor maintains a steady back pressure in order to prevent the
formation of air bubbles when the column is released. It is comparable to a cork on a bottle
of champagne.
Chromatography 81
In-line filters: An in-line filter is fitted between the output of the mixer and position 7 of the
injection valve. It creates a back pressure of maximum 0.5 MPa and filters out any dust
particulates that may clog or block the fluidity of the system.
Programming of the FPLC system: The FPLC system is controlled by an automated software
program. The software allows method validation and process optimization for performing
a better run, along with the efficient evaluation of data. All instrument settings and func-
tions are under the direct control of this software.
4.9.3 Calibrations
The calibrations performed on the FPLC system are as follows:
System component calibration: This involves the calibration of various components including
pH electrode, conductivity flow cell, pump, temperature reading, pressure reading, flow
restrictors, and fraction collectors. An automated program installed with the FPLC system
calibrates the instrument components when commanded.
Sample preparation calibration: The need for sample preparation prior to performing the first
chromatographic step is dependent on the sample type. Samples must be free from par-
ticulate matter. It is important to set objectives for quality and maintenance of the FPLC
instrument along with quantity and biological activity of the sample.
Solvent system (buffer) calibration: Buffer calibration is important to control the pH and pre-
vent changes in the pH in order to resolve sharp and pure peaks. They are most effective at
±0.5 pH units around their acid dissociation constant (pKa) values.
Besides the aforementioned system calibrations, the following individual component calibrations
are required before performing any run in the FPLC system:
Component Calibration Requirements

1. pH electrode (optional) Every day
2. Pressure reading Once a year or when required
3. Cell constant of the conductivity Only necessary if specific conductivity with high
flow cell accuracy is measured
4. Temperature Must be checked when changing the flow cell
5. Entering a new cell constant Must be done when changing the flow cell
6. Sample pump (optional) Whenever the running conditions are changed
4.9.4 Maintenance
Regular maintenance is important for the safe and trouble-free operation of an instrument. The user
should design a daily and monthly maintenance regime. Preventive maintenance should be performed on
a yearly basis by qualified service personnel. For smooth functioning of the FPLC system, regular main-
tenance is necessary. The following are recommendations to maintain the system in working condition:
1. Liquid should not be allowed to spill on the instrument. The surface should be regularly
wiped with a damp cloth. The system should be allowed to dry completely before use.
2. All tubing and flow paths should be properly rinsed, the pH electrode must be calibrated,
and the pump should be regularly checked for any leakage. If there are signs of liquid leak-
age from the assembly, the components must be replaced. The pump should be rinsed with
ethanol (20%), and if leakage is observed the piston must be replaced.
3. The online filters must be replaced every week. The inlet filters should be checked and
replaced if necessary. To clean the titanium filter, the piece must be placed in a beaker
containing 0.1N NaOH and stirred overnight or sonicated for 30 minutes.
4. The back pressure generated by the flow of the restrictor must be calculated using the user
manual and the restrictor should be replaced if it is not within the given limit.
5. Every 6 months, the flow cells of the monitor and the fraction collector should be cleaned
according to the user manual.
6. The valves should be checked for internal or external leakage and the distribution plate
must be replaced yearly.
Some points should be kept in mind for periodic maintenance:
1. The power supply must be disconnected before attempting to replace any item on the system.
2. When using hazardous chemicals, the entire system should be flushed thoroughly with
distilled water before performing service and maintenance.
3. Care should be taken while changing the location of the instrument so that the tubings are
not entangled and no leakage occurs from the connections.
4. During servicing and maintenance of the system, the buffer bottles must be placed on the
laboratory bench to prevent draining.
5. The pH electrode should be removed from the flow cell when the system is not in use and
it should be kept in cover containing a mixture (1:1) of pH 4 buffer and 2 M KNO3.
6. When the sample is loaded in the injector, care should be taken to ensure the needle
inserted is tight; if necessary it should be tightened by hand, but the needle should not be
overly tightened.
4.9.5 Troubleshooting
Common symptoms such as erratic retention times, noisy baselines or spikes in the chromatogram,
and leaks at pump fittings or seals can result in poor chromatography. For the eradication of specific
problems related to the apparatus, troubleshooting problems and their probable causes along with
their remedial measures are listed in Table 4.3.
4.9.6 Advantages
• The use of FPLC columns allows much higher protein loadings as compared to HPLC
along with the use of a wide range of aqueous and biocompatible buffer systems.
• FPLC is an intermediate between classical column chromatography and HPLC. The FPLC
pump delivers a solvent with a flow rate in the range 1–499 mL/h, whereas the HPLC
pump delivers a solvent flow rate in the range 0.01–10.0 mL/min.
• Since lower pressures are used in FPLC (0–40 bar) than in HPLC (1–400 bar), a wider
range of column supports is possible.
• FPLC has many advantages in situations where a nonvolatile or thermally unstable sample
must be separated, as is the case with many biochemicals, and it can also adapt to large-
scale preparative procedures.
4.9.7 Applications
Some applications of FPLC are as follows:
• FPLC has proved to be especially useful in the purification of murine monoclonal

antibodies.
• The FPLC method is useful in quantitatively measuring hemoglobin A2 (HbA2) levels.
• An efficient purification of recombinant his-tagged proteins from bacterial and mamma-
lian and baculovirus-infected cells can be achieved by using His60 nickel resin. Tags,
either N or C terminal, consisting of consecutive histidine residue, bind selectively to
Chromatography 83
TABLE 4.3
FPLC Problems and Their Probable Causes and Remedies
Problem Probable Causes Remedy
Noisy signal or no peaks or 1. Detector lamp off 1. Check that the flow restrictor generates a
small peaks 2. Chances of impurity in buffer back pressure in its limit; if not, there may
be air in the flow cell.
2. Degas buffers before use.
3. Check the connections of the optical unit
and filter setting.
4. Clean the UV flow cell.
Ghost peaks observed in 1. Air in the eluant 1. Check that the mixer is functioning
gradient profile properly.
2. Check loose tubing connections. Use a flow
restrictor.
Baseline drift occurs 1. Column temperature fluctuation. 1. Control column and mobile phase
2. There may be air in the flow cell. temperature; use a heat exchanger before
detector.
2. Check that the column is equilibrated. If
necessary, clean the column.
3. Use HPLC-grade solvents, and high-purity
salts and additives. Degas mobile phase
before use; sparge with helium during use.
4. Flush cell with methanol or some other
strong solvent. If necessary, clean the
cell with 1N HNO3 (never with HCl; never
use nitric acid with PEEK tubings or
fittings).
Waves on the gradient — 1. Check that the pump and the valves are
persist operating properly and are programmed
correctly.
Erratic flow, noisy baseline 1. Air bubbles passing through or 1. Check that there is sufficient eluent in the
signal, irregular pressure trapped in the pump. reservoirs.
trace (higher than the 2. Injector, in-line filter, or tubing. 2. Check all connections for leakage.
usual)
3. Pump valves not functioning 1. Clean the valves according to system manual.
correctly 2. Piston seal leaking. Replace the piston seal
according to the instructions in User
Manual.
4. Blockage or partial blockage of 1. Flush the flow path to clear the blockage.
the flow path 2. If necessary, replace the tubing.
3. Check the inlet tubing filter. It can get clogged
if unfiltered buffers or samples are applied.
Unstable UV baseline, 1. Monitor and mixer 1. Check main cable (power connection).
conductivity curve 2. Use a large mixer chamber.
3. Recalibrate the conductivity cell.
Low eluant flow and noise as 1. Air trapped in pump cylinders 1. Disassemble the pump cylinder and
piston moves; erratic pump 2. Partially blocked solvent filters examine the piston seal.
pressure 3. Leaking connections 2. Follow pump user manual.
4. Piston seal leakage
5. Pump valve malfunction
6. Piston damaged
(Continued)
TABLE 4.3 (Continued)

FPLC Problems and Their Probable Causes and Remedies
Problem Probable Causes Remedy
Variable retention times 1. Leaks, salt buildup, and unusual 1. Change mobile phase composition. (Small
noises in the pump. changes can lead to large changes in
2. Air trapped in pump. (Retention retention times.) Change pump seals if
times increase and decrease at necessary.
random times.) 2. Check makeup of mobile phase. If mobile
3. Column temperature fluctuations phase is machine mixed using proportioning
(especially evident in ion- values, hand mix and supply from one
exchange systems). reservoir.
4. Column overloading. (Retention 3. Purge air from pump head or check valves.
times usually decrease as the Change pump seals if necessary. Be sure
mass of the solute injected to mobile phase is degassed.
column exceeds column 4. Use reliable column oven. (Note: Higher
capacity.) column temperatures increase column
5. Sample solvent incompatible efficiency. For optimum results, heat the
with mobile phase. eluant before introducing it to the column.)
6. Column problem. (Not a 5. Inject smaller volumes (e.g., 10 μL vs. 100
common cause of erratic μL) or inject the same volume after 1:10 or
retention. As a column ages, 1:100 dilutions of a sample.
retention times gradually 6. Adjust solvent. Whenever possible, inject
decrease.) samples in mobile phase.
7. Substitute new column of the same type to
confirm the column is at fault. Discard old
column if restoration procedures fail.
Loss of resolution 1. Mobile phase contaminated/ 1. Prepare fresh mobile phase.
deteriorated 2. If problem persists, the column may be
clogged with strongly retained contaminants;
hence, change or replace the column.
Split peaks 1. Sample solvent incompatible 1. Adjust solvent whenever possible and
with mobile phase prepare sample in mobile phase.
Tailing peak 1. Mobile phase is contaminated or 1. Check mobile phase.
deteriorated and there is an 2. Check column performance with standards.
interfering component in the
sample
immobilize Ni2+ ions. The purification of recombinant his-tagged proteins consists of cell
lysis/extraction, binding, washing, and elution. The His60 nickel resin allows one-step pro-
tein purification under either native or denaturing conditions. Purified recombinant his-
tagged proteins can be eluted with imidazole or by a reduction in pH.
• The FPLC method is used for glutathione-S-transferase (GST)-tagged protein purification.
The GSTs are a family of enzymes that modify toxic substances, such as nitro and haloge-
nated compounds, by adding sulfur from glutathione, leading to their excretion in urine. Many
mammalian GSTs can be purified by affinity chromatography using the immobilized cofactor
glutathione, which is followed by competitive elution with an excess of reduced glutathione.
The GST is the second most commonly used protein tag. The GST gene fusion system
uses pGEX plasmids for inducible, high-level intracellular expression in Escherichia coli
of genes or gene fragments fused with Schistosoma japonicum GST. The GST-tagged
protein can be purified using a GSTrap high pressure (HP) column, and pure, untagged
protein can be obtained. The activity of the tag can be easily measured by an enzyme assay
Chromatography 85
or immunoassay. If necessary, the tag can be cleaved during the purification process to
generate native proteins with high purity, which is suitable for further studies.
• FPLC is used for antibody purification. Affinity purification of monoclonal antibodies has
been largely confined to the use of protein A and protein G chromatography. The anti-
bodies obtained are sufficiently pure for radiolabeling, conjugations (e.g., fluorescein), or
preparation of immunoaffinity columns.
• The FPLC system is used in biotin binding. Nowadays, biotinylated proteins/enzymes bind-
ing to avidin/streptavidin columns are frequently used. The high affinity (Kd = 10−15 M)
between avidin and biotin is one of the strongest known noncovalent interactions, which
can be used in pretargeting by coupling avidin to an antibody and using an effector mol-
ecule comprising biotin and a radionuclide.
• FPLC is used in phosphoprotein enrichment. Protein phosphorylation is probably the most
common and important form of protein modification. Protein phosphorylation provides
detailed methods designed to detect and identify phosphorylated proteins and to analyze
their specific sites of modification using both isotopic and nonisotopic approaches.
• Another application of FPLC is in protein desalting. Desalting columns apply size-
exclusion chromatography to facilitate the removal of low-molecular-weight components
(MW < 1000 Da) from DNA, proteins, or peptides (MW > 5000 Da). Protein desalt-
ing columns desalt or exchange buffers of protein samples and have exceptional desalting
characteristics, with a ≥95% retention of salts and small molecules while providing excel-
lent recovery of proteins greater than 7000 Da. Multiple samples can be processed in less
than 5 minutes without cumbersome column preparation steps.
• An improved ribonucleic acid (RNA) purification method using FPLC size-exclusion chro-
matography allows the preparation of milligram quantities of pure RNA in a single day.
• FPLC is used for the separation of urinary protein and several plasma proteins and for the
diagnosis of β-thalassemia. It is also used to identify protein profiles or variability within
a single protein of clinical significance.
• FPLC in conjunction with nano-HPLC-ESI-tandem mass spectrometry as a new integrated
methodology is suitable for the proteomic analysis of human lipoprotein fractions.
• FPLC is used for measuring levels of tubular proteinuria. Tubular proteinuria is a medical
condition in which a person’s kidney secretes more than 150 mg of urine proteins daily.
FPLC is used for cases of tubular proteinuria to isolate specific proteins from urine to
measure the levels of excreted proteins.
• FPLC is used in the profiling of plasma proteins in cerebrospinal fluid. Using the anion-
exchange column in the FPLC process, plasma proteins, transport proteins, hemoglobin,
and isoenzymes in cerebrospinal fluid are profiled. Protein profiling and monitoring contrib-
utes much to research on various diseases and medical conditions, including Alzheimer’s
disease, leukemia, cerebral hemorrhages, and renal failure.
• FPLC is used in analyzing pancreatitis. FPLC determines the specific protein-related
cause of pancreatitis (presence of pancreatic juice) that potentially leads to disease.
4.10 GAS–LIQUID CHROMATOGRAPHY

4.10.1 Principle
Gas chromatography (GC) as the name suggests is particularly suited for the separation of gases and
volatile liquids or solids in their gaseous state. Compounds of low polarity are best separated by GC.
The technique is highly sensitive and reproducible and has a high speed of resolution. When the sta-
tionary phase is an active solid such as silica, the method is referred to as gas–solid chromatography
(GSC). However, if the stationary phase is a liquid such as polymers of silicone coated on the surface
of an inert granular solid, then the technique is known as GLC. The stationary phase, whether a solid
or a liquid coated as a thin film on the surface of a solid support, is packed in a glass or stainless steel
column, which is narrow, coiled, and 1–3 m long with a 2–4 mm internal diameter. An inert carrier
gas (mobile phase) such as nitrogen, helium, or argon is made to flow through the column. The tem-
perature of the column is maintained high in an oven to keep the compounds separated in their volatile
states. These volatilized compounds get partitioned between the liquid or solid stationary phase and
the gaseous mobile phase, and thus they get separated because of differences in their partition coef-
ficients. After leaving the column, the separated compounds pass through the detector, are sensed, and
are recorded by the recorder. The essential components of GC equipment are presented in Figure 4.17.
Capillary columns with internal diameters of 0.03–1.0 mm and lengths of up to 100 mm made of
glass or steel are used for performing GC. Two types of capillary columns, that is, wall-coated open
tubular columns (WCOTs) and support-coated open tubular columns (SCOTs), are available for this
purpose. In WCOTs, as the name suggests, the walls of the capillary column are coated with the sta-
tionary phase. Since the stationary phase is a liquid and is directly coated on the walls of the capillary
column, only a small amount of the stationary phase is present in this system. Accordingly, only a
small amount of the sample can be applied onto the WCOT column. In SCOTs, the stationary phase is
in the form of a thin layer on the surface of a solid support, which is in turn packed into the capillary
column. Hence, the capacity of the SCOT system is much higher than that of the WCOT system and
a larger amount of sample can be applied to the former (Figure 4.18a and 4.18b). GC can be carried
out only in the column mode. It has high sensitivity, reproducibility, and speed of resolution and it has
proved to be the most versatile of all chromatographic methods. The only limiting factor is that the
components of the mixture must be vaporized to give heat-stable vapors up to a temperature of 300°C.
4.10.2 Solid Support and Stationary Phase

The purpose of the solid support is to provide a large, uniform, and inert surface area for holding
a thin layer of the liquid stationary phase. The support should be inert and have high mechanical
strength, a large surface area, regular shape, and uniform size. The most commonly used support is
celite, the OH groups of which are modified by silanization with hexamethyl disilazane to minimize
the support’s interaction with the sample.
The correct choice of the stationary phase is perhaps the most important parameter in GC.
Ideally, the stationary phase must be nonvolatile and thermostable at the temperature used for analy-
sis. It should be chemically inert toward the solutes of interest at the column temperature. The high
boiling points of organic compounds such as polyethylene glycols; methyl phenyl and methyl vinyl
silicon gums; esters of adipic, succinic, and phthalic acids; polyesters; and polyethylene glycols are
Recorder
Injection port Thermostats
Chromatogram
Column
Detector
Flow
controller
Carrier gas
cylinder
FIGURE 4.17 Schematic diagram of a GC system.

Chromatography 87
Recorder
Amplifier and
data system Igniter
Collector
electrode Outlet
Detector
Carrier gas Air supply

supply Amplifier
Sample injection
point
Hydrogen
supply Flame
Heated
oven
Carrier gas
Oven
temperature
programmer
Chromatographic column
(a)
Detector response
Peak height
Sample injected
Baseline

(b) (c)
FIGURE 4.18 (a) Diagrammatic representation of a gas chromatography system and flame ionization
detector, (b) schematic recorder trace from a gas-liquid chromatograph, and (c) an idealized gas-liquid
recorder peak showing the significance of retention time.
used as liquid stationary phases. At very high temperatures, the organic compounds may get volatil-
ized and cause excessive column bleedings, which may contaminate the detector.
4.10.2.1 Column Packing

The columns are generally dry packed under a slight positive gaseous pressure. Prepacked columns
are also available. After packing, the column is kept in an oven for 24–48 hours at a temperature
near the upper working limit. This is done to condition the column. During conditioning, the carrier
gas is passed through the column at normal flow rates. The column is not connected to the detector;
otherwise, the detector may get contaminated.
4.10.3 Sample Preparation and Application

The sample should be prepared in such a way that it does not get retained on the column for an
excessive period of time. This will lead to poor resolution and peak tailing. Polar groups such as
− NH 2 − COOH, and OH are derivatized by methylation, silanization, and trifluoromethyl silaniza-

tion to increase the volatile character and distribution coefficient of the compounds.
Solvents such as ether, heptane, and methanol are used to dissolve the sample, which is then
injected with the help of a microsyringe onto the column through a rubber septum in the injection
port. The temperature of the injection port is generally maintained higher than the temperature of
the column to ensure the rapid and complete volatilization of the sample. As a rule of thumb, the
temperature of the injection port should be 50°C higher than the boiling point of the sample. Too
high a temperature of the injection port may cause the decomposition of the sample. Therefore,
the temperature of the injection port should be such that it causes rapid vaporization of the sample
without decomposing it.
4.10.4 Carrier Gas

The primary function of a carrier gas is to carry the volatile components through the column. The
gas used should be inert and should not react with either the sample or the stationary phase. Its
secondary purpose is to carry the separated components to the detector, so the carrier gas should be
suitable for detector use. It should be readily available in extra-pure form and inexpensive.
Normally, nitrogen, helium, and argon are the three most commonly used carrier gases. The
column temperature must be high enough that analysis can be accomplished in a reasonable length
of time. The retention time doubles with every 30°C decrease in column temperature. The lower the
temperature the better the resolution and the longer the analysis time. Therefore, a balance has to
be struck between peak retention time and resolution. Chromatographic separation can be achieved
isothermally where a constant temperature is used or by temperature programming where the tem-
perature is increased gradually.
4.10.5 Detectors
Selectivity, sensitivity, response, noise, and minimum detectable quantity and linear range should
be considered when choosing a detector. The detector should be simple to operate, inexpensive and,
as far as possible, insensitive to changes in flow rate and temperature. Some of the commonly used
detectors are as follows:
Flame ionization detector (FID): It responds to almost all organic compounds and is the most
widely used detector. It has a wide linear response range (106) and can detect even at low
concentrations. The detector consists of two electrodes: one of the electrodes is the jet of
the flame produced by introducing a mixture of hydrogen and air into the detector, whereas
the second electrode is made of brass or platinum wire, which is mounted near the tip of the
flame. When the carrier gas carrying the sample components emerges from the column, the
sample components are ionized in the flame and sensed by the detector giving the signal,
which is recorded by the recorder. An FID has an upper temperature limit of 400°C, and the
minimum quantity that can be detected by this detector is on the order of 5 × 10−12 g. A typi-
cal FID is shown diagrammatically in Figure 4.19.
Nitrogen phosphorus detector (NPD): As the name suggests, NPD responds efficiently to
detect compounds containing N or P or both. It shows poor response to compounds that
contain neither of these elements. This detector has an upper temperature limit of 300°C,
a narrow linear response range of 104, and detection limits of 10−11 g·s−1. Its principle of
operation is the same as that of FID, but NPD has the sodium salt fused onto the electrode
system. The NPD is widely used in the analysis of organophosphorous pesticides.
Electron capture detector (ECD): Compounds that have the capacity to capture electrons are
best detected by this detector. Here, a radioactive source (63Ni) ionizes the column gas and
produces electrons, which give a current across the electrodes to which suitable voltage
Chromatography 89
Igniter
Collector
electrode
Amplifier
Air supply
Flame
H2 supply
Carrier gas
FIGURE 4.19 An FID.
is applied. When the carrier gas carrying the electron-capturing substance emerges from
the column, it captures the ionized electrons. This results in a drop in the current, which
is traced on chart paper by the recorder. The detector has an upper temperature limit of
300°C and high detection sensitivity (10−12 g·s−1) but a low linear range (102–104). This
detector is best suited for halogen-containing compounds and is widely used in the analysis
of polychlorinated compounds such as the pesticides DDT, dieldrin, and aldrin.
Thermal conductivity detector (TCD) or Katharometer detector: This detector measures the
change in the thermal conductivity of the carrier gas as a component emerges. This is
measured by means of change in the resistance of a platinum wire. All components of a
mixture, whether organic or inorganic, are detected up to a limit of 10−8 g·s−1.
4.10.6 Amplifiers and Recorders

When components leave the column and pass through the detectors, small and weak electrical sig-
nals are produced, which are amplified by an amplifier before they are fed to the recorder. Recorders
generally consist of two basic parts, that is, a chart paper and a pen; the pen moves on the chart
paper and traces the signals being activated from the amplifier in the form of peaks.
In cases where the identity of a compound is unknown, the GLC system is connected to a mass
spectrometer. Special separators separate the carrier gas from the sample, which is introduced into
the mass spectrometer. The GLC system can also be linked to an infrared (IR) spectrometer and
nuclear magnetic resonance (NMR) spectrometer in order to identify the compounds.
4.11 ION-EXCHANGE CHROMATOGRAPHY

Ion-exchange chromatography is a type of adsorption chromatography in which the retention of a solute
occurs due to its reversible electrostatic interaction with the oppositely charged group on an ion-exchange
substrate. This technique is useful in the separation of compounds that bear a net electric charge, such
as proteins, amino acids, and nucleic acids. Ion exchangers are prepared from either certain synthetic
resins, which are insoluble porous organic molecules, or naturally occurring biopolymers such as cel-
lulose to which various groups known as fixed ions are covalently attached. These fixed ions are bal-
anced by equal and oppositely charged ions from the solution, referred to as counterions. Depending on
the nature of the counterions, ion exchangers are of two types: (1) In cation exchangers counterions are
cationic or positively charged ions, and (2) in anion exchangers counterions are negatively charged ions.
Counterions are mobile and can be easily exchanged by other similarly charged molecules in the sample.
The nature of the resin matrix remains unchanged during this exchange process. Generally, resin-based
ion exchangers are used for the separation of low-molecular-weight biomolecules and cellulosic ion
exchangers are more suitable for the isolation of macromolecules such as proteins and nucleic acids.
4.11.1 Principle
Ion-exchange chromatography depends on the degree of attraction between oppositely charged
particles. Hence, it is used exclusively for the separation of ionic species. These occur mainly in
inorganic systems. However, ionic species occur in organic systems too, for example, amino acids,
proteins, and nucleic acids components have ionizable groups that can carry positive or negative
charge depending on their pKa and the pH of the solution. Separation may be carried out in column,
paper, or thin-layer modes with the help of ion exchangers, which are either positively charged
(anion exchangers) or negatively charged (cation exchangers). The positive and negative charges in
the exchangers are loosely bound to oppositely charged groups. When a group of a stronger charge
is introduced into the matrix structure of the exchanges, they displace the loosely bound groups and
bind strongly as a result of the higher degree of attraction, for example:
Cation exchanger : RSO3 … Na + + N+ H 3 R’ = RSO3 … NH 3 R’ + Na
exchanger counter ion to be exchanged: Charged molecule: bound
molecular ion: exchanged ion
Anion exchanger : ( R )4 N+ … Cl − + OOCR = ( R )4 N+ … OOCR’ + Cl
The exchange molecules are recovered by selective desorption by the eluant and diffusion of the
molecule to the external solution. Selective desorption is brought about by changing the pH or ionic
concentration, or by introducing an ion that has a greater affinity for the exchanger than the bound
molecules (Figure 4.20).
4.11.2 Ion-Exchange Materials

The common ion-exchange materials are resins insoluble in water. These are produced by the
copolymerization of styrene and divinyl benzene. Copolymerization results in cross-linkages, which
renders the polymers insoluble. By varying the amount of the two polymers, the amount of cross-
linking is controlled so that the system swells in water and is susceptible to water molecules and
ionic species. Sulfonic acid groups are introduced after polymerization. This results in the formation
of the anionic group, which binds mobile cations, that is, cation exchangers (Figure 4.21). Anion
exchangers are made by copolymerizing styrene with chloromethyl ether and allowing the chloro
groups to react with tertiary amines, which provides the cationic group that binds mobile anions.
Modified cellulose is now available as an alternative to polystyrene-based anion exchangers with
Fixed ions
Counterions
(a) (b) (c) (d) (e)
FIGURE 4.20 Separation process of solute during ion-exchange chromatography. Demonstration of vari-
ous steps (a to e) in separation of solute during ion exchange chromatography where Δ is a negatively charged
solute and ⚪ and ◽ are positively charged and neutral solutes.
Chromatography 91
SO3
SO3
CH CH2 CH CH2 CH CH2
SO3
SO3
CH CH2 CH CH2 CH CH2 CH CH2
SO3
SO3 CH CH2
Sulphonated polystyrene resin
CH2 CH3
H
CH2 CH2 N
N
CH2 CH2
Cellulose
DEAE cellulose
(diethylaminoethyl cellulose)
O
CH2 C
O
Cellulose
CM cellulose
FIGURE 4.21 Carboxymethyl (CM) cellulose.
better flow and exchange properties are now available, which possess good flow and exchange prop-
erties. In addition, separation is aided by the sieving action of gels and beads of these materials.
4.12 EXCLUSION CHROMATOGRAPHY

4.12.1 Principle
The separation of molecules on the basis of their molecular size and shape is achieved by utilizing
the molecular sieve action of gels. The term gel filtration is used to describe the separation of mol-
ecules of varying molecular sizes utilizing gel materials. Porous glass granules have been used for
this purpose, and the term controlled pore glass chromatography has been coined for this process.
The term exclusion or permeation chromatography is used to describe all separation processes that
utilize the molecular sieve action of gels.
Gels are insoluble hydrophilic semisolid colloids, which swell in buffer to form a 3D network of
pores. In order to explain the molecular sieve actions of gels, consider a mixture of large, medium,
and small particles being eluted through a gel (in equilibrium with a suitable solvent for the mol-
ecules to be separated; see Figure 4.22a). Large molecules, which are completely excluded from
the pores of the gel particles, pass through the interstitial spaces first, whereas small molecules
are distributed between the solvent inside and outside the gel particles and then pass through the
column at a slower rate. Due to variation in the pore size of gel particles, molecules of medium size
penetrate partially, fully, or not at all (Figure 4.22b). Hence the distribution coefficient, Kd, of a
particular solute between the solvent inside and the solvent outside a particular gel system varies
between Kd = 0 for large molecules completely excluded and Kd = 1 for small particles completely
reaching the inner solvent. The intermediate values will be for molecules of medium size. These
variable K values are responsible for the complete separation of the components of a mixture based
on differences in molecular weight or size (Figure 4.22c).
The elution volume for a given solute depends on several parameters given by the following
expression:
Ve = Vo + K dVi (4.1)
where
Vo = void volume (volume of solvent outside gel particles)
Ve = elution volume
Vi = volume of solvent inside gel particles
Kd = partition coefficient
It is noted that Vi can be calculated from Wr, or water regain value, which is the amount of solvent
taken up by l g of dry gel:
Vi = aW r
where a = dry weight of gel.

Thus from Equation 4.1,
Ve − Vo Ve − Vo
Kd = =
Vi aW r
For a molecular species, completely exclude Ve = Vo. Then,
Kd = 0
The molecular weight of a given unknown species can be determined by comparing its ΔV (arbi-
trary volume increments) value with that of compounds of known molecular weight eluted under the
same conditions (Figure 4.23).
4.12.2 Materials and Methods

Gel filtration is usually carried out in the column mode. However, the thin-layer mode can also be
used. The swollen gel is spread on a glass plate without the addition of a binding material. This is
called thin-layer gel filtration (TLG). Similar to TLC, the solvent in the interstitial spaces is the
Chromatography 93
L M S
Swollen
gel
particles
Solvent
inside and
outside gel
particles
(a)
Cross-linked network of
gel particles swollen in
water
Small molecules
can enter
Large molecules
cannot enter
(b)
V0 Vi
V0
Gel matrix
Solute
Solute
Volume of liquid Volume of liquid

accessible to large accessible to small
molecules (V0) molecules (V0 +Vi)
(c)
FIGURE 4.22 Figure showing (a) the molecular sieve action of gels, (b) the principle of gel filtration, and (c)
the diagrammatic representation of exclusion column chromatography.
Concentration of
solute
ΔV
V0 Ve
Fraction number
FIGURE 4.23 Elution diagram for exclusion chromatography.
mobile phase, but unlike TLC the layer in TLG is never dried; hence, there is no solvent front in
TLG. The plate is kept in an airtight jar at an angle of 20° to the horizontal position to facilitate
movement of solvent through the layer. Whereas TLC is used for the separation of amino acids, sug-
ars, oligosaccharides, and lipophilic substances, TLG is used for the separation of hydrophilic sub-
stances, particularly high-molecular-weight biological material such as proteins and nucleic acids.
4.12.3 Applications
Apart from its use for the separation of components of a mixture, gel filtration has further uses
unlike any other chromatographic technique. These include the following:
Determination of the molecular weight of an unknown compound: For determination of the

molecular weight of an unknown compound, V (Ve − Vo) values are compared with the ΔV
values of known compounds eluted under the same conditions.
Concentration of solute: Water and low-molecular-weight substances are absorbed by the swell-
ing gel, whereas high-molecular-weight substances remain in the solution. After 10 min-
utes, gel is removed by centrifugation, leaving behind high-molecular-weight material in
the solution whose concentration has increased without altering pH and ionic strength.
Desalting solutions of high-molecular-weight compounds: High-molecular-weight sub-
stances move with the void volume which is the volume of mobile phase (V0) in a column,
whereas low-molecular-weight substances are distributed between stationary and mobile
phases and hence move slowly. This method of desalting is faster and more efficient than
dialysis, which is used for the same purpose. This is used for removing monosaccharides
from polysaccharides, NH4SO4 from protein preparation, and amino acids from proteins.
Protein binding studies: To study the binding of a ligand to a protein, a protein/ligand mixture
is applied to a column, which has been previously equilibrated with ligand of the same
concentration as that in the mixture. The sample is eluted. Early fractions contain ligand
and protein-bound ligand. Thus by repeating the experiment for a series of ligand concen-
trations, the appropriate binding constants can be calculated.
4.13 AFFINITY CHROMATOGRAPHY

4.13.1 Principle
Unlike all other separation and preparative techniques such as chromatography, centrifugation, and
electrophoresis, which depend on the physical properties (size, molecular weight) of molecules,
Chromatography 95
Spacer
arm
Ligand
Matrix Bound protein Unbound contaminants
Sample
immobilized ligand washed away nonspecific
Affinity or elution by changing pH
specific elution or tonic strength
Protein with altered

Dialysis conformation
Restore the
optimum conditions
Purified protein
FIGURE 4.24 Principle of affinity chromatography applied in the purification of a protein.
affinity chromatography depends on the biological interactions of molecules to achieve purification.

It is therefore very sensitive and extremely efficient in achieving absolute purity in a single process
without destroying the molecules. This factor makes it superior to other forms of chromatography
for which repeated fractionation is necessary to achieve a high degree of purity. It is well known
that an enzyme can bind specifically to a substrate inhibitor or activator. These binding media are
called ligands.
A column is prepared in which a ligand of the required enzyme is covalently bonded to the inert
insoluble matrix when a solution containing the enzyme is passed through this column. It alone
binds to the ligand while all other molecules pass through. Even slightly modified or denatured
molecules do not bind and are thus eliminated. The enzyme is then eluted by changing either the
pH or the ionic strength of the solvent. Originally the technique was developed for the purification
of enzymes, but it has now been extended to the purification of nucleotides, nucleic acids, immuno-
globulins, membrane receptors, and even whole cells and cell fragments. Any molecule is capable
of reversibly binding to a specific ligand, which is attached to an insoluble matrix.
The main limitation found so far is the difficulty in simulating the natural affinity between mac-
romolecules in an artificial system. It requires detailed knowledge of the interactions and conditions
(pH, ionic strength, temperature, etc.) in which binding can take place. Also, the matrix in which the
ligand is bound should have spherical gel particles for a good flow of the unbound molecules to pass
through. Further, the ligand should be attached such that the attachment site for the macromolecule
is well exposed. For this reason, the ligand is not bound directly to the matrix; instead, a spacer arm
is used to separate the two (Figure 4.24).
4.13.2 Materials and Methods

The three important components of an affinity chromatograph are the matrix, ligand, and spacer
arm. The matrix should have a good network of pores through which the unbound molecules can
easily pass. It should be chemically inert and have suitable functional groups to which the ligand
can bind. It should not interact (or interact only weakly) with other molecules so that nonspecific
adsorption does not occur. The most commonly used materials for the matrix are agarose, poly-
acrylamide gels, cellulose, porous glass, and silica. Ligands may be bonded to the matrix by a
cyanogen bromide treatment of the matrix at pH 11 (Figure 4.25), which activates the matrix for
ligand attachment. The length of the spacer arm is usually 6–10 carbon atoms or their equivalent. It
should possess two functional groups, one at either end; one group binds to the matrix and the other
binds to the macromolecule, respectively.
(a) (b)
FIGURE 4.25 Representation of possible arrangements (a and b) of the role of spacer arms in properly bind-
ing a macromolecule.
Experiment: Separation and Identification of Amino Acids by

Descending Paper Chromatography
Introduction
Amino acids in a given mixture or sample aliquot are separated on the basis of the differences in their
solubility and hence differential partitioning coefficients in a binary solvent system. The amino acids
with higher solubility in a stationary phase move slowly compared with the amino acids with higher
solubility in a mobile phase. The separated amino acids are detected by spraying the air-dried chro-
matogram with ninhydrin reagent. All amino acids give off a purple or bluish-purple color on reaction
with ninhydrin, except proline and hydroxyproline, which give off a yellow-colored product.
Safety Guidelines
1. Do not touch the paper with naked hands because sweat contains a significant amount of
amino acids, which may interfere with your result.
2. The spots of the applied sample should be as compact as possible. The larger the spot the
poorer the resolution.
3. At the time of fixing paper in the chromatography chamber, ensure that the baseline on which
the sample has been applied does not dip into the solvent; otherwise, the sample might get
washed away in the solvent.
4. Allow sufficient time for the filter paper to absorb sufficient water (which will act as a sta-
tionary phase) before pouring the solvent into the trough/tank. Inadequate conditioning or
equilibration will result in improper or poor-quality resolution.
5. The solvent front should advance in a straight line and should not zigzag or slip; it should be
parallel to the baseline.
6. Dry the paper thoroughly before spraying with the detection reagent. Wet paper may interfere
with the appearance of evenly shaped compact spots.
7. Chromatography should be carried out in a temperature-controlled room because any fluctua-
tion in temperature will cause the uneven flow of the solvent and may alter the R f value.
Experimental Outline
Saturate the chromatographic chamber with BAOH (n-butanol: acetic acid: water). Develop the chro-
matogram in the solvent. Take the chromatogram out of the solvent after the solvent front reaches the
bottom. Dry the chromatogram completely and spray it with the ninhydrin reagent.
Materials
1. Whatman no. 1 filter paper, which should be cut as per the chromatographic chamber size;
standard amino acid solutions; ninhydrin; n-butanol; acetic acid; and distilled water
2. Micropipette/microsyringe
Chromatography 97
3. Hair dryer
4. Sprayer
5. Oven set at 105°C
6. Chromatographic chamber saturated with solvent vapors
Prelaboratory Preparations
1. Solvent: Take n-butanol, acetic acid, and water in the ratio 4:1:5 in a separating funnel and
mix them thoroughly; saturate the mixture by incubating for 3–6 hours. Allow the phases to
separate out completely. Use the lower aqueous phase for saturating the chamber. The upper
organic phase is used as the mobile phase.
2. Ninhydrin spray reagent: Prepare a fresh solution by dissolving 0.2 g of ninhydrin in 100 mL
of acetone.
3. Standard amino acids: Prepare solutions such as methionine, tryptophan, alanine, glycine,
and threonine (1 mg/mL in 10% isopropanol).
4. Prepare a sample containing a mixture of unknown amino acids.
Method
1. Take Whatman no. 1 filter paper and lay it on rough filter paper. Throughout the experiment, care
should be taken not to handle the filter paper with naked hands; for this purpose gloves should be
used, or filter paper should be handled with the help of a folder piece of rough filter paper.
2. Fold the Whatman no. 1 filter paper about 2–2.5 cm from one edge. Reverse the paper and
again fold it 2 cm down from the first fold.
3. Draw a line across the filter paper with a lead pencil at a distance of about 2 cm from the
second fold. Put circular marks along this line at a distance of 2.5 cm from each other.
4. With the help of a micropipette or microsyringe, apply 20 μL of solution of each standard
amino acid on a separate mark. Also apply a spot of the sample or mixture to be analyzed,
preferably on the mark at the center of this baseline. The size of the spot should be as small
as possible so that the developed spots are compact and do not overlap. If necessary, the wet
sample spot should be dried with the hair dryer before applying additional aliquot.
5. Hang filter papers in a line in a chromatographic chamber, which has previously been satu-
rated with the aqueous phase of the solvent system. This is done by keeping petri plates con-
taining the aqueous phase at the bottom of the chamber. The paper is hung from the trough/
tray and a glass rod is kept to hold it in place. Care should be taken to ensure that the baseline
is not submerged when the mobile phase is added to the trough; otherwise, the spotted mate-
rial will dissolve in the solvent.
6. Close the chamber firmly so that it is airtight. Allow sufficient time for the cellulose fibers of
the paper to fully hydrate.
7. Pour the mobile phase through the holes provided on the lid of the chamber into the trough.
Replace the rubber bungs in the hole and allow the mobile phase to run down the paper until
the solvent front reaches about 5 cm from the opposite edge.
8. Remove the paper and mark the solvent front using a lead pencil, and let it dry at room
temperature.
9. Spray the filter paper (chromatography) with a ninhydrin reagent; after drying it at room
temperature, transfer it to an oven at 105°C. Keep it in the oven for 5–10 minutes.
10. Blue- or purple-colored spots should appear on the paper. Mark the boundary of each spot
with a lead pencil.
11. Measure the distance between the center of the spots and the distance of the solvent front
from the baseline.
12. Calculate the R f value of the standard amino acids as well as of those in the given mixture or
sample as follows:
Distance traveled by unknown amino acid
Rf =
Diistance traveled by the solvent system
13. Identify the amino acids in the mixture or sample by comparing their R f values with those of
the reference standards (Figure 4.26).
Glass plate
Substances Solvent
A BA+B
with Rf s in trough
A and B
Trough
support
Filter
Solvent paper Solvent
movement strip movement
Developing
solvent (to
saturate atmosphere)
FIGURE 4.26 Chromatographic chamber for descending PC. A denotes sample 1, B denotes sample 2, and
A + B denotes the mixture of 1 + 2.
Note: It is advisable to carry out chromatography in three different solvent systems before the identity
of the amino acid in the mixture or sample can be established with any degree of certainty.
Observations
Distance traveled by the solvent = x cm from baseline
Distance traveled by glycine = a cm from baseline
Distance traveled by alanine = b cm from baseline
Distance traveled by threonine = c cm from baseline
Distance traveled by methionine = d cm from baseline
Distance traveled by spot no. 1 in = a cm sample from baseline
Calculations
Rf value of glycine = a/x
Rf value of alanine = b/x
Rf value of threonine = c/x
Rf value of methionine = d/x
Rf value of spot no. 1 = a/x
Conclusion
The sample contains glycine since the R f value of spot no. 1 is identical to the R f value of authentic
glycine standard.
Experiment: Separation and Identification of Amino Acids by

Ascending Paper Chromatography
Introduction
Same as given in the first experiment of this chapter.
Safety Guidelines
Same as those given in the first experiment of this chapter.
Chromatography 99
Materials
Same as those given in the first experiment of this chapter, except that cylindrical chromatography
chambers are needed for this experiment.
Experimental outline is similar to the one given in the first experiment of this chapter.
Same to that given in the first experiment of this chapter.
Method
1. Take a Whatman no. 1 filter paper sheet of appropriate size so that it can be rolled into a cyl-
inder and accommodated in a cylindrical chromatographic jar.
2. Draw a baseline 2 cm from one of the breadthwise edges of the paper. Put small circular
marks along the baseline in such a way that the distance from the edge of the paper to the first
spot and the distance between adjacent spots are not less than 2.5 cm.
3. Apply 20 L aliquots of the standard amino acids and the sample at different spots. The
diameter of the spotted material should be as small as possible and, if required, the applied
solution may be dried prior to loading additional volume.
4. Roll the paper into a cylinder and fasten its edges with a paper clip. Pour a sufficient volume
of the mobile phase into the chromatographic jar, which has been previously saturated with
water vapors by lining the tank with filter paper saturated with the aqueous phase of the sol-
vent system.
5. Gently place the rolled filter paper upright in the jar after ensuring it does not touch the
sides of the chamber; at the same time, take care that the baseline where the spots have been
applied does not dip into the solvent.
6. Close the tank with an airtight lid or a glass plate to which a sufficient amount of silicon
grease has been applied.
7. Leave the setup undisturbed and allow the solvent to move up until it reaches about 5 cm from
the upper edge.
8. Remove the chromatogram from the chamber and air dry it.
9. Spray the paper with a ninhydrin reagent and let it dry again at room temperature prior to
transferring it to an oven at 105°C for 5–10 minutes. Locate the position of the amino acids
from the bluish or purple-colored spots on the chromatogram.
10. Calculate the R f values of the standard amino acids and the amino acids in the sample or
mixture as described in the first experiment of this chapter.
11. Identify the amino acids in the mixture or sample by comparing the R f values with those of
applied standard amino acids.
Experiment: Separation and Identification of Amino Acids

in a Given Mixture by 2D Paper Chromatography
Introduction
Amino acids that have very close R f values in a particular solvent system may appear as single or overlap-
ping spots in a one-dimensional (1D) chromatogram and may be mistaken as a single component. They can
be separated into individual components by developing the chromatogram again in a direction perpendicu-
lar to the first run in a second solvent system in which they have different R f values. The main limitation
of this method is that only one spot of either the sample or a standard amino acid can be applied on each
filter paper sheet, necessitating the running of a large number of chromatograms for standard amino acids.
Safety Guidelines
Develop the chromatographic paper in one solvent after it has been dried; turn round and develop it in
another direction with a second solvent. Calculate the R f values of the amino acids (Figure 4.27).
Materials
Same as the ones listed in the first experiment of this chapter, except that an additional chromatographic
chamber for the second solvent system is required.
Prelaboratory preparations required are the same as those given in the first experiment of this chapter.
Additional preparations required are as follows:
1. Solvent system no. 2: Phenol (distilled) in water (80:20 w/v) is used as the second solvent
system. Add 125 mL of water to 500 g of phenol, and add a few drops of ammonia (0.88%) to
this mixture just before use. (Caution: Phenol is corrosive and can cause burns on the skin.)
2. Standard amino acids: Prepare a 1% solution of standard amino acids such as asparagine,
glycine, serine, and arginine in 10% isopropanol (w/v).
Method
1. Lay the chromatographic paper sheet flat on the rough filter paper using gloves.
2. Draw a baseline 5 cm from one of the edges of the paper.
3. Draw another line perpendicular to the first line, again 5 cm away from the adjacent edge.
4. Apply 60 L of the sample solution or a given mixture containing unknown amino acids at
the point of intersection of the two lines. The sample should be applied in small volumes at
a time with the help of a micropipette with intermittent drying to ensure that the zone of the
applied solution is as small as possible.
5. Repeat the same procedure for a mixture of three standard amino acids using a separate chro-
matographic sheet for each amino acid. The composition of the mixture of standard amino
acids should be such that each amino acid is present in at least two different mixtures so that
its identity can be established.
6. Hang the paper in the chromatographic tank whose interior has been previously saturated
with the aqueous phase of solvent system no. 1 (n-butanol: acetic acid: water mixture in the
ratio 4:1:5).
7. After allowing an equilibrium period of half an hour, pour solvent no. 1 into the trough
of the chamber and let it run until it reaches about 10 cm from the opposite edge of the
paper.
8. Take the paper out, air dry it, and turn it at an angle of 90°C; now develop the paper
in the second chromatographic chamber using solvent system no. 2 (phenol: ammonia:
water).
9. Remove the paper when the solvent has traveled up to about 10 cm from the opposite end.
10. Dry it at room temperature and spray it with the ninhydrin reagent. After air drying it, keep
the chromatogram in an oven at 105°C for 10 minutes. Mark the blue- and/or purple-colored
zones that appear on the paper.
Turn through
Second
90° after
solvent
removing first
system
solvent
FIGURE 4.27 Scheme of 2D chromatography.

Chromatography 101
Observations
Calculate the R f value of the standard amino acids and those in the mixture as given in both the sol-
vents. From these values, identify the amino acids in the given mixture.
Experiment: Separation and Identification of Sugars by

Adsorption TLC
Introduction
Sugars are separated on the basis of differential adsorption onto silica gel. The sugars that have higher
affinities for stationary phases are adsorbed more strongly, and they migrate slowly when the mobile
phase moves over them. On the other hand, those having lower affinities for stationary phases are
weakly adsorbed and more easily carried by the mobile phase. The separated sugars are then located as
colored zones by spraying TLC plates with an aniline diphenylamine phosphate reagent.
Safety Guidelines
1. Only thoroughly cleaned glass plates free of any greasy spots or finger marks should be used.
2. The thickness of the layer should be uniform throughout the length of the plate.
3. The slurry of the chromatographic media should be free of any clumps. This can be ensured
by vigorously shaking it in an Erlenmeyer flask or by gently preparing the slurry using a
pestle and mortar to ensure uniform mixing.
4. The layer on the chromatographic media should not get scraped off when putting marks on
samples.
5. The size of the applied spot should be as small as possible. If a large volume of the sample has
to be spotted, then it should be done in small aliquots with intermittent drying. Overloading
of the sample should be avoided.
6. The chromatographic tank should be airtight and chromatography should be performed under
temperature-controlled conditions.
Preparation of TLC Plates with Silica Gel-G
Develop silica gel-G plates by running glass plates in a chromatographic chamber with ethyl ace-
tate: isopropanol: water: pyridine in the ratio 26:14:7:2. Dry the plates after they are developed, spray
with aniline diphenylamine phosphate reagent, and calculate the R f values of each spot (Figure 4.28).
Cover
Movement
of solvent
Tank
Glass plate
with thin
layer of
silica gel
Solvent
Spots rising differentially

with rising solvent
FIGURE 4.28 TLC chromatographic tank.

Materials
A TLC chromatographic tank, glass plates (20 × 20 cm), a spreader, micropipettes/microsyringe, an
oven maintained at 105°C, a hair dryer, and a sprayer or an automizer.
1. Solvent system: Take ethyl acetate: isopropanol: water: pyridine in the ratio 26:14:7:2.
2. Standard sugar solution: Prepare a 1% solution of standard sugars such as glucose, ribose,
fructose, and sucrose in 10% isopropanol.
3. Aniline diphenylamine phosphate reagent: Mix 5 volumes of 1% aniline, and 5 volumes of
diphenylamine in acetone with 1 volume of 85% o-phosphoric acid.
Method
1. Place thoroughly cleaned and dried glass plates (20 × 20 cm) side by side on a flat plastic tray,
leaving no gap between the two adjacent plates.
2. Prepare a slurry of the stationary phase (silica gel-G) free of clumps in water or an appropri-
ate buffer.
3. Spread a uniform layer of slurry of 250 μm thickness on the glass plates with the help of a
spreader or an applicator by moving it from one end to the other end of the tray. Note that
ready-made thick silica gel–coated aluminum or plastic sheets are also available.
4. Activate the plates by keeping them at 105°C for 30 minutes; allow the plates to cool in a
desiccator before use.
5. Gently put marks in a straight line with the help of a pin at a distance about 2 cm from one
edge of the plate. The adjacent marks should be plotted carefully in such a way that the silica
does not scratch off while putting on the spots.
6. Carefully apply the solution of individual standard sugars and the mixture or alcoholic extract
of the sample on separate marked spots.
7. Gently put marks in a straight line.
8. Develop the TLC plates in the solvent (ethyl acetate: isopropanol: water: pyridine in the ratio
26:14:7:2).
9. Take out the plates after the solvent reaches 2 cm from the bottom.
10. Air dry the plates for at least 12 hours.
11. Identify the sugar species by spraying the plates with an aniline diphenylamine phosphate
reagent.
Experiment: Isolation and Identification of Lipids in a Given

Sample by Thin-Layer Chromatography
Introduction
Lipids, which are a heterogeneous group of biological compounds, are insoluble in water but soluble
in ether, chloroform, and other organic solvents. The hydrocarbon content of lipids contributes to their
hydrophobic nature. Lipids are generally bound to proteins in biological samples and cannot be effi-
ciently extracted with nonpolar solvents alone. In such cases, lipids are extracted with a mixture of
chloroform and methanol and are easily separated and identified by TLC.
Safety Guidelines
Reagents
1. Silica gel
2. Acetone ((CH3)2 CO)
3. Benzene (C6H6)
4. Chloroform (CHCl3)
5. Methanol (CH3OH)
6. Ammonium hydroxide (NH4OH) or ammonia solution
Chromatography 103
A. Extraction of Lipids
1. Centrifuge a known volume of homogeneous algal suspension at 5000 rpm for 10 minutes.
2. Wash the pellet twice in distilled water.
3. Sonicate or grind with glass powder a known weight of the algal pellet with a known volume
of chloroform: methanol (2:1) (v/v).
4. Filter the extract using the filter paper and ensure that the filter paper is free from lipids.
5. Add 1/3 volume of distilled water to the filtrate and vortex thoroughly to remove water-
soluble impurities (upper layer).
6. To remove moisture content in the filtrate, add a small amount of sodium sulfate crystals and
centrifuge (nonclumping of crystals indicate that the filtrate is free of moisture).
7. Transfer the filtrate to a preweighed bottle (weight is A).
8. Dry the filtrate either under nitrogen or in a rotary evaporator.
9. Reweigh the bottle (new weight is B).
10. Weight of lipid (in milligrams per gram) = B − A.
Comments
For storage up to a few hours, the tube is covered with aluminum foil and chilled on ice to minimize
the evaporation of the solvent.
B. The TLC Method for Separation of Lipid Classes

1. Draw a pencil line on a precoated silica gel plate (20 × 20 cm) parallel to and approximately
2 cm from one edge.
2. Redissolve the total lipid extracted earlier in 1 mL of chloroform: methanol (2:1) (v/v).
3. Apply a lipid solution (10–50 μL) as a spot on the pencil line with a microsyringe (evaporate
the solvent quickly with an air blower).
4. Develop the plate with either of the solvent systems:
a. (CH3)2 CO/C6H6/H2O (91:30:8) (v/v)
b. CHCl3/CH3OH/(28%) NH4OH (13:7:1) (v/v)
5. Dry the plate in the fume hood for about 20 minutes.
6. Keep the plate in the iodine chamber until the colored spots develop.
7. Mark the spots, and scrape into a flask for extraction.
8. Calculate the resolution front (Rf) and identify the sample by comparing the standards.
Experiment: Separation of Pigments from Leaves or Flowers by Adsorption

Column Chromatography
Introduction
Different pigments are adsorbed to alumina to different extents. They can be selectively desorbed by
using a mobile phase of increasing polarity in a stepwise manner.
Safety Guidelines
The safety guidelines outlined in the first five experiments of this chapter may be followed.
Prepare a glass column; homogenize leaves in benzene: methanol (26% ratio); and run the extract in an
alumina-packed glass column with appropriate solvents. Different pigment fractions are collected and
identified by their colors.
Materials
Leaves or flowers, pestle and mortar, a glass column or a burette, Whatman no. 1 filter paper, alumina
or icing sugar, sodium sulfate (anhydrous), acetone.
The solvent used is benzene: methanol (2:1).
Method
A. Preparation of Extract
1. Homogenize the leaves or flowers (5 g wet weight) in a pestle and mortar, using sand as an
abrasive, in 20 mL of benzene: methanol (2:1); add a small amount of this extracting medium
at a time.
2. Filter the extract through Whatman no.1 filter paper and transfer the filtrate to a separating
funnel.
3. Add 10 mL of water to the filtrate and after shaking the contents and allowing the phases to
separate out, drain out the lower aqueous methanol layer. Repeat this step; avoid vigorous
shaking.
4. Collect the benzene layer in a beaker and add a small amount of solid anhydrous Na2SO4 to
remove the traces of moisture.
5. Decant the clear benzene layer to another beaker and concentrate the extract by evaporating
the solvent over a boiling water bath.
B. Preparation of Column
1. Mount a burette or glass column vertically on a burette stand with the help of clamps.
2. Lightly place a plug of glass wool at the base of the burette and close the stopcock or outlet at
the bottom of the column.
3. Take 5 g of alumina or icing sugar (adsorbent), which has been previously dried at 120°C for
8 hours, and prepare its slurry in benzene. Pour the slurry carefully into the column or burette
by gently tapping the column or burette so that no air bubbles get trapped in the adsorbent.
4. Allow the adsorbent to settle by opening the outlet. After the adsorbent has completely set-
tled, add 20 mL of benzene and let it pass out of the column. Care should be taken to not let
the adsorbent dry.
C. Application of Sample
1. Allow the solvent at the surface of the column to drain out slowly, and transfer the leaf or
flower extract with the help of a pipette without disturbing the surface of the column adsor-
bent. Let it enter the column, and then add a few drops of benzene to wash away the traces of
the extract sticking to the wall of the column.
2. Add 20 mL more benzene to wash any unabsorbed material out of the column.
D. Column Development
For the desorption of the adsorbed substances, change the polarity of the solvent in a stepwise manner.
After 20 mL of benzene passes through the column, add 10 mL of 5% acetone (v/v) in benzene and
let it percolate through the column; collect 1–2 mL fractions of the effluent from the outlet. Continue
increasing the concentration of acetone in benzene at every succeeding step. Finally, pass pure acetone
through the column.
Result
Note the change in the color of the collected fractions. In the case of the leaf extract, the initial frac-
tions are colorless; they are followed by yellow-colored and then green-colored extracts. The color-
less fractions do not contain any pigments, but it is quite possible that these fractions contain some
UV-absorbing materials.
Experiment: Desalting of Protein Sample by Gel Filtration

Introduction
Separation is based on the fact that proteins are macromolecules, whereas salts are low-molecular-
weight substances. When the sample is passed through a column packed with sephadex G-10 or G-25,
Chromatography 105
proteins remain totally excluded from the gel and move with the void volume, while salts enter the gel
particles and take a longer time to get eluted.
Safety Guidelines
Standard laboratory guidelines may be followed in this experiment for protein purification.
Prepare the column with either sephadex G-10 or sephadex G-25; elute the column with buffer. Collect
2 mL fractions for the eluant and measure the protein content of each fraction.
Materials
Glass column; sephadex G-10, G-25, or G-75; protease; RNAase; sodium phosphate.
1. Prepare 0.1 M Tris-HCl buffer (pH 7.0).
Method
1. Suspend 5 g of sephadex G-25 (coarse) in 0.1 M Tris-HCl buffer (pH 7.0), and allow it to swell
by keeping it for 3–4 hours at room temperature with intermittent stirring.
2. Decant the excess buffer along with any suspended fine particles to obtain slurry of reason-
able thickness.
3. Fix the column upright on a burette stand with the help of clamps.
4. Keep the outlet of the column closed, place a plug of glass wool at the base of the column, and
pour a small volume of the buffer or water into the column.
5. Pour the slurry gradually into the column along the inner surface of its wall and, if necessary,
gently tap the column to expel any air bubbles.
6. Allow the chromatographic media to settle down evenly and then open the outlet to drain
excess liquid from the column.
7. Place a filter paper disk or nylon gauze on the surface of the packed bed to prevent a distur-
bance of the upper layer while loading the sample or feeding the eluant into the column.
8. Prepare a mixture of 10 mg of bovine serum albumin and 40 mg of sodium phosphate in 2 mL
of 0.1 M Tris-HCl buffer (pH 7.0).
9. Apply the mixture to the chromatography column by either of the following two methods:
a. Drain out the mobile phase at the top of the peak until the bed surface is exposed.
Close the outlet and gently apply the sample uniformly over the bed surface using a
pipette; then allow the loaded sample to just enter the column by opening the outlet.
Add a small amount of mobile phase (or buffer) to wash the traces of the sample into
the column.
b. In the second method, add sucrose or glycerol up to a concentration of 1% to the sam-
ple to increase its density. Apply this sample just above the surface of the bed directly
through the layer of the buffer in the column bed. Since the sample has a higher density, it
automatically settles on the surface of the gel. Then open the outlet to facilitate the entry
of the sample into the column. When using this procedure, it is advisable to ensure that
the addition of glycerol or sucrose does not interfere with the separation and subsequent
analysis of the separated compounds.
10. Add a sufficient amount of buffer to the top of the column and connect it to the buffer
reservoir.
11. Collect fractions (2 mL each) either manually or using an automatic fraction collector.
Determine the protein content either by monitoring the absorbance at 280 nm or by applying
Lowry’s method and the phosphate ions method in each of the fractions.
12. Plot a graph of the concentration of protein and phosphate versus the fraction number or elu-
tion volume (Figure 4.29).
Protease
RNAase
Enzyme activity
Protein
Hemoglobin
NaCl
Elution volume Elution volume

(a) (b)
FIGURE 4.29 Figure showing (a) typical elution pattern on sephadex G-25 to separate hemoglobin from salt
and (b) separation of RNAase from a protease in pancreatic extract on G-75.
Experiment: Separation of Amino Acids by Ion-Exchange Column

Chromatography Using Cation Exchanger
Introduction
Ion-exchange chromatography can be used for the separation of substances that possess a net electrical
charge. Anion exchangers reversibly bind negatively charged compounds through electrostatic forces,
whereas positively charged molecules interact with cation exchangers. Different compounds are held
by ion exchangers with varying strengths depending on charge. At very low pH values of 1.0, almost
all amino acids (including acidic amino acids) exist as cations; hence, they can be separated on a cation
exchanger.
Safety Guidelines
The safety guidelines outlined in the first six experiments of this chapter may be followed.
Prepare the glass column by packing it with an ion-exchange resin. Elute the amino acids with a buffer,
collect the eluant, and identify the amino acids.
Materials
Chromatographic column (2.5 × 25 cm), colorimeter
1. Dowex-50 resin in 0.05 M citrate buffer, pH 3.0
2. Citrate buffer 0.05 M, pH 3.0
5. Amino acids (aspartic acid, alanine, lysine, and histidine); 2 mg of each amino acid per
m illiliter of 0.1 M HC1, pH 1.0
6. 4N HCI
7. Ninhydrin reagent
8. 0.1N HCl, pH 1.0
Chromatography 107
Method
A. Preparation of Ion Exchanger
Dowex-50, a cation exchanger, must be fully saturated with H+ first; this H+ form can be converted to
Na+ form so that the resin can function as a cation exchanger.
1. Suspend 10 g of Dowex-50 into sufficient volume of 4 N HCI for 15 minutes to ensure that the
resin is saturated with H+ ions.
2. Filter the suspension and wash it repeatedly with distilled or deionized water until the pH of
the filtrate is neutral.
3. Transfer the resin into 2 N NaOH and keep for 15 minutes to get the Na+ form. Wash it until
the pH of the filtrate is neutral.
B. Equilibration of the Resin

1. Suspend the resin in citrate buffer (of pH 3.0) and allow it to stand for 1 hour.
2. Mount the column upright and pour the suspension with the help of a glass rod while tapping
the column gently.
3. Allow the suspension to settle down, open the outlet, and pass two to three bed volumes of
citrate buffer (0.05 M, pH 3.0) through the column. This will fully equilibrate the resin to pH
3.0. When only a thin layer of buffer remains at the top of the resin, stop the flow by closing
the column outlet.
C. Sample Loading
1. Open the outlet and let the buffer at the top drain into the column surface. Close the stopcock.
2. Load the column with 1 mL of a mixture of amino acids in 0.1 M HCl that have a pH value of 1.0.
3. Add a small amount of buffer to wash away traces of the sample from inside the walls of the
column, and when the level just reaches the surface, close the stopcock.
D. Development of the Column

All the amino acids are in cationic form at pH 1.0 and, thus, they are bound to the cation exchanger.
Gradient elution using increasing pH and ionic strength facilitates sequential elution of the bound
amino acids. Test each eluant with ninhydrin.
Experiment: Determination of the Molecular Weight of a

Given Protein by Gel Filtration
Introduction
During gel filtration, solutes are separated primarily on the basis of their molecular size. Due to the
molecular sieving effect, large molecules are eluted from the column first, followed by compounds of
smaller molecular mass. A plot between Kd or the elution volume versus logarithm to the base 10 of
molecular weight gives a straight line. The molecular weight of a given protein can be established from
its elution volume through the gel filtration column, which has previously been calibrated with standard
marker proteins of known molecular weight.
Safety Guidelines
The safety guidelines are outlined in the first six experiments of this chapter; pack the glass column
with sephadex G-100, avoiding the entrapment of any air bubbles.
1. Preparation of the glass column with sephadex G-100
2. Elution with buffer solution
3. Collecting the protein fractions
4. Calculating the molecular weights
Materials
Glass column (2.5 × 70 cm), sephadex G-100, MgCl2, dithiothreitol (DTT), glycerol, standard protein
markers, blue dextran
1. The HEPES [4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid]–NaOH buffer (20 mM;
pH 8.0)
Method
1. Suspend 15 g of sephadex G-100 in 20 mM HEPES–NaOH (pH 8.0) buffer containing 5 mM
MgCl2 and 5 mM DTT for 5 hours in a boiling water bath.
2. Allow it to cool and pack it into the glass column.
3. Equilibrate the column by passing buffer equivalent to 2–3 volumes of the bed volume.
4. Find out the void volume (Vo) of the column by determining the elution volume of blue dex-
tran solution (2 mg/mL) through the column. Again pass 2 bed volumes of the starting buffer.
5. Apply the mixture of the standard marker proteins of known molecular weight and elute the
column with the buffer.
6. Collect fractions of 2 mL each and determine the protein content in each fraction either by
Lowry’s method or by recording absorbance at 280 nm.
7. Determine the elution volume of standard proteins and prepare a graph of logarithm to the
base 10 of molecular weight versus Ve or Kd, again pass 2 volumes of the starting buffer.
8. Layer the sample containing the protein whose molecular weight must be determined. Elute
it and collect fractions of 2 mL each. Test each fraction for the presence of protein and deter-
mine its Ve.
9. Determine the molecular weight of the given protein from the calibration curve prepared in
step 7 as shown in Figure 4.30.
Ribonuclease A
Cytochrome C
Soybean trypsin inhibitor
Kd
Bovine serum albumin
Bovine serum albumin dimer

Ovalbumin
Thyroglobulin
104 105 106

Molecular weight
FIGURE 4.30 Relationship between Kd and logarithm of the molecular weight of proteins.
Chromatography 109
Experiment: Identification and Quantification of Amino Acids by

High Performance Liquid Chromatography (HPLC)
Introduction
The derivatized amino acids have greater resolutions as well as detectability at picomole levels. There are
two types of reagents used for derivatization: (1) precolumn and (2) postcolumn. Precolumn derivatization
is commonly used, and the reagents used are phenylisothiocyanate (PITC) and ortho-phtalaldehyde (OPA).
Derivatives could be measured above 250 nm. A fluorescence detector could also detect OPA derivatives.
A. Phenylthiocarbamyl Method
Principle
PITC reacts with primary and secondary amino acids, and the reaction yields phenylthiocarbamyl
(PTC) amino acids derivatives. These have strong absorbances between 240 and 260 nm.
Reagents
1. PITC.
2. 6N HCl.
3. Acetate buffers (0.025 M) of pH 5 and pH 7: Prepare 0.25 M of acetic acid (0.23 mL in 100
mL of distilled water) and 0.25 M sodium acetate (3.4 g in 100 mL of distilled water). Add
sodium acetate to 0.25 M acetic acid until the pH of the solution reaches 5 and 7, respectively,
for acetate buffers of pH 5 and 7.
4. Acetonitrile.
5. Coupling buffer: Prepare the coupling buffer by mixing 10 mL of acetonitrile, 5 mL of pyri-
dine, 2 mL of trimethylamine, and 3 mL of water.
Procedure
1. Take commercially available protein hydrolysate and prepare ethanolic solution.
2. Place the samples in the vacuum desiccator and completely dry them under a vacuum.
3. To the dried sample, add 200 μL of coupling buffer and evaporate to dryness.
4. To the sample, again add 200 mL of coupling buffer; this is followed by the addition of 20 μL
of PITC.
5. Incubate the sample at room temperature for 5 minutes and evaporate to dryness.
6. Store the dried sample in the freezer until analysis.
7. Prior to analysis, dissolve the dried sample in 100 μL of acetate buffer adjusted to a pH value of 7.
8. Filter the sample before injection.
Column Conditions
Column: Teledyne Isco, Inc. P.O. Box 82531, Lincoln, Nebraska, 68501 USA (ISCO) C18, 4.6 ×
250 mm, 5 μm pack ink
Mobile phase A: Sodium acetate buffer, pH 5.0
Mobile phase B: 50% sodium acetate buffer/50% acetonitrile (before use, filter and degas)
Flow rate: 1.5 mL·min−1
Detector: ISCO V4 variable wavelength, 5 mm flow cell, and wavelength 254 nm
Result
Run the standard PTC amino acids. From the retention time and peak area, identify and calculate the
amount of individual amino acids in the sample and express the amount as nanomoles per m illigram
dry weight of sample or protein.
B. OPA Method
Principle
Peptides with N-terminal primary amines are derivatized by OPA. One advantage of the OPA derivative
is its enhanced sensitivity; further, it can be detected in a fluorescence detector without interference.
Reagents
1. Borate buffer (0.25 M, pH 9.5): Prepare 0.25 M of boric acid (15.457 g in 100 mL of distilled
water) and 1 M of NaOH (4 g in 100 mL of distilled water). Add NaOH solution to boric acid
solution until the pH reaches 9.5, and make up to 100 mL.
2. Phosphate buffer (0.1 M, pH 6.5): Prepare 0.1 M of K2HPO4 (2.720 g in 100 mL of distilled
water) and 0.02 M sodium acetate (164 mg in 100 mL of distilled water). Take 50 mL of 0.1 M
K2HPO4 and titrate with 0.02 M sodium acetate until the pH reaches 6.5; make up to 100 mL.
3. OPA stock solution: Dissolve 0.26 g of OPA in 20 mL of methanol and make up to 200 mL
with borate stock solution and store the solution in a refrigerator.
4. Derivatizing solution: Add 30 μL of mercaptoethanol to 20 mL of OPA solution (prepare this
on the day of use).
5. Tetrahydrofuran.
6. Acetic acid.
7. Methanol.
Procedure
1. Take commercially available protein hydrolysate and prepare ethanolic solution.
2. Mix equal amounts of ethanolic hydrolysates and derivatizing solution thoroughly before
injection (prior to sampling, filter the solution through a 0.45 μ nylon filter).
3. Load the mixture into the HPLC injection loop and allow the reaction to continue (do the
mixing and injection within 1 minute; for reproducible results, the timing of the injection is
critical).
Column Conditions
Column: ISCO C18, 4.6 × 250 mm, 5 μm packing
Mobile phase A: 10% tetrahydrofuran/90% phosphate buffer (pH 6.5), K2HPO4 (0.1 M), sodium
acetate (0.2 M)
Mobile phase B: 80% methanol/20% acetic acid (0.1 M)
Flow rate: 1.5 mL·min−1
Detector: ISCO FI-2, 9 μL flow cell
Excitation filter: 305–395 nm
Emission filter: 430–470 nm
Calculations
Run the standard OPA amino acids. From the retention time and peak area, identify and calculate the
amount of individual amino acids in the sample and express the amount as nanomoles per m illigram
dry weight of sample or protein.
Experiment: Isolation and Identification of Carbohydrates by GC

A. Hydrolysis of Polysaccharides
Principle
Carbohydrates that occur as trioses (CH2O)3, tetroses (CH2O)4, pentoses (CH2O)5, and hexoses
(CH2O)6 are hydrolyzed to simple sugars by strong acids because of the dehydration of hydroxyl groups.
Reagents
1. Hydrolyzing agent: H2SO4/trifluoroacetic acid (TFA)
2. Neutralizing agent: Barium carbonate [Ba(CO3)2]
Procedure
1. Centrifuge a known volume of homogeneous bacterial/fungal/cyanobacterial suspension at
5000 rpm for 10 minutes.
Chromatography 111
3. To a known weight (10 mg) of the pellet in a tube, add 1 mL of 0.70% H2SO4 and seal.
Hydrolyze at 105°C for 6 hours.
4. Neutralize the hydrolyzed contents with barium carbonate and centrifuge at 5000 rpm for 10
minutes.
5. Evaporate to dryness over a boiling water bath.
B. Identification by Gas Chromatography

Principle
For GC analysis of carbohydrates, the trimethylsilyl (TMS) derivative is recommended to increase the
volatility of the carbohydrates. The chloride present in trimethylchlorosilane acts on hydroxyl groups in
carbohydrates and forms Me3Si-O-carbohydrates in the presence of a pyridine base.
Reagents
1. Anhydrous pyridine (pyridine dried over KOH pellet is suitable)
2. Hexamethyldisilazane (HMDS)
3. Trimethylchlorosilane (TMCS)
Procedure
1. Prepare a trimethylsilation reagent by mixing anhydrous pyridine (5 mL), HMDS (2 mL), and
TMCS (0.5 mL).
2. To the hydrolyzed sugar sample, add 1 mL of the pyridine–silane mixture and shake well
until the sugar dissolves completely.
3. Allow the sample to stand at room temperature for 5 minutes and then perform the injection
using the following column conditions:
Column: 3% OV-225
Column temperature: 190°C
Injection port temperature: 240°C
Detector temperature: 240°C
Gas flow rates:
H2: 15 mL·min−1
N2: 15 mL−1
Air: 300 mL·min−1
or
Column: 3% OV-275
Column temperature: 230°C
Injection port temperature: 275°C
Detector FID
Gas flow rates:
H2: 15 mL·min−1
N2: 15 mL−1
Air: 300 mL·min−1
4. Run standard sugars with TMS derivatives. From the known retention time (RT), find the
sugars of the unknown sample and quantify them using the peak area; express their amounts
as nanogram per milligram dry weight of sample.
SUGGESTED READING
AKTA Design Purification Method Handbook. Amersham Biosciences. Catalog number 18-1124-23. Amersham
Biosciences 2006.
AKTA FPLC, System Manual, Amersham Pharmacia Biotech. http://www.hhmi.umbc.edu/toolkit/aktadesign
.pdf, 18-1140-45 Edition AB.
ÄKTAFPLC, System Manual 18-1140-45 Edition AB. Amersham Pharmacia Biotech AB 2000.
Buffington, R., and M. K. Wilson. 1987. Detectors for Gas Chromatography—A Practical Primer. Hewlett-
Packard Corporation, Part No. 5958-9433.
Chromatography, Theories, FPLC and Beyond. http://www.mnstate.edu/biotech/chrom_fplc.pdf
Cooper, E. H., R. Turner, E. A. Johns, H. Lindblom, and V. J. Britton. 1983. “Applications of Fast Protein
Liquid Chromatography TM in the Separation of Plasma Proteins in Urine and Cerebrospinal fluid.”
Clinical Chemistry 29: 1635–40.
Desai, S. N., R. B. Colah, and D. Mohanty. 1998. “Comparison of FPLC with Cellulose Acetate
Electrophoresis for the Diagnosis of Beta-Thalassaemia Trait.” Indian Journal of Medical Research
108: 145–48.
Ettre, L. 1993. “Nomenclature for Chromatography.” Pure and Applied Chemistry 65: 819–72.
Feinberg, J. G., and I. Smith. 1972. Paper and Thin Layer Chromatography & Electrophoresis, 2d ed. (with
amendments and corrections). London: Longman.
Ferreira, P. O., and M. A. Ferreira. 2002. “Solid Phase Micro-Extraction in Combination with GC/MS
for Quantification of the Major Volatile Free Fatty Acids in Ewe Cheese.” Analytical Chemistry 74:
5199–204.
Gogou, A. I., M. Apostolaki, and E. G. J. Stephanou. 1998. “Adsorption Chromatography.” Journal of
Chromatography A 799: 215.
GST Gene Fusion System Handbook, Amersham Biosciences Corp. 800 Centennial Ave, P.O. Box 1327.
Piscataway, NJ 08855-1327. Company bulletin 18-1157-58 (2002).
Hage, D. S., ed. 2006. Handbook of Affinity Chromatography, 2nd ed. New York: Taylor & Francis.
Hage, D. S., and P. F. Ruhn. 2006. “An Introduction to Affinity Chromatography.” In Handbook of Affinity
Chromatography, 2nd ed., edited by D. S. Hage. New York: Taylor & Francis.
Hill, H. H., and D. G. McMinn, eds. 1992. Detectors for Capillary Chromatography. New York:
John Wiley & Sons.
Jeppsson, J. O., P. Jerntorp, G. Sundkvist, H. Englund, and V. Nylund. 1986. “Measurement of Haemoglobin
A1c by a New Liquid-Chromatographic Assay: Methodology, Clinical Utility, and Relation to Glucose
Tolerance Evaluated.” Clinical Chemistry 32: 1867–72.
Lee, W.-C., and K. H. Lee. 2004. “Applications of Affinity Chromatography in Proteomics.” Analytical
Biochemistry 324: 1–10.
Marz, W., R. Siekmeier, H. Scharnagl, U. B. Seiffert, and W. Gross. 1993. “Fast Lipoprotein Chromatography:
New Method of Analysis for Plasma Lipoproteins.” Clinical Chemistry 39: 2276–81.
Mehler, A. H. 1993. “Glutathione S-Transferases Function in Detoxification Reactions.” In Textbook of
Biochemistry, 3rd ed., edited by T. M. Devlin, 523–24. New York: Wiley-Liss.
Parikh, I., and P. Cuatrecasas. 1985. “Affinity Chromatography.” Chemical Engineering News 63: 17–29.
Gustavsson, P.-E., and Larsson, P.-O. 2003. “Fast Chromatography of Proteins.” In Isolation and Purification
of Proteins, edited by Rajni Hattokoul and Bo Mattiasson. Marcel Dekker, Inc.
Sambrook, J., and W. Russell David. 2001. Protein Interaction Technologies. Molecular Cloning A Laboratory
Manual. New York: Cold Spring Harbor Laboratory Press.
Sandra, J. F. 2002. Gas Chromatography. Ullmann’s Encyclopedia of Industrial Chemistry. Weinheim: Wiley-
VCH VerlagGmbH.
Scouten, W. H. 1981. Affinity Chromatography: Bio-Selective Adsorption on Inert Matrices. New York: Wiley.
Sheehan, D., and S. O’Sullivan. 2003. “Fast Protein Liquid Chromatography.” Protein Purification Protocols
244: 253.
Shibasaki, T., H. Gomi, F. Ishimoto, and T. Miyahara. 1990. “Urinary N-Acetyl-Beta-D-Glucosaminidase
Isoenzyme Activity as Measured by Fast Protein Liquid Chromatography in Patients with Nephrotic
Syndrome.” Clinical Chemistry 36: 102–03.
Smith, I. 1960. Chromatographic and Electrophoretic Techniques. Vol 1. Chromatography. Vol. 2. Zone
Electrophoresis. New York: Interscience Publishers, Inc.
Smith, I., J. Seakins, and T. William. 1976. Chromatographic and Electrophoretic Techniques, 4th ed. London:
William Heinemann Medical Books.
Stahl, E., and M. R. F. Aisworth. 1969. TLC: A Laboratory Handbook, 2nd ed. New York: Springer Verlag.
TC information ab, Uppsala. Printed in Sweden by T. K. i Uppsala AB. Amersham Pharmacia Biotech
AB 1999.
Turkova, J. 1978. Affinity Chromatography. Amsterdam: Elsevier.
Walters, R. R. 1985. “Affinity Chromatography.” Analytical Chemistry 57: 1099A–114A.
Wilson, K., and J. Walker. 2003. Practical Biochemistry: Principle and Techniques, 5th ed. Cambridge:
Chromatography 113
IMPORTANT LINKS
1. Column chromatography: http://www.repligen.com/bioprocessing/products/prepackedcolumn?gclid=
ckogjcjzoksFQl76wodARLC-fw
2. HPTLC: http://www.camag.com/v/products/tlc-ms/
3. HPLC: http://www.hplc.com/Eicom/index.html
4. GLC: http://www.makarandelectronics.com/gas_chromatograph.html
5. Ion-exchange chromatography: http://www.gelifesciences.com/aptrix/upp01077.nsf/Content/Products?
OpenDocument&parentid=5179&moduleid=165889&zone=Labsep
6. Exclusion chromatography: http://www.pall.com/main/Laboratory/Literature-Library-Details.page?id
47506
7. Affinity chromatography: http://www.jenabioscience.com/cms/en/1/browse/1450affinitychromatography
.html
5 Spectroscopy
5.1 INTRODUCTION
5.1.1 Definition and General Principles
As a useful working definition, spectroscopy can be defined as the interaction of electromagnetic
radiation (EM) with matter, although this does not include mass spectroscopy. Several factors have
led to the branching of spectroscopy in different directions. Most significant is the order of mag-
nitude of the energies involved, but additional factors such as the presence of a magnetic field and
instrumentation considerations have led to the techniques of ultraviolet (UV), infrared (IR), nuclear
magnetic resonance (NMR), and electron spin resonance (ESR) spectroscopy. Breakup and analysis
of the above definition will be useful before delving into the details of the different spectroscopic
techniques mentioned. The definition includes
1. Electromagnetic radiation
2. Interaction of EM with matter
3. Matter
EM radiation consists of an electric field perpendicular to a magnetic field and both at right
angles to the direction of propagation of light (Figure 5.1). A fundamental property of EM radiation
is that it can behave as though it exists as discrete quanta or packets of energy:
E = hυ
where
E = energy
h = Planck’s constant = 6.63 × 10−34 J·s
υ = frequency of radiation in Hertz
There are two ways in which EM radiation interacts with matter: absorption and emission.
Absorption occurs when incident radiation increases the energy of a system. An increase in energy
is manifested as a decrease in intensity of emergent radiation. Emission occurs when there is a
decrease in the energy of a system. Decrease in energy may be due to
1. Thermal energy loss: Energy loss by molecular or submolecular motion like a collision,
vibration, or rotation.
2. EM emission: This results in phosphorescence and fluorescence.
3. Photochemical reactions: There is a competition between the three processes, also called
relaxation processes.
Matter is composed of atoms and molecules. The electrons are constrained to certain energy
levels called K, L, M, and so on orbitals. When atoms combine to form molecules, electrons occupy
new energy levels called molecular bonding orbitals. Atoms in the molecule can vibrate and rotate
about the bond axis, giving rise to vibrational and rotational energy sublevels. Electrons usually
remain in the ground state but after receiving energy, for example, from incident EM radiation,
115
Frequency (Hz)
Wavelength
Gamma rays 0.1 Å
1019
1Å
0.1 nm
1018
X-rays
1 nm
400 nm
1017
Electromagnetic
10 nm
1016 Ultraviolet
spectrum
500 nm
100 nm
1015
Visible 1000 nm
Near IR 600 nm
1𝜇m
1014
Infrared 10 𝜇m
1013
700 nm
Thermal IR 100 𝜇m
1012
Far IR 1000 𝜇m
1000 MHz 1mm
1011
UHF Microwaves 1 cm
500 MHz 1010 Radar
10 cm
109
VHF 1m
7-13 108 Radio, TV
100 MHz FM 10 m
VHF 107
2-6
50 MHz 100 m
105 AM
1000 m
Long waves
FIGURE 5.1 (See color insert.) EM spectrum.
they get excited to higher states. This is the absorption of energy. When electrons come back to
their original ground state, the emission of energy takes place. Sometimes all the energy absorbed
is emitted, while at other times some energy is lost in one or all of the relaxation processes. The
amount of energy absorbed or emitted is given by
E = E1 − E2 = h
where
E1 = energy of electron at original level
E2 = energy of electron at final level
h = Planck’s constant = 6.63 × 10−34 J·s
c = velocity of light = 3 × 108 m·s−1
υ = frequency of radiation in Hertz = c/λ
λ = wavelength of radiation, usually in nm
Spectroscopy 117
5.1.2 Beer–Lambert’s Law

When a beam of light passes through a solution, a part of it is absorbed by the components of that
solution. In addition, certain portions (wavelengths) of the light beam are selectively absorbed. The
mathematical relationship between the concentration of a substance and the absorption of light is
provided by the Beer–Lambert, or Lambert–Beer, law. The basis of this law comes from the work
of Lambert on the transmission of monochromatic light by homogeneous solid substances. Beer
applied the law to solutions and found that both the concentration and thickness of the solution
affect light transmission through it.
Lambert’s law may be expressed as follows:
Io
log = K1 b (5.1)
I
where
I o = the original intensity of the light beam
I = the intensity of the beam after passing through the homogeneous substance
h = the thickness of the layer of solution through which the light has passed (usually expressed
in centimeters)
K1 = proportionality constant, the value of which depends on the absorption characteristics of
each compound, units of thickness, temperature, and wavelength
Beer’s law may be expressed as:
Io
log = K 2c (5.2)
I
where
I o = the original intensity of the light beam
I = intensity of the beam passing through solution
c = the concentration of the solution in moles per liter
K2 is similar to K1
Combining the above two formulas, we get
Io
log = Kcb (5.3)
I
The log quantity above is called the optical density (OD), whereas K is called the extinction coef-
ficient and may be written as E for convenience. It is specific to a certain wavelength and is large
when a particular wavelength is absorbed efficiently by a compound. It is possible to use l instead
of b to obtain
OD = Ecl (5.4)
In short, the quantity and quality of light absorbed or transmitted by a solution depends on the
absorption characteristics of the solute and solvent and is directly proportional to the concentration
of the solution and the thickness of the layer used (length of the light path). The Beer–Lambert law
may, therefore, be used to determine the extinction coefficient of substances in a solution and the
concentration of one or more such substances in a specific solution. Examples 5.1 and 5.2 on next
page will illustrate this point.
Example 5.1
Given the following absorption data for two compounds, A and B, at the indicated wavelengths,
calculate the molar extinction coefficients for the two compounds at the two wavelengths. The
concentration of A in both cases is 1.5 × 10 −4 mol/L, and the concentration of B in both cases is
8 × 10−4 mol/L. In all cases, the light path is 1 cm.
CALCULATIONS
Compound A Compound B
Wavelength (μm) OD Wavelength (μm) OD
400 0.55 400 0.07
600 0.04 600 0.75
Compound A
At 400 μm:
0.55 = E (1.5 × 10 −4 )(1.0) (5.5)
0.55 = E (1.5 × 10 −4 ) (5.6)
0.55
E= = 3667 (5.7)
1.5 × 10 −4
where 0.55 is the OD, E is unknown, 1.5 × 10 −4 is the concentration c in molar, and 1.0 is b or
l in centimeters.
At 600 μm:
0.04 = E (1.5 × 10 −4 )(1.0) (5.8)
0.04 = E (1.5 × 10 −4 ) (5.9)
10.04
E= = 267 (5.10)
1.5 × 10 −4
where 0.04 is the OD, E is unknown, 1.5 × 10 −4 is as above, and 1.0 is also as above.
Compound B
At 400 μm:
0.07 = E (8.0 × 10 −4 )(1.0) (5.11)
0.07 × E (8.0 × 10 −4 ) (5.12)
0.07
E= = 87.5 (5.13)
8.0 × 10 −4
where 0.07 is the OD, E is unknown, 8.0 × 10 −4 is the concentration c in molar, and 1.0 is as above.
At 600 μm:
0.75 = E (8.0 × 10 −4 )(1.0) (5.14)

Spectroscopy 119
0.75 = E (8.0 × 10 −4 ) (5.15)
0.07
E= = 87.5 (5.16)
8.0 × 10 −4
where 0.75 is the OD, E is unknown, 8.0 × 10 −4 is as above, and 1.0 is also as above.
Example 5.2
Using the molar extinction coefficients obtained above, calculate the concentration of A and B in
a mixture of the two, which gives the following data: The light path is 1 cm.
• OD at 400 μm is 0.349
• OD at 600 μm is 0.7324
Suppose that:
• Concentration of A = a
• Concentration of B = b
Then at 400 μm:
OD ( A ) = (3667) ( a) (1.0)
OD (B) = (87.5) ( b) (1.0)
OD (mixture A + B) = OD ( A ) + OD (B) (5.17)
Therefore,
0.349 = 3667a + 87.5b (5.18)
and at 600 μm:
OD ( A ) = ( 267) ( a) (1.0)
OD (B) = (938) ( b) (1.0)
OD (mixture A + B) = OD ( A ) + OD (B) (5.19)
Therefore,
0.7324 = 267a + 938b (5.20)
Simultaneously solving Equations 5.18 through 5.20:
a = 0.000024 mol/L = ( 2.4 × 10 −5 M) (5.21)
b = 0.00077 mol/L = (7.7 × 10 −4 M) (5.22)
A spectrum is a plot of absorption or emission versus wavelength. The spectra of atoms are
line spectra since the electrons are present in discrete energy levels. Electrons are present in dis-
crete energy levels in molecules as well (Figure 5.2). However, a group of molecules exists in a
number of different vibrational and rotational states, each state differing from another by
(a)
(b)
Absorbance % Transmittance
Absorbance
Transmittance
Concentraction of solute
FIGURE 5.2 (a) Beer’s law plot and (b) deviation from Beer’s law.
Absorbance peak
FIGURE 5.3 An arbitrary absorption spectrum showing an absorption peak.
a relatively small amount of energy. Thus, a group of molecules absorbs energy over a small range to
give rise to an absorption band over certain wavelength ranges, and the absorbance rises to a maxi-
mum and the transmittance falls to a minimum (Figure 5.3). This is referred to as an absorption peak.
In quantitative analysis, the values of the absorption peak are used so that the measurements
have the greatest sensitivity with respect to solute concentration. Also, the value obtained is the least
sensitive to errors in the wavelength setting of the spectrophotometer.
5.1.3 Mechanics of Measurement

The basic requirements of a spectrophotometer are as follows:
Source: The source provides radiation in the range in which the absorbing species will absorb
or is expected to absorb. A tungsten lamp is used to obtain light in the visible range. In
the near-UV region, a hydrogen lamp, deuterium lamp, or xenon lamp may be used. In the
IR region either a Nernst glower, which is a hollow rod of yttrium and zirconium oxides
heated to about 1450°C, or the globar, which is rod of silicon carbide heated to about
1200°C, may be used.
Spectroscopy 121
Monochromator: This allows only one particular wavelength of light to pass through and be
incident on the solution. These are optical filters, diffraction gratings, or both.
Absorption cell: The solution containing the absorbing species is placed in this absorption
cell.
Detector: The detector measures absorbance, and it is made to compare the intensity of light
transmitted by a cell containing a solvent (I) with that transmitted by a solution containing
the absorbing species (I0). In the visible and UV regions, photoelectric detectors are used.
In the IR region, thermal detectors like bolometers are used.
Meter: This is calibrated in terms of absorbance and transmittance.
Absorbance (A) = log I0/I
Transmittance (T) = I/I0
[Transmittance is given as a percentage (0–100%). The range of absorbance commonly
recorded is 0–2.0. The most accurate range for measurement is 0.1–0.8 (20–85% T).]
5.2 UV–VISIBLE SPECTROSCOPY

5.2.1 Definition
Interaction of EM radiation in the range of 200–400 nm (UV) and 400–700 nm (visible) with matter
gives rise to UV and visible spectroscopy, respectively.
5.2.2 Principle
The absorption of light energy by compounds in the visible and UV regions involves the promotion
of electrons in the σ, π and ν molecular orbitals to an antibonding orbital which is at a higher energy
level. Organic molecules containing several types of molecular orbitals σ and π are called bond-
ing orbitals and are occupied by a pair of electrons in the ground state. There are corresponding
σ* (sigma star) and π* (pi star) antibonding orbitals at higher energy levels, which are unoccupied
in the ground state. A third type of “ν” orbital or nonbonding orbital also occurs in molecules that
contain lone pairs of electrons like oxygen and nitrogen. The electrons here are not directly involved
in bonding and are therefore known as nonbonding orbitals.
The electronic transitions (→) that are involved in the UV and visible regions are of the following
types, in order of energy associated with them:
(σ → σ*) > ( ν → σ*) > (π → π*) > ( ν → π*)
The energy associated with σ and σ* transitions is so high that the corresponding λ falls short of
the visible range. Hence, fully saturated compounds do not show any significant absorption above
200 nm and are therefore colorless compounds that contain nonbonding electrons on oxygen, nitro-
gen, sulfur, or halogen atoms, which are capable of showing absorptions owing to ν → σ* transitions
involving lower energy.
In unsaturated and delocalized systems such as benzene and porphyrins, the π → π* transition
is of sufficiently small energy (long λ) to produce an absorption band in the near-UV (benzene) or
visible (porphyrin) range. This increase in absorbing wavelength due to delocalization is called a
bathochromic shift, whereas a decrease in delocalization caused, for example, by protonating a ring
nitrogen atom causes a hypsochromic shift, which leads to a decrease in absorbing wavelength.
Hyperchromic and hypochromic shifts refer to an increase and decrease in absorbance, respectively.
Electronic transitions within a molecule may be associated with a given group in the molecule
called a chromophore.
5.2.3 Instrumentation
5.2.3.1 Colorimeter
A colorimeter is used to measure the absorbance of particular wavelengths of light by a specific
solution. This instrument is most commonly used to determine the concentration of a known solute
in a given solution by the application of the Beer–Lambert law, which states that the concentration
of a solute is proportional to its absorbance.
The output from a colorimeter may be displayed by an analog or digital meter and may be shown
as transmittance (a linear scale from 0 to 100%) or absorbance (a logarithmic scale from zero to
infinity). The useful range of the absorbance scale is from 0 to 2, but it is desirable to keep within
the range 0–1 because, above 1, the results become unreliable due to the scattering of light. In addi-
tion, the output may be sent to a chart recorder, data logger, or computer. Changeable optical filters
are used in the colorimeter to select the wavelength of light which the solute absorbs the most, in
order to maximize accuracy. The usual wavelength range is from 400 to 700 nm. If it is necessary to
operate in the UV range (below 400 nm), then some modifications to the colorimeter are needed. In
modern colorimeters, the filament lamp and filters may be replaced by several light-emitting diodes
of different colors.
The most important parts of a colorimeter are (Figure 5.4)
• A light source, which is usually an ordinary tungsten lamp
• An aperture, which can be adjusted
• A set of filters in different colors
• A detector that measures the light that has passed through the solution
5.2.3.1.1 Filters
Different filters are used to select the wavelength of light that the solution absorbs the most. This
makes the colorimeter more accurate. Solutions are usually placed in glass or plastic cuvettes. The
usual wavelengths used are between 400 and 700 nm. If it is necessary to use UV light below 400 nm,
then the lamp and filters must be changed.
5.2.3.1.2 Output
The output of the colorimeter may be shown in graphs or tables by an analog or digital meter. The
data may be printed on paper or stored in a computer. It either shows the amount of light that is
absorbed by the solution or the amount of light that has passed through the solution.
Reference Light Lamp

phototube gate Field
lens
Entrance slit
Objective lens
Sample Occluder
Fliter Grating
Measuring Exit Light control
phototube slit
Wavelength
cam
FIGURE 5.4 Schematic diagram of a spectrocolorimeter.

Spectroscopy 123
5.2.3.2 Spectronic 20 Spectrocolorimeter

The Spectronic 20 spectrocolorimeter is a routinely used instrument in most laboratories and edu-
cational institutions. It is therefore described in some detail.
5.2.3.2.1 Description of the Optical System

White light emanating from the tungsten lamp passes through the entrance slit and is focused by
the field lens onto the objective lens. The objective lens focuses an image of the entrance slit at
the exit slit after it has been reflected and dispersed by the diffraction grating. To obtain various
wavelengths, the grating is rotated by means of an arm which rides on the wavelength cam. In set-
ting the wavelengths, the cam rotates the grating so that the desired wavelength passes through the
exit slit. The monochromatic light passes through the exit slit contained in a test tube or cuvette
placed in the light path (the light also goes through the red filter in the IR wavelength range) and
finally terminates at the measuring phototube, where the light energy is converted to an electric
signal. Whenever the sample is removed from the instrument, an occluder automatically falls into
the light beam so that the zero may be set without further manipulation. A light control is provided
to set 100% transmittance or zero absorbance with a reference or standard solution in the sample
compartment. The optics of the lens tube provides an extended range, which goes to 340 nm.
A wall separates the optical system from the electronics, thus preventing dust and dirt from
spoiling the efficiency of the optical system. At the same time, the wall shields the meter to prevent
erroneous readings and fluctuations from stray light entering through the meter face or permitting
error-free operation in bright light or even fluctuating sunlight.
5.2.3.2.2 Description of the Electrical System

The measuring circuit consists of a direct current (DC) wheatstone bridge-type differential ampli-
fier in which variations in characteristics, nonlinearities, and drift of one triode are cancelled by
another. A current gain of 5000 V is obtained from this amplifier.
A wheatstone bridge circuit similar to that in the detection–amplification system is used to balance
and compare the monitoring output with the constant voltage from the power supply voltage regula-
tor tubes. This differential output is further amplified by a transistor cascade (powered by a silicon
hill-wave rectifier circuit), transformed into conductance variation of the two transistors operating on
the center-tapped secondary transformer. Thus, a change in transformed load is reflected back to the
transformer primary and to the 75 Ω and 50 W resistors, causing readjustment of the primary voltage.
The net effect is that an increase or decrease in supply voltage is cancelled out through the feedback
system, providing a constant voltage at the primary of the supply transformer. Since this transformer
supplies the lamp and amplifier tube filament, the lamp output and filament current are independent
of the line voltage. In this way, not only is amplifier stability achieved by a compensating circuit for
variation in tube characteristics, but any second-order errors, due to individual tube filament tem-
perature dependence, are removed by keeping the filament at constant operating conditions.
5.2.3.3 Choice of Instruments for Colorimetry

When the absorption characteristics of a compound are unknown, a spectrophotometer or a record-
ing spectrophotometer should be employed. By scanning the compound through the entire light
spectrum, an absorption curve is obtained. This curve or some of its portions may be utilized in
identifying the compound or in the development of analytical techniques. When a narrow absorp-
tion peak is utilized for such purposes, a spectrophotometer should be employed due to its narrow
wavelength “window.” In instances where peaks are broad or may shift slightly, a colorimeter with
its broader “windows” is the more-useful apparatus.
5.2.3.4 UV–Visible Spectrophotometer

Colorimeters are relatively simple instruments, which are designed to function only in the visible
range. On the other hand, spectrophotometers are equipped to operate both in the visible and UV
ranges. They are fitted with deuterium or hydrogen (for UV light) and tungsten (visible range) as
the light sources. Several models of spectrophotometers of varying degrees of sophistication are
available. These include single-beam, double-beam, recording, and multibeam instruments. In dual-
beam spectrophotometers, the incident light is split into two beams of equal intensity, one of which
passes through the reference cuvette and the other through the sample cuvette. The multibeam
instrument is designed to simultaneously record absorbance changes at two or more predetermined
wavelengths. Recording spectrophotometers can both scan the absorption spectrum of the sample
in the desired range and also record the change in absorbance with time at a fixed wavelength.
Reflectance spectrophotometers are used for determining the spectra of pastes and suspensions like
those of microorganisms. The latter type of spectrophotometers enable measurement of the radia-
tion absorbed when the light beam is reflected by a sample, which is too opaque to allow transmis-
sion of light (Figure 5.5).
The spectrophotometer has the following parts (Figure 5.6). The light source provides EM radia-
tion in the UV and visible regions. For UV, a hydrogen or deuterium lamp is used. An ordinary
tungsten lamp provides visible radiation as used for the colorimeter. The slit S1 allows a thin beam
of light to pass through and reach the monochromator (Figure 5.6).
A monochromator, as the name suggests, produces light of only one particular wavelength from
a multiwavelength source of radiation. The instrument has a provision for selecting the required
wavelength by turning a knob located on the exterior of the instrument. Monochromators are usu-
ally optical filters, diffraction gratings, or both. Often prisms are used, by which refraction produces
light of different wavelengths. Glass prisms are used for visible wavelengths, whereas quartz is used
for UV because glass absorbs radiation below 400 nm. The light emerging from any monochroma-
tor does not consist of a single wavelength in practice. It consists of a group of wavelengths called
bandwidth. Bandwidth is usually defined as twice the half-intensity bandwidth, which is the range
of wavelengths for which transmitted intensity is greater than half the intensity of the chosen wave-
length. Bandwidth varies from 5 to 35 nm depending on the quality of the instrument.
The slit S2 allows only a thin beam of bandwidth light to pass through. A sample is placed in a
cuvette, which is an optically transparent cell made of glass and quartz for visible and UV light,
Sample Detector
Light Slit Monochromator (photoelectric cell or
source (grating prism) photomultiplier tube)
(a) (b)
FIGURE 5.5 (a) A spectrophotometer and (b) schematic representation of a spectrophotometer.
L S1 M S2 S P A R
L = Light source S = Sample

S1 = Slit P = Photocell
M = Monochromator A = Amplifier
S2 = Slit R = Recorder
FIGURE 5.6 Parts of a spectrophotometer.

Spectroscopy 125
respectively. Commonly used cuvettes have an optical path length of 1 cm. A sample of 2.5–3 mL
is required for accurate measurement; there are also microcuvettes requiring a 0.3–0.5 mL sample
that are useful when valuable sample and reagents are being used.
The emergent beam from the cuvette reaches the photocell, which converts radiation to electrical
energy which is amplified, detected, and recorded. In a photocell, photons impinging on the metal
surface in a vacuum cause the emission of electrons. These are attracted by a positive electrode and
hence a current flows, which causes a potential difference across a resistor present in the system.
This potential difference is recorded on the potentiometer, which is calibrated to read absorbance
and transmittance. Absorbance is calibrated as log I0/I, whereas transmittance is calibrated as I/I0,
where I0 and I are the intensities of emergent radiation from solution and pure solvent, respectively.
The corresponding current produced is recorded. Photomultiplier tubes are more sensitive than
simple photocells. In photomultiplier tubes, the emitted electrons are accelerated by high potential
and produce secondary electrons by collision with gas molecules present in the tube. This results in
a large current and thus very small changes can be measured.
5.2.4 Applications
UV-Visible Spectrophotometer is mainly used to provide valuable information on
• Concentration measurement
• Growth kinetics
• Structural studies
• Enzyme kinetics
• Effect of pH, ionic strength, and so on using difference spectroscopy
• Testing purity and homogeneity of sample
• Identification of compounds such as nucleic acid, carbohydrate, lipid, protein, organic
acids, pigment, and so on.
5.2.4.1 Concentration Measurement

This is by far the most important application of this technique. Concentration can be calculated by
using the equation A = EcI at a specific wavelength (λ maxima) for particular compound since I is
also known (1 cm). However, it is normal to construct a calibration or standard curve at the time the
samples are being analyzed and also at the same conditions. To construct a calibration curve, the
absorbance of known concentrations of the substance is read on the spectrophotometer and a graph
of concentration versus absorbance is plotted. Concentration of test samples may then be simply
read off the graph after the measurement of absorbance values. The calibration curve should, how-
ever, embrace all values of concentration to be measured and should be measured under exactly the
same conditions as the samples.
For a mixture of chromophore, quantitative measurement of the constituent chromophore is pos-
sible, provided they exhibit different absorbance at certain wavelengths. For example, if A1 and A2
are absorbance values at two wavelengths of two chromophore whose molar concentrations are
given by [B] and [C] and molar absorption coefficients are eB1, eB2 and eC1, eC2 at wavelengths I1 and I2
then the concentration values [B] and [C] can be solved using the simultaneous equations.
A1 = E1B [ B] + E1C [C]
A1 = E2B [ B] + E2C [C]
There are certain naturally occurring chromophores, such as egg proteins (280 nm), nucleic acids
(260 nm), carotenoids (455 nm), and tetrapyrroles (400 nm). However, for species that do not absorb
in the visible region, a derivative is used. They are made to react quantitatively with some other
reagent, which after reaction gives a colored derivative whose concentration is equal to that of the
original species, for example, amino acids (280 nm) react with ninhydrin to produce a colored com-
plex whose lmax = 570 nm. Proteins are treated with Folin Ciocalteau reagent to produce a colored
complex whose lmax = 650 nm. Absorbance is measured against a reagent blank, which contains all
reagents but not the substance to be measured. A calibration curve is constructed and concentrations
read off it. This technique for producing a colored derivative is called colorimetry. The only draw-
back with the technique is that it is destructive. The compound being assayed is destroyed because
it is made to form a complex with another compound.
5.2.4.2 Growth Kinetics

In situations where light scattering is the predominant factor causing a loss of intensity, measure-
ments of absorbance are actually measurements of turbidity. This reflects the number of particles
per unit volume. This is useful for constructing growth curves for bacteria.
5.2.4.3 Structural Studies

Protein structural studies: The spectrum of a chromophore depends on the polarity of its
environment. Change in the polarity of a solvent changes the spectrum of a constituent
amino acid chromophore without a change in the conformation of a protein. This is called
solvent perturbation. As another example, if denaturation exposes a tyrosine present in an
internal (hydrophilic I to an external hydrophobic) environment, the effect of pH, tempera-
ture, and ionic strength on protein denaturation may be studied (Figures 5.7 and 5.8).
Nucleic acid structural studies: The absorbance at 260 nm of double-stranded DNA in a solu-
tion increases due to denaturation on heating (hyperchromicity). Hypochromicity occurs
on renaturation. Thus, the effects of pH, temperature, and ionic strength on the secondary
structure of DNA can be studied. Solvent perturbation studies can be made, for example,
by replacing normal water with 50% deuterium oxide (DO) in a solution of nucleic acids.
Since DO only changes spectral components due to unpaired nucleotides, the fraction of
unpaired bases like t-RNA can be estimated (Figure 5.9).
4.5
3.5
3
OD at 350 nm
2.5
1.5
0.5
0
1 4 7 10 13 16 19 22 25 28 31 34 37 40 43 46 49 52 55 58 61 64 67 70
Sample no.
FIGURE 5.7 OD measurement of protein samples during different fractions.

Spectroscopy 127
0.45
Relative absorbance (A)
0.0
350 800
Wavelength (nm)
FIGURE 5.8 Absorbance spectra of pigments of cyanobacterium Anabaena sp.
0.55
No.11
0.50
0.45
No.7
Absorbance (280 nm)
0.40
0.35
0.30
0.25
0.20
0.15 No.15
0.10
0.05
0.00
25.0 30.0 35.0 40.0 45.0 50.0 55.0
Elution time (minutes)
FIGURE 5.9 The elution profile of sample at 280-nm absorbance.
5.2.4.4 Enzyme Kinetics and Assays

These are carried out via the estimation of change in absorbance per unit of time with changes in
the concentration of either a substrate or product, for example, the binding of a drug (substrate) to
a liver microsomal monoxygenase causes a blue shift of the cytochrome P450 component of the
enzyme from 420 to 390 nm.
5.2.4.5 Difference Spectra

These are produced by a double-beam spectrophotometer. Here, there are two sample cells, one for
the reference solution and the other for the sample. Two beams of the same wavelength pass through
the sample cells and the difference of absorption by the solutions in the two cells is measured. This
enables the detection of small changes in absorption.
5.2.4.6 Purity and Homogeneity

The characteristic absorption maxima of different chromophores help in the identification of
unknown compounds in both pure state and biological preparations of proteins, nucleic acids, chlo-
rophylls, and so on. The technique may also be used to detect chemical structures and intermediates
occurring in a system by comparing them with the spectrum of pure a compound under similar
conditions. However, for really precise analysis, IR spectroscopy is required (Figure 5.10).
A. Wheel filter instrument B. Tiling spinning filter
Collimating
Interference Light
Light lens Focusing
filters source
source/s lens
Sample
Detector/s
Exit
Chopper slit
Wheel filter
(dark correction)
Sample
Detector/s
C. Predispersive monochromator D.Postdispersive diode array

(Czerney-turney configuration)
Entrance slit Entrance slit
Light Sample
source
Collimating Collimating
Moving Fixed
lens lens
Detector/s grating grating
Sample
Focusing lens Light Imaging lens
Exit slit
source Diode array
detector
(a)
390 Display 300

device
310 IR source
380
350 Optically
Process dispersive
or element
320 Adjustable
aperture
370 IR
detector
360
330 Sampling
accessory
Focusing
optics
(b)
FIGURE 5.10 (a) External view of an IR spectrophotometer and different internal parts of the instrument
depicted from A to C. (b) Schematic operational diagram of IR spectrophotometer.
Spectroscopy 129
5.3 IR (VIBRATIONAL) SPECTROSCOPY

5.3.1 Principle
IR spectra originate from different modes of vibration of a molecule. The absorption of IR energy
(102–105 nm) by a compound causes the excitation of molecules between vibrational energy levels.
The excitation of molecules from the lowest energy vibrational level to the first excited level gives
rise to absorption bands that are referred to as fundamental bands. Additional (nonfundamental)
absorption bands may occur because of the presence of overtones (or harmonics) of reduced inten-
sity at 1/2, 1/3,…the wavelength (twice, thrice the wavenumber).
The spectral position is given in terms of wavenumber or Hertz because it deals with vibrations
(wavenumber = 1/wavelength). When a light wave passes through an atom carrying an electrical
charge, it is pushed first to one side and then to another. In a molecule that has a dipole moment
(e.g., H–Cl), the electrical field of a light wave tends to set the charges into oscillation by stretching
and compressing the HCl bond alternately. The bond has a natural frequency of vibration depend-
ing on the masses of the two atoms and the restoring the force of the bond. An incident light wave
of the same frequency greatly increases the natural frequency of vibration—resonance is said to
occur—and molecules absorb maximum energy at this resonant frequency. This is indicated by an
absorption peak.
Bond vibration modes are one of two types:
1. Stretching—periodic stretching of bond along the bond axis

2. Bending or deformation type—displacement at right angles to b and the axis (Figure 5.11)
Different vibration modes lead to corresponding energy patterns. For a polyatomic molecule,
there are 3–6 modes of vibration of which n−1 are stretching and 2n−5 are of the bending type,
where n is the total number of atoms in the molecule. Thus, C–H has 30 fundamental vibrations.
However, only those that have transient dipole moments are excited by the radiation. That is to say
that in order for a particular vibration to result in the absorption of IR energy, that vibration must
cause a change in the dipole moment of the molecule. Thus, the IR spectrum of benzene contains
Stretching
Asymmetrical Symmetrical
stretching stretching
Bending
+ + – +
– – + –
Scissoring Wegging Twisting Rocking
FIGURE 5.11 Bond vibration modes.

2.5 3.0 4.0 5.0 6.0 7.0 8.0 9.0 10 12 15 20 μ Wavelength

100
Transmittance %T μ = 10–6 meter
Note inverted peaks

50 Top : 100% transmission
O H
Bottom : No transmission
OCH3
OH
Vanillin
(CCl4 solution) Frequency
0 cm–1 = Hz/c
4000 3000 2000 1500 1000 500
Wave number cm–1
FIGURE 5.12 IR spectrum.
less than 30 absorption peaks (Figure 5.12). Although IR spectrum is characteristic of a compound,
the spectra of all molecules contain three common characteristics:
1. In the region 3600–1500 cm, absorption is due to the bonds of the type X–H (e.g., N–H,
O–H, C–H).
2. Below 1600 cm−1, absorption is due to the bonds of the type C–C, C–N, C–O, C–halogen.
3. 1300–650 cm−1 is characteristic of a molecule (this is called the fingerprint region).
A common light source for IR radiation is the Nernst glower, as a molded rod containing a mixture
of zirconium oxide, yttrium oxide, and erbium oxide that is heated to around 1500°C by electrical
means. Either optical prisms or gratings are used to obtain approximately monochromatic light.
The beam is split into two beams: one is made to pass through the sample and one through the
reference cell. Since glass and quartz absorb IR radiation, metal halides like NaCl are used as con-
tainers of absorbing species. About 1 mg of substance and 100–200 mg of alkali halide are ground
together finely and pressed under high pressure to a small disk of 1–2 nm in thickness. When equal
light intensity is transmitted by both the sample and reference beams, no signal is produced. The
absorbance of the sample beam results in the inequality of the two transmitting beams falling on the
detector, which produces a pulsating electrical signal. The detector is a bolometer or a thermocouple
calibrated to give absorbance or transmittance (Figure 5.10a through c).
5.3.3 Applications
The IR spectrum of a compound is a “fingerprint” of that compound; hence, it can be used to identify
a pure compound (Figure 5.13). Compound charts relate molecular structure to absorption bands.
Impurities in a compound may be detected by the appearance of extra absorption peaks in the spec-
trum of a pure compound. IR spectra can even distinguish between isomers of a compound.
Since certain functional groups in a molecule have characteristic natural frequencies that are
relatively independent of the molecule, the presence of such functional groups can be ascertained
in a certain molecule. Fortunately, however, a particular group does not always absorb exactly the
same frequency because of environmental influence. Thus, it is possible to distinguish between C–H
bonds of CH2 and CH3. Since there is a quantitative relationship between the absorbance and num-
ber of absorbing molecules, quantitative chemical analysis is also possible (Figure 5.10d).
Spectroscopy 131
20,000 15,000 10,000 5000

1/cm
20,000 15,000 10,000 5000 20,000 15,000 10,000 5000

1/cm 1/cm
FIGURE 5.13 IR spectroscopic analysis of different preparations of heme with plasma of Plasmodium yoelii
infected mice. The characteristic peaks of hemozoin are indicated by arrows.
Interfacing IR spectroscopy with gas chromatography is a powerful technique for analyzing drug
metabolites. Its most important application is to study carbon dioxide metabolism during photosyn-
thesis and respiration in plants and microorganisms.
5.4 FLAME/ATOMIC ABSORPTION SPECTROSCOPY

5.4.1 Principle
On absorbing energy of the order of 4 × 10 to 4 × 10 kJ·mol, the valence shell electrons of atoms get
excited to higher energy levels, giving rise to absorption line spectra. On returning to the ground
state, energy given off appears as emission line spectra. Atoms give rise to line spectra and not
band spectra–like molecules because electronic transitions take place within discrete energy levels
characteristic of that atom. Atomic line spectra are, therefore, said to be fingerprints of atoms and
can be used to identify an element. Quantitative estimations are also possible since the amount of
radiation absorbed or emitted is proportional to the concentration of the element.
FIGURE 5.14 Atomic absorption spectroscope.
Flame spectroscopy uses a flame to provide energy for the excitation of atoms. The amount of
radiation emitted or absorbed is measured as in UV–visible spectroscopy. This is used to quantify
the element present in the sample, which is dissolved in water.
5.4.2 Instrumentation for Emission Flame Spectroscopy

The instrumentation needed for emission flame spectroscopy is as follows:
• The aspirator, which by vacuum action sucks up the sample solution and takes it to the
nebulizer.
• The nebulizer or atomizer produces small droplets of solution that are sprayed into the
flame.
• The flame serves to volatilize and excite every atom present; temperature can be controlled
by gas and air pressure controls. The gas used is usually oxy-acetylene flame (2000°C). For
higher temperatures of 3500°C, a mixture of oxygen and nitrous oxide is used.
• Emitted light is made to pass through a monochromator that is adjusted to the characteris-
tic wavelength, which will be emitted by the element.
• A photoelectric detector is the same as in UV–visible type.
• The photoelectric detector is connected to a galvanometer calibrated to read concentra-
tions. Alternatively, the instrument is calibrated with known concentrations of solution.
The amount of radiation emitted is proportional to the number of atoms excited by the flame.
However, not all atoms present are excited; hence, quantitative measurements are not very pre-
cise. The technique of atomic absorption spectroscopy provides more sensitivity and precision
(Figure 5.14).
5.4.3 Instrumentation for Atomic Absorption Spectroscopy

The element is excited by means of its characteristic spectra produced from a cathode tube whose
cathode is made of the element being assayed. The tube contains an inert gas, usually neon, at low
Spectroscopy 133
Monochromator
Detector
Lens Lens Detector
Hollow
cathode Monochromator
lamp Hollow Atomized
Flame
cathode sample
Test lamp
Nebulizer
Data Readout Amplifier
solution
processor
FIGURE 5.15 Functional view of atomic absorption spectroscope.
temperature. A high voltage is used to produce an arc spectrum of the element. The nebulizer,
detector, and recorder are the same as in emission spectroscopy. To increase the optical path length
of the sample, burners producing 10 cm flame are used (Figure 5.14).
In recent years, the flame has been replaced by electrothermal heating in a graphite furnace. The
sample to be analyzed is deposited on a graphite tube in the presence of an inert gas and the tem-
perature raise to 3000°C by electric current. The element in the sample gets volatilized and excited
(Figure 5.15).
5.4.4 Applications
Since this technique can detect elements as small as less than 1 ppm, it is widely used in biochemi-
cal research for assay of various samples. More than 20 elements can be detected. These include
sodium, calcium, potassium, iron, manganese, copper, nickel, chromium, zinc, cadmium, lead,
lithium, and silver.
A diagnosis of certain clinical conditions can be made by observing the departure from the usual
composition of elements from urine, milk, blood, saliva, and cerebrospinal fluid. In food chemistry,
foodstuffs and beverages can be analyzed for the presence of trace elements or contamination by
pesticides. When assaying biological samples like cells and tissues, ashing is carried out to remove
organic molecules.
5.5 FLUORESCENCE SPECTROSCOPY

5.5.1 Principle
Fluorescence is a phenomenon whereby a molecule, after absorbing the radiation of a particular
wavelength, emits radiation of a larger wavelength. This is called the Stokes shift. When the emit-
ted wavelength falls in the visible region, a glow can be seen. Measurement of the intensity of this
glow with respect to the intensity of incident radiation is called fluorescence spectroscopy, or simply
fluorometry (Figure 5.16).
Absorption and emission are almost instantaneous, with a time lag of only seconds, approxi-
mately during which a molecule exists in an excited state. Most organic molecules in their ground
state are singlets (paired); on absorbing radiation, they are excited to a higher energy state without
a change of spin. These are called excited state singlets. An excited state with the lowest energy is
the first excited singlet (Figure 5.17).
Fluorescence occurs when the first excited singlets relax to the ground state. The intensity of
fluorescence (If ) is related to incident radiation (I0) by
I f = I 0 2.3eλcdQ
Excitation Detection
Photo-
diode
Photonic crystal Prism
fiber spectrometer Slit
Acousto-
Fiber optic Confocal Signal
microscope Detector
laser tunable
filter
Computer
(a) (b)
FIGURE 5.16 (a) Fluorescence spectrophotometer and (b) functional view.
n=3
n=2
Decay
n=1
First excited state
hν1 hν2 hν3
n=0
Ground state
FIGURE 5.17 The emission process.
where
c = concentration of fluorescing solution (M)
d = light path in the fluorescing solution (cm)
ε = molar absorptivity coefficient for the absorbing material at wavelength λ (dm3·mol−1·cm−1)
Q = quantum efficiency that is equal to the number of quanta fluoresced divided by the num-
ber of quanta absorbed
If the initial absorption generates a higher excited state, this will relax quickly and nonradia-
tively to the first excited singlet (decay), which may then fluorescence. The nonradiative relaxation
mechanisms include:
• Thermal relaxation transfer of energy to molecular and submolecular motions like colli-
sion, rotation, and vibration.
• Photochemical reactions. When such processes win the competition with radiative energy
loss, quenching of fluorescence is said to occur.
Spectroscopy 135
The efficiency of these nonradiative processes depends on the environment of the molecule; therefore, so
does fluorescence intensity. Thus, the fluorescence of an emitter is a probe (indicator) of its environment.
Figures 5.18 and 5.19 show the main components of a spectrofluorimeter. The source is a mercury lamp
or xenon arc. The M1 monochromator is for selecting a chosen wavelength of irradiation. The M2 mono-
chromator enables determination of the fluorescence spectrum of a specimen. The photocell detector
and recorder are the same as in a UV–visible spectrophotometer. The fluorescence from a sample is
emitted in all directions but is examined at right angles so that the transmitted light does not interfere.
5.5.3 Pre- and Postfilter Effects

Prefilter absorption reduces the amount of incident radiation reaching fluorescent molecules fur-
thest from the light source, and postfilter effects reduce the amount of fluorescence escaping from
the cuvette. Use of (1) microcuvettes (Figure 5.20a) and/or (2) front-face illumination (Figure 5.20b)
reduces both pre- and postfilter effects.
5.5.4 Applications
5.5.4.1 Concentration Measurement
The intensity of fluorescence is directly proportional to the concentration of fluorophore the (sub-
stance emitting fluorescence) according to the relation
I f = I 0 2.3cIQ
that is,
If ∝ c
Hence, concentration can be found as in absorption visible spectrophotometry. Since fluores-

cence has high absolute sensitivity, that is, even very small amounts can be detected, it is far better
than absorption visible spectrophotometry at concentrations too low for absorption spectral analysis.
Sample cell
Source M1
M2
Photocell
Recorder
FIGURE 5.18 Main components of a spectrofluorimeter.

Excitation filter
Source or Sample
monochromator
Beam
attenuator
Emission filter
or
monochromator
Reference Sample
photomultiplier photomultiplier
Difference amplifier
Output
FIGURE 5.19 Functions of spectrophotofluorimeter.
If the sample lacks intrinsic fluorescence, it can be made to bind to a fluorophore or probe
and the so-called extrinsic fluorescence can then be measured. Some extrinsic fluorophores
include dansyl chloride, l-anilinonaphthalene-8-sulphonate (ANS), fluorescein, ethidium bro-
mide, and so on.
5.5.4.2 Compound Identification/Excitation Spectrum

The comparison of both the fluorescence and excitation spectra of a compound may help to iden-
tify it. An excitation spectrum is obtained by keeping the emission monochromator of the fluo-
rimeter fixed at a particular wavelength and then successively changing the wavelength of the
excitation monochromator and recording the photocell output. The spectrum produced is similar
to an absorption spectrum, but it has the added advantage that it enables a fluorescent material
to be detected and quantified in the presence of a nonfluorescent material that absorbs at the
same wavelength. Hence, an absorption spectrum of such a mixture would give overlapping peaks
(Figure 5.21a).
5.5.4.3 Kinetic and Structural Studies

Use is made of extrinsic fluorophores to label any biological structure under study (Figure 5.21b).
For example, the fluorimetric assay of β-galactosidase enzyme is made using fluorescein di-(β-d-
galactopyranoside) as a substrate. Even a single molecule of enzyme can be detected by this process.
Membrane structure and effects of temperature and pH can be studied using ANS and MNS
(N-methyl-2-anilino-6-naphthalenesulphonate) as probes. These contain both hydrophobic and
hydrophilic groups and therefore become attached to the water–lipid interface of the membrane.
Spectroscopy 137
Prefilter Absorption
Excitation radiation
Microcuvette
Postfilter absorption
Fluoresced
radiation
(a)
45°
Cuvette
(b)
FIGURE 5.20 Reduction of filter effects (a) using microcuvette and (b) using front-face illumination.
5.6 ESR SPECTROSCOPY

5.6.1 Principles
ESR is the interaction of an unpaired electron with a microwave field (−1010 Hz). Different from
other forms of spectroscopy, energy levels arise from the application of a static magnetic field. Also,
only molecules in which there are unpaired electrons can be detected. These include:
• Free radicals like CH3O, C2H5O, and C6H5O

• Odd electron molecules such as paramagnetic molecules NO, N2O, and O
• Paramagnetic ions and complexes such as those of transition metals
An electron not only moves around the nucleus of an atom but also rotates about its own axis either
clockwise or counterclockwise, giving rise to a spin quantum number, S + 1/2 or −1/2, depending on
the direction of spin. This motion may be likened to the flow of an electric current through a loop.
Such a flow creates a magnetic field. A similar magnetic field is created due to the motion of the
electron, which therefore has a magnetic moment. This field can interact with an external magnetic
60,000 Toluene Benzene Control Xylene p-NP
50,000
Fluorescence intensity (arb)
40,000
30,000
20,000
10,000
0
600 650 700 750 800
Wavelength (nm)
(a)
120
00
550 600 650
Wavelength (nm)
(b)
FIGURE 5.21 (a) Laser-induced chlorophyll florescence of Synechococcus elongates PCC 7942 under
organic stress. (b) Fluorescence spectra of wild type and Het− Fix− mutant strain of Anabaena variabilis in
the presence and absence of nitrate at an excitation wavelength of 435 nm.
field. When an external magnetic field H is applied, the electron is aligned either parallel to it in a
low-energy state or antiparallel to it in a high-energy state, depending on the spin of the electron
(Figure 5.22). Thus, there are two energy levels after the application of the magnetic field.
Spectroscopy 139
With field
+ 1 g βH
2
Without field
gβH
S = 1 and – 1
2 2
With field
– 1 gβH
2
FIGURE 5.22 Energy levels after the application of magnetic field.
The unpaired electron can absorb energy from the microwave region of the EM spectrum and
change from a low-energy state (spin parallel to H) to a high-energy state (spin antiparallel to H).
This spin reversal (resonance) occurs if the energy, E, absorbed is equal to
E = hυ = gβH
where
h = Planck’s constant
υ = frequency of wavelength absorbed
g = constant called spectroscopic splitting factor
H = applied magnetic field
β = magnetic moment of electron called Bohr magneton
From the above relationship, it follows that the frequency of absorbed radiation depends on β and
H. In practice, however, it is usual to keep β constant and vary H. This gives rise to an absorption
peak when the magnetic field is enough to cause resonance. Such a peak corresponds to a para-
magnetic species in the sample. The area under the peak is a measure of the concentration of that
species, which may be quantified if a standard containing a known amount of unpaired electrons is
available. In practice, ESR spectra contain many peaks and a fine structure due to hyperfine split-
ting. This is due to the interaction of the electron with the magnetic nuclei within the molecule.
The requirements of an ESR spectrophotometer are as follows:
• Klystron source of monochromatic microwave (3 × 10−2 m/9000 MHz) radiation.

• Sample cell. Samples must be in a solid state so biological samples are usually frozen in
liquid nitrogen.
• Magnetic field of 50–500 mT surrounding the sample. The magnetic field is generated by
electromagnets. An auxiliary sweep of 10–100 mT is also present.
• Detector used to determine the resonance condition when the sample absorbs microwave
radiation. The detector is a bolometer or a crystal detector.
• Pen recorder that records dA/dH, that is, the change in absorption A with the change in mag-
netic field H. Therefore, unlike the absorption spectrum, there is a nonsymmetrical peak
adjacent to a nonsymmetrical trough and together they are called an ESR line (Figure 5.23),
which is characteristic of the molecule in which the unpaired electron is present.
dA
A dH
H
(a) (b)
FIGURE 5.23 (a) ESR absorption curve and (b) ESR line.
5.6.3 Applications
Several transition metals constitute prosthetic groups of a number of enzymes and other proteins.
Since the transition metals show intense paramagnetism, this technique is particularly useful in stud-
ies on metalloproteins such as those containing copper (e.g., cytochrome oxidase), iron (cytochromes,
ferredoxin, iron-sulphur proteins, nitrite reductase, etc.), and molebdenum (aldehyde oxidase, xan-
thine oxidase, nitrate reductase, nitrogenase, sulfite oxidase, etc.). These metal ions possess ESR
peaks in one of their oxidation states. Thus by monitoring their ESR signals their role in the activity of
such metals containing isolated enzymes can be studied. ESR spectroscopy has also provided useful
insight into the functioning of complex multienzymic systems such as mitochondria and chloroplast
electron transport systems. The ESR spectroscopic data provides information about the environment
around the metal component which contributes towards understanding structure of the molecule.
Since free radicals can be detected by ESR spectroscopy, this technique can also be extended to
study macromolecules that do not contain unpaired electrons by using spin-labels. In spin-labeling,
a stable and unreactive free radical is attached to the biomolecule. For example, the later movement
and the “flip” rates of glycerophosphatides in the lipd bilayers of biomembranes has been examined
by spin-labeling glycerophosphatides with nitroxide free radicals. ESR spectroscopy has also been
employed quite extensively for investigations on generation of free radicals following irradiation of
biological materials.
5.7 NMR SPECTROSCOPY

5.7.1 Principle
NMR is the absorption of energy from a radiofrequency (approximately ∼108 HZ) of EM radiation
by a system containing unpaired nuclear spins in a strong static magnetic field. The separation of
energy levels and hence the frequency of absorption depends on the strength of the magnetic field.
Like electrons spinning about their own axes, protons in a nucleus also spin either clockwise or
counterclockwise about their axes. The positive spinning charge gives rise to a magnetic field with
a magnetic moment. Pairs of protons have net magnetic moments of zero. However, an odd proton
in the nucleus imparts a magnetic moment to the molecule, which can interact with an applied mag-
netic field. In an applied magnetic field H, it can exist either in a low-energy state aligned parallel to
the direction of the applied magnetic field or antiparallel to it in a high-energy state. Upon absorbing
energy from the radiowave region of the EM region, a proton can change from a low-energy state
to a high-energy state, causing resonance to occur and giving rise to NMR, which is therefore also
known as proton magnetic resonance (PMR). For reasons already explained, NMR can occur only
in atoms containing an odd number of protons, for example, protons like lH, 13C, 15N, 19F, and 31P.
Spectroscopy 141
The resonance condition is given by
υ = H /hI
where
υ = frequency of EM radiation absorbed
μ = nuclear magnetic moment
H = magnetic field strength
h = Planck’s constant
I = nuclear spin quantum number characteristic of an atom
The above relationship shows that the frequency of radiowaves absorbed during NMR depends on
both the atom being studied (as described by I) and the strength of the magnetic field. It is com-
mon practice, however, to vary the magnetic field, H, and keep frequency constant in the radiowave
region, rather than vice versa.
The instrumentation needed for NMR spectroscopy is as follows:
• Source is a radiofrequency transmitter to irradiate the sample.

• Sample cell containing a sample dissolved in a solvent that lacks the atom containing the
unpaired electron that is going to be analyzed. For example, in PMR, D2O or CDCl3 is used.
• Electromagnets providing fields of 1–10 T, in conjunction with auxiliary sweep coils to
vary the magnetic field over 1–100 mT.
• Radio receiver that serves as a detector of the absorption signal.
• Recorder that plots energy absorbed against the magnetic field strength applied (Figure 5.24).
5.7.3 Chemical Shifts

The nuclear resonance of a particular atom is not always the same in a given applied static magnetic
field. This is because the adjacent electron clouds interact with the applied field to give rise to small
NMR spectrometer: Overview
Magnet
RF transmitter
Computer
RF receiver ADC
Gradient
controller
2H lock
transmitter Console
2H lock
receiver
Pre-amp Field/shim
regulation
(a) (b)
FIGURE 5.24 (a) NMR spectroscope and (b) functional view.

induced magnetic fields that alter the effective magnetic field felt by each nucleus. Thus, the actual
field experienced by a proton depends on its molecular environment; for example, the NMR spectra
of ethyl alcohol show that it has three different types of protons: (1) those in the CH3 group, (2) those
in the CH2 group, and (3) those in the OH group. If the induced field opposes the applied field, a
higher applied field is required to make the nucleus resonate. Such nuclei are said to be shielded.
On the contrary, nuclei are deshielded if the induced field augments the applied field. Such spectral
shifts in different structural environments are called chemical shifts. The extent of the chemical
shift is measured relative to the PMR of tetramethylsilane (TMS) and is called the tau (τ) value:
τ = 10 −
( frequency difference from TMS) × 106
instrument frequuency in Hertz
The chemical shift is influenced by
• The electronic configuration around the nucleus and therefore the molecular structure.
• The solvent in which the sample is dissolved. This is because the process of dissolution
involves the bonding electrons of the solute and solvent.
• The temperature, in the case of molecules with hydrogen bonding, because it affects the
strength of the hydrogen bond.
5.7.4 Applications
NMR spectroscopy is of great importance due to chemical shifts, which make the spectra very pre-
cise and the ultimate in structural analysis. Chemical shifts are utilized for studying the following
situations: The presence of neighboring aromatic rings can be detected due to abnormal shifts of a
particular nucleus. Specific probes can be introduced to cause changes in the shifts making it pos-
sible to study the effect of the probes on molecular structure.
In a covalent bond, the electronic magnetic moment is zero because electrons are paired. However,
the nuclear magnetic moment causes the electrons to be polarized slightly. This effectively transmits
the direction of the spin of one nucleus to another. Such an interaction between like or different
spins through the bonding electrons, called spin–spin interactions, cause the splitting of the NMR
absorption peak already separated by chemical shifts. This splitting is called hyperfine splitting, and
it is used to detect and identify the number and kind of chemical groups, bond angles, and isomers
present. These can be extended to biomolecules such as nucleotides, hormones, peptides, and so on.
Just like other spectroscopic techniques, NMR spectra is mainly used for studying the structure of
molecules, conformational changes in macromolecules, qualitative and quantitative analysis, and at
times for kinetic investigations (Figure 5.25).
5.7.5 Comparison of ESR and NMR

Both ESR and NMR provide information about the structure of a molecule at the atomic level, which
is not possible by any other form of spectroscopy. The two differ in the instrumentation involved and
practical applications. ESR requires a magnetic field of 0.1–1 T, whereas NMR requires a higher
magnetic field (10 fold higher) of 1–10 T. ESR absorbs in the microwave region of the spectrum,
whereas NMR absorbs in the radiowave region of lesser energy. Both forms are nondestructive and
can be used under nearly the same physiological conditions.
NMR is universally applicable since all biological molecules contain protons and most contain
31P. ESR can only be observed in molecules with unpaired electrons, which restricts the technique
to molecules containing free radicals on paramagnetic centers. NMR is, however, less sensitive than
ESR because smaller energy changes are involved. Also, NMR spectra are more complicated due
to chemical shifts and spin–spin interactions. In contrast, ESR spectra are simpler, with only one or
two peaks corresponding to paramagnetic centers.
Spectroscopy 143
Aliphatic carbon
13C NMR
Fish oil
36 34 32 30 28 26 24 22 20 18 16 ppm
160 140 120 100 80 60 40 ppm
Sn1, 3
Sn1, 3 20:5
Sn2 22:5
Sn1, 3 18:4 Sn2 18:4
Sn2
Sn2 20:5
Carboxyl carbons Sn1, 3 22:6 Sn2 22:6
172.9 172.7 172.5 172.3 172.1 171.9 171.7 ppm
FIGURE 5.25 NMR spectra of fish oil. (From Aursand et al., 2007, J Agric Food Chem, 55:38-47.)
5.8 MALDI-TOF MASS SPECTROMETRY

5.8.1 Introduction
The characterization of polymeric materials is vital for predicting and elucidating polymer proper-
ties and morphology. Characterization typically involves (1) molecular mass analysis utilizing gel
permeation chromatography, light scattering, osmometry, or viscometry, (2) a sequence of repeat
units utilizing NMR spectroscopy, (3) end-group analysis utilizing titration, NMR spectroscopy, or
Fourier transform infrared (FT-IR) spectroscopy, and (4) purity examination utilizing NMR spec-
troscopy, elemental analysis, and FT-IR spectroscopy. Until recently, no single technique could
completely describe these characteristics of a polymer sample. The powerful capabilities of matrix-
assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry are realized
with the fast and accurate determination of molar masses, sequencing of repeat units, and recogni-
tion of polymer additives and impurities.
5.8.2 MALDI-Mass Spectrometry in Chemical Identification

Mass spectrometry (MS) has been appropriately used for the analysis of the molar masses of mol-
ecules for the past 50 years. However, the application of MS to large biomolecules and synthetic
polymers has been limited due to the low volatility and thermal instability of these materials.
These problems have been overcome to a great extent through the development of soft ionization
techniques such as chemical ionization, secondary ion mass spectrometry, field desorption, fast
Target plate spotted with

proteins of interest
Pulsating light Detection Reflection

Sample plate
Laser
Ionization
Protein identification
FIGURE 5.26 Functional view of MALDI-TOF.
atom bombardment (FAB), and matrix-assisted laser desorption/ionization mass spectrometry

(MALDI-MS). The MALDI-MS technique, in particular, allows for the mass determination of large
biomolecules and synthetic polymers with molar masses greater than 200,000 Da by ionization and
vaporization without degradation (Figure 5.26).
MALDI-TOF MS is an emerging technique offering a promise of fast and accurate determina-
tion of a number of polymer characteristics. The MALDI technique is based upon a UV-absorbing
matrix pioneered by Hillenkamp and Karas. The matrix and polymer are mixed at a molecular level
in an appropriate solvent with a ~104 molar excess of the matrix. The solvent prevents the aggrega-
tion of the polymer. The sample/matrix mixture is placed onto a sample probe tip. Under vacuum
conditions, the solvent is removed, leaving cocrystallized polymer molecules homogeneously dis-
persed within matrix molecules. When the pulsed laser beam is tuned to the appropriate frequency,
the energy is transferred to the matrix that is partially vaporized, carrying intact polymer into the
vapor phase, and charging the polymer chains. Multiple laser shots are used to improve the signal-
to-noise ratio and the peak shapes, which increases the accuracy of the molar mass determination.
In the linear time-of-flight (TOF) analyzer (drift region), the distribution of molecules emanating
from a sample are imparted with identical translational kinetic energies after being subjected to the
same electrical potential energy difference. These ions will then traverse the same distance down
an evacuated field-free drift tube; the smaller ions arrive at the detector in a shorter amount of time
than the more massive ions.
Separated ion fractions arriving at the end of the drift tube are detected by an appropriate
recorder that produces a signal upon the impact of each ion group. The digitized data generated
from successive laser shots are summed, yielding a TOF mass spectrum (Figures 5.26 and 5.27).
The TOF mass spectrum is a recording of the detector signal as a function of time. The TOF for a
molecule of mass m and charge z to travel this distance is proportional to (m/z)1/2. This relationship,
t ~ (m/z)1/2, can be used to calculate the ion’s mass. Through the calculation of the ion mass, conver-
sion of the TOF mass spectrum to a conventional mass spectrum of the mass-to-charge axis can be
achieved (Figures 5.28 and 5.29).
MALDI is a “soft” ionization technique in which the energy from the laser is spent volatil-
izing the matrix rather than degrading the polymer. The preparation of an appropriate polymer/
matrix mixture is one of the critical limiting factors for the universal application of MALDI
to the synthetic polymers. With the advent of MALDI in 1992, the challenge has been to dis-
cover appropriate matrix materials for use with synthetic polymers since previous efforts were
Spectroscopy 145
Ultraviolet Data
laser analysis
Optics
Oscilloscope
Sample
probe
Detector
Trigger
Drift
region (m/z)
Vacuum Amplifier
Deflection Vacuum
plates
Voltage
potential
FIGURE 5.27 Schematic of a MALDI-TOF MS.
To
TOF MS
Pulsed laser
beam N2 ~ 337 nm
Ions
Sample
30º
Sample
holder
FIGURE 5.28 MALDI-TOF MS sample ionization.
Drift
tube (m/z)
Data analysis
Detector
TOF spectrum Mass spectrum
T ~ (m/z)1/2 t = Time-of-flight
FIGURE 5.29 Conversion from TOF spectra to conventional spectra.

Intensity/arbitrary units
(A)
47
450.1689
434.1509
1345.5668
1343.5670
185.1508
1330.5684
2430.7588
2634.8189
0
200 400 600 800 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 3000 3200 3400
m/z
FIGURE 5.30 Peptide mass fingerprinting of a 70 kDA protein spot showing different peptide peaks of dif-
ferent molecular mass from an antigen of Aspergillus fumigatus.
centered around biopolymers. Synthetic water-soluble polymers have been shown to be capable
of analysis using similar conditions to those of biopolymers. Synthetic, organic-soluble poly-
mers, however, have exhibited analysis complications due to their seeming incompatibility
with the matrix materials. Because of this fact, only structurally simplistic, synthetic, water-
soluble and organic-soluble polymers have been investigated to date using MALDI analysis
The purpose of the matrix material, as alluded to previously, is twofold: (1) absorption of energy
from the laser light, thus preventing polymer decomposition, and (2) isolation of the polymer mol-
ecules from one another. Matrices for biopolymers have traditionally utilized just the biopolymer
and the matrix material. Synthetic polymers, particularly organic-soluble polymers, have differing
solubilities in the common solvents and often do not have large concentrations of ionized species.
Most of the commonly used matrices are 2,5-dihydroxybenzoic acid derivatives, sinapinic acid
derivatives, and indoleacrylic acid derivatives. Few compounds are as useful as matrix materials
due to the numerous stipulations involved: common solubility in a given solvent (water, acetonitrile,
ethanol, etc.), absorption, reactivity, and volatility are conditions that must be considered before
an appropriate matrix might be found for a particular synthetic polymer. In addition to the matrix
material, a cationizing species is often added to increase the concentration of ionized species. Some
linear homopolymers and condensation polymers have been shown to yield adequate spectra for
analysis without a cationizing species, but often alkaline salts (LiCl, NaCl, KCl) or silver trifluoro-
acetate have been included as the cationizing agent to increase the yield of cationized species and
allow a more homogeneous cationization. Surfactants are being investigated for use with organic-
soluble polymers, where homogenization is not always possible or reproducible. Enhancement of
spectra is expected where the surfactant can potentially play a dual role as both a matrix emulsifier
and a cationization agent.
Spectroscopy 147
×104
1904.268
2.5
2.0
Intensity (a.u)
1.5
1.0
1511.137
2273.332
2163.203
1653.192
2013.394
1463.075
0.5
3300.244
1225.027
1824.743
2704.964
1320.781
881.447
2349.432
3052.913
0.0
1000 1500 2000 2500 3000 3500

Mass (m/z)
FIGURE 5.31 Representative MALDI-TOF spectrum of Spot 8114 antigen fragment (SWISSPROT acces-
sion number Q8SNCO; MHC class II antigen fragment of Mycobacterium tuberculosis).
5.8.3 Synthetic Polymer Analysis

The structural investigation of homopolymers using MALDI has been limited to a discrete number
of water-soluble and organic-soluble systems. MALDI studies have been shown to be applicable to
polymers of a broad range of chemistry, from water-soluble polymers such as poly(ethylene glycol)
(PEG), poly(propylene glycol) (PPG), poly(styrene sulfonic acid), and poly(acrylic acid) to organic-
soluble polymers such as poly(styrene) and poly(butyl methacrylate). Other MALDI studies in the
homopolymer, condensation polymer realm have included fluorinated polymers, polymer blends,
and polymer additives. MALDI was originally designed for the analysis of architecturally specific
synthetic polymer systems such as copolymers, grafted polymers, living block copolymers, and
dendrimers for which no standards exist. Statistical models for the mass spectra of the composi-
tion and microstructure of copolymers were also developed. These studies utilized principles of
laser desorption, FAB, field ionization, and electron impact, methods in which fragmentation is
observable. Actual studies utilizing MALDI analysis with copolymers have had limited investiga-
tions. Copolymers under investigation have been poly(butyleneadipate-co-butylenesuccinate) and
poly[(N-vinylpyrrolidone)-co-(vinylacetate)]. The results of copolymer studies cannot be compared
with other MALDI analyses since MALDI was used strictly as a detector after polydisperse copo-
lymers were segmented with gel permeation chromatography (GPC)-MALDI.
The investigation of synthetic polymers utilizing MALDI techniques included the studies of PPG
and PEG. Mixing occurs between the polymer and matrix materials on a molecular level in the sol-
vent followed by homogeneous vacuum cocrystallization. Figure 5.32 shows the resultant spectra for
one of the first successful MALDI analyses. The spectra are for a low-molar-mass (5300 g/mol) PPG
sample. Due to the low molar mass of the polymer, the molar mass distribution is easily derived as
58 g/mol from the peak-to-peak mass increments. The molar masses obtained through MALDI, listed
as Mn, Mw, and Mp, agree quite well with the value specified by the manufacturer of PPG-5300.
∆m = 58 g/mol
100 CH3
Polymer: Poly(propylene glycol)
MW: 5300 (By GPC) O CH CH2
Matrix: 2, 5-Dihydroxyhenzoic acid 75 n
Solvent: Water/ethanol, 1:1 (v/v)
% Int.
Mn = 5157
Mw = 5227 50
PDI = 1.01
Mp = 5280
25
4000 5000 6000 7000

m/z
FIGURE 5.32 MALDI-TOF spectra for PPG.
Molecular ion ∆m = 104 g/mol

[Mn]+
Polymer: Poly(styrene) 100
MW: 20,000 (By GPC)
Matrix: 2-Nitrophenyl octyl ether
silver trifluoroacetate (CH2 CH)
75 n
Dimer
Mn = 19,337
Mw = 19,509 50 [MnMm]+
PDI = 1.01
Mp = 19,740
Trimer
25
Tetramer
10,000 20,000 50,000
FIGURE 5.33 MALDI-TOF spectra for poly(styrene).
The MALDI technique was investigated for a PEG sample having a higher molar mass of 23,000
(Figure 5.32). At m/z 23,000, the mass resolution is not sufficient to resolve adjacent oligomer
molecular ions with a difference of 44 mass units. Therefore, the resultant spectra show a convolu-
tion of the molecular ions, which results in a continuous distribution. Typically, there is a limit to
the peak-to-peak resolving capabilities of MALDI, which has been observed by researchers to be
around 20,000 g/mol. However, a MALDI study showed samples of PEG-23,600 g/mol that had
the same molecular convolution of the spectrum; they were able to discern the peak-to-peak mass
resolution of 44 g/mol due to the improved resolving power of more recently manufactured MALDI
instruments. Even with the continuous distribution of the spectra, the data for the PEG-23,000 g/
mol sample shows that the polymer distribution is 20,000–25,000 g/mol, possessing a maximum of
the distribution at 22,930 and the centroid mass at 22,950. This data still exhibits a good agreement
with the manufacturer’s value of 23,000. Mixing between the polymer and matrix materials occurs
on a molecular level in the solvent followed by homogeneous vacuum cocrystallization. Figure 5.33
shows the resultant spectra for MALDI analysis of poly(styrene).
Spectroscopy 149
In the low mass range, only peaks for the matrix ions appear. These spectra have a continu-
ous distribution due to convolution of the molecular ions; however, the molar mass for individual
oligomers is apparent, as shown in the inset, with a peak-to-peak mass resolution of 104 g/mol.
This sample utilized 2-nitrophenyl octyl ether, a viscous liquid, as the matrix material because
using 2,5-dihydroxybenzene matrix resulted in separation of the matrix and polymer. No results
can be obtained from sample preparations with inhomogeneity between the matrix and polymer
because the polymer is either directly ionized, resulting in the degradation of the sample (fragmen-
tation), or the polymer is not fully ionized, leaving ion levels below the limits of detection. Spectra
obtained from studies displayed good homogenization between the matrix and the polymer and
do not show the dimer, trimer, or tetramer oligomer ion distributions. Here, the matrix material
is possibly better in absorbing energy from the laser light, thus shielding the polymer from over
ionization.
5.8.4 Impurity in Oligocarbons

Certain condensation polymers have been investigated using MALDI. Contrary to most polymer-
ization products, condensation polymers tend to possess low molar masses. However, it is the com-
plex polymer structure of most condensation polymers that renders them interesting for MALDI
studies. MALDI studies of condensation polymers have included phenolic resins, epoxy resins, and
polycarbonates, all of which are important technical products. MALDI samples of the two oligocar-
bonates, containing the matrix material of dithranol and LiCl and the oligocarbonate, were mixed
on a molecular level in a THF solvent solution and homogeneously vacuum cocrystallized. LiCl
was added as part of the matrix to increase the formation of cationized species. Spectra A and B in
Figure 5.34 are the resultant distributions derived from MALDI-TOF MS analysis.
Spectra A have straightforward molar mass distributions with peak-to-peak mass increments of
254 g/mol, equaling exactly the mass of the repeating unit of bisphenol A-based oligocarbonates.
The end-group can be derived through multiple subtraction of the repeat unit from any one of the
mass peaks. The end-group of spectra A has, therefore, been derived as 228 g/mol, which corre-
sponds to oligomers with hydroxyl end-groups. Spectra B include the same molar mass distribution
with peak-to-peak mass increments of 254 g/mol, equaling exactly the mass of the repeating unit of
bisphenol A-based oligocarbonates. However, observance of further oligomeric series in the spec-
trum is significant because it is representative of inhomogeneity in the sample. The peaks in the
denoted oligomer series are offset by 134 g/mol from the major oligomer sample (Figure 5.35). It
has been suggested that these oligomers contain cresol, which would be present as a purposefully
added chain terminator or an impurity in the reaction mixture, as shown in Figure 5.36.
100 100
∆m = 254 g/mol ∆m = 254 g/mol
%Int.
% Int.
0
0 500 1000 1500 2000 2500 3000
1000 2000 3000 4000 5000
m/z
m/z
(a) (b)
FIGURE 5.34 Oligocarbonate studies utilizing MALDI-TOF MS: (a) molar mass distribution with peak to
peak mass increments and (b) mass of repeating unit of bisphenol A-based oligocarbonates.
M = 254n + 228
O M + Li+ = 254n +235
H O O C O OH
n Repeat
End-group
unit
FIGURE 5.35 A pure oligocarbonate sample.
O O M = 254n + 362
M + Li+ = 254n + 369
O C O O C O OH
n
CH3 Repeat End-group
unit
FIGURE 5.36 Determination of an impurity in an oligocarbonate.
O
O O C
O n
H O O C O OH
n O
M + Li+ = 254 n + 219 M + Li+ = 254 n + 217
Repeat End-group Repeat End-group

unit unit
FIGURE 5.37 Speculation of the side reactions in the oligocarbonate.
5.8.5 Side Reaction in Oligocarbons

The peaks in the minor oligomer series denoted by the peaks with the + above them are again
indicative of oligocarbonates due to the m/z 254 peak-to-peak mass increment. End-group calcula-
tions allow for the speculation of the two structures shown in Figure 5.37.
5.9 CIRCULAR DICHROISM (CD) SPECTROSCOPY

5.9.1 Principle
CD spectroscopy measures the differential absorption of right (R) and left (L) circularly polarized
light as a function of wavelength. Light consists of EM waves vibrating in all directions perpendicu-
lar to the direction of the propagation of light. After passing through a Nicol prism or polaroid, light
becomes plane polarized, that is, it consists of waves oscillating only in one plane. When two plane-
polarized waves of equal amplitude and wavelength but differing in their planes of polarization by
90° are superimposed, circularly polarized light is obtained. It can be either right (R) circularly
polarized or left (L) circularly polarized depending upon the relative positions of the peaks of the
two component plane-polarized waves.
For an optically active compound, εL ≠ εR, that is, the molar absorption coefficients of L and R
circularly polarized light are unequal. It may absorb either the L or R circularly polarized light more
than the other. Maximum absorption occurs when the electric field vector is parallel to the direction
Spectroscopy 151
in which there is maximum electronic displacement within the absorbing molecules because of the
differential absorption of the R and L circularly polarized light; the resultant light is elliptically
polarized. It is this ellipticity (θ) rather than absorbance which is measured as a function of wave-
length, and a CD spectrum is obtained.
CD spectroscopy is different from other forms of spectroscopy in the following ways:
• It requires the use of circularly polarized light as incident radiation.

• It gives information about the shape or 3D structure of an optically active molecule.
• Only optically active molecules can be analyzed. This is not a handicap for biological
investigations since most biomolecules are optically active; for example, amino acids (gen-
erally of l-configuration), nucleotides (containing the sugars d-ribose and d-deoxyribose),
and carbohydrates (d and l configurations) are the units from which polypeptides, pro-
teins, nucleic acids, and polysaccharides are built up.
Figure 5.38 diagrammatically shows the components of a CD spectrophotometer. R and L circu-
larly polarized radiation is produced by passing plane-polarized light in an electro-optic modulator
through which an alternating current is passed. Depending on the polarity of the electric field, the
R or L component of light is transmitted.
The photomultiplier detector produces a voltage proportional to the ellipticity of polarization of
the combined beam falling on it. This is recorded against the wavelength by the recorder.
180
θ = 2.303Δ E
4π
Radiation source
Monochromator
Monochromatic radiation
Linear polarizer
Plane-polarized radiation
Electro-optic
Alternatively R or L
modulator
circularly polarized
radiation
Sample
Elliptically
polarized radiation
Detector
Amplifier/signal
processor
Recorder
FIGURE 5.38 The main components of a CD spectrophotometer.

where
θ = ellipticity
ΔE = difference in the absorption of R and L waves
5.9.3 Applications
5.9.3.1 Protein Conformation
It is possible to study the 3D secondary structure of proteins. The CD spectra of α-helix,
β-conformation, and random coil of poly-l-amino acids are known and can be used for calculating
the amount of secondary structure present in a protein.
5.9.3.2 Nucleic Acid Structure

The CD spectrum of a single-stranded nucleic acid can be calculated from its nearest neighbor fre-
quency. Any difference in the measured CD spectrum can be a result of conformational changes in
the nucleic acid, that is, double-strandedness. These can therefore be studied in detail with the help
of a CD spectrum.
5.9.3.3 Secondary Structures of Proteins

The technique is particularly useful for proteins which cannot be analyzed by x-ray diffraction
studies.
Experiment: Isolation and Quantification of Pigments

A. Chlorophyll a (Chl a)
Principle
Cyanobacteria have only Chl a, and its quantitative estimation is important for the evaluation of growth
and photosynthetic rates. Chl a is completely extractable in solvents like acetone/methanol and exhibits
characteristic absorption at 663 nm.
Reagent
80% methanol.
Procedure
1. Centrifuge a known volume of homogenous cyanobacterial suspension at 5000 rpm for
10 minutes.
3. Suspend the pellet in 4 mL of methanol and vortex thoroughly.
4. Cover the mouth of the test tube with aluminum foil to prevent evaporation of the solvent.
5. Incubate the tube in a water bath at 60°C for 1 hour (preferably in the dark) with occasional
shaking.
6. Cool the tube and centrifuge the contents at 5000 rpm for 5 minutes.
7. Transfer the supernatant to another tube and once again add 4 mL of the solvent and extract
again like before.
8. To ensure complete extraction, add 2 mL of the solvent to the pellet and repeat the process.
9. Pool the supernatants and make up the volume to 10 mL with methanol (to compensate the
solvent loss during heating).
10. Read at 663 nm in a spectrophotometer against methanol blank.
Comments
Chl a is not stable in light and easily gets oxidized. Care should be taken to extract Chl a in dim light
or in the dark.
Spectroscopy 153
Calculations
A663 × 12.63 × volume of sample

Chl a ( g·mL–1 ) =
Volume of methanol
where
A663 = absorbance at 663 nm
12.63 = correction factor
Using the above formula, calculate and express Chl a as µg·mL−1.
B. Carotenoids
Principle
Carotenoids include pigments like carotenes and xanthophylls. They are soluble in solvents like acetone
and/or methanol, exhibiting a characteristic absorption at 450 nm.
Reagent
85% acetone.
Procedure
10 minutes.
3. Homogenize the pellet with 3 mL of acetone.
4. Centrifuge the contents at 5000 rpm for 5 minutes and store the supernatant in the refrigerator.
5. Repeat the extractions until the acetone remains colorless.
6. Pool the supernatants and make up to a known volume with acetone.
7. Measure the absorbance at 450 nm against the acetone blank.
Calculation
D × V × f × 10
Caretonoids (mg·mL–1 ) =
2500
where
D = absorbance at 450 nm
V = volume of the sample
f = dilution factor
2500 = extinction coefficient
With the formula given above, calculate and express caretonoids as mg·mL −1
C. Phycobilins or phycobiliproteins
Principle
Phycobilins, which generally account for 24% of the dry weight of the soluble proteins of cyanobacte-
rial cells, are important for physiological, biochemical, and ecological studies. These, namely phyco-
cyanin, phycoerythrin, and allophycocyanin, are water-soluble pigments and are extracted in phosphate
buffer (pH 6.8).
Reagent
Phosphate buffer (0.05 M), pH 6.8. Dissolve 1.72 g of dipotassium hydrogen phosphate (K 2HPO4) and
1.36 g of potassium dihydrogen phosphate (KH2PO4) in 100 mL distilled water separately and set the
pH to 6.8 by adding KH2PO4 to K 2HPO4.
Procedure
10 minutes.
2. Wash the pellet in distilled water (check for the loss of pigments).
3. Suspend the pellet in 3 mL of PO4 buffer and homogenize/sonicate the contents.
4. Freeze–thaw the contents repeatedly and centrifuge at 5000 rpm for 5 minutes.
5. Store the supernatant in the refrigerator.
6. Repeat the same process until the pellet becomes colorless to ensure complete extraction.
7. Pool the supernatants and measure the absorbance at 565, 615, and 652 nm, respectively,
against PO4 buffer blank.
Calculation
A 615 − 0.474( A652)
C-Phycocyanin (PC) mg mL−1 =
5.34
−1 A 652 − 0.208( A615)
allo-Phycocyanin (APC) mg mL =
5.09
A 562 − 2.41( PC ) − 0.849( APC )
C-Phycoerythrin (PE) mg mL−1 =
9.62
The values obtained from the calculation are for the extract (mg mL−1). From this, the values for the
original sample has to be calculated, based on the volume of the sample/culture used.
Experiment: Measurement of Absorption Spectra

A characteristic absorption spectrum is simply a plot of absorbance of light by a compound at different
wavelengths. Absorption spectra of oxidized and reduced forms of cytochrome c are presented in Figure
5.39a. For instance, the presence of cytochromes, ham or flavins, as a prosthetic group of a number of
enzymes was largely deduced from spectral studies. This technique has also been extremely useful in
indicating the involvement of certain compounds in various complex processes. A notable example
of this is in establishing the role of quinones, flavins, and various cytochromes in the mitochondrial
electron transport chain as well as in the photosynthetic electron transfer chain. Special investigations
revealed that, under anaerobic conditions, the addition of NADH to mitochondrial preparations results
in the reduction of cytochrome c. It undergoes rapid oxidation on the introduction of oxygen, thereby
suggesting that it acts as an intermediate carrier of electrons during their transport from NADH to oxy-
gen via the mitochondrial electron transfer system. Such studies are generally carried out by examining
100
Optical density of a millimolar solution
80
Extinction coefficient
Oxidized 275
60 Reduced Ubiquinone
Protein
bond δ α
24
β
40
20
Ubiquinol
0 250 350 450 550 00 0 260 280 300 320
Wavelength in millimicrons Wavelength (nm)
(a) (b)
FIGURE 5.39 (a) Absorption spectra of oxidized and reduced forms of cytochrome c. (b) Absorption and
difference spectra of ubiquinone and ubiquinol.
Spectroscopy 155
2.50 Aº
(0.500
/div)
0.00 Aº
(100/div) 800.0 nm
FIGURE 5.40 Absorption spectra of a cyanobacterium Spirulina platensis.
the difference spectra, because the various states of a compound exhibit qualitative alteration in their
spectral characteristics. For example, the oxidized and reduced forms of quinones, flavins, and cyto-
chromes have distinctive spectral difference. As the name denotes, the difference spectra is a graphical
representation of the difference in the absorbance of light at different wavelengths by two forms of a
compound. The absorption spectra and difference spectra of ubiquinone and ubiquinol are shown in
Figure 5.39b.
Spectrophotometric analysis has been helpful in the identification of chromophores in light-medi-
ated responses and processes. First, the rate of the light-dependent response or process is determined
at varying wavelengths. A plot of the rate of the process (such as photosynthetic oxygen evolution) at
various wavelengths is prepared. Such a plot is known as an action spectrum. An attempt is made to
isolate the compound from the tissue that has an absorption spectrum superimposable on the action
spectrum. This approach has successfully been employed in establishing the central role of chlorophylls
as the primary light-harvesting pigments in photosynthesis and of phytochrome in red-/far-red-induced
responses in plants.
Chl a was qualitatively measured by a spectrophotometer on samples filtered onto Whatman GF/C
filters, extracted in 90% acetone, and scanned in a wavelength range of 400–700 nm through UV–VIS
Spectrophotometer (Shimadzu; Kyoto, Japan) (Figure 5.40).
Experiment: Determination of the Molar Extinction

Coefficient of NADH
Introduction
Quantitative colorimetric estimations are based on two laws, namely, Lambert’s law and Beer’s law.
Although Lambert’s law defines the relationship between the length of the light path through the solu-
tion, Beer’s law states that the fraction of the length of the light transmitted is inversely proportional
to the concentration of the light-absorbing compound in the solution. The amount of transmitted light
is inversely related with the absorption of light by the media. Hence, as a corollary, the extent of light
absorbed by a compound is directly proportional to its concentration. The experiment is designed to
verify the validity of Beer’s law.
Reduced forms of nictotinamide adenine nucleotides (NADH and NADPH) show a distinctive
absorption peak at 340 nm. These nucleotides are required as cofactors by several oxidoreductases. The
spectrophotometric determination of activities of such enzymes is based on the measurement of the rate
of utilization or production of NADH by monitoring the change in absorbance at 340 nm. According
to Beer’s law, the absorbance of light that is often referred to as optical density (OD units) should be
directly proportional to the concentration of NADH in the reaction mixture.
The molar extinction coefficient of NADH is defined as the absorption of light by 1 M concentration
of a compound at an optimal wavelength with a fixed light path of 1 cm, and it is represented as ε with
the wavelength shown as a subscript (for NADH at 340 nm, it is written as ε340 = (6.2 × 103). From this
value, the concentration of the compound in a sample can directly be calculated without preparing a
standard or reference curve.
1. Prepare an NADH standard solution of different molarities.
2. Record the absorbance of the sample.
Safety Guidelines
1. Prepare the NADH solution freshly as and when the absorption measurements are made.
2. Prepare NADH in a Tris–HCl (pH 7.5) buffer.
Materials
UV–visible spectrophotometer, standard quartz silica cuvettes with a light path of 1 cm, pH meter,
NADH, Tris–hydroxylamine, and HCl.
Prelaboratory Precautions
NADH solution: 10 mL of 1 mM solution of NADH solution. Prepare 10 mL solution of NADH in 0.05
M Tris–HCl (pH 7.5).
Method
1. Switch “on” the spectrophotometer. Set the wavelength to 340 nm and after 1–2 minutes,
switch “on” the UV (or deuterium) lamp and allow the instrument to warm up for 15–20 min-
utes (follow the instructions given in the operator’s manual of the instrument supplied by the
manufacturer).
2. Take a silica cuvette and add 3 mL of 0.05 M Tris–HCl. Place the cuvette in the cuvette holder
and again adjust it to “zero” absorbance (or 100% transmission) using this blank (buffer
alone) cuvette.
3. Check the “zero” and 100% transmission as described in step 2 to make sure that the instru-
ment is properly adjusted.
4. In another matched cuvette, take 0.1 mL of 1 mM solution of NADH and 2.9 mL of 0.05 M
Tris–HCl buffer so that the total volume in cuvette is 3 mL. Mix the contents thoroughly and
record the absorbance of this sample solution (it corresponds to 33 μM NADH or 0.1 μmol in
3 mL).
5. Pour out the solution from the sample cuvette and rinse it with distilled water. Add 0.2 mL of
NADH and increase the final volume 2.8 mL of 0.05 M Tris–HCl buffer. Record its absorbance.
6. Repeat step 5 by taking 0.40 mL of NADH solution and 2.6 mL of 0.05 M Tris–HCl buffer.
Record its absorbance.
7. Repeat step 5 by taking 0.6 mL of NADH solution and increase the volume to 3 mL with
0.05 M Tris–HCl buffer, and record the absorbance of this solution.
Calculations
1. Present the result obtained in the form of a table as follows:
mL of NADH Conc. of Fold Conc. of

Sample No. Solution NADH (μM) NADH A340 Ratio
1 0.10 33.3 1.0 – 1.0
2 0.20 66.6 2.0 – –
3 0.40 133.3 4.0 – –
4 0.60 200.0 6.0 – –
Calculate the ratios of A340 for samples 2, 3, and 4.
Spectroscopy 157
2. Check whether the calculated values of the ratios for samples 2, 3, and 4 correspond with
the increase in the fold concentration of NADH in this sample as compared to sample 1.
3. Prepare a graph of A340 against the concentration of NADH in the sample. A straight line
denotes the increasing concentration of NADH in the sample. This graph can be used as a
standard curve for NADH. One can determine the concentration of NADH in the sample
from its A340 by referring to this standard curve.
4. Calculate the molar extinction coefficient (ε340 nm) for NADH as below
a. Suppose 133.3 μM solution of NADH gives A340 of x.
b. 1 μM solution of NADH would correspond to (x/133.3) absorbance.
c. 1 M solution of NADH would give A340 value of ( x /133.3) × 10 6.
This is the ε 340 for NADH. Thus, the concentration of NADH in an unknown sample can
directly be calculated from its A340 by using the molar extinction coefficient of NADH.
Experiment: Preparation of Absorption Spectra of NADH

Introduction
The absorption spectrum refers to the absorbance of light of different wavelengths by a compound.
Every compound or group of compounds has some characteristic features in its absorption spectra,
which is used in analyzing the substance quality and also helps in estimating the quantity. For exam-
ple, flavin adenine nucleotides (FAD) have broad absorption spectra with peaks at 370 and 450 nm.
Enzymatic or chemical reduction of flavin nucleotides is accompanied by the disappearance of the peak
at 450 nm. Thus, the presence of flavin nucleotides in a sample can be established by examining its
absorption spectra before and after its reduction. Similarly, the oxidized form of cytochrome c shows a
prominent peak at 415 nm and a broad but less intense peak at around 550 nm. Reduction with sodium
dithionite leads to the appearance of a sharp distinct absorbance peak at 554 nm (∝-band), another peak
524 nm (β-band), and an intense peak at 419 nm. The amount of cytochrome c can be quantitatively
estimated from A554, which has a molar extinction coefficient value 27.7. Absorption spectra also helps
in identifying wavelength which is characteristic and unique for a particular compound; for example,
absorption peak at 340 nm is unique for NADH, and even though the peak at 260 nm is much more
intense, it cannot be used for detection and quantitative estimation of NADH because NAD and other
adenine nucleotides (like ATP, ADP, AMP) also show intense absorption at 260 nm but not at 340 nm.
The absorption spectra was obtained by examining the absorbance of light at different wavelengths
by the compound. A dual beam spectrophotometer with a facility for scanning is required. In these
spectrophotometers the wavelength changes in a predetermined range continuously at a constant rate
(say, 25 nm per minute), and the difference in absorbance between the blank and the sample preparation
is automatically recorded on chart paper. However, absorption spectra can also be obtained manually
with simple single-beam spectrophotometer. At each wavelength, the instrument has to be set again to
zero absorbance. The absorbance by the sample is then determined and is plotted in form of a graph of
the absorbance value versus wavelength.
1. Preparation of 1 μm solution of NADH.
2. Measurement of absorption spectra at different wavelengths with UV–visible spectrophotometer.
Safety Guidelines
1. Prepare NADH solution as and when the experiment is carried out.
2. Prepare NADH in a Tris–HCl buffer.
Materials
Spectrophotometer, pH meter, NADH, Tris hydroxylamine, hydrochloric acid, NADH solution.
Prelaboratory Preparation
NADH solution: Prepare 1 mM solution of NADH in 0.05 M Tris–HCl.
Method
1. Switch “on” the spectrophotometer and after 1 minute, switch “on” the UV lamp.
2. Take two matched silica cuvettes. In the reagent blank cuvette, add 3 mL of 0.05 M Tris–HCl
buffer (pH 7.5). In the sample cuvette, add 0.4 mL of 1 mM NADH solution and 2.6 mL of
0.05 Tris–HCl (pH 7.5).
3. Set the instrument at 200 nm using the reagent blank cuvette (Tris–HCl buffer alone) as
described in steps 2 and 3 of the first experiment of this chapter and determine the absorption
of the sample (containing NADH) against the blank.
4. Now reset the instrument at 210 nm with reagent blank and record the reading of the sample.
Repeat this step at intervals of 10 nm each up to 40 nm. For taking readings beyond this
wavelength, switch “off” the deuterium lamp and switch “on” the tungsten lamp.
5. Draw a graph of absorbance value versus the wavelength to obtain the absorption spectrum of
NADH.
Experiment: Determination of Difference Spectra of

Oxidized–Reduced NAD
Introduction
As the name indicates, the difference in the spectra represents or highlights the difference of the
absorption of light by two forms of the same compound, for example, oxidized–reduced states of a
compound like NAD and NADH, the oxidized form of FAD and its reduced form FADH2, and so on.
The differential spectra provides useful information as to which is the optimal wavelength to differenti-
ate between the two states of the compound. In fact, the selection of the most appropriate wavelength to
differentiate and specifically estimate the particular state of the compound from the other state is based
on their difference spectra.
For obtaining difference spectra, an automatic, dual-beam scanning spectrophotometer is used,
where NAD is placed in a blank position of the cuvette holder and that containing NADH in the sample
position. The scanning range (say, 210–400 nm) and scanning speed (20 nm/min) are adjusted as per
requirement of the investigations. The speed of recorder is synchronized (say, 1 cm–20 nm), scanning
speed (20 nm/min) is adjusted, and the scanning operation is initiated. Such a spectrum will provide a
graphical figure of the differences in the absorption spectra of the two states of the compounds, which
is automatically recorded on scanning spectrophotometer. One can determine separately the absorption
spectra of these two compounds by ordinary uv-vis spectrophotometer if scanning spectrophotometer
is not available. Calculate the difference in absorption of light at different wavelengths and draw a
graph of the difference in values of light absorbance versus wavelength. The value in the difference
spectra will be zero and only peaks with positive values will appear at the wavelengths where the two
compounds absorb light to the same extent; the blank (NAD solution) shows lesser absorption than the
sample (reduced NAD). The absorption band of negative value will be obtained where the absorption
of light by the sample is less.
1. Preparation of NAD solution.
2. Determination of absorption of light at different wavelengths.
Safety Guidelines
Same as the first two experiments of this chapter.
Materials
Same as the first two experiments of this chapter.
1 mM NAD solution in 0.05 M Tris–HCl (pH 7.5).
Spectroscopy 159
Method
Determine the absorption of light of different wavelengths by taking 0.1 mL of NAD manually as
described in steps 1–4 of the second experiment of this chapter using 0.05 M Tris–HCl as the blank.
Repeat the experiment using NADH in place of NAD in the sample cuvette.
Calculations
1. Subtract the absorbance values for NAD from those for NADH at each of the wavelengths.
2. Draw a graph of obtained differences in absorbance versus wavelength to obtain the differ-
ence spectra of oxidized–reduced NAD.
Experiment: Determination of Polyamines by Fluorescence

Spectrophotometer
Introduction
Polyamines (PA) play an important role in biological process such as in proliferation of cells, growth
and differentiation and in clinical disorders. They are highly conserved organic compound having two
or more primary amino groups –NH2. The most common PAs are putrescine (Put), cadavarine (Cad),
spermidien (Spd), and spermine (Spm). Due to their cationic nature, PAs can associate with the amino
components of biomembranes such as pectin. PAs may regulate DNA replication, transcription and
translation, cell division, differentiation, and other morphogenetic processes. They are regarded as
hormonal second messengers and as some of the reserves of carbon and nitrogen. In addition to free
amines, PAs can bind covalently to protein and conjugate hydroxycinnamic acid and hydroxyferulic
acid. The phenolic acids exhibit fluorescence when separated on TLC and viewed under UV light. They
can be quantified with a spectroflurometer.
1. The extraction of free (soluble-free cations), soluble-conjugated (with phenolic acids and
other low-molecular-weight compounds), and bound-conjugated (with macromolecules and
cell walls) PAs.
2. Estimation of free, conjugated, and bound PAs.
3. Identification of PAs by UV fluorescence.
4. Quantitative estimation by using a spectrofluorimeter.
Safety Guidelines
Follow standard laboratory precautions.
Materials
Animal or plant tissue, proline, mortar and pestle, acetone, refrigerated centrifuge, dansyl chloride,
perchloric acid (PCA), PA standards, hydrochloric acid, putrescine, benzene, spermidine, cyclo-
hexane, spermine, ethyl acetate, agmatine, glass plates, chromatographic chambers, silica gel G,
spectrofluorimeter.
10% PCA Take 10 mL of PCA and increase the volume to 100 mL with distilled water
6 N HCl Take 50 mL of conc. HCl and increase the volume to 100 mL with distilled water
PA standard Prepare 1 mM solutions
Dansyl chloride Weigh 50 mg of dansyl chloride and mix in 100 mL of water
Proline Weigh 100 mg of proline and dissolve in 1 mL of distilled water
Method
Extraction and measurement: Homogenize the tissue in a prechilled mortar with 10% (v/v) PCA in the
ratio of 100 mg fresh weight of tissue/PCA 10 mL. Incubate the homogenate at 4°C for 1 hour and then
centrifuge at 16,000 × g for 20 minutes. After centrifugation, separate the supernatant and pellet. The
supernatant contains free PAs, and PCA-soluble, conjugated, and bound PAs are released from 200 μL
of original supernatant pellet and suspension, respectively, by acid hydrolysis with 200 μL 12 N HCl
(1:1 v/v) for 16–18 hours at 110°C in flame-sealed glass ampoules. Filter the hydrolyzate through glass
wool and wash with six drops of 6 N HCl, dry at 70°C on a dry bath in an exhaust hood, and resuspend
in 20 μL of PCA. Dansylate aliquots of 200 μL nonhydrolyzed pellet containing bound PAs along with
PA standards (1 mM) as control. Briefly, mix 100 μL of the samples and standard PA mixtures with 100
μL of saturated Na2CO3 and 200 μL of freshly prepared dansyl chloride (5 mg/mL of acetone). After
vortexing, incubate the mixture overnight in the dark at 26 ± 1°C in reagent. Add 50 µL of proline (100
mg/mL H2O) and incubate for a minute under dark conditions.
Extract dansylated PAs in 250 μL of benzene. Collect clear organic phase in glass vials loaded onto
high-resolution silica gel TLC plates, and develop chromatogram developed for 1 hour with cyclo-
hexane: ethyl acetate (5:4 v/v). After TLC, the bands can be detected and marked under a UV transil-
luminator and then scraped and eluted in 3 mL of ethyl acetate. Measure the fluorescence by using a
Shimadzu RF 540 dual-wavelength spectrofluorimeter with excitation wavelength at 350 nm and emis-
sion wavelength at 495 nm.
Calculations
Calculate the PA content from standard graph made from any one of the PAs.
Experiment: Determination of Melting Temperature (Tm) and

Base Composition of DNA from Thermal Denaturation
Characteristics
Introduction
If the dilute aqueous solution of double-stranded DNA is heated, the two strands become separated
due to the disruption of hydrogen bonds between the complementary bases. Such DNA is referred to
as denatured DNA, and the process is called denaturation. Denaturation is a reversible process; if the
heated DNA solution is slowly allowed to cool to room temperature, the complementary strands of
DNA recombine to give duplex DNA. DNA is then said to be reannealed or renatured, and process is
called reannealing or renaturation of DNA.
During denaturation, the absorbance of DNA at 260 nm is increased by 30–40% due to the exposure
of the bases. The process of absorption increase is called the hyperchromic effect. Heating through the
temperature range of 25°C to about 80°C results in only a minor increase in absorbance at 260 nm, fol-
lowed by a sharp increase within a narrow temperature range (80–90°C), and then A260 becomes constant
when DNA is fully denatured (Figure 5.41). A graph between absorbance at 260 nm and temperature
gives a thermal denaturation curve, a temperature profile, or the melting curve of DNA. The temperature
corresponding to the midpoint of the curve is defined as Tm, the transition temperature or melting tem-
perature of DNA, and it denotes the temperature at which 50% of the DNA has undergone denaturation.
Tm is largely dependent on the (G+C) content of DNA; the higher the (G+C) content, the higher the
Tm. Under standard conditions of ionic strength and pH, (G+C) content is related with Tm in accordance
with the following equation:
%(G + C) = Tm − 69.3 × 2.44
Each species of DNA has a characteristic value that can be used for the purposes of identification and
characterization.
Safety Guidelines
The extracted DNA should be pure. The glassware must be washed thoroughly with double-distilled
water. Wear a lab coat.
Spectroscopy 161
1.4
1.3
A260 1.2 Midpoint of inflexion
1.1
1.0
60 70 80 Tm 90 100
Temperature (ºC)
FIGURE 5.41 Melting curve of DNA sample.
1. The measurement of DNA samples with a spectrophotometer at different ranges of tempera-
ture from 25 to 100°C recording the absorbance at 260 nm.
2. Plotting a graph of absorbance against temperature.
Materials
UV spectrophotometer with thermoprogrammer, quartz cuvettes, sodium chloride, and sodium citrate.
1. Saline sodium citrate (SSC): Prepare 0.015 M sodium citrate solution (pH 7.0) and dissolve
NaCl in it so that its final concentration in solution is 0.15 M.
2. DNA: Dissolve 50μg DNA/mL in SSC.
Method A
1. Switch “on” the spectrophotometer and after allowing a sufficient period for warming, set it
to zero absorbance at 260 nm with SSC.
2. Measure A260 of the DNA samples at 25°C.
3. Heat the DNA solution at a rate of 1°C rise/min up to 100°C with the help of a thermopro-
grammer. Record the absorbance values.
4. Calculate A260 (T°C)/A260 at 25°C for each of the following temperatures: 25, 35, 50, 70, 75,
80, 85, 90, 95, and 100°C, and plot the absorbance ratio against the temperature.
5. Determine the midpoint of increase in absorbance and by extrapolation find the correspond-
ing temperature that represents Tm for the DNA sample.
6. Calculate % (G+C) content of the DNA using the following equation:
% (G + C) = Tm − 69.3 × 2.44
Method B
If a UV spectrophotometer with a thermoprogrammer is not available, then the following procedure
can be adopted:
1. Arrange a series of constant temperature water baths maintained at 25, 50, 75, 80, 85, 90, 95,
and 100°C, respectively.
2. Record the absorbance at 260 nm of a DNA sample solution (50 mg/mL) kept at 25°C.
3. Distribute the above solution into eight test tubes and put one tube each in the water baths
maintained at different temperatures. Allow the tubes to stand for 15 minutes. After incuba-
tion, quickly cool all the tubes (except one at 25°C) by placing them in a nice bath for 10
minutes.
Note: Reannealing occurs only if the sample is cooled gradually, but reannealing is negligible
if the cooling is instantaneous.
4. Record the A260 of these samples.
5. Then proceed as in steps 4–6 of the procedure described earlier.
SUGGESTED READING
Allen, D., C. Cooksey, and B. Tsai. 2010. Spectrophotometry. http://www.nist.gov/pml/div685/grp03/
spectrophotometry.cfm (accessed October 5, 2010).
Bassler, G. C., and T. C. Morrill. 1981. Spectrometric Identification of Organic Compounds, 4th ed. New York:
John Wiley and Sons.
Edisbury, J. R. 1967. Practical Hints on Absorption Spectrometry. New York: Plenum Press.
Hilton, W. A. 1974. Experiments in Optical Physics, 3rd ed. Liberty, MO: Department of Physics, William
Jewell College.
Schwedt, G. 1997. The Essential Guide to Analytical Chemistry. Translated by Brooks Haderlie, 16–7.
Chichester, NY: Wiley.
Sharma, B. K. 1991. Instrumental Methods of Chemical Analysis, 11th ed. New Delhi, India: Goyal Publishing
House.
Snavely, B. B. 1969. “Flashlamp-Excited Organic Dye Lasers.” Proceedings of the IEEE 57: 1374–90.
Westermeier, R., and T. Naven, 2002. Proteomics in Practice: A Laboratory Manual of Proteome Analysis, 3rd
ed. Darmstadt Wiley-VCH Verlag Gmbh.
Wilson, K., and J. Walker. 2003. Practical Biochemistry: Principle and Techniques, 5th ed. Cambridge:
IMPORTANT LINKS
1. UV–visible spectroscopy: http://www.uv-groebel.com/pms_spek1.php
2. Infrared spectroscopy: http://www.perkinelmer.com/Catalog/Product/ID/L1280002
3. Fluorescence spectroscopy: http://www.perkinelmer.com/Catalog/Category/ID/Fluorescence%20Spectroscopy
4. ESR spectroscopy: http://www.jeol.com/PRODUCTS/AnalyticalInstruments/ElectronSpinResonance/
tabid/98/Default.aspx
5. NMR spectroscopy: http://www.magritek.com/kea.html
6. MALDI-TOF MS: http://www.thermoscientific.com/ecomm/servlet/productsdetail?productId=11962154&
groupType=PRODUCT&searchType=0&storeId=11152&gclid=CLaVoIr-oKsCFYh_6wodyVEXfA
7. Circular Dichroism spectroscopy: http://www.biocompare.com/ProductDetails/665635/FVS-6000-
Vibrational-CD-Spectrometer.html
6 Centrifugation
6.1 INTRODUCTION
Centrifugation is one of the most important and widely applied research techniques in biochemistry,
cellular and molecular biology, and medicine. Current research and clinical applications rely on the
isolation of cells, subcellular organelles, and macromolecules, often in high yields.
A centrifuge uses centrifugal force (g-force) to isolate suspended particles from their surround-
ing medium on either a batch or a continuous-flow basis. There are many applications for centrifu-
gation, including the sedimentation of cells and viruses; separation of subcellular organelles; and
isolation of macromolecules such as DNA, RNA, proteins, and lipids.
6.1.1 Increasing the Effect of Gravity: The Centrifuge

Many particles or cells in a liquid suspension, given time, eventually settle at the bottom of a con-
tainer due to gravity (1 g). However, the length of time required for such separations is impracti-
cal. Other particles, which are extremely small in size, do not separate at all in a solution unless
subjected to a high centrifugal force. When a suspension is rotated at a certain speed or revolutions
per minute (RPM), centrifugal force causes the particles to move radially away from the axis of
rotation. The force on the particles (compared to gravity) is called relative centrifugal force (RCF).
For example, an RCF of 500 g indicates that the centrifugal force applied is 500 times greater than
Earth’s gravitational force. Table 6.1 illustrates common centrifuge classes and their applications.
6.2 PRINCIPLE OF CENTRIFUGATION

A centrifuge is a device for whirling an object with a high angular velocity. The consequent large
acceleration ϖ2r is equivalent to increasing the value of g. The acceleration due to gravity and such
processes as sedimentation (settling of particles or precipitates out of a solution) can be greatly
accelerated in this way. Hence, ϖ2r is expressed as “number times g” or relative centrifugal field
(RCF). This is the ratio of the weight of the particle in an applied centrifugal field to the weight of
the same particle when acted upon by gravity alone. The force acting on a body moving in a circular
path can be broken down into two components: (1) normal and (2) tangential to the path. Centrifugal
force (F) is the force on a rotating object, which acts tangentially outward, therefore,
F=M⋅ 2
r
where
M = mass of the particle
ϖ2 = angular acceleration of the particle moving in a circle of the square of angular velocity
r = the radial distance of the particle from the axis of rotation.
6.3 TYPES OF CENTRIFUGES

The different types of centrifuges are as follows:
1. Small benchtop centrifuges have a maximum rate of 3000 g–7000 g. They are used to
precipitate coarse granules, yeast cells, and so on (Figure 6.1).
2. Large-capacity refrigerated centrifuges have a maximum rate of 6500 g with a capacity of
100 cc. They are refrigerated to control the temperature.
163
TABLE 6.1
Classes of Centrifuges and Their Applications
Centrifuge Classes
Low Speed High Speed Ultra/Micro-Ultra
Maximum speed (rpm × 103) 10 28 100/150
Maximum RCF (×103) 7 100 800/900
Pelleting applications Yes Yes (Yes)
(bacteria)
Animal and plant cells Yes Yes (Yes)
Nuclei Yes Yes (Yes)
Precipitates Some Most (Yes)
Membrane fractions Some Some Yes
Ribosomes/polysomes – – Yes
Macromolecules – – Yes
Viruses – Most Yes
FIGURE 6.1 Small benchtop centrifuges.
3. High-speed refrigerated centrifuges have a maximum rate of 60,000 g; are refrigerated;

and are used to sediment small microorganisms, cellular debris, and large cellular organ-
elles (Figure 6.2).
4. Continuous-flow centrifuges are unlike other centrifuges where tubes are attached to the
rotor; in continuous-flow centrifuges, the rotor itself is tubular. Particles are sedimented
against the wall of the centrifuge and supernatant continuously flows out; they are used in
the large-scale harvesting of bacteria.
5. A preparative ultracentrifuge has a maximum rate of 600,000 g. The rotor chamber is
refrigerated, sealed, and evacuated to minimize heat production due to friction between air
and the spinning rotor.
Centrifugation 165
FIGURE 6.2 A large-capacity high centrifuge.
FIGURE 6.3 An ultracentrifuge.
6. In an analytical ultracentrifuge, a sample being spun can be monitored in real time through
an optical detection system, using ultraviolet light absorption and/or interference optical
refractive index sensitive system known as the (a) Schlieren optical system (Figure 6.3) or
the Rayleigh interferometric system (Figure 6.4). This allows the operator to observe the
evolution of the sample concentration versus the axis of rotation profile as a result of the
Solvent Boundary
Meniscus Solution
Air
“Bottom” of cell
“Top” of cell
Centrifugal
force
Center section of
ultracentrifuge cell
showing sector-shaped
cavity containing
sample material
Armored casing
Before After
10,000 rpm
Supernatant
Pellet
5 cm
Axis
Rapidly rotating rotor Centrifugal force
FIGURE 6.4 A rotor.
applied centrifugal field. With modern instrumentation, these observations are electroni-
cally digitized and stored for further mathematical analysis. Two kinds of experiments are
commonly performed on these instruments: (1) sedimentation velocity experiments and
(2) sedimentation equilibrium experiments. An analytical ultracentrifuge has a maximum
rate of 500,000 g.
In the Schlieren optical system, when light passes through different density zones it is refracted at
the boundary between the zones. In the sedimenting material in the analytical cell, a boundary is
formed between the solvent, which has been cleared of particles, and the remainder of the solution
containing the sedimenting material. Light is refracted at the boundary. The Schlieren system plots
refractive index gradient against distance along the analytical cell. Concentration can be deter-
mined from the area of the peak.
A centrifuge is a device for whirling an object with a high angular velocity. The consequent large
acceleration (ϖ2r) is equivalent to increasing the value of g, the acceleration due to gravity, and
processes such as sedimentation (settling of particles or precipitates out of a solution) can be greatly
accelerated in this way. Hence, ϖ2r is expressed as the “number times g,” or relative centrifugal
force (RCF). This is the ratio of the weight of a particle in an applied centrifugal field to the weight
of the same particle when acted on by gravity alone.
In an applied centrifugal field, the rate of sedimentation of a particle suspended in solution
depends on the following factors:
1. Density and size of the particle

2. Density and viscosity of the medium in which the particle is suspended
3. Extent to which the particle’s shape deviates from spherical
Centrifugation 167
1. Density and size of particle: The net force on a particle suspended in a medium in a cen-
trifugal field (F) is
F = M ϖ2 r
4 3
or F =
3
πr rp (ρp − ρm ) ϖ2 r (since M = volume × density )
where
ρp = density of particle
ρm = density of medium
r = radial distance of particle from axis of rotation
rp = radius of particle
ϖ2 = angular velocity
2. Density and viscosity of the medium: Due to viscosity of the medium, the frictional force
(fo) on a spherical particle, opposes motion through the medium.
fo = 6π η rp ν
where
η = coefficient of viscosity
ν = velocity of the particle
rp = radial distance from axis of rotation to the bottom of the tube
The particle continues to accelerate until
F = fo
and in this condition
4 3
or F = πrp (ρp − ρm )ϖ2 r = 6π η rp ν
3
dr 2rp3
or v = = (ρp − ρm )ω 2 r (6.1)
dt 9 η
9η lnr
or t = = b (6.2)
2rp2 (ρp − ρm )ω 2 r rt
where
rt = radial distance from axis of rotation to meniscus of liquid medium
r b = radial distance from axis of rotation to the bottom of the tube
t = time in seconds
Extent to which the particle’s shape deviates from spherical: The ratio of functional force f on a
nonspherical particle to the functional force fo on a spherical particle is equal to one (f/fo = l), whereas
for a nonspherical particle the ratio is greater than one, therefore, the velocity of sedimentation v is
2rp2 (ρp − ρm )ω 2 r lnrb

or, t = =
9 η ( f /fo ) rt
Thus, nonspherical particles sediment at a slower rate. Centrifugation is based on the principle that
solution, occurs in an applied centrifugal field due to differences in shapes and masses of particle.
If the composition of the suspending medium is defined, the rate of sedimentation is propor-
tional to ϖ2r and Equation 6.1 simplifies to v = sϖ2r, where s is the sedimentation coefficient.
Sedimentation coefficients are usually very small for biological particles; hence, a basic unit of 10−13
seconds is taken for convenience. This is called the “Svedberg unit” (S). Thus, a sedimentation coef-
ficient of 15 × 10−13 seconds is represented by 15S.
6.4 TYPES OF CENTRIFUGAL SEPARATIONS

6.4.1 Differential Centrifugation
Separation is achieved primarily based on the size of the particles in differential centrifugation. This
type of separation is commonly used in simple pelleting and in obtaining partially pure preparations
of subcellular organelles and macromolecules. For the study of subcellular organelles, sample tis-
sue or cells are first disrupted to release their internal contents. This crude disrupted cell mixture is
referred to as a homogenate. During centrifugation of a cell homogenate, larger particles sediment
faster than smaller ones, which provides the basis for obtaining crude organelle fractions by dif-
ferential centrifugation. A cell homogenate can be centrifuged at a series of progressively higher
g-forces and times to generate pellets of partially purified organelles (Figure 6.4).
When a cell homogenate is centrifuged at 1000 g for 10 minutes, unbroken cells and heavy nuclei
pellet to the bottom of the tube. The supernatant can be further centrifuged at 10,000 g for 20 minutes
to pellet subcellular organelles of intermediate velocities such as mitochondria, lysosomes, and micro-
bodies. Some of these sedimenting organelles can be obtained with partial purity and are typically con-
taminated with other particles. The repeated washing of the pellets by resuspending them in isotonic
solvents and repelleting may result in the removal of contaminants that are small in size (Figure 6.5).
Partial purification of organelles by differential centrifugation serves as the preliminary step for fur-
ther purification using other types of centrifugal separation methods (e.g., density gradient separation).
First spin Second spin Third spin
Starting Pellet 1 Pellet 2 Pellet 3

suspension
Wash Wash
Pellet 1 Pellet 2
FIGURE 6.5 Demonstration of sedimentation and pelleting by centrifugation.

Centrifugation 169
6.4.2 Density Gradient Centrifugation

Density gradient centrifugation is the preferred method for purifying subcellular organelles and
macromolecules. Density gradients can be generated by placing layer after layer of gradient media
(Table 6.2) such as sucrose in a tube with the heaviest layer at the bottom and the lightest at the top
in either a discontinuous or continuous mode. The cell fraction to be separated is placed on top of
the layer and centrifuged. Density gradient separation can be classified into two categories: (1) rate-
zonal (size) separation and (2) isopycnic (density) separation.
1. Rate-zonal (size) separation: Rate-zonal separation takes advantage of particle size and
mass instead of particle density for sedimentation. Figure 6.5 illustrates a rate-zonal sepa-
ration process and the criteria for successful rate-zonal separation. Examples of common
applications include separation of cellular organelles, such as endosomes, and separation
of proteins, such as antibodies. Antibody classes have very similar densities but different
masses. Thus, separation based on mass separates the different classes, whereas separation
based on density is not able to resolve these antibody classes. Certain types of rotors are
more applicable for this type of separation than others (see Section 6.5 on rotor categories
and Table 6.3).
TABLE 6.2
Application of Density Gradient Media for Isopycnic Separation
Gradient Media Cells Viruses Organelles Nucleoproteins Macromolecules
Sugars (e.g., sucrose) + +++ +++ + –
Polysaccharides (e.g., Ficoll) ++ ++ ++ – –
Colloidal silica (e.g., Percoll) +++ + +++ – –
Iodinated media (e.g., ++++ ++ ++++ +++ +
Nycodenz)
Alkali metal salts (e.g., CsCl) – ++ – ++ ++++
Notes: + + + + denotes excellent, + + + denotes good, + + denotes good for some applications, + denotes limited
use, and − denotes unsatisfactory. Other rotors include continuous-flow and elutriation rotors.
TABLE 6.3
Types of Rotors and Their Applications
Rate-Zonal
Type of Rotor Pelleting Sedimentation Isopycnic
Fixed-angle Excellent Limited Variablea
Swinging-bucket Inefficient Good Goodb
Vertical NS Good Excellent
Zonal NS Excellent Good
Note: NS = Not suitable.

a Good for macromolecules, and poor for cells and organelles.
b Good for cells and organelles, caution needed if used with CsCl.
Sample zone
1.1 g/mL
1.2 g/mL
1.3 g/mL
1.4 g/mL
1.5 g/mL
1.6 g/mL
1.7 g/mL
Sample before Sample after

centrifugation centrifugation
FIGURE 6.6 Isopycnic separation.
The criteria for successful rate-zonal centrifugation are as follows:

• Density of the sample solution must be less than that of the lowest-density portion
of the gradient.
• Density of the sample particle must be greater than that of the highest-density por-
tion of the gradient.
• Path length of the gradient must be sufficient for the separation to occur.
• Time is important. If you perform runs that are too long, particles may all pellet at
the bottom of the tube.
2. Isopycnic separation: In this type of separation, a particle of a particular density will sink
during centrifugation until a position is reached where the density of the surrounding
solution is exactly the same as the density of the particle. Once this quasi-equilibrium is
reached, the length of centrifugation does not have any influence on the migration of the
particle. A common example for this method is the separation of nucleic acids in a CsCl
gradient (Figure 6.6). A variety of gradient media can be used for isopycnic separations;
their biological applications are listed in Table 6.2.
The criteria for successful isopycnic separation are as follows:
• Density of the sample particle must fall within the limits of the gradient densities
(Figure 6.7).
• Any gradient length is acceptable.
• The run time must be sufficient for particles to band at their isopycnic point.
Excessive run times have no adverse effect.
6.5 ROTOR CATEGORIES

Rotors can be broadly classified into three common categories: (1) swinging-bucket rotors, (2) fixed-
angle rotors, and (3) vertical rotors (Figure 6.8; Table 6.3). Note that each type of rotor has strengths
and limitations depending on the type of separation.
Centrifugation 171
Sample before Sample after

centrifugation centrifugation
FIGURE 6.7 Rate-zonal (size) separation.
(a)
Rmin
(b)
Rmin
(c)
Rmin
Rmax
FIGURE 6.8 Figure showing rotor types: (a) swinging-bucket, (b) fixed-angle, and (c) vertical rotors.
In swinging-bucket rotors, the sample tubes are loaded into individual buckets that hang verti-
cally while the rotor is at rest. When the rotor begins to rotate, the buckets swing out to a horizontal
position (Figure 6.8). This rotor is particularly useful when samples are to be resolved in density
gradients. The longer path length permits a better separation of individual particle types from a
mixture. However, this rotor is relatively inefficient for pelleting. Also, care must be taken to avoid
“point loads” caused by spinning CsCl or other dense gradient materials that can precipitate.
In fixed-angle rotors, the sample tubes are held fixed at the angle of the rotor cavity. When the
rotor begins to rotate, the solution in the tubes reorients (Figure 6.8). This rotor type is most com-
monly used for pelleting applications. Examples include pelleting bacteria, yeast, and other mam-
malian cells. It is also useful for isopycnic separations of macromolecules such as nucleic acids.
In vertical rotors, sample tubes are held in the vertical position during rotation. This type of rotor
is not suitable for pelleting applications but is most efficient for isopycnic (density) separations due
to the short path length. Applications include plasmid DNA, RNA, and lipoprotein isolations.
6.6 SELECTION OF CENTRIFUGE TUBES

Tables 6.4 and 6.5 illustrate properties of centrifuge tubes and the proper rotors in which they
should be used. Selection of the appropriate centrifuge tube
• Prevents sample leakage or loss

• Ensures chemical compatibility
• Allows easy sample recovery
Major factors considered in the selection of a tube (plastic) material are as follows:
• Clarity.
• Chemical resistance.
• Sealing mechanism (if needed).
• Check product guide pages or tube packaging for notes on recommended sample volume
and maximum speed.
• Always run thin-walled, sealed tubes full in a fixed-angle or vertical rotor with open top
tubes with multiple sealing assemblies and reseal tubes.
• Autoclave tubes only if it is absolutely necessary and only at 121°C for 15 minutes.
TABLE 6.4
Chemical Compatibility of Popular Tube Materials
Tube Plastic Type Clarity Chemical Resistance
Polypropylene (PP) Opaque Good
Polyallomer (PA) Opaque Good
Polycarbonate (PC) Clear Poor
Polyethylene terephthalate (PET) Clear Poor
TABLE 6.5
Tube Type and Rotor Compatibility
Rotor Type
Tube Type Fixed Angle Swinging Bucket Vertical
Thin wall, open top No Yes No
Thick wall, open top Yes Yes No
Thin wall, sealed Yes Some tube types Yes
Oak ridge Yes No No
Centrifugation 173
• Avoid cleaning plastic tubes in automated dishwashers or glassware washers, which may
produce excessively hot temperatures.
• We recommend that you clean tubes with a mild laboratory detergent in warm water, rinse,
and then air dry.
• Tube must be carefully matched with rotor type to prevent sample loss and/or failure, as
illustrated in Table 6.5, and to prolong tube life and avoid tube breakage or collapse.
6.7 COMMON CENTRIFUGATION VOCABULARY AND FORMULAS

This section discusses common centrifugation vocabulary and formulas.
• Pellet: Hard-packed concentration of particles in a tube or rotor after centrifugation.

• Supernatant: The clarified liquid above the pellet.
• Adapter: A device used to fit smaller tubes or centrifugal devices in rotor cavities.
• RPM: Revolutions per minute (speed).
• Rmax: Maximum radius from the axis of rotation in centimeters.
• Rmin: Minimum radius from the axis of rotation in centimeters.
• RCF: Relative centrifugal force; 1 RCF = 11.17 × Rmax (RPM/1000)2.
• K-factor: Pelleting efficiency of a rotor. The smaller the K-factor the better the pelleting efficiency:
2.53 × 1011 ln( Rmax / Rmin )

K=
(RPM)2
• S-value: The sedimentation coefficient is a number that gives information about the molec-
ular weight and shape of a particle. The S-value is expressed in Svedberg units. The larger
the S-value the faster the particle separates. (For more information on sedimentation coef-
ficients, refer to the suggested readings section of this chapter.)
• Pelleting time: Time taken to pellet a given particle. T = K/s, where T is pellet time in
hours, K is the K-factor of the rotor, and s is the sedimentation coefficient.
• Rotor conversion formula: If the time to pellet a sample in an “old” rotor is known, one
can determine the time it takes to pellet the same sample in a “new” rotor. The formula for
this determination is as follows:
T1 T K1
= 2 → T1 = T2
K1 K 2 K2
where
T1 = time to pellet in the new rotor
T2 = time to pellet in the old rotor
K1 = K-factor of the new rotor
K2 = K-factor of the old rotor
An example of a rotor conversion is as follows. The old rotor used is a Beckman® JA-10
and the new rotor used is a Sorvall® SLC-1500:
T2 = 20 minutes, K ∂ = 3610; T1 = 10 minutes, K1 = 1676
It is noted the old pelleting time is 20 minutes and new pelleting time is 9.2 minutes.
6.8 ANALYTICAL ULTRACENTRIFUGE

The ultracentrifuge is a centrifuge optimized for spinning a rotor at very high speeds; it is capable
of generating accelerations as high as 1,000,000 g (9,800 km/s²). There are two kinds of ultracentri-
fuges: (1) preparative and (2) analytical. Both classes of instruments find important uses in molecu-
lar biology, biochemistry, and polymer science.
The analytical ultracentrifuge was first developed by Svedberg and associates in the 1920s. This
tool proved invaluable in the study of macromolecules and provided some of the first evidence
that proteins are indeed macromolecules comprising a huge number of atoms linked by covalent
bonds. Since its creation, the ultracentrifuge has helped in further understanding the behavior of
macromolecules.
6.8.1 Theory of Ultracentrifugation

A particle suspended in a solvent that is subjected to a gravitational field experiences several forces.
We can draw the following diagram describing three forces acting on such a solute particle:
Ff
Fb
Constant velocity = u
m
Fs
The sedimenting, or gravitational, force, Fs, is proportional to the mass of the particle and accel-
eration. For a particle subjected to a rotation, the acceleration is determined by the distance of the
particle from the axis of rotation, r, and the square of the angular velocity, w (in radians per second),
such that
M 2
Fs = mω 2 r = ω r
N
where m is the mass of the single particle in grams, M is the molar weight of the solute in grams per
mole, and N is Avogadro’s number.
The buoyant force, Fb, from Archimedes’ principle, is equal to the weight of the fluid displaced
by the particle:
Fb = − m0 ω 2 r
where m 0 is the mass of fluid displaced by the particle:
M
m0 = m νρ = νρ
N
Here, νρ is the volume in milliliters occupied by each gram of solute in the solution and r is the
density of the solvent in grams per milliliter. If the density of a particle is greater than that of the
Centrifugation 175
solvent, the particle will sediment or sink. As the particle begins to move along a radial path toward
the bottom of the cell, its velocity, u, will increase because of increasing radial resistance. Since the
particle is moving through a viscous fluid, it will experience a frictional drag, Ff, which is propor-
tional to the velocity:
Ff = − fu
where f is the coefficient of friction, which depends on the size and shape of the particle.
Within a very short time (on the order of 10−6 second), the forces come into balance. Then we can
write the following force balance equation:
Fs + Fb + Ff = 0
M 2 M
ω r− vρω 2 r − fu = 0
N N
Rearranging, we get the following equation:
M
(1 − vρ)ω 2 r − fu = 0
N
Collecting the terms that relate to particle size on one side and terms that relate to experimental
conditions on the other side of the equation, we can write
M (1 − vρ) u
= 2 ≡s
Nf ω r
The term u/w2r is defined as, the velocity of the particle per unit gravitational acceleration, as the
sedimentation coefficient. This coefficient depends on the properties of the particle and, in particu-
lar, it is proportional to the buoyant effective molecular weight of the particle. Also, it is indepen-
dent of the operating conditions. Therefore, molecules with different molecular weights or different
shapes and sizes, will, in general, move with different velocities in a given centrifugal field, that is,
they will have different sedimentation coefficients.
6.8.2 Analytical Ultracentrifugation

An analytical ultracentrifuge spins a rotor at an accurately controlled speed and temperature. The
concentration distribution of the sample is determined at known times using absorbance measure-
ments. The concentration, c, is determined for solutes obeying the Beer–Lambert law:
A = ε⋅c⋅l
where the absorbance of the sample, A, is measured at a given wavelength, ε, knowing the fixed
position in the cell, l.
Figure 6.9 displays a schematic diagram of the Beckman Optima XL-A absorbance system.
A high-intensity xenon flask lamp allows the use of wavelengths between 190 and 800 nm. The
lamp is fired briefly as a selected sector passes the detector.
Sedimentation velocity (SV) cells are cylindrical and have double-sector centerpieces (Figure 6.10
is a top-down view of the cylindrical centerpiece). One sector is for loading samples, and the other is
the reference sector and contains the solvent. The reference sector is filled slightly more than the sam-
ple sector so that the reference meniscus does not obscure the sample profile (Figures 6.11 and 6.12).
Reference
Top
Toroidal view
diffraction
grating Sample
Incident
light
detector
Reflector
Sample/reference
cell assembly
Rotor
Imaging system for

radial scanning
Slit (2 nm)
Aperture
Xenon
flash lamp
Photomultiplier tube
FIGURE 6.9 Schematic diagram of the Beckman Optima XL-A absorbance system.
Sample Reference
FIGURE 6.10 Top-down view of the cylindrical centerpiece.
For an SV experiment, an initially uniform solution is placed in a cell and a sufficiently high
angular velocity is applied to cause rapid sedimentation of the solute toward the cell bottom. As a
result, there is a depletion of solute near the meniscus, causing a characteristic spectrum as shown
in Figure 6.13. A sharp boundary occurs between the depleted region and the sedimenting solute
(the plateau).
Although the velocity of individual particles in SV experiments cannot be resolved, the rate of
movement of the boundary region can be measured. From this, the sedimentation coefficient, s,
Centrifugation 177
Mirror Light path

Detector
Lens
Boundary
Ultracentrifuge Air Solvent Solution
Motor
Rotor
Cooling
Anmored
chamber Sample cell
Motor Vacuum
pump
UV light
source
Schlieren optics
(schematic)
Rotor
Balance cell Sample cell
goes here
Centrifugal force
Graph of solute concentration Schlieren optics record boundary

in terms of concentration gradient
FIGURE 6.11 Rotor movement in an analytical centrifuge.
Turbine Oil seal
Air inlet
Air bearing
Shaft
Oil seal
Rotor
Vacuum
chamber
Sample Reference
FIGURE 6.12 Examination of SV.

Boundry
Solvent Plateau
region
Absorbance
meniscus
Sample
meniscus
0.4 0
Top Bottom
A280
0.2
Sanole
Reference
Radius ω2r
FIGURE 6.13 Determination of SV. “A” stands for absorbance at 280 nm.
can be determined. Remember that s depends directly on the mass of solute particles and inversely
on the frictional coefficient, which is a measure of the size of the solute particles (Figure 6.10).
6.8.3 Examination of SV
Sedimentation equilibrium (SE) experiments have a lower rotor speed than SV experiments. Solute
particles do not pellet at the bottom of the cell; instead, the process of diffusion opposes the pro-
cess of sedimentation until, after a period of time, the two opposing forces reach equilibrium and
the apparent concentration profile does not change. At equilibrium, the concentration of the solute
increases exponentially toward the cell bottom. Each column displays a different absorbance profile,
because the concentrations of sample are varied in each (Figure 6.14).
There are six columns in the SE experiment. One row is the sample row, and the other is the refer-
ence row containing only the solvent (specifically, the sample buffer). As in the SE experiment, the
reference columns are filled more than the sample columns. In the solvent columns concentrations
are varied, usually 0.25, 0.5, and 0.8 optical density (OD) (280), or the same fraction of absorbance
is obtained at any selected wavelength where that wavelength is monitored by analytical ultracen-
trifugation (AU).
Several scans are taken at a given rotor speed to try to ascertain definitely that equilibrium has
been reached (if it has been reached in scan 1 and you take scan 2 an hour later, both scans should
look the same).
6.8.4 Examination of Sample Purity

Sample heterogeneity can be examined by both SE and SV methods. In SE experiments, each
species of a heterogeneous solution will be distributed at SE such that higher-MW species will be
distributed toward the cell bottom and lower-MW species will dominate the distribution at the top
of the cell.
SV techniques assess sample heterogeneity through the detection of sedimentation boundaries.
The general rule (although stated in an oversimplified manner) is that a single sedimentation bound-
ary exists in a homogeneous solution, whereas multiple boundaries indicate heterogeneity.
Centrifugation 179
1.380
24,000 rpm
20°C
18 hours
Absorbance (278 nm)
Data
from
within the
solution column
–0.305
6.799 Radius (cm) 7.199
Solution
sector
Solvent
(reference)
sector
FIGURE 6.14 Autoscanning of absorbance during AU.
6.8.5 Determination of Molecular Weight

AU techniques for MW measurement are superior because they work with small sample sizes. The
method is applicable to MW ranges from 100 to 1,000,000 (i.e., proteins, nucleic acids, and carbohydrates
work with AU methods). AU techniques do not rely on assumptions or calibration; they work on any
substance whose absorbance differs from that of the solvent. A final advantage is the fact that experi-
mental design is simple in comparison with some other techniques of MW determination.
The molecular weights of biological materials can be determined using the analytical centrifuge.
The molecular weight, M, is related to the sedimentation coefficient, s, of a molecule by the follow-
ing equation:
RTs
M=
D (1 – vρ)
where
D = diffusion coefficient of the molecule
V = partial specific volume of the molecule (volume increases when l g of solute is added to
an infinite volume of solution)
ρ = density of solvent at 20°C
8.0
7.5
7.0
In cr
6.5
6.0
5.5
5.0
49.0 50.0
r 2 (cm2)
FIGURE 6.15 Sedimentation equilibrium for bovine serum albumin in 0.1 M NaCl at 27,700 rpm and 20°C.
The sample containing the molecule is centrifuged at high speeds in an ultracentrifuge. The
molecules move radially outward, creating a distinct boundary between the solvent containing the
molecules and the solvent without the molecules. This boundary moves radially outward depending
on the sedimentation coefficient of the molecule. The movement is recorded by either Schlieren or
Rayleigh optical system; thereby, D is found. Since
v = s 2r
v
s =
2r
Here, ϖ2r and v are known values; hence, s can be found and used to calculate M.
As a better alternative, equilibrium sedimentation can be used to determine the molecular weight.
Centrifugation is continued until the solute particles acquire a static position in the tube. This hap-
pens when there is equilibrium between sedimentation due to diffusion. Using the concentration
gradient, the molecular weight (M) can be calculated from the following formula:
2 RT c 1
M= In r ⋅ 2
(1 − νρ)ω 2 cα r − a 2
where, RT is the gas constant at temperature T, νρ is patial specific volume, cr is the concentration
of the solute at a distance r from the axis of rotation and cα is the distance of the meniscus from the
axis of rotation. Hence, a plot of In (normal log) cr versus r 2 is a straight line from whose slope M
can be calculated (Figure 6.15).
6.8.6 Detection of Conformational Changes

Since the rate of sedimentation varies with not only the size but also the shape of a molecule,
changes in conformation, for example, change of dsDNA to ssDNA, cause the molecule to band at
different isodensity positions, thereby revealing the change in conformations.
Centrifugation 181
Assembly state Kinetics
Affinity Thermodynamics
FIGURE 6.16 Demonstration of conformational changes of protein due to association and affinity binding.
6.8.7 Analysis of Associating Systems

Sedimentation analysis can yield valuable information relating to changes in molecular weight when
a molecule associates to form more complex structures (Figure 6.16). Note that SE experiments can
yield the following:
• The monomer MW
• The complex MW
• The stoichiometry of heterogeneous components
• The strength of interactions between components
• The thermodynamic nonideality of the solution
6.8.8 Ligand Binding

Absorbance measurement is well suited for the study of ligand binding because since the technique
can distinguish ligands from acceptors. Ligands and acceptors can be labeled with a chromophore,
provided that the modification does not alter the binding. When a ligand and an acceptor differ
greatly in sedimentation coefficient, AU analysis of ligand/acceptor binding interactions is a simple
matter.
6.8.9 Cell Fractionation and Metabolic Studies

The metabolic function of individual cell organelles and soluble components within the cell can
be studied by separating the cell components from each other by centrifugation. When cells are
subjected to high shear forces, the cell membrane ruptures and its contents are released into the
medium. This is usually done by grinding animal or plant tissue in a pestle and mortar, and the
process is called homogenization. Chloroplast material, blood cells, unicellular organisms, plant
and animal tissue homogenates can also be ruptured in a pressure cell and sonication. Pressure
cells, for example the French pressure cell, use hydraulic pressure controlled by a motor-driven
pump to produce shear forces. The sonicator uses ultrasonic waves to produce cavitational forces
within the suspending medium, which cause the cells to burst.
The homogenate is then suspended in a medium, which should be cheap, uncharged, and
metabolically inert. Following this, either density gradient centrifugation or differential cen-
trifugation can be used to separate the cell components. As described in Section 6.4.2, the cell
components band at the isodensity positions. In differential centrifugation, the homogenate is
separated into a number of fractions by centrifuging at various g values. The cell components
sediment to form pellets at different rates according to their size and density. For example, rat
liver homogenate can be separated into different components by subjecting it to differential
centrifugation.
TABLE 6.6
Application of Centrifugation for Different Cell Organelles
Centrifugation Time
Conditions g Values (minutes) Major Components in Fraction
500 5 Nuclei, whole cells
8,000 10 Mitochondria, some lysosomes
15,000 10 Mitochondria, lysosomes
100,000 60 Microsomes (membrane fragments, endoplasmic
reticulum), ribosomes, soluble components of the cell
Final supernatant
Certain tissues, for example pig brain tissues, are very heterogeneous in nature; thus, differ-
ential centrifugation of pig brain tissues gives rise to fractions with different compositions than
those of rat liver (Table 6.6). Each fraction contains a very complex mixture of components, and
density gradient centrifugation is required to purify them further.
Experiment: Isolation of Chloroplasts by Differential Centrifugation

Requirements
Fresh spinach; clean, sharp sand; 50 mL 0.5 M sucrose (17% w/v); cheesecloth; 12 × 12 in ice; ice bath;
25 mL graduated cylinder; mortar and pestle (or blender); table top clinical centrifuge; glass filter fun-
nel; two 16 × 150 mm test tubes in rack; three 13 × 100 mm test tubes in rack; plastic-capped 15 mL
centrifuge tube; double pan balance; glass stirring rods.
Procedure
1. Grind 8 g of deveined spinach with ½ teaspoon clean, sharp sand in a mortar and pestle to a
paste.
2. Suspend in 0.5 M sucrose. Measure out 16 mL ice-cold 0.5 M sucrose solution in a 25 mL
graduated cylinder. Add in 3–4 mL increments; grind to a smooth pulp with each addition
(a blender may be used for volumes greater than 100 mL).
3. Filter the solution. Homogenate the solution through about eight layers of clean cheesecloth
in a glass funnel into an ice-cold 16 × 150 mm test tube.
4. Pour the filtrate back into the 25 mL cylinder and record the volume. Save approximately
0.5 mL of the filtrate (F1) in a labeled 13 × 100 mm test tube to examine at 400× under a
microscope to determine the composition, and illustrate the observations in a notebook. Note
the appearance of components and degree of heterogeneity (label cells, ghosts, chloroplasts,
mitochondria, and debris).
5. Centrifuge at low speed. Prepare a balance tube against the filtrate in a 16 × 150 tube and spin
at 50 g for 10 minutes (speed 2 on the clinical centrifuge).
6. Decant the top 10 mL into a clean cold centrifuge tube, discard sediment, and record the vol-
ume. Save ~0.5 mL supernatant (S1) to examine under the microscope in order to determine
composition; illustrate and label as in step 2.
7. Centrifuge the supernatant from step 3 opposite a carefully balanced tube at 1000 g for
10 minutes (speed 7) to precipitate chloroplasts. How does the supernatant appear? Does it
appear as a precipitate? Carefully decant all the supernatant into the 16 × 150 mm tube, but
save the pellet. Discard the supernatant if you have a significant pellet (you will lose some soft
pellet, but there is no need to worry).
8. Resuspend the pellet from step 4 to one-tenth the volume of the step 2 filtrate in ice-cold
0.5 M sucrose with a clean, ice-cold stirring rod. Record the final volume. Keep on ice at all
times. Examine the suspended organelles (SOs) under the microscope to determine composi-
tion; illustrate as in step 2.
Centrifugation 183
Experiment: Isolation of Plasmid DNA by Centrifugation

The isolation of plasmid DNA from E. coli is a common routine in research laboratories. You will
perform a widely practiced procedure that involves alkaline lysis of cells. This protocol, which is often
referred to as plasmid “miniprep,” yields fairly clean DNA quickly and easily.
Procedure
1. Fill a microcentrifuge tube with saturated bacterial culture grown in LB broth + antibiotic.
Spin the tube in a microcentrifuge for 1 minute, and make sure the tubes are balanced in the
microcentrifuge. Dump the supernatant and drain the tube briefly on a paper towel.
2. Repeat step 1 of the first experiment in the same tube, filling the tube again with more
bacterial culture. The purpose of this step is to increase the starting volume of cells so that
more plasmid DNA can be isolated per preparation. Spin the tube in a microcentrifuge for
1 m inute. Pour off the supernatant and drain the tube on a paper towel.
3. Add 0.2 mL ice-cold solution 1 to a cell pellet and resuspend cells as much as possible
using a disposable transfer pipette. Solution 1 contains glucose, Tris, and ethylene-diamine-
tetraacetic acid (EDTA). Glucose is added to increase the osmotic pressure outside the cells.
Tris is a buffering agent used to maintain a constant pH of 8.0. The EDTA protects the DNA
from degradative enzymes (called DNAses); the EDTA binds divalent cations that are neces-
sary for DNAse activity.
4. Add 0.4 mL solution 2, cap the tubes, and shake five time gently by inverting to mix uni-
formly. Let the tubes sit at room temperature for 5 minutes. Solution 2 contains NaOH and
sodium dodecyl sulfate (SDS; a detergent). The alkaline mixture ruptures the cells, and the
detergent breaks apart the lipid membrane and solubilizes cellular proteins. The NaOH also
denatures the DNA into single strands.
5. Add 0.3 mL ice-cold solution 3, cap the tubes, and invert five times gently. Incubate tubes on
ice for 10 minutes. Solution 3 contains a mixture of acetic acid and potassium acetate. The
acetic acid neutralizes the pH, allowing the DNA strands to renature. The potassium acetate
also precipitates the SDS from solution, along with the cellular debris. The E. coli chromo-
somal DNA, a partially renatured tangle at this step, is also trapped in the precipitate. The
plasmid DNA remains in the solution.
6. Centrifuge the tubes for 5 minutes. Transfer the supernatant to a fresh microcentrifuge tube
using a clean disposable transfer pipette. Try to avoid taking any white precipitate during
the transfer. It is better to leave a little supernatant behind to avoid accidentally taking the
precipitate. This fractionation step separates plasmid DNA from the cellular debris and chro-
mosomal DNA in the pellet.
7. Fill the remainder of the centrifuge tube with isopropanol. Let the tube sit at room tem-
perature for 2 minutes. Isopropanol effectively precipitates nucleic acids, but it is much
less effective with proteins. A quick precipitation can therefore purify DNA from protein
contaminants.
8. Centrifuge the tubes for 5 minutes. A milky pellet should form at the bottom of the tube. Pour
off the supernatant without dumping out the pellet. Drain the tube on a paper towel. This
fractionation step further purifies the plasmid DNA from contaminants. Cap the tubes and
store them in a freezer.
9. Add 1 mL of ice-cold 70% ethanol. Cap the tube and mix by inverting it several times. Spin
the tubes for 1 minute. Pour off the supernatant (one must be careful not to dump out the pel-
let) and drain the tube on a paper towel. Ethanol helps to remove the remaining salts and SDS
from the preparation.
10. Allow the tube to dry for about 5 minutes. Add 50 μL Tris EDTA buffer (TE) to the tube. The
DNA is ready for use and can be stored indefinitely in the freezer.
Solutions
Solution 1:
50 mM glucose per 500 mL
25 mM Tris–HCl pH 8.0 9 mL 50% glucose
10 mM EDTA pH 8.0 12.5 mL 1 M Tris–HCl pH 8.0

Add H2O to 500 mL 10 mL 0.5 M EDTA pH 8.0
Solution 2:
1% SDS per 500 mL
0.2 N NaOH 50 mL 10% SDS
Add H2O to 500 mL 100 mL 1N NaOH
Solution 3:
3 M K + per 500 mL
5 M acetate 300 mL 5 M potassium acetate
Add H2O to 500 mL TE 57.5 mL glacial acetic acid
10 mM Tris–HCl pH 8.0 per 100 mL
1 mM EDTA 0.5 mL 1 mL 1 M Tris–HCl pH 8.0
Add H2O to 100 mL 0.5 M EDTA pH 8.0
Optional: RNAse can be added to TE at a final concentration of 20 μg/mL.
SUGGESTED READING
Birnie, G. D., and D. Rickwood. 1978. Centrifugation Separations in Molecular and Cell Biology. London:
Butterworth.
Ford, T. C., and J. M. Graham. 1991. An Introduction to Centrifugation. Oxford: Bios Scientific.
Griffith, O. M. 1983. Techniques in Preparative, Zonal and Continuous flow Ultracentrifugation, 4th ed. Palo
Alto, CA: Beckman instruments Inc.
Ralston, G. 1993. Introduction to Analytical Ultracentrifugation. Palo Alto, CA: Beckman Instruments Inc.
Rickwood, D. 1984. Centrifugation, 2nd ed. Published in the Practical Approaches to Biochemistry series.
Oxford/Washington, DC: IRL press.
Rickwood, T. C., and Steensgard, F. J. 1994. Centrifugation Essential Data. London: John Wiley & Sons Ltd.
Sharpe, P. T. 1998. “Laboratory Techniques in Biochemical and Molecular Biology.” In Methods of Cell
Separation, vol. 18, edited by R. H. Burden, and P. H. van Knippenberg. New York: Elsevier.
Van Holde, K. E., W. Johnson, and P. Shing Ho. 1998. Principles of Physical Biochemistry. Upper Saddle River,
NJ: Prentice Hall.
Wilson, K., and J. Walker. 2003. Practical Biochemistry-Principles and Techniques, 5th ed. Cambridge:
IMPORTANT LINKS
1. Centrifuge: https://www.beckmancoulter.com/wsrportal/wsr/research-and-discovery/products- and ser-
vices/centrifugation/avanti-j-e/index.htm
2. Ultracentrifuge: https://www.beckmancoulter.com/wsrportal/wsr/research-and-discovery/products- and
services/centrifugation/optima-tlx/index.htm
7 Electrophoresis
7.1 INTRODUCTION
Gel electrophoresis (GE) is a method that separates macromolecules on the basis of size, electric
charge, and other physical properties. The term electrophoresis describes the migration of charged
particles under the influence of an electric field. “Electro” refers to electricity and “phoresis,” from
the Greek word phoros, means “to carry across.” Thus, GE refers to a technique in which molecules
are forced across a span of gel, motivated by an electrical current. The driving force for electrophore-
sis is the voltage applied to electrodes at either end of the gel. The properties of a molecule determine
how rapidly an electric field can move it through a gelatinous medium. The complete GE assembly
along with the power pack is shown in Figure 7.1, whereas the various positions in which electropho-
resis can be carried out, that is, upright, horizontal, and vertical, are shown in Figures 7.2 and 7.3.
Many important biological macromolecules (e.g., amino acids, peptides, proteins, nucleotides, and
nucleic acids) possess ionizable groups and, at any given pH, exist in a solution as electrically charged
species, either as cations (+) or anions (–). Depending on the nature of the net charge, the charged particles
migrate either to the cathode or to the anode. For example, when an electric field is applied across a gel
at a neutral pH, the negatively charged phosphate groups of DNA cause it to migrate toward the anode.
7.1.1 Structure of the Agarose GE Instrument

7.1.1.1 Components of the Agarose GE Instrument
The components of the agarose GE instrument are as follows (Figure 7.4):
Gel casting trays: Gel casting trays are available in a variety of sizes and comprise UV-
transparent plastic. The open ends of the tray are closed with tape while the gel is being
cast; the tape is removed prior to electrophoresis.
Sample combs: Molten agarose is poured around sample combs to form sample wells in the gel.
Agarose: A natural colloid extracted from seaweed, agarose is a linear polysaccharide (aver-
age molecular mass is ~12,000 Da) made up of the basic repeated unit agarobiose, which
comprises alternating units of galactose and 3,6-anhydrogalactose. Agarose gels have large
“pore” sizes and are used primarily to separate large molecules with molecular masses
greater than 200 kDa. Table 7.1 gives the recommended agarose gel concentration for
resolving linear DNA molecules.
Electrophoresis buffer: The electrophoretic mobility of DNA is affected by the composition
and ionic strength of the electrophoresis buffer. Several buffers are available for electropho-
resis of native double-stranded DNA. These contain EDTA (pH 8.0) and tris-acetate (TAE),
tris-borate (TBE), or tris-phosphate (TPE) at a concentration of approximately 50 mM (pH
7.5–7.8). Electrophoresis buffers are usually prepared as concentrated solutions and stored
at room temperature. TBE was originally used at a working strength of 1× for agarose GE.
Marker DNA: For a given voltage and agarose gel and buffer concentrations, migration dis-
tance depends on the molecular weight of the starting material. Therefore, marker DNA of
a known size should be loaded into slots on both right and left sides of the gel. A marker
generally contains a defined number of known DNA segments, which makes it easier to
determine the size of the unknown DNAs if any systematic distortion of the gel occurs
during electrophoresis.
185
FIGURE 7.1 The GE apparatus.
Cathode
Buffer
Gel tube Analytes band
Buffer
(a)
Sample Power supply

wells
Cathode
Anode
Buffer Buffer
(b)
Sample
wells Buffer
Cathode
Power supply
Anode
(c)
FIGURE 7.2 Schematically, GE can be performed in (a) an upright tube. Alternatively, flat rectangular slab
gels can be used, which are positioned (b) horizontally or (c) vertically.
Loading buffer: The DNA samples to be loaded onto the agarose gel are first mixed with the
loading buffer, which usually comprises water, sucrose, and a dye (e.g., xylene cyanole,
bromophenol blue, bromocresol green). The loading buffer serves three purposes:
1. Increases the density of the sample, ensuring that the DNA drops evenly into the well.
2. Adds color to the sample, thereby simplifying the loading process.
3. Imparts a dye to the sample that moves toward the anode at a predictable rate in an
electric field.
Electrophoresis 187
Platinum electrodes
Upper buffer
Connecting vessel
Cover cord
Gasket
Teflon comb
Acrylic
spacers Basic unit
Spirit level
Leveling screws
Lower buffer
Clamps and vessel
screws Rectangular and notched
glass plates
FIGURE 7.3 Vertical slab GE apparatus.
Lid Comb stand
Basic unit
Connecting
cord
Platinum electrodes
Combs
Gel platform
FIGURE 7.4 Parts of a submarine GE apparatus.
Ethidium bromide: Ethidium bromide is a fluorescent dye used for staining nucleic acids. This
fluorescent dye intercalates between bases of DNA and RNA. It is often incorporated into the
gel so that staining occurs during electrophoresis; the gel can also be stained after electro-
phoresis by soaking in a dilute solution of ethidium bromide. Ethidium bromide is a known
mutagen and should be handled as a hazardous chemical; wear gloves while handling it.
Transilluminator: A transilluminator is a UV light box, which is used to visualize ethidium
bromide–stained DNA in gels.
TABLE 7.1
Recommended Agarose Gel Concentrations for
Resolving Linear DNA Molecules
Agarose (%) DNA Size Range Base Pair [bp]
0.75 10,000–15,000
1.0 500–10,000
1.25 300–5000
1.5 200–4000
2.0 100–2500
2.5 50–1000
7.2 PRINCIPLES OF GE
GE is a technique used for the separation of nucleic acids and proteins. The separation of macromol-
ecules depends on two variables: (1) charge and (2) mass. When a biological sample, such as DNA, is
mixed in a buffer solution and applied to a gel, these two variables act together. The electrical current
from one electrode repels the molecules, whereas the other electrode simultaneously attracts the mol-
ecules. The frictional force of the gel material acts as a “molecular sieve,” separating the molecules by
size. The separation principle of electrophoresis is shown diagrammatically in Figure 7.5.
During electrophoresis, macromolecules are forced to move through the pores; their rate of
migration through the electric field depends on the following:
• Strength of the field

• Size and shape of the molecules
• Relative hydrophobicity of the samples
• Ionic strength and temperature of the buffer in which the molecules are moving
To completely understand the separation of charged particles in GE, it is important to look at

the simple equations relating to electrophoresis. When a voltage is applied across the electrodes, a
potential gradient, E, is generated; it can be expressed by the following equation:
E = V /d (7.1)
where V, measured in volts, is the applied voltage and d is the distance in centimeters between the
electrodes.
When the potential gradient, E, is applied, a force, F, on a charged molecule is generated, which
is expressed by the following equation:
F = Eq (7.2)
where q is the charge in coulombs bearing on the molecule. It is this force, measured in newtons,
that drives a charged molecule toward an electrode.
––
– – ––
– –– – ––
– ––
–– – Cathode – –– + Anode
–– – – –
– – –– – ––
–
Analyte Run buffer at Compound A Compound B
mixture constant pH
FIGURE 7.5 The separation principle of electrophoresis. Particles with different charges, in this case nega-
tive charges, and different sizes migrate toward the electrodes at different velocities in an applied electric field.
Electrophoresis 189
7.3 WORKING WITH THE ELECTROPHORESIS APPARATUS

A direct current (DC) power source is connected to the electrophoresis apparatus and an electrical
current is applied. Charged molecules in the sample enter the gel through the walls of the wells.
Molecules with a net negative charge migrate toward the positive electrode (anode), whereas net
positively charged molecules migrate toward the negative electrode (cathode). Within a range, the
higher the applied voltage the faster the samples migrate (EDVOTEK Manual). At the end of a run,
the separated molecules can be detected in position in the gel by staining or autoradiography and
quantified by scanning with a densitometer, and the gel can be dried for permanent storage.
7.3.1 Applications of GE
Major applications of GE are as follows:
• GE is used in forensics, molecular biology, genetics, microbiology, and biochemistry.

• The results can be analyzed quantitatively by visualizing the gel with UV light and a gel
imaging device. The image is recorded with a computer-operated camera, and the inten-
sity of the band or spot of interest is measured and compared against standard or markers
loaded on the same gel. The measurement and analysis are mostly done with specialized
software.
• Depending on the type of analysis being performed, other techniques are often imple-
mented in conjunction with the results of GE, providing a wide range of field-specific
applications (Figure 7.6).
1 2 3 4 5 6 1 2 3 4 5 6 7
(a) (b)
M 1 2 3 4 5 6 kDa M 1 2 3 4 5 6
kDa
205 205
116 116
97.4 97.4
46 46
43
43
29
29
(c) (d)
FIGURE 7.6 (See color insert.) Top: Protein profile of different fractions of metabolic antigens of
Aspergillus fumigates obtained by size-exclusion chromatography on 12% SDS-PAGE stained with Coomassie
blue: (a) Arrow shows 70–72 kDa protein doublet bands and (b) arrow shows 18 kDa purified protein.
(c) Protein profile of metabolic antigens of Aspergillus fumigates precipitated by graded saturation of ammo-
nium sulfate. (d) Identification of immunogenic proteins by Western blotting. Lane M, molecular weight
marker; 1-, 2-, 3-, 4-, and 5-proteins precipitated at 20%, 40%, 60%, 80%, and 100% saturation of ammonium
sulfate in culture filtrate, respectively.
7.4 DENATURING GRADIENT GE

Denaturing gradient GE (DGGE) is a robust method for point mutation detection that has been
widely used for many years. It is a polymerase chain reaction (PCR)-based method, the principle
being the altered denaturing temperature of a PCR product with a mutation compared to the wild-
type product. Figure 7.7 shows different components of the DGGE instrument. DGGE is used to
detect changes (mutations) in the genetic code within a sample and can detect as little as one base
pair difference between strands of DNA.
7.4.1 Structure of the DGGE Instrument

7.4.2 Principle of DGGE
The principle of this technique is to separate DNA strands based on their actual base composition or
the ratio of GC to AT base pairs that make up a particular segment of DNA. This is accomplished by
exposing the DNA to a gradient of denaturant at elevated temperatures within a polyacrylamide gel.
The products are run on an acrylamide gel with a gradient of denaturing agents, urea and for-
mamide. The working principle of DGGE is diagrammatically shown in Figure 7.8. These denatur-
ing agents alone are not sufficient. In addition to their action, the gel is run at a high temperature,
usually 60°C. During electrophoresis, the PCR products will run through the gel as double-stranded
DNA until they reach the point where they start to denature.
Once denatured, the PCR products continue running through the gel as single-stranded DNA, but
the fragments have to remain precisely where they denatured. To achieve this, a so-called GC clamp
is attached to prevent complete denaturing. This GC clamp is a string of 40–60 nucleotides compris-
ing only guanine and cytosine and is attached to one of the PCR primers. A PCR with a GC clamp
results in a product with one end having a very high denaturing temperature. A PCR product running
through a DGGE gel will therefore denature partially. The GC clamp remains double stranded. The
fragment will form a Y-shaped piece of DNA that sticks firmly at its position on the gel.
Buffer siphon Heater

pump assembly stirrer
Single Vapor
cassettes shield
Thermometer
Comb (2)
Glass plate assembly (2)
Spacers
(2 pairs)
Clamps
Gelwarp (2)
Mini-pump (optional) DGGE
tank
GM-40
FIGURE 7.7 Components of a DGGE apparatus.

Electrophoresis 191
GC-clamp primer 1 Primer 2

5΄ 3΄
3΄ 5΄
Low melting
Mixture of PCR products
Denaturant
Single-size band
on agarose gel High melting
FIGURE 7.8 Working principle of DGGE.
7.4.3 Working with the DGGE Instrument

DGGE gels are poured and run to separate similarly sized PCR products. Gels are created by
combining two solutions containing acrylamide (structural material) and differing amounts of
denaturants (urea and formamide) to form a gradient of denaturant in which double-stranded DNA
fragments of differing sequences are denatured during electrophoresis. The gel is stained and visu-
alized to reveal band patterns, which can be used to determine the similarity of sampled microbial
communities.
7.4.4 Applications of DGGE

Applications of DGGE include the following:
• DGGE is a useful tool for tracking a contamination to its source. For example, if a certain
microbial contaminant is appearing in a particular product, DGGE can be used to track
this organism to its source. This can be particularly useful in production facilities in food,
pharmaceutical, and various manufacturing systems industries.
• Using DGGE, the amplified segments of DNA can be separated into individual species
bands, recovered, and then used for sequencing to identify each organism within the
sample.
• DGGE is a rapid and economical way of comparing large numbers of samples to one
another without having to culture, isolate, and analyze each sample individually.
• The ability of DGGE to separate individual species within a sample also enables one to
follow the progression of communities over a period of time. This application is extremely
useful for remediation studies. In such cases, sample sites require sampling over extended
periods of time to follow the degradation of contaminants and the organisms degrading
them.
• DGGE eliminates several problems by eliminating the need for media, minimizing sample
volumes, and being able to detect organisms that either are unculturable or may have per-
ished during transit from the sample site to the lab.
• DGGE also allows the researcher to examine which organisms are forced out of a com-
munity over time, which organisms are stable, and what new organisms may be appearing.
• DGGE is a method to identify small mutations (e.g., point mutations). However, there are
more types of small mutations, such as deletions or insertions of one or more nucleotides,
which can be identified by DGGE as well.
• With the breadth of PCR primers available, DGGE can also be used to investigate broad
phylogenies or specific target organisms such as pathogens or xenobiotics degraders.
• DGGE has been used to elucidate and characterize microbial populations in many bio
leaching environments, including bioreactors, acidic mining-impacted environments, and
bioleaching heaps.
7.5 TEMPERATURE GRADIENT GE

Temperature gradient GE (TGGE) is a powerful technique for the separation of nucleic acids or
proteins. The TGGE method, which is covered by patents, uses the temperature-dependent changes
of conformation for separating molecules. Figure 7.9 shows the complete apparatus of TGGE along
with a power pack system. Since the introduction of the first commercially available TGGE appa-
ratus in 1989, TGGE has gained much interest in scientific and clinical research laboratories due
to its unprecedented resolution capability and ease of analysis. The range of scientific publications
using the TGGE method is broad and covers all disciplines using molecular biology methods, such
as oncology, virology, immunology, RNA viroid research, prion research, and population analysis.
The TGGE method has also been used for quantitative analysis in the industry and for the confor-
mational analysis of proteins.
7.5.1 Structure of the TGGE Instrument

7.5.1.1 Components of the TGGE Instrument
A typical TGGE instrument consists of different parts, which are diagrammatically shown in
Figure 7.10.
7.5.1.2 Electrophoresis Unit

The electrophoresis unit consists of four parts:
1. A safety lid with two electric plugs (anode and cathode)

2. Two removable electrophoresis chambers, each with platinum wires and electric connectors
(maximum volume: 250 mL)
3. Housing with Peltier-element-powered gradient block
4. Thirty-seven pins connecting the cable to the control unit
7.5.1.3 Controller Unit

The controller is a highly integrated microprocessor-driven unit for controlling the tempera-
ture, ramping time, and ramping rate of the gradient block, as well as supplying the power for
FIGURE 7.9 The TGGE unit.

Electrophoresis 193
Safety lid
Buffer chambers
Electrophoresis unit
Control cord plug
FIGURE 7.10 Different components of a TGGE instrument.
the electrophoresis unit. During the run, the display of the controller continuously shows the
current parameters.
7.5.2 Principles
Conventional protein or nucleic acid electrophoresis separates molecules according to their size or
charge. TGGE adds a new parameter for separation: the melting behavior of a molecule. Figure 7.11
describes the basic principles of TGGE. The melting behavior is determined by primary sequence
and the secondary and tertiary structures of the molecule and can be changed by external influences
such as temperature, salt concentration, and pH.
During electrophoresis, the sample migrates along a temperature gradient. As the temperature
rises, the molecules start to denature. Working with PCR fragments, for example; during electropho-
resis it starts separating from double stranded molecules. At a certain temperature, the DNA starts
to melt, resulting in a forklike structure (partial single strand). In this conformation, the migration
is slowed down compared to a DNA fragment of same size that is completely double stranded. Since
the melting temperature strongly depends on the base sequence, DNA fragments of the same size
but different sequences can be separated. This is used in mutation detection, where PCR fragments
of identical size but different sequences are separated. Thus, TGGE not only separates molecules
but also gives additional information about the melting behavior and stability of molecules.
7.5.3 Working with the TGGE Instrument

The sample is loaded directly to the gel. The gel is connected with the buffer chambers by paper
wicks soaked with the running buffer. To protect the gel from drying, it is covered with a gel cover
film. The complete setup, consisting of gel with cover film and buffer wicks, is covered with the gel
cover plate. The gel cover plate has two sealings and fits precisely onto the thermoblock. It holds
the buffer wicks in place and helps to build a humidity chamber around the gel. This is important
to prevent evaporation during a run.
Cold
ssDNA
Electrophoresis
Partial single strand
ssDNA
Warm
FIGURE 7.11 Different conformations of DNA during TGGE.
7.5.4 Applications of TGGE

Applications of TGGE include the following:
• Study community complexity.

• Monitor population shifts.
• Analyze enrichment cultures and the isolation of bacteria.
• Detect sequence heterogeneities of 16S rRNA genes in single genomes.
• According to a recent investigation, TGGE can be utilized to examine mutations in the
mitochondrial DNA of an individual.
• Compare DNA extraction methods.
• Screen clone libraries.
• Determine PCR and cloning biases.
7.6 PULSED-FIELD GE
DNA molecules larger than 15–20 kb migrating through a gel will essentially move together in a
size-independent manner. In 1984, Schwartz and Cantor described pulsed-field GE (PFGE), thereby
introducing a new way to separate DNA. In particular, PFGE resolved extremely large DNA for the
first time, raising the upper size limit of DNA separation in agarose from 30–50 kb to well over
10 Mb (10,000 kb). The complete instrument of PFGE is shown in Figure 7.12. The development of
PFGE expanded the range of resolution of DNA fragments by as much as two orders of magnitude.
7.6.1 Structure
7.6.2 Principles
During electrophoresis, DNA above 30–50 kb migrate with the same mobility regardless of size.
This is seen in a gel as a single large diffuse band. If, however, the DNA is forced to change direc-
tion during electrophoresis, fragments of different sizes within this diffuse band begin to separate
from each other. With each reorientation of the electric field relative to the gel, smaller DNA begin
moving in the new direction more quickly than larger DNA. Larger DNA lags behind, providing
a separation from smaller DNA. The basic principle underlying the PFGE process is described in
Figure 7.13.
Electrophoresis 195
FIGURE 7.12 The PFGE unit.
Condenser
Pump
A(+)
A(+)
B(+)
B(+/–)
B(+/–)
B(–)
A(–)
A(–)
Reorientation angle Reorientation angle

120°
120°
120°
120° 120°
120°
120° 120° 120°

120°
120° 120° 120°
120°
(a) (b)
FIGURE 7.13 (a) Basic principle of PFGE and (b) principle of PFGE. In the figure, arrows denote the net
direction of DNA movement, solid lines the actual path of DNA molecules, and dashed lines the trajectory
created by electric fields.
Here, the direction of electric field is periodically altered, requiring electrophoresing mol-
ecules to assume new orientations for productive motion through the gel matrix. Accordingly,
the net electrophoretic mobility strongly correlates, in a size-dependent way, with the frequency
of the applied electrical fields. Consequently, as molecules approach complete orientation they
move more effectively through the gel matrix with vanishing electrophoretic size dependencies.
As such, PFGE pulsing routines use switching frequencies that optimize the periods in which
molecules undergo size-dependent reorientation, causing zigzag traversals and separations up
to 12 Mb.
7.6.3 Working with the PFGE Instrument

The basic components of a PFGE system are a gel box with some means of temperature regulation,
a switching unit for controlling the electric fields, a cooler, and a power supply.
7.6.3.1 Gel Box

The basic design of PFGE boxes consists of an immobilized gel within an array of electrodes and a
means for circulating the electrophoresis buffer. Voltage gradients of 10 V/cm are commonly used
in PFGE. Voltage gradients as high as 15 V/cm have been used in field inversion separations of cos-
mid clones. The temperature of the buffer is controlled by a heat-exchange mechanism. Generally,
the buffer is recirculated throughout the gel box using inlet and outlet ports.
7.6.3.2 High-Voltage Power Supply

Precise control of the electric field gradient is necessary to obtain consistent PFGE separations.
The output ratings of the power supply should therefore be high enough to meet both voltage and
current requirements of the gel box. To achieve the commonly used range of voltage gradients of
1.5–15 V/cm, one requires a power supply with a maximum voltage rating of 750 V. The current
drawn at this voltage in most PFGE boxes is about 0.5 A at 14°C using 0.5× TBE (1× TBE is 89 mM
Tris pH: 7, 89 mM boric acid and 2 mM EDTA) as running buffer.
7.6.3.3 Switch Unit

The ability to reproducibly control the switch interval is critical for separation. Such switching units
are commonly based on the use of metal oxide semiconductor field-effect transistors (MOSFETs) in
both switching and electrode voltage control circuits.
7.6.3.4 Computer Program

Careful control of the switch interval is crucial in controlling the resolution in PFGE. A versatile switch-
ing unit should have software with the same characteristics. The algorithm should be fast enough so that
switch times at least as short as 1 millisecond can be achieved, and switch interval increments should
have at least 1 millisecond resolution. Linear switch interval ramping is the most commonly used pro-
cedure because of its simple implementation. The maximum run time should be about two weeks to
allow for the separation of very large DNA molecules. This is controlled by a computer program.
7.6.3.5 Cooler
DNA molecule migration is sensitive to temperature, and thus a uniform temperature across the
gel is needed to ensure even migration in each of the lanes. Buffer is recirculated through the gel
chamber by a reciprocating solenoid pump at a rate of about 450 mL/min. The buffer is chilled in
its reservoir tank by circulating cold water (5°C) through a glass tubing heat exchanger. Buffer tem-
perature is thus maintained at 13°C–15°C throughout a typical run.
7.6.4 Applications
Applications of PFGE include the following:
• The advent of PFGE techniques for the resolution of large DNA molecules provides a new
analytical approach for bacterial genomes. The PFGE of DNA fragments obtained using
different enzymes is a powerful technique for quick resolution of the bacterial genome into
a small number of large fragments.
• PFGE is an amazing and useful tool for microbial strain identification and epidemiological
tracking and tracing. PFGE techniques are precise, reliable, and reproducible.
Electrophoresis 197
• PFGE techniques may be used for genotyping or genetic fingerprinting.

• Yeast artificial chromosome (YAC) libraries have been constructed by PFGE.
• PFGE helps in identifying restriction fragment length polymorphisms (RFLPs) and con-
struction of physical maps.
• PFGE is commonly considered a gold standard in epidemiological studies of pathogenic
organisms.
• PFGE helps in detecting in vivo chromosome breakage and degradation.
7.7 CAPILLARY ELECTROPHORESIS

Capillary electrophoresis (CE) was developed in the 1980s by James Jorgenson and Krynn Lukas.
They separated derivatized amino acids in a tube of 75 μm inner diameter. The technique has vari-
ously been referred to as high-performance CE (HPCE), capillary zone electrophoresis (CZE), free
solution CE (FSCE), and simply CE. The CE method (Figure 7.14) can be used to separate a wide
spectrum of biological molecules including amino acids, peptides, proteins, DNA fragments (e.g.,
synthetic oligonucleotides), and nucleic acids as well as many small organic molecules such as drugs
or even metal molecules.
7.7.1 Principles
CE is based on the same principle as GE. Charged analytes can be separated in an applied electric
field based on their mobility. In contrast to GE, however, separations are carried out in a capillary
with a small diameter containing a free solution of electrolyte rather than on a slab gel. Moreover,
convective flows due to Joule heating occur more easily in a free solution than in a gel. In contrast
to GE, electroosmotic flow is often part of the separation process.
7.7.2 Structure of the CE Instrument

The instrumentation required for CE is relatively simple, consisting of vials with samples and buf-
fer, a high-voltage power supply, a capillary enclosed in a thermostatically controlled compartment,
an on-column detector, and a data output system as well as a vacuum system for sample injection.
The parts of a typical CE instrument are discussed in Sections 7.7.2.1 through 7.7.2.4.
Integrator or
Capillary
computer
Detector
Anode + + – Cathode
Source vial Sample vial Destination vial

High-voltage
power supply
FIGURE 7.14 Schematic of a typical CE instrument.

7.7.2.1 Capillaries
The capillaries used in CE have internal diameters of 20–100 nm and outer diameters of about
400 nm. They are typically between 10 and 100 cm long. The most popular capillary material used
is fused silica, that is, amorphous quartz, which is transparent to UV and visible light. These capil-
laries are externally coated with a polyimide layer of about 10 nm thickness to increase flexibility.
The capillary is usually enclosed in a thermostatically controlled environment for temperature
control. This is because the viscosity of the buffer varies with temperature and Joule heating must
be dissipated effectively to avoid temperature fluctuations, which can have dramatic effects on the
efficiency and reproducibility of CE separations.
7.7.2.2 Buffer
A buffer is also referred to as a carrier electrolyte or background electrolyte. The purpose of a buffer
is to maintain the pH as well as the conductivity during an electrophoretic separation. A controlled
pH is crucial for maintaining a constant net charge on the biomolecules and thus maintaining their
electrophoretic mobility. Buffer concentrations in CE are typically on the order of 10–100 mM.
7.7.2.3 Injection System

The injection system must be capable of reproducibly introducing very small sample volumes into
the capillary. Two injection methods are commonly used:
1. In electrokinetic injection, voltages are used to introduce the sample into the capillary. The
source ends of the capillary together with the source end of the electrode are placed into
the sample solution. A high voltage is applied over the capillary between the sample vial
and the destination vial for a given period of time. This causes the sample to move into the
capillary according to its apparent mobility.
2. Hydrodynamic injection can be performed in three different ways: (1) In pressure injec-
tion, a precisely controlled external pressure is used to force a controlled amount of sample
into the capillary. (2) In vacuum injection, a vacuum is applied to the buffer reservoir at the
detector end of the capillary for a controlled period of time at a regulated reduced pressure.
(3) For gravity flow injection, the sample vial with one end of the capillary is elevated to a
certain height above the other end of the capillary for a given period of time. Gravity forces
a sample plug into the capillary.
7.7.2.4 Detectors
Detection schemes used for CE include the measurement of UV absorption, fluorescence, and
refractive index. Electrochemical signals and conductivity as well as radioactivity from radioiso-
topes have also been measured. The signals obtained are plotted against the migration time in the
form of an electropherogram.
The detection of UV absorption at a chosen wavelength is the most commonly used scheme.
Peptides are usually measured at λ = 210 nm, and proteins and DNA at λ = 260 nm or λ = 280 nm.
The absorbance is measured directly through a detection window in the capillary, approximately
1 mm long.
7.7.3 Working with the CE Instrument

The source vial, destination vial, and capillary are filled with an electrolyte such as an aqueous buf-
fer solution. To introduce the sample, the capillary inlet is placed into a vial containing the sample
and then returned to the source vial. The migration of analytes is then initiated by an electric field
that is applied between the source and destination vials and is supplied to the electrodes by the
Electrophoresis 199
high-voltage power supply. The output of the detector is sent to a data output and handling device
such as an integrator or a computer. The data is then displayed as an electropherogram, which
reports detector response as a function of time. Separated chemical compounds appear as peaks
with different retention times in an electropherogram.
7.7.4 Applications
• CE can be used to quantify DNA. For example, CE analysis of PCR products from Human
Immunodeficiency Virus-I [HIV-I] allowed the identification of between 200,000 and
500,000 viral particles per cubic centimeter of serum.
• A range of small molecules, drugs, and metabolites can be measured in physiological solu-
tions such as urine and serum.
• Point mutations in DNA, such as those occurring in a range of human diseases, can be
identified by CE.
• Chiral compounds can be resolved using CE. Most of the efforts to this end have been car-
ried out in a free solution using cyclodextrins as chiral selectors.
Experiment: GE of Proteins
Principles
Any charged ion or group will migrate toward the electrodes when placed in an electric field. Negatively
charged particles in solution move toward the positive electrode and vice versa. These particles move at
different speeds in solution depending on their net charge and size of the molecule.
SDS–Polyacrylamide GE (SDS-PAGE)
SDS, in the presence of the reducing agent beta-mercaptoethanol, dissociates proteins into their sub-
units and binds in large quantities with the protein. This completely masks the natural charge of the
protein, giving a constant charge to mass ratio. Therefore, the larger the molecule the greater the charge.
The electrophoretic mobility of the complex depends on the size (molecular weight) of the protein.
Protein Sample Preparation

A. For Bacteria
1. Raise 50 mL of the culture.
2. Centrifuge at 6000g for 10 minutes. Wash the pellet three times with 0.1 M Tris buffer
(pH 6.8).
3. Resuspend the pellet in 2 mL of 0.1 M Tris buffer (pH 6.8) containing 15% glycerol and SDS
to a final concentration of 1% (w/v).
4. Heat it in a boiling water bath for 10 minutes.
5. Centrifuge and store the supernatant containing proteins.
6. Mix 100 μL of protein sample with 100 μL of sample solubilizing buffer. Heat it at 100°C for
3 minutes.
B. For Cyanobacteria
1. Take 500 mg of cyanobacterial pellet and add 5 mL of 10% cold trichloroacetic acid (TCA).
2. Incubate in ice for 30 minutes.
3. Centrifuge at 12,000g for 5 minutes.
4. Wash the pellet with ethanol–ether (1:1 v/v) repeatedly to remove the TCA.
5. Dissolve the TCA precipitate to 0.0625M Tris–HCl (pH 6.8).
6. Subject the sample to SDS-PAGE.
Reagents
1. Acrylamide stock: Dissolve in 100 mL of distilled water. Store at 4°C in a dark bottle.
Acrylamide 29.2 g
NN′-methylene bisacrylamide 0.8 g
2. Resolving gel buffer (pH 8.8): Dissolve the salt in 50 mL of distilled water and adjust the pH
with 6N HCl. Make up to 100 mL with distilled water. Store at 4°C.
Tris 18.15 g
SDS 0.4 g
3. Stacking gel buffer (pH 6.8): Dissolve the salt in 50 mL of distilled water and adjust the pH
with 6N HCl. Make up to 100 mL with distilled water. Store at 4°C in a dark bottle.
Tris 6.05 g
DSD 0.4 g
4. Reservoir buffer: Dissolve and make up to 1000 mL with distilled water.
Tris 3.0 g
Glycine 14.4 g
SDS 1.0 g
5. Protein stain: Dissolve and make up to 500 mL with distilled water.
Coomassie brilliant blue-R250 1.25 g

Methanol 200 mL
Acetic acid 35 mL
6. Destaining solution: Mix and make up to 1000 mL with distilled water.
Methanol 500 mL
Acetic acid 75 mL
7. Storing solution:
Methanol 5 mL
Acetic acid 7 mL
Distilled water 87.5 mL
8. Sample buffer (stock):
0.0625 M Tris–HCl, pH 6.8 1.2 mL

SDS 1g
Glycerol 3 mL
Beta-mercaptoethanol 200 μL
Bromophenol blue (1mg/mL) 2 μL
Distilled water 5 mL
Electrophoresis 201
Procedure
1. Clean the glass plates by soaking them in chromic acid overnight; rinse them with water and
then with ethanol. Keep the plates down on a clean tissue paper, with the side that is to be in
contact with the gel facing upward, and swab them with an acetone-soaked tissue held in a
gloved hand. After a final rinse with ethanol, allow the plates to air dry.
2. Fix the gel plate with appropriate spacers on the gel maker. To avoid leakage, apply vacuum
grease on both sides of the spacers.
3. Prepare the resolving gel solution. Degas the mixture and then add
Acrylamide (A) 10 mL
Distilled water 12.5 mL
Resolving gel buffer 7.5 mL
Pour the solution into a glass plate up to a level such that 1–2 cm is allowed for stacking the gel.
Remove air bubbles, if any.
TEMED 45 µL
Ammonium persulfate (APS)
(APS 1.5%) 150 µL
4. Add an even layer of isobutanol on the top of the separating gel solution to get a flat surface
on top of the gel.
5. Allow it to polymerize for 30 minutes, remove the isobutanol layer, and wash it with water.
6. Prepare the stacking gel solution by mixing
Acrylamide (A) 1 mL
Stacking gel buffer (C) 2.4 mL
Degas the mixture and then add
TEMED 20 μL
1.5% APS 100 μL
7. Insert the comb between the plates. Pour the solution carefully on the top of the separating gel
and remove the bubbles, if any.
8. After 20 minutes, remove the bottom spacer and fix the gel plate with the slab-gel unit.
Remove the comb and fill up the wells with reservoir buffer (D).
9. Add equal volume of sample buffer (I) to the sample solution and boil in a water bath for
3 minutes.
10. Load about 100–200 μL of the aforementioned sample mixture into each well and, instead
of the sample, load an equal amount of standard protein mixture to any one of the wells to
compare the molecular weight of the sample proteins.
11. Add a reservoir buffer to the anode and cathode chambers until the buffer touches the gel.
12. Connect the power supply and apply 60 V until the marker dye enters the separating gel. Then
increase the voltage to 100–200 V.
13. Continue the power supply until the marker dye reaches the bottom of the gel. Disconnect the
power supply and remove the slab-gel setup.
14. Remove the glass plate and place the gel in Coomassie brilliant blue R-250 stain (E) for
2–4 hours.
15. Destain the gel in the destaining solution mixture (F) until a clear background is obtained.
16. Store the gel in the storing solution (G; Figure 7.15).
(a)
kDa M 1 2 3 4 5 6
205
116 70 kDa
97.4
66
45
29
A 18 kDa
B
(b)
FIGURE 7.15 Protein profiles: (a) whole cell protein profile of Anabaena variabilis under different physi-
ological conditions with lane 1 as marker, and (b) (See color insert) electrophoretic protein profile of a fungus
Aspergillus fumigates with known-molecular-weight marker protein.
Experiment: Determination of the Molecular

Weight of Plasmid DNA by Agarose GE
Introduction
DNA molecules are negatively charged at neutral or alkaline pH and migrate toward the anode when an
electric field is applied. The charge/mass ratio in nucleic acids is unity; thus migration occurs largely on
the basis of the molecular size of the DNA molecules (Figure 7.16).
1. Preparation of agarose gels
2. Loading plasmid DNA preparation along with the standard
3. Conducting electrophoresis
4. Examining the gels under UV light
Safety Guidelines
High-purity chemicals and water should be used. Other guidelines are as follows:
1. All glassware, plasticware, and solutions should be sterile.
2. Ethidium bromide is a carcinogen. Gloves must be worn while handling gels in ethidium
bromide solution.
3. Wear safety glasses while viewing the gel on a UV transilluminator.
4. Do not touch the electrophoresis chamber or the electrical leads while electrophoresis is in
progress.
5. At the time of casting the gel, ensure that no air bubbles are entrapped in the gel.
Materials
Plasmid DNA (isolated and standard); minigel horizontal agarose gel electrophoretic unit, which
comprises
• Gel casting plate
• Electrophoretic tank
• Comb
Electrophoresis 203
kb
M 1 2 3 4 5 6 7 8 9 10 11 1213 14 15 M
10 kb
9 kb
8 kb
7 kb
12 3 4 5 6 7 8
5 kb
2 kb 1.0 kb kb
0.9 kb
0.8 kb
0.7 kb
0.6 kb
0.5 kb
0.4 kb
0.3 kb
0.2 kb
0.1 kb
1 2 3 4 5 67 8
(a) (b)
FIGURE 7.16 Figure showing (a) agarose GE of plasmid DNA with known ladder, and (b) genomic library of a
bacterium with chromosomal DNA from wild and mutant strains after DNA digestion with restriction analysis.
• Electrophoretic leads
• Adhesive tape
• Power pack (0–500 V), UV transilluminator with camera, micropipette or syringe
• Gloves
1. TAE stock solution (5×): A fivefold concentrated TAE buffer stock solution. Adjust the pH of
the aforementioned solution to pH 9 and add water to make 1 L. Dilute five times before use
to obtain the working buffer (1× buffer).
Tris–base 24.2 g
Glacial acetic acid 7.71 mL
0.5 M EDTA 10 mL
2. 1% agarose in 1× TAE buffer: Dissolve 0.75 g agarose in 75 mL of 1× TAE buffer (working

TAE buffer), by boiling and maintaining it at 50°C until it is to be used.
3. Gel loading solution: Dissolve 10% glycerol and 0.025% bromophenol blue in water.
4. Ethidium bromide: Dissolve 10 mg of ethidium bromide per milliliter of the 1× TAE buffer.
Gloves must be worn while preparing this solution.
5. Plasmid DNA preparation: To 20 μL of plasmid DNA preparation, add 10 μL of gel loading
solution and mix properly.
6. Standard DNA marker: Take 20 μL of the λ DNA–Hind III Digest; add 10 μL of gel loading
solution and mix well.
Method
1. Take a clean, dry gel casting plate and make a gel mold using adhesive tape along the sides of
the plate to prevent the material to be poured on the plate from running off.
2. Pour 50 mL of 1% agarose solution kept at 50°C onto the casting plate. Immediately place the
comb about 1 cm from one end of the plate, ensuring that the teeth of the comb do not touch
the glass plate. Wait until a firm layer of gel is formed.
3. Remove the comb and the tape surrounding the plate carefully and transfer the gel plate to the
electrophoresis tank such that the wells are toward the cathode.
4. Pour l× TAE buffer into the tank until the gel is completely submerged. Connect the elec-
trodes to the power supply.
5. Load the plasmid DNA preparation and the standard DNA markers into separate wells with
the help of a micropipette or a syringe.
6. Turn on the power supply and run at 100 V (10–15 mA). Monitor the progress of the fast-
running tracking dye (bromophenol blue) during electrophoresis.
7. Turn off the power supply when the tracking dye reaches near the opposite edge of the gel.
8. Transfer the gel from the casting plate onto a UV-transparent thick plastic sheet, place it in a
staining tray containing ethidium bromide solution, and stain for 20–30 minutes.
9. Place the gel for destaining in water for 15–20 minutes.
10. Observe the gel on a UV-transparent sheet with a UV transilluminator for the presence of orange-
colored bands. The gel may be photographed for a permanent record (Figure 7.16). (Caution: UV
light is extremely injurious to eyes; wear UV protection glasses while viewing the gel.)
11. Measure the distance moved by each band from the edge of the loading well. Draw a graph
of logarithm to base 10 of the molecular weight of the standard DNA markers versus the dis-
tance traveled by each of them.
12. From the distance traveled by the supplied plasmid DNA preparation, determine its molecular
weight using the calibration curve prepared in step 11.
Experiment: Electroblotting (Western Blotting

of Proteins from SDS Polyacrylamide Gel)
Introduction
When an electric field is applied, proteins migrate from cathode to anode. Nitrocellulose sheets are able
to bind proteins. The proteins get immobilized onto the sheet, forming an exact replica of protein bands
on the nitrocellulose sheet as they come in contact.
Transfer the proteins separated on polyacrylamide gels onto the nitrocellulose sheet. Examine the blue
bands of the transferred proteins (Figure 7.17).
Safety Guidelines
1. Do not touch the nitrocellulose sheet using your hands.
2. Wear gloves while handling the gel and the nitrocellulose sheet.
3. Avoid the entrapment of bubbles in the assembly.
4. The proteins get immobilized onto the sheet and form the exact replica of protein bands on
the nitrocellulose sheet.
70 kDa
FIGURE 7.17 Western blot on a Whatman no. 3 nitrocellulose sheet.

Electrophoresis 205
Materials
1. Western blot apparatus consisting of gel holder, sponge, and transfer tank
2. Power pack and electrical leads
3. Slab gel containing separated proteins (use the gel obtained after the electrophoresis of pro-
teins on SDS-PAGE in the first experiment of this chapter)
4. Nitrocellulose sheet cut to size
5. Whatman no. 3 MM paper cut to size of the gel
Prelaboratory Precautions
Transfer buffer consists of
Tris 3g
Glycine 14.7 g
Methanol 200 mL
After mixing the aforementioned components, adjust the pH of the solution to 8.3 and make the final
volume 1 L with distilled water.
Method
1. Take the gel obtained after electrophoresis in the first experiment of this chapter. Do not stain
it, and mark it by cutting off one corner. Place the gel for 30 minutes in the transfer buffer for
equilibration.
2. Take a nitrocellulose sheet, cut it to the size of the gel, and dip it in the transfer buffer by
carefully wetting one edge and then slowly lowering the sheet into the buffer. Leave it in the
buffer for 30 minutes.
3. Soak the sponge in transfer buffer and place the wet sponge on the gel holder. Now keep a
sheet of Whatman no. 3 MM paper (presoaked in transfer buffer) on the sponge.
4. Place the equilibrated gel carefully on the filter paper, avoiding trapping any air bubbles.
5. Carefully lay down the nitrocellulose membrane with its shining side toward the gel on top of
the gel. Gently roll a sterile 10 mL pipette over the membrane to remove air bubbles to ensure
good contact between the membrane and the gel.
6. Complete the sandwich by placing a wet Whatman no. 3 MM filter paper over the membrane
and a second sponge on the filter paper. Close the gel holder and place it in the transfer tank
containing sufficient quantity of the transfer buffer to completely cover the blot.
7. Connect the setup to the power supply and run for 5 hours at 60 V or at 30 V overnight.
8. When the transfer is complete, lift the membrane from the gel. Stain and destain it using the
Coomassie brilliant blue R-250 stain. Examine the nitrocellulose sheet for the presence of
blue bands of the transferred proteins.
SUGGESTED READING
Amersham. 1999. Protein Electrophoresis: Technical Manual. USA: Amersham Biosciences Inc.
Andreas, M., P. Nicole, and L. Dimitri. 2004. Bioanalytical Chemistry. London: Imperial College Press.
Arakawa, T. et al. 1993. “Analysis of the Heat-Induced Denaturation of Proteins Using Temperature Gradient
Gel Electrophoresis.” Analytical Biochemistry 208:255–9.
Baughman, K. 2005. Principles and Applications of DGGE. Microbac Laboratories, Inc.
Baumstark, T., and D. Riesner. 1995. “Only One of Four Possible Secondary Structures of the Central Conserved
Region of Potato Spindle Tuber Viroid Is a Substrate for Processing in a Potato Nuclear Extract.” Nucleic
Acids Research 23:4246–54.
Biometra a Whatman company. 1999. TGGE System Manual. Göttingen: Biometra, biomedizinische, Analytik
GmbH.
Biometra a Whatman company. 2002. TGGE System Manual, Version 6.0. Goettingen: Biometra, biomed-
izinische, Analytik GmbH.
Birmes, A. et al. 1990. “Analysis of the Conformational Transition of Proteins by Temperature-Gradient Gel
Electrophoresis.” Electrophoresis 11:795–801.
Birren, B. W., E. Lai, S. M., Clark, L. Houd, and M. I. Simon. 1988. “Optimized Conditions for Pulsed-Field
Gel Electrophoretic Separations of DNA.” Nucleic Acids Research 16:7563–81.
Carle, G. F., and M. V. Olson. 1984. “Separation of Chromosomal DNA Molecules from Yeast by Orthogonal-
Field-Alternation Gel Electrophoresis.” Nucleic Acids Research 14:5647–63.
Chrambach, A., M. J. Dunn, and B. J. Radola. 1983. Advances in Electrophoresis, vol. 4, 189–95. Weinheim:
VCH Verlagsgesellschaft.
Dempsey, J. A. F., W. Livaker, A. Madhure, T. L. Snodgrass, and J. G. Cannon. 1991. “Physical Map of the
Chromosome of Neisseria Gonorrhoea FA1090 with Locations of Genetic Markers, Including Opa and
Pil Genes.” Journal of Bacteriology 173:5476–86.
EDVOTEK Manual. 2003. EDVO-Kit # 101 Principles and Practice of Agarose Gel Electrophoresis, 1–31.
Washington, DC: The Biotechnology Education Company.
Gardiner, K. 1991. “Pulsed-Field Gel Electrophoresis.” Analytical Chemistry 63:658–65.
Hecker, R. et al. 1988. “Analysis of RNA Structure by Temperature-Gradient Gel Electrophoresis: Viroid
Replication and Processing.” Gene 72:59–74.
Henco, K., and M. Heibey. 1990. “Quantitative PCR—The Determination of Template Copy Numbers by
Temperature Gradient Gel Electrophoresis.” Nucleic Acids Research 18:6733–4.
Herschleb, J., G. Ananiev, and D. C. Schwartz. 2007. “Protocol: Pulsed-Field Gel Electrophoresis.” Nature
Protocols 2:677–84.
Horn, D. et al. 1996. “Three Novel Mutations of the NF1 Gene Detected by Temperature Gradient Gel
Electrophoresis of Exons 5 and 8.” Electrophoresis 17:1559–63.
Instruction Manual. 2011. Denaturing Gradient Gel Electrophoresis Systems. Del Mar, CA: C.B.S. Scientific
Company, Inc.
Jeroen, H. R., and J. M. P. Dorien. 1998. “Denaturing Gradient Gel Electrophoresis (DGGE).” In Medical
Biomethods Handbook, edited by J. M. Walker and R. Rapley. Totowa, NJ: Humana Press, Inc.
Joppa, B., S. Li, S. Cole, and S. Gallagher. 1992. HIS Laboratories, Hoefer Scientific Instruments. Fall San
Francisco: Probe Volume 2(3).
Kappes, S. et al. 1995. “p53 Mutations in Ovarian Tumors, Detected by Temperature-Gradient Gel
Electrophoresis, Direct Sequencing and Immunohistochemistry.” International Journal of Cancer 64:
52–9.
Kuhn, J. E. et al. 1995. “Quantitation of Human Cytomegalovirus Genomes in the Brain of AIDS Patients.”
Journal of Medical Virology 47:70–82.
Lai, E., B. W. Birren, S. M. Clark, M. I. Simon, and L. Hood. 1989. “Pulsed-Field Gel Electrophoresis.”
Biotechniques 7:34–42.
Lessa, E. P., and G. Applebaum. 1993. “Screening Techniques for Detecting Allelic Variation in DNA
Sequences.” Molecular Ecology 2:119–29.
Linke, B. et al. 1995. “Identification and Structural Analysis of Rearranged Immunoglobulin Heavy Chain
Genes in Lymphomas and Leukemia.” Leukemia 9:840–7.
Loss, P., M. Schmitz, G. Steger, and D. Riesner. 1991. “Formation of a Thermodynamically Metastable Structure
Containing Hairpin II is Critical for the Potato Spindle Tuber Viroid.” EMBO Journal 10:719–28.
Menke, M. A., Tiemann, M., Vogelsang, D. et al. 1995. Temperature gradient gel electrophoresis for analysis
of a polymerase chain reaction-based diagnostic clonality assay in the early stages of cutaneous T-cell
lymphomas. Electrophoresis 16: 733–8.
Milde-Langosch, K. et al.1995. “Presence and Persistence of HPV and p53 Mutation in Cancer of the Cervix
Uteri and the Vulva.” International Journal of Cancer 63:639–45.
Nubel, U. et al. 1996. “Sequence Heterogeneities of Genes Encoding 16S rRNAs in Paenibacillus Polymyxa
Detected by Temperature Gradient Gel Electrophoresis.” Journal of Bacteriology 178:5636–43.
Orbach, M. J., D. Vollrath, R. W. Davis, and C. Yanofsky. 1998. “An Electrophoretic Karyotype of Neurospora
Crassa.” Molecular Cell Biology 8:1469–73.
Prischmann, J. 2011. Basics and Theory of Electrophoresis (ppt). Diagnostic Lab, North Dakota State Seed
Department.
Richter, A., L. Plobner, and J. Schumacher. 1997. “Quantitatives PCR-VerfahrenzurBestimmung der
Plasmidkopienzahl in rekombinanten Expressionssystemen.” BIOforum 20:545–7.
Riesner, D. 1998. “Nucleic Acid Structures.” In Antisense Technology. Practical Approach Series, 1–24. Oxford, UK:
Oxford University Press.
Electrophoresis 207
Riesner, D., K. Henco, and G. Steger. 1991. Temperature gradient gel electrophoresis: A method for the
analysis of conformational transitions and mutations in nucleic acids and proteins. Adv Electrophoresis
4:169–250.
Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. “Gel Electrophoresis of DNA.” In Molecular Cloning: A
Laboratory Manual, edited by J. Sambrook, E. F. Fritsch, and T. Maniatis. Cold Spring Harbor, NY: Cold
Spring Harbor Laboratory Press. Chapter 6.
Schwartz, D. C., and C. R. Cantor. 1984. “Separation of Yeast Chromosome-Sized DNAs by Pulsed Field
Gradient Gel Electrophoresis.” Cell 37:67–75.
Sheffield, V. C., D. R. Cox, L. S. Lerman, and R. M. Meyers. 1989. “Attachment of a 40-Base-Pair G+C-
Rich Sequence (GC-Clamp) to Genomic DNA Fragments by the Polymerase Chain Reaction Results in
Improved Detection of Single-Base Changes.” Proceedings of the National Academy of Sciences of the
United States of America 86:232–6.
Skoog, D. A., F. J. Holler, and S. R. Crouch. 2007. Principles of Instrumental Analysis, 6th ed. Belmont, CA:
Thomson Brooks/Cole Publishing.
Westermeier, R. 1997. Electrophoresis in Practice: A Guide to Methods and Applications of DNA and Protein
Separation. Weinheim: VCH.
Wieland, U. et al. 1996. “Quantification of HIV-1 Proviral DNA and Analysis of Genomic Diversity by
Polymerase Chain Reaction and Temperature Gradient Gel Electrophoresis.” Journal Virology Methods
57:127–39.
Wiese, U. et al. 1995. “Scanning for Mutations in the Human Prion Protein Open Reading Frame by Temporal
Temperature Gradient Gel Electrophoresis.” Electrophoresis 16:1851–60.
Wilson, K., J. Walker. 2000. Practical Biochemistry: Principles and Techniques, 5th ed. Cambridge: Cambridge
University Press.
IMPORTANT LINKS
1. DGGE: http://www.cbsscientific.com/dgge.aspx
2. TGGE: http://www.cbsscientific.com/ttge.aspx
3. PFGE: http://www.biolabo.com/Electrophoresis/Pulsed-Field-Gel-Electrophoresis-PFGE-system
4. CE: http://www.biocompare.com/ProductDetails/3177514/Agilent-7100-Capillary-Electrophoresis-
System.html?fi=3177514
8 X-Ray Microanalysis
8.1 INTRODUCTION
X-ray microanalysis makes it possible for chemical analysis to be performed on biological tissue
within very small and well-defined regions of specimens. All elements from Na to U can be detected
while observing a specimen through an electron microscope. Using x-ray microanalysis, as little as
10−17–10−18 g of an element can be detected. It is used in such diverse scientific areas as metallurgy,
physics, electronics, mineralogy, environmental pollution, geology and, lately, in pathology, zool-
ogy, biochemistry, and other biological fields. The excess energy of an electron that migrates to an
inner shell to fill a newly created hole can do more than emit an x-ray. Often, instead of x-ray emis-
sion, the excess energy is transferred to a third electron from a further outer shell, which prompts its
ejection. This ejected species is called an Auger electron, and the method for its analysis is known
as Auger electron spectroscopy (AES).
8.2 PRINCIPLES
Atoms, when struck by electrons from an external source, yield x-rays, which are characteristic of
those atoms and are used to identify and quantify the elements present in a molecule. X-ray micro-
analysis combines electron microscopy and x-ray spectroscopy. When a specimen is observed
through the electron microscope, the sample is bombarded with high-energy electrons, which
generate characteristic and continuous background x-rays in the irradiated area of the sample.
If the exciting electron beam is focused to a diameter of 100 nm on an ultrathin section of same
thickness, a lightly conical electron probe of this size is formed within the specimen and x-ray
emission is restricted to this probed area. Thus, we can observe the specimen in the electron
microscope, select the feature of interest, focus the electron beam onto this feature, and record
the generated x-ray spectrum.
In Figure 8.1, a nucleus comprising neutrons and protons is surrounded by orbital electrons
distributed in different energy levels: K, L, M, and so on. X-ray microanalysis is based on
the excitation of these electrons to produce an emitted x-ray spectrum that is characteristic of
the element concerned. If one of the orbital electrons is removed from its energy level by an
incident electron, then the atom is said to be in an excited state. When this occurs, an electron
from a higher energy state will fall down into the gap to stabilize the atom. Because of the dif-
ference in potential energy levels, the excess energy is emitted during this electron transition
as an x-ray photon. Thus, if an electron in the K shell is removed a second electron from the
L shell may instantaneously replace it, giving off its excess energy as a photon of energy (E L –
E K), which is generally called “Eα radiation.” Now, the filling of the vacancy in the K shell by
an electron from the L shell will also produce a vacancy in the L shell, which in turn may be
filled with an electron from the M shell and so on; each electron transition is associated with
the production of x-ray photons of energies determined by the orbital energies. Thus, a single
ionization can give rise to a whole spectrum of characteristic x-rays, and this energy spectrum
identifies the atom.
A primary electron beam may, instead of interfering with the orbital electrons to produce charac-
teristic x-rays, interact with the nucleus. As the incoming electron beam is decelerated by the field of
nuclear charge, it radiates energy, which can be anything from the maximum energy originally car-
ried by the electrons to a small fraction of it. Figure 8.2 shows the energy spectrum produced by this
209
Incident electron
M shell
X-ray photon
White radiation
Scattered Nucleus
electron
FIGURE 8.1 Simple schematic representation of an atom showing x-ray production.
Characteristic
X-ray intensity
White
radiation
Eo X-ray wavelength
FIGURE 8.2 X-ray continuum.
effect, with the maximum energy being that of the primary electron beam Eo. This general spec-
trum is called “x-ray continuum,” “continuous radiation,” “white radiation,” or “Bremsstrahlung.”
It forms the background on which the characteristic x-ray lines are superimposed at specific wave-
lengths or energies.
White radiation forms a basic limitation to the ability to detect a characteristic “line” and it is
considered x-ray noise. However, it is useful in calculating elemental concentrations.
8.3 INSTRUMENTATION
For viewing biological material, there are two methods: (1) thin specimens are viewed in transmis-
sion and (2) bulk specimens are viewed by reflection. Accordingly, instrumental arrangements are
of two types:
1. Scanning electron microscope and x-ray detection system

2. Transmission electron microscope and x-ray detection system
X-Ray Microanalysis 211
X-ray detection systems used generally are also of two types: (1) wavelength-dispersive crystal
spectrometers and (2) energy-dispersive solid-state detectors. Wavelength-dispersive crystal spec-
trometers work on the principle that of the x-rays leaving the specimen, a narrow cone falls on a
curved crystal and a fraction of this signal is reflected into a detector, which is usually a gas flow
or a sealed, proportional counter. In the detector, the x-rays are converted to electrical signals that
are amplified and transferred to a multichannel analyzer. The individual channels are calibrated
by energy and the channel number or energy position gives qualitative analytical information. The
fraction of signal that is reflected depends on the crystal’s ability to “diffract” a particular wave-
length maximally and is governed by Bragg’s law, which states that for crystals,
2d sinθ = nλ

where n is an integer, λ is the x-ray wavelength maximally diffracted, d is the lattice spacing of the
crystal, and θ is the angle of incidence (and of reflection) of the x-ray beam at the crystal. Every
element in the periodic table has x-ray lines corresponding to characteristic wavelength (λ) values.
A crystal having a value of maximally diffracted wavelength the same as the λ value of x-rays emit-
ted by an element not only detects this element but also quantifies it. In order to extend the range of
elements detected, a number of crystals are incorporated in the x-ray differection system. All the
crystals have different d values or lattice spacings, so that for the same θ range the wavelength (λ)
range is large, thereby covering a number of elements.
The energy-dispersive solid-state detector can detect all x-ray energies leaving the specimen
at once, unlike the crystal spectrometer, which can detect only one x-ray energy at a time. The
solid-state detector provides an energy spectrum of all elements analyzed simultaneously. Here,
the incoming x-rays are sorted and analyzed by their energies and the apparatus consists of a liquid
nitrogen–cooled Si/Li semiconductor.
Figure 8.3 illustrates the incorporation of crystal detectors or solid-state detectors, or both, at
appropriate positions with respect to the electron microscope either in the scanning mode or the
transmission mode. In a scanning electron microscope, the detectors can be easily brought close to
the specimen for greater sensitivity.
Condenser
Scanning
coils
Objective
Solid-state
detector
Crystal
Secondary
electron X-ray detector
detector
Transmitted-electron
detector
FIGURE 8.3 Schematic representation of a scanning electron microscope incorporating x-ray microanalysis.
Liquid nitrogen
X-rays
Solid-state
detector
Crystal
Detector
Probe
Specimen
Image
FIGURE 8.4 Schematic representation of x-ray microanalysis of thin sections with TEM.
Both 1D and 2D analysis can be performed with a scanning electron microscope. For 2D analy-
sis, the detector is set so as to collect x-rays from only a particular element, and then the focused
electron beam is made to scan the specimen. The x-ray signal from the detector is displayed on a
cathode ray oscilloscope by synchronizing it with the electron beam raster. For one-dimensional
analysis, that is, a line trace, the output is fed to a chart recorder so that changes in elemental content
can be monitored across that line in the specimen. To analyze a particular area of interest, a static
probe is directed over that area and x-ray emission is analyzed over a period of time (Figure 8.4).
Almost any electron microscope can thus be converted to an x-ray analyzer by attaching a suit-
able detector to the specimen region. This idea was first given by Castaign in 1949, and in 1968 the
first electron microscope with an x-ray analyzer was constructed.
8.4 APPLICATIONS OF X-RAY MICROANALYSIS

Several problems can be tackled using this technique:
• The natural elemental composition of tissues can be demonstrated by analysis of normal

physiological levels after appropriately preparing the specimen for analysis.
• Accidentally introduced foreign material, for example, toxic chemicals, can be located and
identified within the tissue.
• Deliberately introduced elements, for example, administration of drugs, can be traced
throughout the tissue and related to morphological changes that follow.
• The histochemistry and immunochemistry of living systems can be studied in situ by
analysis of biochemical events.
8.5 T
ECHNIQUES FOR THE ANALYSIS OF SECONDARY, TERTIARY, AND
QUATERNARY PROTEINS BY X-RAY CRYSTALLOGRAPHY
8.5.1 Introduction
Protein x-ray crystallography is a technique used to obtain the 3D structure of a particular protein by
x-ray diffraction of the crystallized form of the protein. This 3D structure is crucial in determining
a protein’s functionality. X-ray crystallography can reveal the precise 3D positions of most atoms in
a protein molecule because x-rays and covalent bonds have similar wavelengths and, therefore, this
method currently provides the best visualization of protein structure. The specificity of the protein’s
active sites and binding sites is completely dependent on the protein’s precise conformation. It was
x-ray crystallography that made it possible for J. D. Watson and F. H. C. Crick to figure out the
double-helix structure of DNA.
The technique imparts knowledge of the cellular mechanism and the 3D structure of enzymes
and other macromolecules. It is critical that we understand better how each chemical reaction that
occurs in a cell needs a specific enzyme for it to happen. Two common techniques used for the
analysis of protein structure are nuclear magnetic resonance (NMR) and x-ray crystallography.
X-ray crystallography can be used to analyze different compounds up to a molecular weight of 106
(g/mol), for instance, whereas NMR is restricted to the analysis of biopolymers (polymers produced
by a living organism such as starch, peptides, and sugars) of molecular weights not more than
30,000 (g/mol). It can also measure compounds that are very small because the appropriate size
to measure the distance between atoms in a molecule is 0.5–1.5 Ǻ. X-rays are used as the form of
radiation to this end because their wavelengths are on the same order of magnitude as the bond
length of a covalent bond (~1 Ǻ or 1 × 10−10 m) and this is necessary to obtain a diffraction pattern
that reveals information about the structure of the molecule. If the radiation had a wavelength much
bigger or much smaller than the bond length of a covalent bond, the light would not diffract and no
new knowledge of molecular structure would be obtained.
8.5.2 Principles of X-Ray Crystallography

Crystals, including those of globular proteins, consist of repetitions of a basic structural component
called a “unit cell,” which may be a single molecule or a symmetrical arrangement of several mol-
ecules. Thus, each atom in a crystal must lie in a specific position with respect to all other atoms in
the crystal, enabling the structure to be determined by x-ray diffraction analysis. This consists of
directing a beam of x-rays of a single wavelength on a crystal and studying the characteristics of the
emerging rays. Most rays pass straight through the crystal without being affected, but the rays that
come into contact with an atom in the crystal are scattered by the clouds of electrons surrounding it.
More precisely, these electrons act as secondary sources of x-rays, which then radiate out from the
atom in all directions. The intensity of the x-rays leaving an atom of high electron density, such as
a heavy metal, is much greater than that of x-rays leaving an atom of low electron density, such as
hydrogen; thus, areas of high electron density can be said to scatter x-rays more strongly than areas
of low electron density.
X-rays, similar to other forms of electromagnetic radiation, are best regarded as waves of charac-
teristic lengths and amplitudes (Figure 8.5); the intensity of a ray is proportional to the square of its
amplitude. If two rays of identical wavelength are traveling on a common path so that they are exactly
in phase, that is, the crests and troughs of the waves correspond exactly, then they will combine to
give a ray of the same wavelength and phase but greater amplitude. The amplitude, and hence inten-
sity, obtained under these conditions will be the maximum that can be obtained by any combination
of these two rays. If the two rays are one quarter of a cycle out of phase, the intensity of the combined
ray will be about one-quarter of the maximum possible value, and the phase of the combined ray will
Ω
Component
rays
Combined
ray
(a) (b) (c)
FIGURE 8.5 The combination of rays of identical wavelength (λ) and amplitude (Ω) when directed along a
common path. The component rays are (a) exactly in phase, (b) one-quarter of a cycle out of phase, and (c) half
a cycle out of phase.
Crystals
X-ray
Film
FIGURE 8.6 Diffracted x-rays.
be a combination of the phases of its component rays. If the two rays are exactly half a cycle out of
phase, the waves will cancel each other out and the intensity of the combined ray will be zero.
The scattered x-rays emerging from a crystal can combine in the following way: Rays emerging
at certain angles to the incident ray will combine to give rays of maximum intensity, whereas those
emerging at other angles will cancel each other out. The results can be observed by placing a photo-
graphic plate behind the crystal to register the impact of emerging rays. In general, development of
the plate will show a spot at the center caused by the undeflected x-rays, which will be in phase; this
is surrounded by a pattern of other spots corresponding to the angles where emerging rays combine
to give intensity maxima. The overall effect is known as a “diffraction pattern” (Figure 8.6).
Before discussing x-ray crystallography in more detail, let us consider why we cannot observe
the atoms in a molecule by the use of optical or electron microscopy. Vision consists of two pro-
cesses: The beam of light (another form of electromagnetic radiation) that strikes an object is
scattered by the atoms, and these scattered rays are brought back together (focused) by the lens in
the eye to produce an image of the object on the retina. A magnified image may be produced by
the use of further lenses (optical microscopy), enabling one to clearly distinguish (resolve) features
that are too close to be seen separately by the unaided eye. The limit of resolution in micros-
copy depends on the wavelength of the type of electromagnetic radiation used and the focusing
properties of the instrument. With optical microscopy, the limit of resolutions is about half the
wavelength of the light used. Hence, individual atoms separated in a molecule by distances on the
order of 1–2 Å (1 Å = 0.1 nm) cannot be resolved by an optical microscope, since the wavelength
of visible light is in excess of 4000 Å.
Electron microscopes give a much greater resolving power than optical microscopes, but despite
the very low wavelengths of electron beams it is still not possible to visualize individual atoms
using an electron microscope because of the generally poor performance of the electromagnetic
lenses used in electron microscopy. Similarly, x-rays have wavelengths much smaller than those of
light rays; in fact they are of the same order of magnitude as inter-atomic distances. However, no
procedure has yet been devised for focusing x-rays, therefore no image can be produced using them.
Nevertheless, the detailed structure of a crystal scattering x-rays can be deduced from the diffrac-
tion patterns obtained.
Although each unit cell in a crystal may contain many atoms in a complex arrangement, let us
for the moment consider a unit cell simply as a region of high electron density, which can act as a
scattering center for x-rays. Thus the crystal consists of a regular arrangement of major scattering
centers, each corresponding to a unit cell, as shown in Figure 8.7.
First of all, let us look at the plane of scattering centers containing A, B, and C, which is inclined
at an angle (θ) to the incident beam of x-rays (Figure 8.7). Some rays will be scattered by the
electron-dense regions in the plane, whereas most of the rays will pass straight through the plane.
Each scattered ray has the same wavelength and phase as the incident ray and regarded as being
deflected. Rays will be scattered in all directions, so some will emerge at an angle ϕ to the plane.
Those leaving A and B at the same angle to the incident beam will reach a given point after travel-
ing exactly the same distance through space (so that distance QAU = distance RBT in Figure 8.7)
only when ϕ = θ. This is known as the “reflection condition” since the phenomenon of reflection at
a planar surface is also characterized by these angles being equal. Therefore, all rays reflected by
the scattering centers on the plane ABC, that is, all rays emerging at an angle such that ϕ = θ, will
be exactly in phase and will combine to give a ray of maximum intensity.
Now, let us consider a second plane of scattering centers containing D, E, and F, which is parallel
to the plane ABC and is separated from it by a distance d. Rays leaving B and E in the same direc-
tion can never reach a given point after traveling the same distance through space since distance
PES must be greater than distance RBT. However, if the difference in distance (d1 + d2 = dsinθ +
dsinϕ) is exactly a whole number of wavelengths, the emerging waves will still be exactly in phase.
Therefore, rays that emerge at the same angle to the incident beam from scattering centers on dif-
ferent but parallel planes will combine to give a ray of maximum intensity if nλ = dsinθ + dsinϕ,
where n is a whole number and λ is the wavelength of the rays. In summary, all the scattering centers
in a single plane will combine to give a diffracted ray of maximum intensity at the angle where the
reflection condition is met, whereas centers in different planes will combine to give rays of maxi-
mum intensity at angles where nλ = dsinθ + dsinϕ. If these two conditions are put together, rays
E
P
d1 ϕ
Incident Q A F
beam d2
θ ϕ d
R
B ϕ
C
S
T
U
FIGURE 8.7 Regular arrangements of major scattering centers.

emerging from all the scattering centers on any number of parallel planes that are at a distance d
apart will combine to give an intensity maximum where nλ = 2dsinθ. This was first stated by Bragg
and Bragg (father and son) in 1913 and is known as the “Bragg condition.”
Thus, it can be seen that regular repeating units are essential for the establishment of clear dif-
fraction patterns, since patterns from different scattering centers may reinforce each other under
these conditions. Crystals are rotated in a beam of x-rays, allowing time in each position for the
investigation of the diffraction pattern, until the pattern obtained indicates that planes of scatter-
ing centers are inclined at a suitable angle to the incident beam for reinforcement of patterns to
take place. A clear diffraction pattern may be obtained without rotating the specimen if the crystal
in question is not a single crystal but comprises separate regions of repeating units set at random
angles to each other and, thus, to the incident beam; this is often the case where the specimen is a
powder of fine crystals or a natural fiber.
In general, the greater the repeating distances within a specimen the closer the intensity maxima
on the photographic plate. If clear diffraction patterns can be obtained with a crystal in three differ-
ent orientations, then the dimensions of the unit cell and arrangement of unit cells within the crystal
can be deduced from the maxima values nearest to the center, which correspond to the largest repeat
distances.
If we now turn our attention to the structure of the molecule or molecules making up a unit cell,
we immediately realize that not all the atoms in a complex molecule can lie on the same plane.
Hence, although we have hitherto considered a unit cell to be a single scattering center lying on
a specific plane, a unit cell may in fact consist of a large number of component scattering cen-
ters (atoms) of which some lie at various distances in front of the plane and some at various dis-
tances behind the plane. This inevitably affects the diffraction pattern obtained. If intensity (and
hence amplitude) and phase is known for each x-ray causing a spot in the diffraction pattern, then
a 3D contour map showing the distribution of electron density within the unit cell can be drawn
up using a mathematical procedure called Fourier synthesis. From this map, the structure of the
molecule can be deduced. The intensity of an x-ray can be determined from a photograph of a dif-
fraction pattern or measured directly using a Geiger counter; however, there is no direct method for
determining the phase of the x-ray. This is called the phase problem.
The phase problem can be overcome in one of two ways: (1) A model may be having a built of
possible data on a molecular structure and the theoretical diffraction patterns. This may be useful in
explaining certain repeating features, but otherwise the number of possible structures of a complex
molecule is too immense to enable the successful implementation of this method when used alone.
(2) The alternative method is that of isomorphous replacement, which was introduced by Perutz in
1954. A heavy metal atom, such as mercury or uranium, is attached to a specific site of each mol-
ecule in the crystal without altering the 3D structure of the molecule. The heavy metal atoms, being
in regions of very high electron density, will cause appreciable changes to the amplitude and phase
of the rays producing a diffraction pattern. If the intensities of the spots in this case are compared
to those of the spots in the original diffraction pattern, it is possible to deduce the location of the
substituted atoms within the unit cells. The contribution of rays from the heavy metal atoms to each
spot in the diffraction pattern may then be calculated, in terms of both phase and amplitude. This
enables two possible solutions of the phase problem to be obtained for each spot, one in which the
phase of the original ray is in advance of that of the ray from the substituted atom, and one in which
it is an equal distance behind. It is possible to determine which of the alternative solutions is correct
by substituting between the amplitude and the phase of the rays producing a diffraction pattern with
a heavy metal atom in a different place, or possibly several different places. It is thereby possible to
deduce the complete structure of a molecule.
Low-resolution analysis (to about 5 Å), showing the main features of the molecular structure but
not the fine detail, may be performed using only the spots near the center of the diffraction pat-
tern. All the spots must be used for high-resolution analysis, showing the complete structure of the
molecule. Isomorphous replacement inevitably introduces some changes, however slight, in the 3D
structure, and the higher the resolution attempted the more significant these changes. Hydrogen atoms
are extremely weak scatterers of x-rays, so they are very difficult to pinpoint using these techniques.
It has often been found advantageous to use model-building and isomorphous replacement tech-
niques to complement each other. Low-resolution studies indicate the general shape of the molecule,
and from this information models can be built to elucidate the fine structure. X-rays are commonly
obtained in the x-ray tube by accelerating electrons to a high velocity released from an indecent
tungsten filament against a copper target. This produces rays of approximate wavelength 1.5 Å.
A more recent development is that x-rays selected from the electromagnetic radiation emitted
by highly expensive devices called “synchrotrons” or electrons to rings are of higher intensity
than those obtained from a conventional source. This is advantageous for the determination of
the structure of proteins of high molecular weight where the crystalline structure is unstable over
the exposure period to weak radiation. Another possibility is the use of neutron beams, which are
scattered by atomic nuclei rather than electrons, for high-resolution analysis, since they are scat-
tered strongly by hydrogen atoms. Also, they cause very little radiation damage to macromolecules,
enabling irradiation to be carried out for far longer periods than is possible with x-rays.
8.5.3 Some Results of X-Ray Crystallography

In 1939, Pawling and Corey and their coworkers began a systematic investigation of the 3D structures
of amino acids, dipeptides, and other molecules to provide data with a view to the eventual elucida-
tion of protein structure. X-ray diffraction analysis soon showed that the C–N bond length on a pep-
tide bond is shorter than what is expected for a single covalent bond. Therefore, some double-bond
character must be present; the actual structure deduced between two extremes is shown as follows:
A consequence of the presence of this partial double-bond character is that rotation about the
axis is restricted and all the atoms involved lie in the same plane. Two isomer arrangements are
possible in the trans form, with the oxygen and hydrogen atoms lying diametrically opposite to
each other, and the cis form, with these atoms lying adjacent to each another. In fact, only the trans
isomer is found.
The most significant factor accounting for the stability of the trans form is the spacing between
the carbon atom and the oxygen atom (2.8 Å), which is marginally less than the van der Waals con-
tact distance between these atoms (3.4 Å), so repulsion is slight between the atoms. In the unstable
cis form, the two (3.4 Å) atoms lie adjacent to each other and are separated by a distance (2.8 Å)
more than the van der Waals contact distance between two carbon atoms (4.0 Å), so repulsive forces
would be high between the atoms (Figure 8.8).
Pawling and Corey and their colleagues also noted that, in crystals, there is a high degree of
hydrogen bonding between oxygen atoms in one peptide bond and nitrogen atoms in another. The
distance between such atoms is often about 2.9 Å, which is much less than the van der Waals contact
distance between nonbonded oxygen and nitrogen atoms, thus indicating the presence of the hydro-
gen bond. Furthermore, the N–H…O linkage is usually approximately linear. On the basis of these
findings, they suggested various theoretical types of secondary structures that might be found in pro-
teins. In particular, both right- and left-handed α-helices seemed consistent with the available data,
but the arrangement of London dispersion forces (LDFs) was more favorable in the former structure.
Astbury had already used x-ray scattering to demonstrate regular features in the structures of
several fibrous proteins, and in some cases these were found to be consistent with the postulated
right-handed α-helix. The main features of the x-ray diffraction pattern of α-keratin (Figure 8.9a)
2.8 Å
O CHRʺ CO
1.2
7Å
Free rotation
1 .4
Å
allowed
1.32 Å
Free rotation C N
allowed
Rotation
1.0
3Å
restricted
4Å
1.5
H
HNRʹHC
FIGURE 8.8 Dimensions of the peptide bond.
C
C R
N R
O
C H C
H O N
C
R
N C
H C O
R
C
N
O H
Equivalent C
to 5.2 Å R
C N
O R
H C
5.2 Å C
N
H C
Equivalent to 9.7 Å R
C
O
R N
(a) C
C
O
(b)
FIGURE 8.9 Figure showing (a) the main features of the x-ray diffraction pattern of α-keratin and (b) a
polypeptide chain in the form of a right-handed α-helix (note the α-hydrogen atom has been omitted from the
diagram to minimize congestion).
are a periodicity of 5.2 Å along the axis of the fibers, which is the distance between the turns of the
α-helix (Figure 8.9b), and a periodicity of 9.7 Å at right angles to this axis, which is presumably the
distance between adjacent α-helices.
An α-helix contains approximately 3.6 amino acid residues per turn. This results in each pair
of peptide oxygen and nitrogen atoms being in a suitable position to form hydrogen bonds with
the corresponding atoms in the next turn of the helix (Figure 8.9b); these hydrogen bonds are all
approximately parallel to the axis of the helix.
Other types of secondary structures have also been demonstrated. If α-keratin is stretched
under humid conditions, it is converted to β-keratin, which has characteristic periodicities of
3.3 Å along the axis of the fiber and 4 and 9.7 Å perpendicular to the axis, which gives evi-
dence of a more extended form of secondary structure called a β-pleated sheet. Again, hydrogen
bonds can be formed between oxygen and nitrogen atoms in different peptide bonds, but in this
instance they are perpendicular to the axis of the fiber. The structure is unstable in keratin but
not in other fibrous proteins such as silk fibroin. Keratin is said to form parallel β-pleated sheets,
since the N-termini of adjacent polypeptide chains lie in the same direction, whereas silk fibroin
forms antiparallel β-pleated sheets, the N-termini of adjacent chains being in opposite directions.
Antiparallel β-pleated sheets may also be formed by the doubling back of a single polypeptide
chain (Figure 8.9a and b).
The stability of these α-helix and β-pleated sheet structures depends on the nature of the amino
acid side chains present; large or charged side chains tend to be disruptive. Hence, fibrous proteins
usually consist only of amino acids with small and uncharged side chains and have well-developed
secondary structures. Proline, because of the restricted rotation resulting from its ring structure, is
another amino acid that cannot form part of an α-helix or a β-pleated sheet, but it is incorporated
into the unique triple-helix structure of the fibrous protein collagen. The first globular protein to
have its 3D structure elucidated by x-ray crystallography was sperm whale myoglobin. Myoglobin
is an iron- and oxygen-binding protein found in the muscle tissue of vertebrates in general and in
almost all mammals. It is related to hemoglobin, which is the iron- and oxygen-binding protein in
blood, specifically in the red blood cells. This close relative of hemoglobin is a single polypeptide
chain of 153 amino acid residues; despite its relatively small size, over 10,000 diffraction spots
had to be accurately analyzed to give a resolution to 2 Å. Shortly afterward, the structural analysis
of hemoglobin itself was completed. Each of the four component polypeptide chains was found
to have a tertiary structure almost identical to that of myoglobin. Kendrew for his work on myo-
globin structure and Perutz for his studies on hemoglobin were awarded the Nobel Prize in 1962.
The structure of lysozyme, an enzyme from egg white consisting of 129 amino acid residues in a
single chain, was given by Blake and Phillips and their colleagues in 1965. These and other stud-
ies on globular proteins have shown that a limited degree of secondary structure is usually present
in them. Lysozyme has about 25% of its amino acids in α-helical zones and some in sections of
β-pleated sheet (Figures 8.10 and 8.11).
The amino acids at the positions where the secondary structure is disrupted are, as expected,
those with large side chains, for example, proline and leucine, or those with charged side chains
where two or more with like charges are close together. The molecules are very compact, with space
for very few water molecules within the interior. Most of the amino acids with nonpolar side chains
R R
R O C H
H C N
C
N C N
C N C C H
C C H O
O H
H O N C
N C N
H C H
O
N R O C
C
R
R R
FIGURE 8.10 A section of antiparallel β-pleated sheet (note the α-hydrogen atom has been omitted from the
diagram to minimize congestion).
Pleated sheet
region
NH3
Asp-52
Aspn-37 Trp-62
Trp-63
Glu-35
Substrate
S binding
cleft
S
COO
Asp-101
FIGURE 8.11 Simplified representation of the 3D structure of egg white lysozyme as revealed by x-ray dif-
fraction studies. Only the backbone of the polypeptide chain is shown, and α-helical regions are represented
by cylinders. The amino acid side chains fill up most of the available space within a molecule, but a clearly
defined cleft for the binding of substrate is apparent. The positions of certain important amino acid residues
are indicated.
are found within the interior of the molecule, where they are unlikely to come into contact with
water, whereas those with polar side chains are usually exposed to the solvent.
8.5.4 Investigation of Protein Structure in Solution

X-ray diffraction analysis is not suitable for investigating proteins in solution, since the molecules
are not fixed in a regular arrangement. However, other techniques may be used to give information
on the structures of proteins in solution, particularly on the degree of secondary structure present.
There will be differences in both IR and UV spectra between a polypeptide chain in an α-helix
conformation and one existing as a random coil (i.e., one without regular, repeating 3D features);
these are due to the presence or absence of hydrogen bonding between atoms in different peptide
bonds. Also, since a right-handed α-helix is an asymmetric structure, there will be differences in
optical rotation between a polypeptide in such a conformation and one consisting of the same amino
acid residues in a random coil.
Such investigations have helped to demonstrate that polypeptide chains can exist as α-helices
in solution. Such a structure is most readily formed if all amino acid side chains present are
small and uncharged, as is the case with polyalanine, a synthetic polypeptide consisting entirely
of L-alanine residues. If all the side chains are large, as with polyisoleucine, no α-helix is
formed. In the case of synthetic polypeptides with ionizable side chains, for example, polyglu-
tamic acid, the structure in solution varies with pH. At acid pH, glutamic acid side chains are
uncharged and an α-helix is formed. However, at alkaline pH, the side chains will have a nega-
tive charge; these repel each other and the α-helix is disrupted as shown by optical rotation
measurements. The reverse effect is found with polylysine, whose side chains are uncharged at
alkaline pH but have a positive charge at acid pH. Today, direct measurements of optical rotation
are rarely carried out as similar information can be obtained more easily by the use of circular
dichroism (CD) spectroscopy, which measures the differential absorption of right and left circu-
larly polarized light over a range of wavelengths.
Spectrophotometry may give useful information about protein structure since peptide bonds,
aromatic and imidazole side chains, and disulfides all give absorbance bands in the ultraviolet (UV)
range, which may vary according to the conformation of the protein and the micro-environment
of the absorbing group. Spectrofluorimetry too may be of value, for example, in investigations of
the fluorescence of tryptophan side chains. The electron spin resonance (ESR) technique, which
detects unpaired electrons, is useful for the investigation of metal ions in enzymes, whereas NMR
spectrometry currently gives the best structural information about proteins in solution. The NMR
technique detects atoms with an odd number of protons in their nuclei by giving them a magnetic
moment. If a kilogauss magnetic field is applied, such nuclei will move around with a frequency
depending on the magnetic moment (m) and the magnitude of the applied field (H0); if a radiofre-
quency around 100 MHz field is then generated so that its magnetic vector rotates perpendicular
to the kilogauss field and the conditions are adjusted, resonance will occur when the frequency of
oscillation of the field corresponds to the precession of a nuclear dipole, which can enable the nuclei
concerned to move to higher energy levels. For the single proton in the hydrogen nucleus, for exam-
ple, there are two possible orientations: One, aligned with the kilogauss field, has an energy level
given by –μH0, whereas the other, aligned against the field, has an energy level of +nH0. Therefore,
moving from the orientation of lower energy to that of higher energy requires an energy input of
2μH0, and the resonance frequency (ν) is given by hν = 2 H 0.
In this expression, h is Planck’s constant. This resonance is detected as the absorption of
energy (= 2 H 0 ) by the proton from the radiofrequency field. In general, the intensity of a reso-
nance absorption line is directly proportional to the number of nuclei in an identical environment.
However, chemical shifts in resonance frequency for identical nuclei in different electronic envi-
ronments can be detected, as can the splitting of resonance peaks into multiple fine structures
because of the interaction between neighboring nuclear spins. Switching off the radiofrequency
field and studying the characteristics of the change back (termed relaxation) to the original dis-
tribution of nuclei at different energy levels can also give information about interactions between
neighboring nuclei. Among the nuclei that can be investigated by NMR techniques, there are
1H, 13C, and 15N. Isotopes such as 13C and 15N, which do not occur naturally, can be used in the
.
investigation of protein structure. They must first be incorporated into the protein, for example, by
utilizing bacteria to synthesize the protein in a medium rich in the isotope, depending on the type
of investigation consistent with the assumption that 3D structures found in protein crystals may
also occur in solution.
Experiment: Analysis of Proteins by X-Ray Crystallography

Principle
The technique imparts knowledge of the cellular mechanism and the 3D structure of enzymes and
other macromolecules (Figure 8.12). It is critical that we understand better how each chemical reaction
that occurs in a cell needs a specific enzyme for it to happen. Two common techniques used for the
analysis of protein structure are NMR and x-ray crystallography. X-ray crystallography can be used to
analyze any different compounds up to a molecular weight of 106 (g/mol), for instance, whereas NMR is
restricted to the analysis of biopolymers (polymers produced by a living organism such as starch, pep-
tides, and sugars) of molecular weights no more than 30,000 (g/mol). It can also measure compounds
that are very small because the appropriate size to measure the distance between atoms in a molecule
is 0.5–1.5 Ǻ. X-rays are used as the form of radiation because their wavelengths are on the same order
of magnitude as the bond length of a covalent bond (~1 Ǻ or 1 × 10 −10 m), which is necessary to obtain
a diffraction pattern that reveals information about the structure of the molecule. If the radiation had a
wavelength much bigger or much smaller than the bond length of a covalent bond, the light would not
diffract and no new knowledge of the molecular structure would be obtained.
FIGURE 8.12 (See color insert.) Computer-generated tertiary structures of crystallographic data of ferre-
doxin proteins FdxH1 and FDxH2 from the cyanobacterium Anabaena variabilis.
The three components needed to complete an x-ray crystallography analysis are a protein crystal, a
source of x-rays, and a detector.
Procedure
A. First Step
The process begins by crystallizing a protein of interest. Crystallization of protein causes all the protein
atoms to be orientated in a fixed way with respect to one another while maintaining their biologically
active conformations, which is a requirement for x-ray diffraction. A protein must be precipitated out
or extracted from a solution. The rule of thumb here is to get as pure a protein as possible to grow lots
of crystals (this allows the crystals to have charged properties and surface-charged distribution for bet-
ter scattering results). Four critical steps are performed to achieve protein crystallization, as follows:
1. Purify the protein. Determine the purity of the protein; if it is not pure (usually greater than
99%), then it must undergo further purification.
2. Precipitate the protein. This is usually done by dissolving the protein in an appropriate sol-
vent (water–buffer solution with an organic salt such as 2-methyl-2,4-pentanediol; if the pro-
tein is insoluble in water–buffer solution or water–organic buffer solution, then a detergent
such as sodium dodecyl sulfate [SDS] must be added).
3. The solution must be brought to supersaturation (condensing the protein from the rest of the
solvent-forming condensation nuclei). This is done by adding a salt to the concentrated solu-
tion of the protein, thereby reducing its solubility and allowing the protein to form a highly
organized crystal (this process is referred to as salting out). Other methods include batch
crystallization, liquid–liquid crystallization, vapor diffusion, and dialysis.
4. Let the actual crystals grow. Since nuclei crystals are formed, this will lead to actual crystal
growth.
B. Second Step
For the next step, x-rays are generated and directed toward the crystallized protein. X-rays can be gener-
ated in four different ways:
1. By bombarding a metal source with a beam of high-energy electrons
2. By exposing a substance to a primary beam of x-rays to create a secondary beam of x-ray
fluorescence
3. From a radioactive decay process that generates x-rays (gamma rays are indistinguishable
from x-rays)
4. From a synchrotron (a cyclotron with an electric field at constant frequency) radiation source
The first and the last methods utilize the phenomenon that an accelerating charge gives off radiation.
Then the x-rays are shot at the protein crystal, which results in some of the x-rays going through the
crystal and the rest being scattered in various directions. The scattering of x-rays is also known as x-ray
diffraction. Such scattering results from the interaction of electric and magnetic field of the radiation
with electrons in the atoms of the crystal.
The patterns are a result of the interference between the diffracted x-rays, which is governed by
Bragg’s law. It gives the expression 2dsinθ = n × λ, where d is the distance between two regions of elec-
tron density, θ is the angle of diffraction, λ is the wavelength of the diffracted x-ray, and n is an integer.
If the angle of reflection satisfies the condition
(n × λ )
sin θ =
2d
the diffracted x-rays will interfere constructively. Otherwise, destructive interference occurs. Figure 8.13
shows an example of constructive interference. Here is an example of destructive interference:
Constructive interference indicates that the diffracted x-rays are in phase or lined up with each
other, whereas destructive interference indicates that the x-rays are not exactly in phase with each other.
The result is that the measured intensity of the x-rays increases and decreases as a function of angle and
distance between the detector and the crystal.
The x-rays that have been scattered in various directions are then caught on an x-ray film, which
shows a blackening of the emulsion in proportion to the intensity of the scattered x-rays hitting the film,
or by a solid-state detector, similar to the ones found in digital cameras. The crystal is rotated so that
the x-rays are able to hit the protein from all sides and angles. The pattern on the emulsion reveals much
information about the structure of the protein in question. The three basic physical principles underly-
ing this technique are as follows:
1. Atoms scatter x-rays. The amplitude of the diffracted x-ray is directly proportional to the
number of electrons in the atom.
2. Scattered waves recombine. The beams reinforce one another at the film if they are in phase
and cancel one another out if they are out of phase. Every atom contributes to a scattered
beam.
3. The 3D atomic arrangement determines how the beams recombine.
The intensities of the spots and their positions are thus the basic experimental data of the analysis.
C. Final Step
The final step involves creating an electron density map based on the measured intensities of the dif-
fraction pattern on the film. A Fourier transform can be applied to the intensities on the film to recon-
struct the electron density distribution of the crystal. In this case, the Fourier transform takes the spatial
arrangement of electron density and gives out the spatial frequency (how closely spaced the atoms are)
in the form of the diffraction pattern on the x-ray film. An everyday example of Fourier transform is the
music equalizer on a music player. Instead of displaying the actual music waveform, which is difficult
to visualize, the equalizer displays the intensity of various bands of frequencies. Through the Fourier
transform, electron density distribution is illustrated as a series of parallel shapes and lines stacked on
top of each other (contour lines), similar to a terrain map. The mapping gives a 3D representation of the
electron densities observed in x-ray crystallography. When interpreting the electron density map, the
resolution needs to be taken into account. A resolution of 5–10 Å can reveal the structure of polypep-
tide chains, 3–4 Å the structure of groups of atoms, and 1–1.5 Å the structure of individual atoms. The
resolution is limited by the structure of the crystal, and for proteins it is about 2 Å.
Diffracted wave 1 Diffracted wave 2 Constructive interference
FIGURE 8.13 Diffracted wave and constructive interference.

SUGGESTED READING
Goldstein J., D. Newbury, D. Joy, C. Lyman, P. Echlin, E. Lifshin, L. Sawyer, and M. Joseph. 2003. Scanning
Electron Microscopy and X-Ray Microanalysis. New York: Springer.
Kraut, J. “How Do Enzymes Work?” Science. 242:534.
National Institutes of Health. 2006a. NIH Publication No. 06-474 July 2006 Medicine by Design. 25–27.
http://www.nigms.nih.gov.
National Institutes of Health. 2006b. NIH Publication No. 06-474 July 2006 Medicine by Design. 31. http://
www.nigms.nih.gov.
National Institutes of Health. 2007. NIH Publication No. 07-5423 September, 2007 Structure of Life. 37–38,
40, 44. http://www.nigms.nih.gov.
Orr, P. J., and S. L. Kearns. 2011. “X-Ray Microanalysis of Burgess Shale and Similarly Preserved Fossils.”
Quantifying the Evolution of Early Life. Topics in Geobiology 36:271–99.
Shafranovskii, I. I., and N. V. Belov. 1962. “E. S. Fedorov.” In 50 Years of X-Ray Diffraction, edited by Paul
Ewald, 351. New York: Springer.
Viadiu, H. November 2011. “Why Do We Need Crystals?” UCSD Lecture.
IMPORTANT LINK
1. X-ray microanalysis: http://www.thermoscientific.com/ecomm/servlet/newsdetail?contentId=52420&
storied=11152&gclid=CNS785KeoasCFYEa6wodZWwYFA
9 Techniques with
Radioisotopes
9.1 INTRODUCTION
A radioisotope is a version of a chemical element that has an unstable nucleus and emits radiation
during its decay to a stable form. Radioisotopes have important uses in medical diagnosis, treat-
ment, and research. A radioisotope is so named because it is a radioactive isotope, an isotope being
an alternate version of a chemical element that has a different atomic mass.
Most radioisotopes are made by bombarding a stable element with neutrons in the core of a
nuclear reactor (see fission). The radiations given off by radioisotopes are easy to detect (hence
their use as tracers), can in some instances penetrate substantial thicknesses of materials, and have
profound effects (such as genetic mutation) on living matter. Most natural isotopes of relative atomic
mass less than 208 are not radioactive. Those from 210 and up are all radioactive.
Radioisotopes have many uses in medicine, for example, in radiotherapy and radioisotope scan-
ning. The use of radioactive isotopes in the diagnosis, investigation, and treatment of disease is
called nuclear medicine. The nucleus of a radioisotope is unstable and undergoes changes by break-
ing down into a more stable form. A radioisotope decays over a period of time into a new element.
As it decays, it emits radiation energy in the form of alpha and beta particles and gamma radiation.
The time taken for half of the original atoms to decay is known as the half-life. The product of
radioactive decay is called a “daughter” atom.
9.2 ISOTOPES AND RADIOACTIVITY

There are many different types of radiation. Some types have a particulate character; others, called
electromagnetic (EM) radiation, have wave-like properties. Alpha particles result from the decay of
relatively heavy radioisotopes. They consist of two neutrons and two protons, bound together and
identical to helium nuclei, He:
210
84 Po → 206
82 Pb + 42 He (α -particle)
The particles move relatively slowly, but due to their mass, they have a high-momentum travel in
straight lines not deflected from their path. Normally, they are only deflected by direct collision
with a nucleus (Figure 9.1). Americium 241 (Am-241) is a familiar example, commonly found in
household smoke detectors.
In beta decay, a neutron converts to a proton, emitting a beta particle in the process. The beta
particle is identical to an ordinary electron. Beta particles are electrons released from the nucleus
by the decay of a neutron into a proton and an electron (Figure 9.2). Their energy spectrum depends
on the speed with which the electron leaves the nucleus. Beta particles are emitted from a given
radioisotope over a continuous range of energy up to a maximum value (Emax), which is the charac-
teristic of each radioisotope. They have little mass—about 1/7400 the mass of alpha particles. As
a beta particle traverses material, it causes the ionization and excitation of orbital electrons. Beta
particles produced by 3H and 14C are weak, with little penetrating power (“soft” beta particle), but
those produced by 32P are more energetic (“hard” beta particles) and have greater penetrating power.
225
Alpha particle radiation
Daughter
nucleus
Th-231 4α++
Parent nucleus 2
U-235
Alpha particle
(helium nucleus)
FIGURE 9.1 Alpha radiation and decay process.
Beta particle radiation
Daughter
nucleus
Calcium_-40
0ν
0
Antineutrino
Parent nucleus 0 –
Potassium-40 –1β
Beta particle
FIGURE 9.2 Beta radiation and decay process.
Carbon 14 (14C) is a radioisotope of carbon, which undergoes beta decay and may be familiar for its
use to establish the age of ancient artifacts (“carbon dating”):
14
6 C → 147 N + beta particle
Gamma rays are emitted if a nucleus still has excess energy following the decay and emission of
other particles. They are electromagnetic in nature (called photons), with a discrete, unique energy
(this is used to identify different radioisotopes). Gamma rays are not physical particles, but their
interactions with matter are described by assigning them particle-like properties (Figure 9.3).
Techniques with Radioisotopes 227
Beta particle
Gamma-ray radiation
0 –
–1β
Gamma rays
Parent nucleus
Cobalt-60 Daughter nucleus
Ni-60
FIGURE 9.3 Gamma radiation and decay process.
Radioisotopes or unstable versions of an element that emit radiation as they try to reach more
stable forms are critical in modern medicine. The nucleus of an atom of a radioactive isotope has a
certain probability, characteristic for that isotope, that it will decay at any instant. The probability
remains constant independent of chemical reactions the atom may undergo. It is also independent of
temperature or other physical conditions. The probability is constant for all atoms of a given isotope
in a specialized period of time; a constant fraction of the nuclei will have decayed. The half-life
(T1/2) of an isotope is a period of time during which half the radioactive atoms originally present will
have decayed. It is mathematically related to the radioactivity decay constant, which is as follows:
0.693
T1/2 =
λ
99Mo is used to produce 99Mo/99mTc generators (a generator technology developed at Brookhaven
National Laboratory) for use in nuclear medicine. 99mTc is the most widely used radionuclide in
nuclear medicine, both for the detection of disease and for the study of organ structure and function.
More than 15 million procedures are performed each year in the United States using 99mTc.
9.3 IONIZATION EFFECTS

Because alpha particles are relatively massive and doubly charged, when they pass close to another
atom, they may strip some orbital electrons from that atom, producing positive ions. An alpha par-
ticle with energy of 1.5 MeV can produce about 2 × 105 positive ions in the air before its energy is
expended. Beta particles also lead to the ionization of materials through which they pass. Being less
massive, they travel faster and hence spend less time in the vicinity of other atoms and have less
time to remove electrons from them. The ionization effects caused by alpha particles are therefore
much less intense than those produced by beta particles. Gamma rays being uncharged have no
appreciable force fields; they do not lead directly to the ionization of materials. However, they inter-
act with matter in three unique ways, indirectly producing energetic electrons:
1. Low-energy gamma radiation (<0.5 MeV) can transfer all their energy to the orbital
electrons of atoms of the absorbing medium. The energy is thus transformed to the kinetic
energy of the electrons, which ejects out as the “photoelectron.”
2. Medium-energy gamma radiation (0.5–1.0 MeV) may interact with electrons by inelastic
collision and transfer only a portion of their energy in the process. The electron ejected
(now termed the “compton electron”) has lesser energy than the energy of the incident
gamma radiation.
3. High-energy gamma rays having energy more than 1.02 MeV react directly with the nucleus
producing an electron–positron pair. This is a unique process in which high-energy gamma
rays are transformed into matter. The resulting positron reacts with the surrounding matter
by colliding with an electron. The mass of both the positron and electron are annihilated
to become two 0.51 MeV photons.
Several devices for the measurement of radioactivity are based on the measurement of this ioni
zation in gas-filled chambers, gas ionization detectors such as ion chambers, proportional counters,
and Geiger–Mueller counters. Before considering any of the measurement techniques, it makes
sense to first make ourselves familiar with the measurement units of radioactivity.
9.4 MEASUREMENT UNITS

Measurement units can be classified into three types:
1. Unit of exposure of radioactivity, that is, the amount of radiation energy directed at a mate-
rial. The most common unit is Rontgen (R), which is defined as the quantity of X radiation
or gamma radiation in the air, an ion of either sign carrying a charge of 2.58 × 104 C/Kg of
air. Rontgen was restricted to radiations below 3 MeV. Because of the difficulty of measur-
ing the ionizations in air of the very energetic secondary electrons, radiation absorbed dose
(RAD) was introduced.
2. Radiation absorbed dose or RAD is the unit of absorbed radiation energy. It is defined
as the absorption of 10 −2 J of radiation energy per kilogram of material. The SI unit of
absorbed dose is Gray (Gy) defined as 1 J/kg and therefore one hundred times larger than
RAD. Since the energy absorbed in tissue corresponding to an exposure to 1 Rontgen is
0.0095 J/Kg, 1 Rontgen gives al1 absorbed dose of 0.95 RAD.
3. Unit of activity: This was until recently Curie (Ci), defined as the number of disintegrations
per second (dps) occurring in 1 g of pure radium (236Ra). It was arbitrarily fixed at 3.7 ×
1010 dps. That is,
1 Ci = 3.7 × 1010 dps
In SI, the Curie has been replaced by the Becquerel (Bq). The two are related as
2.703 × 10 −11 Ci = 1 Bq
3.7 × 1010 Bq = 1 Ci
Specific activity is defined as the amount of radioactivity in a given weight of material and
is usually expressed as Curies, disintegrations rate, or count rate, per unit mass of element;
for example, the specific activity of C is 19 counts per minute per gram.
9.5 MEASUREMENT TECHNIQUES

Radioactivity is detected and calculated by measurements made by observing physical or chemical
changes in appropriate devices. The most common method is by measuring the amount of ioniza-
tion caused in air or other gases. Though this is the most important dosimetric method, there are
many other systems of detection, some of which are discussed next.
Scintillation detectors convert the radiation energy of ionizing particles into pulses of light. The
size of the pulse is proportional to the energy deposited in the crystalline or liquid scintillant. Some
semiconductors show an altered conductivity during exposure to radiation. This method is similar
to the ionization chamber measurement, except that the current is flowing in the solid semiconduc-
tor crystals and not in the gas of the ionization chamber. In the ferrous sulfate dosimeter, FeSO4 is
converted to Fe2(SO4)3 when irradiated. Chemical titrations with K 2Cr2O7 may be used to determine
the amount of ferric ion and therefore the radioactivity present.
Calorimetry involves the measurement of the rise in temperature produced by radiation in an
insulated mass of unknown thermal capacity. When LiF and many other crystals are heated after
being exposed to radiation, they emit light; this is called thermoluminescence. The absorption of
radiation energy causes free electrons to be trapped in the lattice imperfections of the crystalline
structure. These trapping levels lie between the valence band and the conduction band; the electrons
can remain trapped for a considerable time. If the temperature of the crystal is raised, the electrons
are excited from the trapping levels to the conduction band and then return to the valence level with
the emission of light. Thermoluminescence devices may be used as powders in capsules or sachets.
Thermoluminescent dosimeters are widespread in laboratories for personnel monitoring.
Photographic emulsions consist of AgX crystals or grains dispersed in gelatin. Radiation absorbed
in an individual grain forms a latent image, and the chemical action of development reduces the
grain to silver. The blacker the film is, as measured by densitometry, the more doses it has received.
This again is used for personnel protection, in the form of film badges. Certain plastics and glasses
become increasingly opaque with increasing radiation dose.
9.5.1 Scintillation Counting Systems

Scintillation counting is a means of detecting radiation through the production of light flashes (scin-
tillation). The energy of radiation is used to produce pulses of light, which are counted. Substances
called “fluors” or scintillators fluoresce upon irradiation. The phenomenon of fluorescence has been
discussed elsewhere, and here it should suffice to say that fluorescence is the emission of radiation
of longer wavelengths as compared to the wavelengths of incident radiation. This may appear in the
visible region of the spectrum, and energy is emitted as photons, which are counted by associated
electronic equipment.
Figure 9.4 shows the mechanism of scintillation counting. The photomultiplier tube transforms
the emitted photons into an electrical signal; the magnitude of this signal is increased by more than
a million times. An extremely stable high-voltage power must be supplied in order to maintain the
reproducibility in multiplication. The preamplifier further multiplies the photomultiplier output.
This allows high counting rates to be achieved using scintillation counting.
High-voltage supply
Photons Electrical signal
Ionizing
radiation
Pulse
counting
Scintillator Photomultiplier tube Preamplifier system
FIGURE 9.4 Simplified mechanism of scintillation counting.

The pulse height analyzer differentiates among the energies of the incident gamma rays. This
analyzer classifies pulses according to their height or amplitude. A single channel pulse height ana-
lyzer consists of two variable discriminators, which allow for the selection of lower and upper levels
of detection. The lower discriminator setting is termed the base. The upper discriminator setting
is selected by adding a voltage increment to the base. These two discriminators, together with an
anticoincidence circuit, allow only those energies between the two discriminator levels to pass to
the scaler. The scaler displays the counts accumulated during the counting period, that is, it registers
the number of pulses received.
Depending on whether the fluor is a solid or liquid, there are two systems, namely solid scintil-
lation counting and liquid scintillation counting. The fluor generally used for solid scintillation
counting is a single large crystal of sodium iodide containing thallium as an activator. The crystal
surrounds the sample to increase counting efficiency. The sodium iodide crystals, being hygro-
scopic (absorb water) in nature, are kept in light-reflecting aluminum sachets, which are completely
closed except where attached to the photomultiplier tube through a transparent window.
Low-energy beta emitters like 3H and 14C cannot be counted by solid scintillation counting
because the weak emissions cannot traverse the aluminum envelope of the scintillation crystals.
This necessitates an intimate mixture of the isotope dissolved in liquid fluor so that there is no
self absorption of beta or alpha particles and efficient energy transfer occurs. Liquid scintillation
derives its name from the liquid mixture composed of isotope sample, the fluor dissolved in an
organic solvent. The mixture of an organic solvent (usually toluene) and the fluor is often called a
“cocktail.” For samples containing water, dioxane can be used as a solvent. The fluors are generally
complex heterocyclic, organic compounds that when excited emit photons in the near ultraviolet
and visible regions. The fluors generally comprise less than 1% of the cocktail. Some organic fluors
used are PPO and POPOP. PPO is the primary solute. POPOP is the secondary solute and is used
to shift the fluorescence of PPO to a longer wavelength for better matching to the spectral response
of photomultiplier tubes. This procedure increases the counting yield and is generally used in the
measurement of H.
The emissions from the sample interact with the material surrounding them and cause exci-
tation first of the solvent molecules. This excitation energy of the solvent is transferred to the
solute and the fluor, causing the excitation of fluor electrons. The excited electrons in the fluor
emit photons of light as they fall back to the ground state. These photons of light are detected by
the paired photomultiplier tube (PMT) and result in electrical pulses as in solid-state counters
(Figure 9.5).
Since the low-energy ranges of beta emissions result in a photomultiplier output of the same
magnitude as the thermionic emission, coincidence circuitry has been used. This ensures that only
pulses seen simultaneously (usually within less than 20 nanoseconds) are registered. Pulses from
PMT
CH3 CH3
Fluor
Disintegration
Excited solvent
FIGURE 9.5 Liquid scintillation counting.

the two detection circuits are passed through a coincidence circuit and electronically added up.
Pulses then pass to two or more channels, each consisting of a linear amplifier, pulse height ana-
lyzer, and scaler, as in solid-state systems (Figure 9.6)
Liquid scintillation counting, though ideal for counting weak emissions, poses the problem of
“quenching.” This is especially true of biological samples, which may contain a great variety of
chemical compounds. Even oxygen in the air and chemicals in the sample result in quenching.
Quenching is of three types: chemical, chromatic, and optical. Chemical quenching is caused by
various polar absorbing energies from excited solvent molecules partly preventing the excitation of
the fluor. Color quenching can be expected whenever the fluor solution does not have its character-
istic light blue color due to impurities. Yellow and red solutions especially may absorb the blue light
emitted by the fluors. Optical quenching results when the mixture of the scintillation cocktail and
sample results not in true solutions but in suspensions. Quenching decreases the detectable energy
released by isotopes, hence it should be minimized. Because quenching is often unavoidable and the
Sample
PMT + PMT
fluor
High-voltage supply
Coincidence
circuit
Amplifier
Pulse height analyzer
Scaler
(a)
(b)
FIGURE 9.6 (a) Block diagram of a liquid scintillation counter; (b) a liquid scintillation counter.
degree of quenching is unpredictable, therefore, it should be corrected. Correction for quenching,

that is, the determination of efficiency (E), can be brought about by using the following relationship:
cpm
%E = × 100
dpm
Disintegrations per minute (dpm) is an absolute number proportional to the isotopic content of a
sample, while counts per minute (cpm) refers to the detected counts, which is always less than dpm
due to quenching.
9.5.2 Geiger–Mueller Counter

The Geiger–Mueller counter utilizes the ionizations produced in air or gas by radioactive disin-
tegrations. A Geiger counter, also called a Geiger–Müller counter, is a type of particle detector
that measures ionizing radiation. They detect the emission of nuclear radiation: alpha particles,
beta particles, or gamma rays. A Geiger counter detects radiation by ionization produced in a low-
pressure gas in a Geiger–Müller tube. Each particle detected produces a pulse of current, but the
Geiger counter cannot distinguish the energy of the source particles. Geiger counters are popular
instruments used for measurements in health physics, industry, geology, and other fields, because
they can be made with simple electronic circuits.
The electrical signal is produced by a special tube (Figure 9.7). The tube consists of a chamber
with the inner surface coated with an electrical conductor and it acts as a cathode. At the central
axis of the chamber is a wire (anode) insulated from the cathode. The tubes are of different designs.
In the most common end–window tube, the end of the tube is covered with a thin membrane or
window that is permeable to particles of sufficient energy. The inside of the chamber is filled with
a monoatomic gas, usually argon or helium containing a small amount (0.1%) of halogen or organic
Cathode
Input
window
Anode
Gamma
radiation
Counter Resistor
Voltage
R
source
FIGURE 9.7 Geiger–Mueller counter.

gas. This type is used mostly for quantitative estimations on solid materials. Other designs include
the thin wall type used mainly inside contamination monitors. There are others not discussed here,
which are useful for measuring activity in liquids. These include the dipping, liquid flow, annular
well, and tissue probe types.
For accurate quantitative work, Geiger–Mueller tubes (Figure 9.8) are contained in a lead block,
which also surrounds the sample chamber to shield the tube and chamber from outside radiations
giving rise to counts in the apparatus when no sample is present. When a radioactive emitter is
brought close to the window of the tube, some of the ionizing radiation (gamma) or particles (alpha
and beta) penetrate the window and pass into the gas inside the tube, leading to the formation
of pairs of ions—positive ions and electrons. If a high, potential difference is applied across the
electrodes, these ions are accelerated toward the electrode of the opposite charge. The accelerated
ions also react with gas atoms of the tube to produce more ions, and this chain reaction continues
to produce an avalanche of ions. An amplification of about 106 –108 is normally obtained; when the
ion avalanche reaches the electrodes, it is neutralized, producing a flow of electrons in the external
circuit and giving a measurable potential of 1–10 V. Thus, the reaction is terminated and another
particle can be detected. The halogen gas inside the tube absorbs some of the energy of the accel-
erated ions, thereby quenching them and helping to terminate the reaction in a very short time.
Therefore, sufficient quenching gas must be added to return the tube to its unionized state in less
than a millisecond from the particle’s entry.
The electronic circuits associated with the tube can be designed to indicate the average current
flow (a rate meter) or to total the number of electrical pulses (a scaler). The count rate is dependent
upon the potential applied across the electrodes. This can be shown by varying the applied voltage
and determining the count rate on a suitable sample. On plotting the electrical potential against the
count rate, a characteristic curve is obtained (Figure 9.9). At low voltages, the curve is exponential,
and slight changes in voltage cause considerable changes in the count rate. At higher voltages, the
curve becomes linear over this region; the voltage across electrodes is a great enough to cause par-
ticles to move sufficiently fast to produce maximum ionization of the tube gas.
At even higher voltages, the count rate increases exponentially as the Geiger tube goes into
continuous discharge, the voltage being great enough to break down the insulating properties of
the gas inside the tube. For maximum stability, the tube is operated in the plateau region where
Glass bead
Metalized
cathode surface
Anode wire
Insulated
base
Thin-wall type End-window type
FIGURE 9.8 Types of Geiger–Muller tubes.

Continuous
discharge
Count rate
Plateau
Sigmoid region
Electrical potential
FIGURE 9.9 Characteristic sigmoid curve.
changes in voltages have little effect upon the count rate. In the plateau region, the tube is operating
at near its maximum efficiency; therefore, no distinction can be made between particles of differing
energy content (that the particles have sufficient energy to penetrate the tube window). This method
of counting is therefore an all-or-nothing process. As in the case of scintillation counters, the effi-
ciency of the tube is cpm/dpm × 100.
When the energy of radiation is low, as from 3H particles, most of the particles are absorbed
either before they reach the Geiger tube of the counter or by the window material. Hence, tritium
cannot be counted on in this type of system unless special windowless gas-flow tubes are used.
The condition under which a Geiger–Mueller tube is usually operated is such that the tube gas
is almost totally ionized, and hence the electrical pulse size is not influenced by the nature of the
incident radiation. However, at low voltages, alpha and beta particles produce different degrees of
ionization and different intensities of signal. Consequently, by the use of suitable discriminator
circuits either in a normal Geiger system or in a low-voltage ionization chamber, alpha and beta par-
ticles from same or different sources can be detected. This type of counting is termed “proportional
counting” since the size of the signal is proportional to the amount of ionization produced by the
incident radiation and therefore varies with the nature of this radiation.
9.6 AUTORADIOGRAPHY
Autoradiography is the detection of radioactivity using photographic emulsions. This is a technique
by which radioactivity can only be detected and not measured. However, this factor does not in any
way lessen its importance as a unique technique in biology. In conjunction with several other tech-
niques, autoradiography is widely used in molecular biology. A photographic emulsion consists of
very small crystals of silver bromide in gelatin mounted on a glass or flexible support, and the silver
bromide also contains small quantities of silver sulfide and colloidal silver. Also, the lattice struc-
ture is not perfect but contains spaces or “holes” in the structure where ions should be, and there are
silver ions out of place and in between the other ions (interstitial ions). When a radioactive emission
passes into a photographic emulsion, it causes ionization and sets electrons free in the ionic silver
bromide lattice. The electrons migrate over short distances to areas known as “sensitivity specks,”
which are probably composed of silver sulfide, and these in turn become negatively charged. This
charge attracts interstitial silver ions, and upon reaching the speck, they are neutralized to silver,
forming a so-called latent image. Thus, the specks act as loci for the growth of the nuclei of metal-
lic silver, the amount of metallic silver formed at these points being dependent upon the amount of
radiation received.
During development of the film, the developer supplies electrons and causes the reduction of
silver ions to metallic silver atoms, which are responsible for the visible image. However, because
of the catalytic effect of the metallic atoms already produced by the radiation, the silver ions in the
region of the latent image are reduced by the developer much faster than those regions where there is
no latent image. Hence, if development is correctly timed, only the former produces a visible image,
which will reflect the sites of exposure of the emulsion to radiation. Thiosulfate present in the fixer
solution removes unexpected silver bromide and thereby stabilizes the image.
9.7 COUNTING STATISTICS

If a single radioactive sample is counted several times under identical conditions and the count
rate is corrected for radioactive decay or the decay correction is negligible, the individual count
rates will deviate about a mean value. These deviations are due to the random nature of radioac-
tive decay. Understanding these statistical effects is necessary in the consideration of experimen-
tal design and in the interpretation of experimental results. Counting statistics closely follow the
Poisson probability distribution. By a special property of the Poisson distribution, the standard
deviation (D) of a registered number of counts, C, is equal to the square root of that number for c
registered counts:
D= c
The standard deviation increases as the square root of the number of counts but decreases as a
percentage of the counts. If in the equation directly above both sides are divided by the period of
counting, t, the result is the standard deviation of the count rate, r:
D c
= = Dr
t t
since c = rt
rt
Dr =
t
The number of counts, C, collected in any counting interval is due to the true counts of the sam-
ple plus those due to background. There is significant background radiation in almost any location.
This is due to cosmic rays, cosmic ray-induced activity such as 14C, and naturally occurring radioac-
tive materials in the Earth’s crust, for example, 226Ra, 232Th, and 4OK. The latter all have associated
gamma rays. The cosmic ray contribution varies with altitude, and the composition of the Earth’s
crust varies with location. All radiation detector counter systems have an associated background
counting rate due to the above-mentioned sources and also electronic noise. The background count
rate is commonly reduced by shielding or by special electronic circuitry. The background radiation
will be a function of the type of detector shielding, location, discriminator settings, and so on.
The variations of background are independent of the variations of the sample activity and the
appropriate error terms added as the sum of the squares. Therefore, the variance (D2) due to the
sample activity alone is
Ds2 = D a2+ b + Db2
where
Ds2 = Variance due to sample alone

D2a+b = Variance due to count of sample plus background
D b2 = Variance due to background
For a total of C accumulated counts due to sample and background counts, the standard deviation
of the sample count is given by
Ds = Ca + b + Cb
where
Ca+b = Total counts due to sample plus background

Cb = Total counts due to background counted alone
If ts is the counting time for a sample in the presence of background and t b is the counting time
for background, then the standard deviation of the sample counting rate Drs is as follows:
ra + b rb
Drs = +
ts tb
In tracer experiments, discussed in Section 9.8, the net counting rate of the samples very com-
monly approaches, or is even less than, the background counting rates. In order to choose the best
division of time for counting the sample and for counting the background to obtain the minimum
error, the following equation may be used:
tb r
= b
ts ra + b
9.8 BIOLOGICAL USES OF RADIOISOTOPES

Radioisotopes are widely used to study the physiological processes of biology. A small quantity of
radioisotope called a tracer or label is introduced into the system to be studied, and its behavior is
observed by tracing the position of the radioisotope within the system. The substance to be traced
is called a tracee. The label is incorporated into the tracee through biological growth, chemical
synthesis, or exchange processes.
Radioisotopes have many uses in medicine, for example, in radiotherapy and radioisotope scan-
ning. The use of radioactive isotopes in the diagnosis, investigation, and treatment of disease is
called nuclear medicine. The nucleus of a radioisotope is unstable and undergoes changes by break-
ing down into a more stable form. A radioisotope decays over a period of time into a new element.
As it decays, it emits radiation energy in the form of alpha and beta particles and gamma radiation.
The time taken for half of the original atoms to decay is known as the half-life. The product of
radioactive decay is called a “daughter” atom.
9.9 TRACER DILUTION TECHNIQUE

The tracer dilution technique introduced by Hevesey is particularly useful when quantitative sepa-
rations are not possible or are too tedious for the systems under study. If a radioactive specimen of
one of the compounds present in the mixture is added to the mixture, the label becomes uniformly
distributed throughout the mixture. When the compound is reisolated, some of the label will be
present and hence can be counted, and the specific activity of the sample can be calculated. The
concentration of the nonradioactive compound in the mixture can be determined from the extent to
which it has diluted the radioactive additive, that is,
specific activity additive

Weight of unlabeled material = weight labeled −1
specific activity isolatte
It is not necessary to isolate all material under study from the mixture because the label will
be uniformly diluted in it. It is, however, necessary to purify the extract rigorously to remove any
radioactive contaminants. A variation of the tracer dilution technique called inverse tracer dilution
enables the determination of the amount of tracer in a system by the addition of a known amount
of tracee.
9.10 RADIOIMMUNOASSAY
Radioimmunoassay (RIA) is one of the most important techniques in the clinical and biochemical
field for quantitative analysis of steroids, hormones, and drugs and is especially useful for testing
the sera from immunized animals for antibody response and for screening hybridomas for secretion
of a specific antibody. Immunoassays are very sensitive and specific and therefore are commonly
used for a great variety of measurements in both research and analytical laboratories. Several
refinements of the basic technology have been developed. The most common techniques use a
radioactively labeled antigen or antibody and involve competition for antibody binding between
labeled and unlabeled antigens. The technique is based on the competition between an unlabeled
antigen and a finite amount of the corresponding radiolabeled antigen for a limited number of
antibody-binding sites in a fixed amount of antiserum. At equilibrium (with excess antigen), there
will be both free antigen and antigen bound to the antibody. Under standard conditions, the amount
of labeled antigen bound to the antibody will decrease as the amount of unlabeled antigen in the
sample increases:
4 Ag * + 4 Ab 4 Ag * Ab
4 Ag + 4 Ag * + 4Ab 2Ag * Ab + 2Ag Ab + 2Ag + 2 Ag *
12 Ag + 4 Ag * + 4Ab Ag Ab + 3Ag * Ab + 3Ag * + 9 Ag
where Ab, Ag, Ag*, and AgAb are antibody, unlabeled antigen, labeled antigen, and antibody–
antigen complex, respectively.
By using known amounts of unlabeled antigen and a fixed amount of antibody and labeled anti-
gen, the amount of labeled antigen bound as a function of the total antigen added is measured, and a
calibration curve is constructed (Figure 9.10). This calibration curve may then be used to determine
the amount of antigen in samples treated similarly.
RIAs offer the following potential advantages: (1) sensitivity, (2) simplicity, (3) specificity, and
(4) the ability to measure any compound that is immunogenic, which means the technique can be
universally applied. In spite of these advantages, RIA is not free from drawbacks, including the
high cost of instruments used for measuring radioactivity and also the dangers involved in handling
100
Bound labeled
antigen (%)
0 4 8 12
Unlabeled antigen added
FIGURE 9.10 Calibration curve.

radioactive compounds. Hence, alternative labels such as enzymes (ELISA—enzyme linked immu-
nosorbent assay) or fluorochromes (fluorescence immune assay) have been used.
9.11 MISCELLANEOUS USES OF RADIOISOTOPES

It is often left to the researcher’s imagination to determine the number of ways in which he or she
can use a particular technique. One such enterprising scientist has been Southern, after whom
the technique of Southern blotting is named. Molecular biology involves the analysis of DNA in
many ways. Electrophoresis of DNA results in the separation of DNA according to size. Now, it is
often required to detect whether the required DNA piece is present or not. This can be achieved
by transferring the DNA from the intact gel onto a piece of nitrocellulose paper placed in contact
with it, using denaturation conditions, so that the DNA becomes bound to the paper in exactly the
same pattern as that originally on the gel. This transfer, called the Southern blot, can be achieved
electrophoretically or by drawing large volumes of buffer through both gel and paper. DNA thus
transferred can now be treated with a radiolabeled DNA molecule acting as a “probe” to discover
which bands of DNA contain sequences complementary to the probe after autoradiography of
the paper. The use of radiolabeled DNA probes together with subsequent autoradiography has been
put to practice in many molecular biology techniques, such as colony hybridization to detect and
locate mutant colonies of microorganisms growing on a petri plate.
9.11.1 A Short Guide to Isotopes

The simplest way to envision an atom is to imagine a nucleus, which consists of protons and neu-
trons, surrounded by a cloud of electrons. The number of protons in the nuclei of any element’s
atoms determines the chemical character of that element.
Different isotopes of an element all contain the same number of protons, but different numbers
of neutrons, and hence have different atomic masses. While some isotopes are stable, others are not;
for the 82 stable elements, there are about 275 associated stable isotopes and 800 unstable isotopes
or radioisotopes. (The U.S. Nuclear Science Advisory Committee [NSAC], in the report quoted
above, estimates the number of natural and artificial radioactive isotopes as exceeding 3200 and
“growing every year.”)
The nuclei of unstable isotopes usually stabilize through radioactive decay (hence the name
“radioisotope”). That is, as the isotope tries to reach a more stable form, it kicks off alpha particles,
which consist of two protons and two neutrons, and/or beta particles, which are electrons or posi-
trons. These beta particles are often (but not always) accompanied by the emission of gamma rays
or EM radiation.
Unstable isotopes rarely occur in nature and are nearly always produced artificially. For example,
99Tc is produced as the artificially produced radioisotope. 99Mo decays, through gamma ray emis-
sion (and a rearrangement of its nucleus), to become 99Tc.
9.11.2 Using Radioisotopes

Naturally occurring or artificially produced radioisotopes are useful because they emit radiation,
whether alpha, beta, or gamma. Carbon dating uses a naturally occurring isotope of carbon, 14C
(carbon-14); 14C can measure the age of water up to 50,000 years old. According to the Australian
Nuclear Science and Technology Organisation (ANSTO), smoke detectors represent “the largest
number of devices based on radioisotopes used worldwide.” (The devices use a minute quantity of
Americium-241, which is a product of the decay of plutonium-241.) Around 200 different radioiso-
topes are currently used in a variety of applications, such as in food and agriculture, industry, and
medicine.
9.11.3 Food and Agriculture

In food and agriculture, the radiation emitted by radioisotopes is used in a variety of different ways.
9.11.3.1 Insect Eradication

Each year, insects probably destroy around 10% of global harvests. In developing countries, this
figure has been estimated as high as 25–35%. In what is called the sterile insect technique (SIT),
huge numbers of insects are bred, irradiated with gamma rays to sterilize them, and then released
en masse in infested areas. Since they are sterile, they cannot reproduce, and subsequently, after
a series of such releases, the insect populations in the areas in which they are released can be
decimated. SIT has been used successfully against such insects as the Mediterranean fruit fly (in
Argentina, Chile, and Mexico), the screwworm (in Mexico and the southern United States), and the
tsetse fly (in Africa).
9.11.3.2 Food Preservation

Irradiation, using gamma rays, is now an acceptable method of destroying bacteria, insects,
and various harmful organisms in a number of different foodstuffs, for example, cereals, fresh
fruit, seafood, and vegetables. Indeed, it is the only way to kill bacterial pathogens in frozen and
raw food.
9.11.3.3 Fertilizer Labeling

When used as labels, the two radioisotopes, nitrogen-15 (15N) and phosphorus-32 (32P), can indicate
how much fertilizer is taken up or lost by plants.
9.11.3.4 Genetic Alteration

Either gamma or neutron irradiation can be used to help with genetic modification and the produc-
tion of strains of plants that are either more productive or resistant to pests.
9.11.3.5 Sterilization
Gamma rays are also used to sterilize such things as archival documents, wood, and raw wool
(before it is exported from Australia).
9.11.4 Industry
Radioisotopes also have a range of industrial uses, including nuclear gauging, gamma radiography,
and tracing.
9.11.4.1 Nuclear Gauging

Beta radiation can be used to gauge (and control) the thickness of anything from continuous
sheets of paper to metal, glass, and plastic film as they speed through the machinery that makes
them. In the coal industry, gamma radiation is used to measure not only the ash content of coal
as it passes on a line but also its sulfur and moisture contents. When the coal is in its hoppers,
gamma radiation is used to gauge exactly how full the hoppers actually are. In addition, radio-
isotopes are used both in borehole logging and, more simply, to measure the water content of soil
and its density.
9.11.4.2 Gamma Radiography

Gamma rays can be used to produce images much in the same way as x-rays. However, gamma rays
can not only produce an image of the object through which they are passing but also help provide a
degree of analysis of the object itself. This is one reason why gamma radiography is often used to
screen luggage at airports. More mainstream uses of gamma radiography include weld inspections
in gas and oil pipelines using “pipe crawlers” and stress testing, for example, of the structural integ-
rity of jet turbine blades. Autoradiography and neutron radiography can also be used to locate things
that might otherwise be difficult to see, for example, detecting corrosion and moisture entrapment,
especially in aircraft structures.
9.11.4.3 Tracing
Since the tiniest amount of a radioactive material can be easily traced, radioisotopes are ideal when
conditions are particularly harsh or complex. Measuring liquid flows through, for instance, a blast
furnace is an example of the former. Using a radioisotope to detect leaks in, say, a power station is an
instance of the latter. One other fascinating example is provided by the World Nuclear Association
in their article “Radioisotopes in Industry”: “The extent of termite infestation in a structure can be
found by feeding the insects radioactive wood substitute, then measuring the extent of the radioac-
tivity spread by the insects. This measurement can be made without damaging any structure as the
radiation is easily detected through building materials” (see Table 9.1).
9.11.5 Medicine
Radioisotopes are key in modern nuclear medicine. Three of their most important uses are steriliza-
tion, medical diagnostics, and medical treatments.
TABLE 9.1
Some Common Industrial Radioisotopes
Radioisotope Half-life Decay Some Uses
Carbon-14 a 5,730 years Beta Dating. Tracer in photosynthesis studies
Chlorine-36a 301,000 years Beta Measuring age of water—up to 2 million years
Hydrogen-3a (tritium) 12.32 years Beta Measuring age of “young” (up to 30 years)
groundwater. In red building-exit signs
Lead-210a 22.3 years Beta Dating layers of sand and soil up to 80 years
old
Americium-241 432 years Alpha Smoke alarms and neutron gauging
Caesium-137 30.2 years Beta Tracing and thickness gauging
Cobalt-60 5.3 years Beta and gamma Gamma radiography, gauging, and sterilization
Gold-198 2.69 days Beta Tracing factory waste pollution in oceans
Iridium-192 73.83 days Beta Gamma radiography
Krypton-85 10.76 years Beta and gamma Industrial gauging and locating leaks
Magnesium-27 9.5 minutes Beta and gamma Locating leaks
Manganese-54 312.2 days Gamma Predicting the behavior of heavy metals in
effluents from mining wastewater
Nickel-63 100.1 years Beta Light sensors in cameras and thickness gauging
Selenium-75 119.78 days Gamma Gamma radiography and nondestructive testing
Sodium-24 15 hours Beta and gamma Locating leaks
Strontium-90 28.8 years Beta− Thickness gauging
Ytterbium-169 32 days Gamma Gamma radiography
Zinc-65 244.26 days Gamma Predicting the behavior of heavy metals in
effluents from mining wastewater
Note: Beta− is positron emission.

a Naturally occurring.
9.11.5.1 Sterilization
Many medical devices that cannot be sterilized in any other way are sterilized using gamma radia-
tion. This applies, in particular, to single-use devices such as gloves, syringes (and needles), alcohol
wipes, and scalpel blades. In addition, irradiation is used to sterilize plasma, serum, and tissue that
is going to be transplanted.
9.11.5.2 Medical Diagnostics

Some 10,000 hospitals around the world use radioisotopes for diagnostic tests. Whether taken orally,
inhaled, or injected, medical isotopes are used in a wide variety of different procedures. They are
used, for example, to assess bone damage; to know how the heart, kidneys, liver, and lungs are
functioning; and, extensively, for testing for cancer, heart, and thyroid diseases. On a more mundane
level, they are commonly used in biochemical analyses in vitro (known as radio immunoassays)
to test blood, urine, hormones, and serum, among other biological samples. Some 15 million such
analyses are undertaken each year in Europe alone.
9.11.5.3 Medical Treatments

Irradiation can control or even eliminate some cancerous growths. Some radioisotopes, for exam-
ple, strontium-89 and samarium-153, are excellent for reducing the pain induced by certain cancers.
Tiny seeds, or sometimes wires, of radioisotopes are used in the treatment of various cancers found
in the breast, head, prostate, and thyroid (see Table 9.2). (Interestingly, however, the frequency of
use of radioisotopes in therapeutics is only about a tenth of their use in diagnosis.)
9.12 RADIOISOTOPE PRODUCTION

Although a number of radioisotopes occur naturally, nearly 200 are being used on a regular basis
and are produced artificially. This mainly occurs via three methods: (1) nuclear reactors, (2) research
reactors, and (3) cyclotrons and linear accelerators.
9.12.1 Nuclear Reactors

While not the most common source of radioisotopes, a number of power reactors do produce radio-
isotopes. Put at its simplest, isotopes are made in a nuclear reactor through neutron gain; that is,
some of the million errant neutrons winging around inside the core of the reactor are absorbed by
the nuclei of particular materials placed in the reactor’s core. So, for example, if one of cobalt’s
stable isotopes, cobalt-59, is stuck in the core of a nuclear reactor and exposed to a high flux of
TABLE 9.2
Some Commonly Used Isotopes in Medicine
Radioisotope Half-life Decay Some Uses
Bismuth-213 46 minutes Alpha Cancer therapy
Cobalt-60 5.27 years Gamma Sterilization
Erbium-169 9.4 days Beta− Relief of pain from arthritis
Iodine-125 60 days Gamma Treatment of brain and prostate cancer
Phosphorous-32 14 days Beta Treatment of excess red blood cells
Technetium-99m 6 hours Gamma Many different imaging applications
Thallium-201 73 hours Gamma Diagnosis of coronary artery disease
Xenon-133 5 days Beta− Pulmonary ventilation studies
Note: Beta− is positron emission.

neutrons, it can absorb some of these neutrons (adding one to each of its nuclei) and become the
radioisotope cobalt-60.
9.12.2 Research Reactors

Currently, radioisotopes are most commonly produced in research reactors through fission, or the
splitting of the nuclei in atoms. Rather than being absorbed by the nuclei of other atoms, they are
instead hurled at those other atoms to break up their nuclei and create by-products in the form of
radioisotopes. The speed of these neutrons and the temperature will determine exactly which radio-
isotopes are produced.
9.12.3 Cyclotrons and Linear Accelerators

Radioisotopes can be produced in either cyclotrons or linear accelerators. In both of these, a beam
of protons is accelerated, using magnets, and smashed into a target to produce the required radio-
isotope. One major difference between using a cyclotron and using a nuclear reactor is that a cyclo-
tron needs neither fissionable material nor uranium to produce radioisotopes. On the other hand,
however, it can only accelerate charged particles, and only protons can be added in this way to
atomic nuclei.
In fact, while reactors produce neutron-rich nuclei, cyclotrons and linear accelerators, by adding
protons, produce neutron-deficient nuclei. Because neutron-deficient and neutron-rich radioisotopes
decay by different means, they will have different properties and are better suited for different
purposes.
9.13 MOST WIDELY USED RADIOISOTOPES

By far the most widely used radioisotopes, excluding those used in power production, are three that
are used for medical purposes: cobalt-60, technetium-99m (molybdenum-99), and thallium-201 in
that order. A 2008 article by Lawrence Kidd in Nuclear Engineering International estimated total
yearly global production of cobalt-60 at 60 million Curies, while production of molybdenum-99/
technetium-99m was some 468,000 6-day Curies. While these figures may reflect how things were
back in July 2008, the scene has changed radically since Kidd published his groundbreaking article.
Both cobalt-60 and molybdenum-99 are produced in reactors. But perhaps surprisingly, both
radioisotopes are produced only in a handful of power and research reactors, a couple of which
have now not been operating for quite some time. This has recently led to a major supply crisis for
molybdenum-99 and, hence, technetium-99m.
Before it closed for repairs, the National Research Universal (NRU) reactor probably produced
more than 80% of the world’s cobalt-90 and nearly 40% of its molybdenum-99. Today it produces
nothing. The latest update indicates that only 56% of the repair work necessary to return the reactor
to service has been completed. Then, in late February, the high flux reactor (HFR) at Petten in the
Netherlands, which is estimated to have produced 25% or more of the world’s molybdenum-99, was
also shut down for repairs. This reactor is not expected to start operating again for at least several
years (see Table 9.3).
Experiment: Distribution of 14CO2 in Different Plant Parts

Introduction
The objectives of this activity are (1) feeding plants with 14 CO 2 and (2) determining the radioactivity in
different plant parts and fractions. 14C (radioactive carbon) and 12C (naturally occurring nonradioactive
isotope of carbon) have the same atomic number with the same chemical properties. Living organisms,
including plants, are unable to differentiate between these two isotopes of carbon. Thus, the plant
TABLE 9.3
Some of the World’s Major Radioisotope-Producing
Reactors
Radioisotope Source Country
Cobalt-60 Atucha 1 Argentina
Embalse Argentina
Bruce B 1 and 2 Canada
NRU Canada
Qinshan 1 & 2 China
Leningrad 1 Russia
Wolsong 1 & 2 South Korea
Clinton BWR United States
Molybdenum-99 BR-2 Belgium
HFR Netherlands
NRU Canada
Osiris France
Maria Poland
Safari-1 South Africa
leaves utilize 12C and 14C carbon dioxide at the same rate. The photosynthetically fixed carbon is then
partitioned between various plant organs, namely roots, shoots, seeds, fruits, and so on. The partition-
ing of assimilates is influenced by a variety of factors such as plant species, age, stage of development,
and environmental factors. The partitioning pattern can be quantitatively determined by estimating the
radioactivity in different plant parts following exposure of the seedlings to 14CO2 in light. The percent
distribution of 14C in various parts is then calculated.
Safety Guidelines
Radioisotopes emit ionizing radiations and affect all life forms. They are dangerous if used indis-
criminately. The use of radioactive materials in laboratories is controlled under a license with stringent
restrictions on use and waste disposal due to the health hazards involved. One must follow the simple
precautions listed below
1. The place where the isotopes are to be used must be kept very clean.
2. Never pipette by mouth in a radioactive laboratory, even if a particular liquid is not radioac-
tive. It may be contaminated.
3. Wear a laboratory coat or apron.
4. Always spread some disposable sheets of cellophane or absorbent paper, or at least an old
newspaper, on your work tables.
5. Wipe all spillage several times using tissue paper.
6. Discard the wiped papers, used containers, or the soluble waste in their respective containers.
7. Clearly mark all glassware used as “radioactive.”
8. Wash all the glassware personally first with “carrier” solution. (This is a solution that con-
tains the same nonradioactive compound that was used in the experiment. When we use 14C
glucose in the experiment, normal glucose solution will be the carrier solution.)
9. It is advisable to use a pair of rubber gloves.
10. Wash your hands well after the completion of the experiment, before using the counters. If
you handle planchets or planchet holders with contaminated hands, they may increase the
counting rate and mess up the background counting.
11. Never prepare the samples in the counting room where the counters are placed.
12. Subscribe for film badge service and get the dosage level reported once every 15 days.
13. Using an ordinary rate meter, check the background activity as often as possible.
Disposal of Radioactive Waste

Keep all glassware, paper, towels, and so on used in experiments in a separate container, and do not
mix them with other materials in the laboratory. It is advisable to use a foot-operated bin for radioac-
tive waste material. It should be periodically emptied and buried. Liquid waste is best kept diluted and
stored in carboys, which can be disposed of from time to time.
Where to Buy the Isotopes

Compounds labeled with radioactive isotopes are manufactured by regulatory authorities in respective
countries. Permission should be obtained for the recognition of the department or laboratory, enclos-
ing details of the space, and other facilities available. For film badge service, apply to the Radiation
Protection Service. Isotopes can be obtained from Amersham Inc., England.
Experiment: Determination of Radioactivity in Different Parts of Plants

1. Feeding plants with 14CO2.
2. Determination of radioactivity in different parts of the plants.
Materials
Syringes, double-walled (water-jacketed) Perspex chamber, airtight circulation pump, Geiger–Muller
counter, gas proportional counter or liquid scintillation counter, planchets or scintillation vials, HCl
and NAOH scintillation fluid, 14C sodium bicarbonate, fully grown plants of wheat, pea or tomato, PPO
(p-terphenyl, 2,5-diphenyloxazole) and POPOP (1,4-bis-2-(5-phenyloxazolyl)-benzene) and toluene,
reagent bottles, balance, clinical centrifuge, water bath.
1. 0.1 N HCl: Take 8.3 mL of hydrochloric acid, and increase the volume to a liter with distilled
water.
2. 0.2 N HCl: Take 16.6 mL of HCl and dilute to 1 L with distilled water, 14C-labeled NaHCO3
(specific activity of 50 mCi/mmol).
3. 0.1 N NaOH: Weigh 4.12 g of sodium hydroxide, and dissolve in a liter of distilled water.
4. Scintillation fluid: Dissolve 4 g of POP (2,5 diphenyloxazole) and 100 g of POPOP (1,4 bis
2) (phenyl oxazole) benzene in 1 L of toluene.
Method
A. Feeding of Plants with 14CO2
1. Enclose the plant (e.g., wheat, tomato or pea plant) in a double-walled Perspex chamber of an
appropriate size and place it under natural sunlight.
2. Circulate water between the chamber walls through the water jacket to prevent any rise in
temperature in the chamber during the feeding period.
3. Connect the outlet of an airtight CO2-generating tube with a flexible propylene or rubber tub-
ing to the inlet of the airtight circulating pump and the outlet of the pump to the inlet of the
chamber. With different tubing, connect the outlet of the chamber with the inlet of the CO2-
generating tube.
4. Place 1–2 μmol of NaH14CO3 (specific activity 50 mCi/mmol) at the bottom of the CO2-
generating tube.
5. Release 0.1 N HCl from the stopper into the NaH14CO3-containing CO2-generating tube so
that 50–100 μCi of labeled 14C is liberated.
6. Circulate the evolved 14CO2 through the Perspex chamber (in which the plant has been
enclosed) using a small airtight electrical pump.
7. Allow the plant to fix 14CO2 for an appropriate time (5 minutes to 1 hour).
8. Remove excess 14CO2 diverting the circulation of gas through NaOH trap, which is attached
via a three-way stop clock in between the CO2-generating tube and the pump.
9. Return the 14C-fed plants to natural growth conditions.
10. After 24 hours of feeding, harvest the plants and separate the parts, for example, leaf, stem,
roots, seeds, fruits, and so on.
11. Dry different parts separately in an oven at 65°C to a constant weight and record their weight.
B. Extraction and Measurement of Radioactivity

Radioactivity can be measured by any one of the following methods after suitably processing the plant
sample.
Method 1
1. Grind the oven-dried sample of different plant parts to fine powder.
2. Place a known weight of the sample in a planchet with some adhesive material on its surface
so that the sample gels stuck to the planchet.
3. Count the dpm either by a gas proportional counter or by Geiger–Muller counter or liquid
scintillation counter.
Method 2
Prepare the ethanol-soluble and ethanol-insoluble factions of the powder sample, and then determine
the radioactivity in each of them individually.
1. Take an appropriate amount of the dry sample in a centrifuge tube.
2. Add 5 mL of 80% aqueous ethanol (v/v), and place in a water bath at 40°C for 1 hour. Shake
the tube occasionally.
3. Centrifuge at 5000×g for 15 minutes, and decant the supernatant.
4. Extract the residue in the similar manner with 50% (v/v) aqueous ethanol, centrifuge, and
collect the supernatant.
5. Finally extract the residue with water, centrifuge, and collect the supernatant.
6. Pool all the supernatants obtained in steps 3–5, which will constitute the ethanol-soluble
fraction.
7. Suspend the residue in 2 N HCl, and autoclave at 15 kg/cm2 for 1 hour.
8. Centrifuge the hydrolyzed material, and wash the pellet twice with 2 N.
9. Pool all the acid fractions representing the ethanol-insoluble fraction.
10. Evaporate both the fractions (ethanol soluble and insoluble) separately to dryness, and redis-
solve each of them in 2 mL distilled water.
11. Pipette 0.2 mL of the above extract on a planchet, dry under an infra-red lamp, and then
record the counts in a gas-flow proportional counter.
Method 3
Measurement of radioactivity by a liquid scintillation counter:
1. Take a suitable aliquot (1 mL) of the above fractions in scintillation vials and dry it.
2. Add 10 mL of scintillation fluid to each vial.
3. Record the counts on a liquid scintillation counter with an appropriate correction for
quenching.
Calculations
Determine the total amount of 14C assimilates in the plant by adding the radioactivity (dpm) in both
the fractions of all plants. While doing this, take into account the weight of the part used for sample
preparation, dilution factors (if any in case of fractions), and the total weight of that plant or organ in
the plant. For example, if radioactivity is determined in a powdered nonfractionated leaf sample, then:
dpm × total weight of leaves on the plant

Total 14 C-labeled material =
weight of powdered sample taaken
For the fractionated sample, take into account the dilution factor as well, that is, the volume of the
fraction used for determination of radioactivity and the total volume of the fraction.
1. Calculate the total 14C-labeled assimilates in each plant part, a, b, c, and d for leaves, stem,
seeds, and roots, respectively, from the sum of the counts in both the fractions of an organ.
2. Compute the percent distribution of 14C in different parts as follows:
% 14C in leaves = a/X× 100 dpm
% 14C in stem = b/X× 100 dpm
% 14C in seeds = c/X× 100 dpm
% 14C in roots = d/X× 100 dpm
where X is the total 14C assimilated by the entire plant and a, b, c, and d represent total
14C-labeled material in each of these plant parts.
Result
Tabulate the results of 14C labeling in each plant part in terms of percent incorporation.
Experiment: Photosynthetic 14CO2 Reduction

to the Primary Metabolic Product
Introduction
The mechanism of photosynthetic CO2 assimilation in plants varies with species and may occur via
either the C3 or C4 pathway. The C3 or C4 mechanism in a particular plant can be established by identify-
ing the first product of a CO2 fixation reaction. In case of the C3 pathway, 3-phosphoglycerate (3-PGA)
is the first product, whereas in the C4 type the initial product of carboxylation reaction is a C4 organic
acid such as oxaloacetate, which is rapidly converted to either malate or aspartate. When plants are
exposed to 14CO2, the label is incorporated into the primary products. Determination of these primary
products (namely, 3-PGA or malate and aspartate) for radioactivity provides the confirmatory evidence
for operation of a particular photosynthetic pathway in a plant species.
Safety Guidelines
Follow all the safety guidelines given in the experiment.
1. Feed 14CO2 to the actively photosynthesizing leaves.
2. Trace 14CO2 photo assimilates by the paper chromatographic method.
3. Identify the chemical nature of the assimilate by using specific spray reagents.
Materials
Experimental plants (select one C3 and one C4 plant), chamber made of Perspex or glass for feeding the
plants with 14CO2, gas mixture pump, 14C-labeled sodium bicarbonate (NaH14CO3), chromatographic
chamber for descending paper chromatography, Whatman no. 1 filter paper, PGA, glucose-6 phos-
phate, malic acid, POP (2,5-diphynyl oxazole), POPOP (1,4 bis (-2,4,5-phyny1 oxazole)) benzene, tri-
cine, KOH, sorbitol, liquid scintillation counter, 50 mM tricine-KOH buffer (pH 7.5) containing 0.33 M
sorbitol buffer, n-butanol, propionic acid.
1. Prepare the scintillation fluid by dissolving 8 g 2,5-diphenyl oxazole (POP) and 100 mg of
1,4-bis (-2,4,5-phenyl oxazole) benzene (POPOP) in 1 L of toluene.
2. Authentic standards: Prepare a solution containing 1 mg/mL of authentic sample of 3-PGA,
glucose-6-phosphate, aspartic acid, and malic acid.
3. Solvent system for paper chromatography: Mix n-butanol:propionicacid:water in the ratio of

10:5:7 (v/v), and use as the solvent system.
4. Detection reagents: Prepare various spraying reagents as given in step 2 in the following
procedure.
5. 50 mM Tris-KOH buffer.
Method
1. Soak the glass fiber discs in 50 mM tricine-KOH buffer (pH 7.5) containing 0.33 M sorbitol.
2. Quickly transfer 0.1 g plant leaf segments on these glass discs to prevent dehydration of plant
tissues. Place these glass fiber discs in steel planchets. Prepare five such planchets and place
them on a strip with a well in its center. Add 2 N HCl to this central well and keep the strip in
the Perspex chamber (19 × 12 × 37 cm) with an internal volume of 50 mL.
3. Expose the chamber to direct sunlight for 5 minutes. Then inject NaHl4CO3 through a rubber
septum into the acid-containing well on the strip such that the concentration of 14CO2 in the
chamber is 0.1%, and circulate the air through the chamber with the help of an airtight gas
mixture pump.
4. Remove the samples from the chamber after 20, 40, 60, 120, and 300 seconds of exposure to
14CO .
2
5. Immediately kill the tissue by dropping it in boiling ethanol.
6. Extract the plant material with 80% (v/v) ethanol, centrifuge the homogenate at 8000×g, and
collect the supernatant.
7. Extract the residue with distilled water, centrifuge again, and carefully decant the supernatant.
Pool the obtained supernatants and increase the volume to a known final volume of 10 mL
with 80% ethanol.
8. Take 1 mL of the extract in a scintillation vial containing 1.5 mL scintillation fluid and evapo-
rate it to dryness. Record the counts in a liquid scintillation counter.
9. Take another aliquot of the extract, evaporate to dryness, and extract chlorophyll from the
residue with chloroform. Evaporate off the excess chloroform from this preparation, and dis-
solve the residue in water.
10. Apply a suitable aliquot of the above water extract onto Whatman no. 1 filter paper sheet in the
form of a spot. Perform descending paper chromatography using n-butanol:propionicacid:water
in the ratio of 10:5:7 as the mobile phase.
11. Remove the chromatogram and dry it at room temperature. Spray the chromatogram for
developing color using the different spraying reagents detailed as follows:
Compound Detected Spray Reagent

Malate sucrose 0.08% (w/v) bromocroesol green in ethanol 1.5 g benzidine + 10 mL
glacial acetic acid + 10 mL 40% (w/v) TCA and ethanol to increase
the volume to 100 mL
3-PGA and glucose-6- 5 mL 60% (w/v) HClO4 + 25 mL 4% (w/v) ammonium molybdate +
phosphate 10 mL N HCl + water to increase the final volume to 100 mL
Aspartate 0.4% (w/v) ninhydrin in 95% (v/v) acetone
After spraying, dry it at room temperature, and then keep it at 80–100°C in an oven for 5 min-
utes. Colored spots appearing on the chromatogram are due to malate, aspartate, and sucrose.
12. Autoclave the paper for 2 minutes at 8–10 psi for detecting 3-PGA and glucose-6-phosphate.
The paper becomes blue. Now expose the paper to ammonia vapors. The blue color of the
phosphomolybdate is due to the reaction with phosphorylated compounds, while the blue
color of the background disappears.
13. Identify the compounds by comparing their Rf values with those of authentic standards
run parallel. Punch the area of paper containing labeled compounds from the developed
and sprayed chromatograms, and count in the scintillation counter. Make sure that necessary
corrections for quenching are made for any colored segments of the chromatogram.
Conclusions
By examining the kinetics of distribution of 14C label in 3-PGA and C4 dicarboxylic organic acids, the
mode of photosynthetic CO2 assimilation can be deduced. If at the initial stages the 14C label is initially
present predominantly in C4 dicarboxylic acids (oxaloacetate, malate, or aspartate) but little in 3-PGA,
and this is followed by decrease in 14C label in C4 acids accompanied by concomitant increase of 14C in
3-PGA, then this is an indication of a C4 pathway of CO2 fixation. If, in contrast, at the early stages the
14C is largely in 3-PGA and 14C labeled dicarboxylic acids appear at a much later stage, this denotes a
C3 mechanism of photosynthetic CO2 assimilation.
Result
Express your results as a percentage incorporation of radio activity in each fraction.
Autoradiography
Radioactive isotopes of various elements can be used to follow the specific molecules biochemically;
one of the earliest uses of radioactivity was to trace the chemical pathway of carbon during photosyn-
thesis. The soluble contents can be separated by paper chromatography (either by ascending, descend-
ing, or two-dimensional); small molecules containing 14C atoms derived from CO2 can be detected by
a sheet of x-ray film placed over the dried chromatogram enclosed in a x-ray cassette. The cassette is
kept in the dark room for 48–72 hours. Remove the x-ray film, and develop the film in the dark room in
the manner that is followed for the development of photographic film. The metabolites formed can be
identified. The location of the individual molecules blotted on the x-ray film can be compared with the
compounds identified on the chromatographic paper with the help of spray reagents. After identifica-
tion of the compounds, each area on the chromatogram is cut and eluted in ethanol and added to the
scintillation vial containing scintillation fluid, and the radioactivity of each biomolecule is measured.
SUGGESTED READING
Biilington, D., G. G. Jayson, and P. J. Maltby. 1992. Radioisotopes. Oxford: Bios Scientific.
Chapman, J. M., and G. Avery. 1981. The Use of Radioisotopes in the Life Sciences. London: George Allen &
Unwin Ltd.
Connor, K. J., and I. S. Mclintock. 1994. Radiation Protection Handbook for Laboratory Workers. Leeds, UK:
H and H Scientific Consultants.
Slater, R. J. 1995. “Radioisotopes in Molecular Biology.” In Molecular Biology and Biotechnology: A
Comprehensive Desk Reference, edited by R. A Myers, 209–20. New York: VCH.
Slater, R. J. 2000. Radioisotopes in Biology—A Practical Approach, 2nd ed. Oxford: IRL Press.
IMPORTANT LINKS
1. Scintillation counter: http://www.hidex.com/products/hidex-300-sl.aspx
2. Autoradiography: http://www.gelifesciences.com/aptrix/upp01077.nsf/Content/na_blotting_site~na_
detection~na_autoradiography_cassettes?opendocument&cmpid=ppcaw100
10 Fermentation
10.1 INTRODUCTION
Fermentation is typically the conversion of sugar to alcohol under anaerobic conditions in the pres-
ence of yeast. Chemical conversion of carbohydrates into alcohols is a general example of fermenta-
tion. When fermentation stops prior to the complete conversion of sugar to alcohol, it is called stuck
fermentation. The science of fermentation is known as zymology. The French chemist Louis Pasteur
was the first known zymologist; he defined fermentation as “respiration without air.” The German
scientist Eduard Buchner, winner of the 1907 Nobel Prize for chemistry, found that the secretion of
zymase in yeast is responsible for fermentation.
Fermented foods have been with us since the dawn of civilization. They will be with us far
into the future, as they are the source of alcoholic foods, beverages, vinegar, pickled vegetables,
sausages, cheeses, yogurts, vegetable protein amino acid/peptide sauces and pastes with meat-like
flavors, and leavened and sourdough breads. All consumers today have a considerable portion of
their nutritional needs met through the consumption of fermented foods and beverages.
10.2 HISTORY
Fermentation is an ancient process by means of which bread, wine, beer, and cheese are made.
Egyptians found that uncooked dough left standing became lighter and softer. The Egyptians and
the Romans discovered that the use of yeast produced lighter and leavened bread. Around 4000
BC, wine was made from grape juice through a fermentation process. Beer-making by the ancients
involved soaking barley in water; at the time, beer was probably a serendipitous by-product of bread
making.
For the production of yogurt, cheese, wine, vinegar, and different types of sauces, microorgan-
isms were used by the Chinese. Earlier, cheese was made by storing milk in animal skins or blad-
ders made from animal stomachs. The bacteria and enzymes present in these urns would cause the
separation of casein (milk protein) to form curd.
Louis Pasteur in the late nineteenth century was the first individual who understood the process
of fermentation; his understanding was based on his experience and implicit knowledge. Antony
van Leeuwenhoek, a Dutch biologist, was the first to see microorganisms in samples of fermenting
beer through a microscope in 1680. Pasteur, a French chemist, discovered that yeasts convert sugars
to alcohol and carbon dioxide during fermentation.
For the first time, large-scale aerobic fermentors were used in Central Europe in the 1930s for
the production of compressed yeast. The fermentor consisted of a large cylindrical tank with air
introduced at the base via a network of perforated pipes. In later modifications, mechanical impel-
lers were used to increase the rate of mixing and to break up and disperse air bubbles, which led to
the requirement of compressed air. Baffles on the walls of the vessels prevented the formation of
a complex vortex in the liquid and later a system was patented in which aeration tubes were intro-
duced with water and steam for cleaning and sterilization.
Fermentation is the process by which alcoholic beverages or acidic dairy products (cheeses,
yogurt) are manufactured. It is a way for a cell to obtain energy without using oxygen. During
the process, complex organic substances are broken down into simpler ones. The cell (microbial
249
or animal) obtains energy through glycolysis, that is, the splitting of a sugar molecule to release
electrons. The by-product of this process is excreted from the cell in the forms of substances such
as alcohol, lactic acid, and acetone. With the development of microbiology and technologies such
as biotechnology, microorganisms are subjugated to produce an extensive assortment of products
using fermentation. These include
Dairy products: Cheese, yogurt.

Beverages: Beer, wine.
Single-cell proteins (SCPs): SCPs are cell monocultures of bacteria, fungi, and algae. Since
the cells contain large amounts of protein, SCPs are used as food or food supplements for
humans and cattle. They are regarded as cheap sources of dietary protein and are produced
from methanol and the by-products of cheese production and papermaking.
Antibiotics: Antibiotics are one of the most important compounds produced by fermen-
tation. In 1929, Alexander Fleming was the first to discover penicillin, an antibiotic.
Large numbers of antibiotics are produced today by fermentation using various bacteria
and fungi.
Chemicals: Citric and acetic acids, amino acids, enzymes, vitamins.
Fuels: Ethanol, methanol, methane.
10.3 PRINCIPLES OF FERMENTATION

Fermentation is a metabolic pathway by which cells catabolize, or break down, a carbon source to
produce energy. The cells consume carbohydrates, leading to an increase in cell mass by replication
and the production of carbon dioxide and other organic compounds. To track the consumption and
production of various carbon products, we analyzed the following carbon balance:
Cglucose consumed = CCO2 + Ccell mass − Cinitial cell mass + Cethanol
The calculation of carbon for the components in the aforementioned equation is relatively simple
and self-explanatory, except for the cell mass. To obtain these experimental values, we estimated
that 70% of the dry cell mass is water by weight and approximately half of the remaining mass is
carbon. Thus, the experimental dry cell mass is multiplied by 0.15 to calculate the mass of carbon
in the cell mass.
Microorganisms undergoing fermentation go through four distinct phases of growth, that is, lag,
exponential, stationary, and death (Figure 10.1). They are described as follows:
1. Lag phase: The period of apparent inactivity in which cells are adapting to a new envi-
ronment and preparing for reproductive growth. Cells are usually synthesizing new com-
ponents. In practice, bacteria from one medium to another, where there are chemical
differences between the two media, typically results in a lag in cell division. This lag in
division is associated with a physiological adaptation to the new environment. Cells may
increase in size during this time, but they simply do not divide (by binary fission). The lag
phase varies considerably in length depending on the condition of the microorganisms and
the nature of the medium.
2. Log (exponential) phase: The period in which organisms are growing at the maximal rate
possible given their genetic potential, the nature of the medium, and the conditions under
which they are growing. In this stage, yeast consumes food and multiplies to form new
cells at a high rate. Here, the production of carbon dioxide rises rapidly and the concentra-
tion of glucose decreases rapidly.
3. Stationary phase: Eventually, population growth ceases and the growth curve becomes
horizontal. The increase in cell number due to cell divisions is exactly balanced by a
Fermentation 251
Lag Log Death

phase phase Stationary phase phase
Number of microbes
Time
FIGURE 10.1 Bacterial growth pattern.
decrease in cell number due to cell death. Carbon dioxide production levels off and glucose
consumption also slows down.
4. Death phase: The stationary phase in a standard bacterial growth curve is followed by a
die-off of cells, called the death phase. It is the period in which cells die at an exponential
rate. Some of the reasons for cell death are continued accumulation of wastes and the loss
of a cell’s ability to detoxify toxins. During this period, both sugar concentration and car-
bon dioxide production approach zero.
In addition, stirring rates may also affect the rate of fermentation reactions as yeast cells need to
be in contact with sugar and oxygen (in aerobic fermentation) in order to react. The yeast cells are
incapable of swimming; if they are just suspended in the fermentor broth, they quickly exhaust the
surrounding resources and smother in their own waste products.
10.4 INTRODUCTION TO MICROORGANISMS

Microorganisms are unicellular, that is, they contain only a single cell. Cellular organisms are
broadly classified into prokaryotes and eukaryotes, aerobic and anaerobic, and according to the type
of metabolism.
10.4.1 Prokaryotes
These include simple bacteria and archaea (Figure 10.2). They are molecules surrounded by a mem-
brane and a cell wall. The cells of these organisms do not contain membrane structures such as mito-
chondria or a nucleus. Chromosomes are present as circular DNA distributed in the cytoplasm; they
can be classified into archaebacteria and eubacteria with further classifications under those types.
Archaebacteria include:
• Methanogens: Anaerobic methane-producing bacteria

• Extreme halophiles: Bacteria that require high salt concentrations to survive
• Extreme thermophiles: Bacteria that require high temperatures and sulfur to survive
Eubacteria include:
• Gram-positive bacteria: Bacteria whose cell walls retain crystal violet dye during iodine
treatment, for example, lactic acid bacteria
• Gram-negative bacteria: Bacteria that vary in cell-wall structure and do not retain crystal
violet dye during iodine treatment
10.4.2 Eukaryotes
The cells of these organisms contain mitochondria, nucleus, plasma membrane, cytoplasm, and
other membranes. In these organisms, bound structures and chromosomes are present in the nucleus,
for example, multicellular organisms and fungi (Figure 10.3).
Cytoplasm
Nucleiod
Capsule
Cell wall
Cytoplasmic
membrane
Ribosomes
Pili
Flagellum
FIGURE 10.2 Prokaryotic cell structure.
Lysosome
Plasma
Cell wall membrane
Nucleus Organelles
Centrioles
Golgi
apparatus
Ribosomes
Mitochondria
Endoplasmic
reticulum
FIGURE 10.3 Eukaryotic cell structure.

Fermentation 253
10.5 TYPES OF FERMENTATION METABOLISM

Fermentation is commonly defined as the process in which energy is formed by the oxidation of
organic compounds such as carbohydrates and sugars. This leads to the conversion of these organic
compounds into an acid or an alcohol, which releases energy. It can be carried out by microorgan-
isms with and without the help of oxygen.
10.5.1 Aerobic Fermentation

The fermentation process that includes fresh air and is similar to vat, crock, tank, and polyethylene
pail is referred to as aerobic fermentation. The presence of air is most important for the growth of
yeast, and it reproduces and increases in density and alcohol is produced in a conductive manner.
Aerobic fermentation needs adequate aeration. The quantity of air that is needed per hour is almost
60 times the fermentation medium volume. An adequate supply of clean air is more essential in aer-
obic fermentation in a bioreactor and clean air is usually sparged inside the fermentation medium.
Aerobic fermentation has a mechanism for the complete mixing and stirring of the fermentation
medium and biological cells (Figure 10.4).
When oxygen is present (i.e., under aerobic conditions), most organisms undergo two more steps,
Kreb’s cycle and electron transport, to produce adenosine triphosphate (ATP). In eukaryotes, these
processes occur in the mitochondria, whereas in prokaryotes they occur in the cytoplasm. These are
microorganisms that can grow and live in the presence of oxygen. In compost heaps, bacteria of this
type generate heat when they convert carbon and nitrogen, reducing the volume of waste. As they
exhaust the oxygen in the compost pile, they die, leaving behind a germ-free product.
10.5.1.1 Acetyl Co-A: The Transition Reaction

Pyruvic acid is first altered in the transition reaction by removing a carbon atom and two oxy-
gen atoms (which forms carbon dioxide). When the carbon dioxide is removed, energy is released
and nicotinamide adenine dinucleotide (NAD+) is converted into the higher energy form NADH.
Coenzyme A attaches to the remaining 2-C (acetyl) unit, forming acetyl Co-A. This process is a
prelude to the Kreb’s cycle.
Glycolysis
Fermentation
Glucose Glycolysis
Pyruvate Glucose
Cellular respiration Pyruvate

Cytosol
Lactic acid
Matrix or ethanol
Citric
acid
cycle
Cytosol
Mitochondrion Prokaryotic cell
FIGURE 10.4 Biochemical reactions in prokaryotic and eukaryotic cells.

10.5.1.2 Kreb’s Cycle (the Citric Acid Cycle)

The acetyl Co-A (2-C) is attached to a 4-C chemical (oxaloacetic acid [OA]). The Co-A is released
and returns to await another pyruvic acid. The 2-C and 4-C make another chemical known as
citric acid, which is a 6-C. Thus, Kreb’s cycle is also known as the citric acid cycle. The process
that occurs after citric acid is formed essentially involves the removal of carbon dioxide; release of
energy in the form of ATP, guanine triphosphate (GTP), NADH, and FADH2; and, finally, regen-
eration of the cycle. Between isocitric acid and α-ketoglutaric acid, carbon dioxide is given off and
NAD+ is converted into NADH. Between α-ketoglutaric acid and succinic acid, a release of carbon
dioxide and reduction of NAD+ into NADH happens again, resulting in a 4-C chemical, that is,
succinic acid. The GTP (which transfers its energy to ATP) is also formed here (GTP is formed by
attaching a phosphate to GDP).
The remaining energy carrier–generating steps involve the shifting of atomic arrangements
within the 4-C molecules. Between succinic and fumaric acids, such molecular shifting does not
release enough energy to make ATP or NADH outright; instead, this energy is captured by a new
energy carrier, flavin adenine dinucleotide (FAD). FAD is reduced by the addition of two Hs, result-
ing in FADH2. FADH2 is not as rich an energy carrier as NADH, the former yielding less ATP than
the latter.
The last step, between malic acid and OA, reforms OA to complete the cycle. Energy is given off
and trapped by the reduction of NAD+ to NADH. The carbon dioxide released by cells is generated
by the Kreb’s cycle, as are the energy carriers NADH and FADH2, which play a role in the next step
(Figure 10.5).
10.5.1.3 Electron Transport Phosphorylation

Whereas Kreb’s cycle occurs in the matrix of the mitochondrion, electron transport system (ETgS)
chemicals are embedded in the membranes known as cristae. Kreb’s cycle completely oxidizes the
carbons in the pyruvic acids, producing a small amount of ATP and reducing NAD and FAD into
higher-energy forms. In ETS these higher-energy forms are cashed in, producing ATP. Cytochromes
are molecules that pass the “hot potatoes” (electrons) along the ETS chain. Energy released by the
“downhill” passage of electrons is captured as ATP by adenosine diphosphate (ADP) molecules.
The ADP is reduced by the gain of electrons. ATP formed in this way is made by the process of
oxidative phosphorylation. The mechanism for the oxidative phosphorylation process is the gradi-
ent of H+ ions discovered across the inner mitochondrial membrane. This mechanism is known as
chemiosmotic coupling. This involves both chemical and transport processes. Drops in the potential
Cellular respiration
2 NADH Mitochondrion
6 NADH 6 CO2
Citric acid
cycle
2 FADH2 2 ATP
Respiratory chain 32 ATP

and oxidative
phosphorylation
Total energy yield 36 ATP
FIGURE 10.5 Biochemical reactions depicting energy yield in complete oxidation.

Fermentation 255
2 FADH2
32 ATP
Respiratory chain
and oxidative
phosphorylation
Total energy yield 36 ATP
FIGURE 10.6 Depiction of total energy yield in oxidative phosphorylation.
NADH + H+
NAD+ NADH-Q
reductase QH2 red H2O
Cytochrome Cytochrome Cytochrome

Ubiquinone reductase
c oxidase
Q ox O2
Succinate-Q
reductase
Succinate
Fumarate FAD
FADH2
FIGURE 10.7 The ETS.
energy of electrons moving down the ETS chain occur at three points. These points turn out to
be where ADP + P are converted into ATP. Potential energy is captured by ADP and stored in
the pyrophosphate bond. NADH enters the ETS chain at the beginning, yielding three ATPs per
NADH. FADH2 enters at Co-Q, producing only two ATPs per FADH2 (Figures 10.6 and 10.7).
10.5.2 Anaerobic Fermentation

When fermentation is carried out in the absence of oxygen, it is called anaerobic fermentation.
Anaerobic fermentation can be supported with the help of an equation that describes the substrates
used in the fermentation process to give the desired products. One of the examples of anaerobic
fermentation is alcoholic fermentation, whose equation is given here to illustrate how the process of
anaerobic fermentation occurs:
Acetaldehyde + NADH + H + ⎯dehydrogenase

⎯⎯⎯⎯→ Alcohol + NAD +
In this reaction, anaerobic respiration occurs in the sugars to cause fermentation, with the help of
the fungus yeast, which is not in contact with the atmosphere or oxygen. Acetaldehyde and NADH
are substrates of the reaction, which are fermented along with one hydrogen ion to form the product,
that is, alcohol. This reaction takes place in presence of the active enzyme alcohol dehydrogenase
to give the alcohol and a cofactor, which is one ion of NAD. This is what anaerobic fermentation
in yeast produces and this reaction follows the decarboxylation of pyruvate with the help of the
ADPADP ATP
ATP
+ Pi Pi
Glucose
2 Pyruvate
NAD+ NADH CO2
NAD+ NADH CO2
+ H H+
+
2 Acetaldehyde
2 Ethanol
FIGURE 10.8 Alcoholic fermentation reaction.
ADPADP ATP
+ Pi Pi ATP
Glucose
NAD+ NADH
NAD+ NADH 2 Pyruvate
+ H+ H+
2 Lactate
FIGURE 10.9 Lactic acid fermentation reaction.
enzyme pyruvate decarboxylase, thiamine pyrophosphate (TPP), and two Mg ions. After this acet-
aldehyde is produced, CO is formed to give the aforementioned reaction.
Under anaerobic conditions, that is, the absence of oxygen, pyruvic acid can be routed by the
organism into one of three pathways: (1) lactic acid fermentation, (2) alcohol fermentation, or (3)
cellular (anaerobic) respiration. Humans cannot ferment alcohol in their own bodies; we lack the
genetic information to do so. These biochemical pathways with their myriad reactions catalyzed
by reaction-specific enzymes, which are all under genetic control, are extremely complex. Alcohol
fermentation is the formation of alcohol from sugar. Yeast, under anaerobic conditions, converts
glucose to pyruvic acid through the glycolysis pathway and then goes one step further to convert
pyruvic acid into ethanol, a C-2 compound (Figure 10.8).
Many organisms also ferment pyruvic acid into other chemicals, such as lactic acid. Humans
ferment lactic acid in the muscles where oxygen becomes depleted, resulting in localized anaerobic
conditions. This lactic acid causes the muscle stiffness that couch potatoes feel after beginning
exercise programs. The stiffness goes away after a few days since the cessation of strenuous activ-
ity allows aerobic conditions to return to the muscle, and the lactic acid can be converted into ATP
through normal aerobic respiration pathways (Figure 10.9).
10.5.2.1 Anaerobic Fermentation and Glycolysis

Anaerobic fermentation is defined as a form of metabolism in which an organic compound serves
as both the electron donor and electron acceptor and ATP is produced by substrate level phosphory-
lation. Fermentation products can be grouped into two general categories: alcoholic fermentation
products and acidic fermentation products.
Glycolysis, which is defined as the process of converting glucose to pyruvate, can happen
anaerobically. This method of transforming glucose into pyruvate with the help of a very limited
amount of oxygen is known as anaerobic glycolysis. The word “lysis” means breakdown and “glyco”
means glucose; so from this pathway, there is fermentation or breakdown of glucose to pyruvate,
which is a by-product of the same. This process produces energy (38 ATP molecules) in about 10
seconds to 2 minutes and is carried out in the cytoplasm of muscle cells. This energy is stored in the
Golgi apparatus inside these cells and then transported when required throughout the body.
Fermentation 257
Anaerobic glycolysis starts when glucose is phosphorylated into glucose-6-phosphate in the first
step. This product is further converted into fructose-6-phosphate, which is then converted into fruc-
tose-1,6-bisphosphate. This product gives two further products, phosphoglyceraldehyde (PGAL)
and dihydroxyacetone phosphate (DHAP), which are interconvertible by a reversible reaction.
The PGAL then produces 1,3-bisphosphoglycerate by reducing one ion of NAD and an inorganic
phosphate to NADH. This is followed by the production of 3-phosphoglycerate and 2-phospho-
glycerate one after the other with the formation of one ATP molecule. The 2-phosphoglycerate
then gives phosphoenolpyruvate (PEP) by the dehydrogenation of one water molecule. This PEP is
converted to pyruvate with the generation of another ATP molecule, and thus energy is produced by
the anaerobic fermentation of glucose.
Anaerobic microorganisms are useful in biodegradation, breaking down organic chemicals into
smaller compounds, and producing methane and carbon dioxide. Some anaerobic organisms can
break down organic chemicals by fermentation. Such organisms are useful in hazardous-waste sites.
10.5.3 Pathways/Fermentation
10.5.3.1 Fatty Acid and Hydrocarbon Pathway
Microbes utilize fatty acids and hydrocarbons for their metabolism and are usually added to various
fermentation reactions, such as the manufacture of antibiotics. Fats and hydrocarbons are converted
to fatty acids, which are finally converted to acetyl-CoA by a series of reactions. This is also called
β-oxidation.
10.5.3.2 Oxidation of Methane and Methanol

Microorganisms using methane as the carbon source are called methanotrophs, and those using
methanol are called methylotrophs. Methane is oxidized initially to methanol and finally to carbon
dioxide in a reaction involving a series of steps. The overall reaction can be summarized as follows:
Methane → methanol → formaldehyde → formic acid → carbon dioxide
10.5.3.3 Oxidation of Amino Acids

Amino acids are metabolized by microorganisms through oxidation and are utilized as excellent
sources of carbon and nitrogen.
10.5.3.4 Oxidation of Polymers

A polymer is a compound with a large number of monomeric units linked together. As an example,
polysaccharides (starch, cellulose, etc.) contain a large number of monomeric sugar (carbohydrate)
molecules linked together. Proteins contain a large number of amino acids linked together to form
large chains. Microorganisms metabolize polymers by breaking the chains into individual mono-
meric units in a process called hydrolysis, a process that requires the presence of enzymes called
hydrolytic enzymes or hydrolases.
10.6 FERMENTATION PROCESS

10.6.1 Selection of Substrates in a Culture Medium
Although specific media requirements depend on the type of microorganism being used in the fer-
mentation process, the basic requirements remain the same, that is, all media should contain sources
of energy, water, carbon sources, nitrogen sources, vitamins, and minerals. Designing media for
small-scale laboratory purposes is relatively easy, but media for industrial purposes are difficult to
prepare.
The culture medium should allow for a high yield of the desired product at a fast rate; allow
for a low yield of undesired products; be sterilized easily; yield consistent products, that is, have
minimum batch variation; be cheap and readily available; be compatible with the fermentation pro-
cess; and not pose environmental problems before, during, or after the fermentation process.
The culture medium will affect the design of the fermentor. For example, hydrocarbons in some
media require high oxygen content, so an air-lift fermentor (ALF) should be used in such cases.
Natural media ingredients are cheap, but they have high batch variation. On the other hand, pure
ingredients (also called defined media or formulated media) have very little batch variation but are
expensive. The media should support the metabolic process of the microorganisms under study and
allow biosynthesis of the desired products. Media are designed based on the following equation
using minimum components required to produce maximum product yield:
Carbon and energy source + nitrogen source + O 2

→ biomass + products + CO 2 + H 2 O + heat
Knowledge of the elemental composition of process microorganisms is required for solving the
elemental balance equation. Some microorganisms cannot synthesize specific nutrients, for exam-
ple, amino acids, vitamins, and nucleotides. Once a specific growth factor is identified, it can be
incorporated into a medium in adequate amounts as a pure compound or as the component of a
complex mixture. The carbon substrate plays a dual role in biosynthesis and energy generation; the
carbon requirement for biomass production under aerobic conditions may be estimated from the
“cellular yield coefficient,” which is defined as follows:
quantity of cell dry matter produced

Cellular yield coefficient =
quantity of carbon substrrate utilized
The other nutrient required is oxygen, which is provided by aerating the culture; this aspect is
considered in detail in Section 10.8. The design of a medium and selection of substrates will influ-
ence the oxygen demand of a culture in that more reduced carbon sources result in a higher oxygen
demand. Energy for growth comes from either the oxidation of medium components or light. Most
industrial microorganisms are chemoorganotrophs; therefore, the most common sources of energy
will be carbon sources such as carbohydrates, lipids, and proteins. Important components of the
medium are carbon sources, nitrogen sources, minerals, growth factors, chelating agents, buffers,
antifoaming agents, air, steam, and fermentation vessels.
10.6.1.1 Carbon Sources

Product formation is directly dependent on the rate at which the carbon source is metabolized; also,
the main product of fermentation determines the type of carbon source to be used. Carbon sources
include carbohydrates, oils and fats, and hydrocarbons.
10.6.1.2 Carbohydrates
Starch is an easily available carbohydrate obtained from maize, cereals, and potatoes. It is widely
used in alcohol fermentation. Grains such as maize are used directly in the form of ground powder
as carbohydrates. Malt and beer made from barley grains contain high concentrations of different
carbohydrates such as starch, sucrose, cellulose, and other sugars. Sucrose is obtained from sugar
cane and molasses. Molasses is one of the cheapest sources of carbohydrate. It contains a high sugar
concentration and other components such as nitrogenous substances and vitamins; it is used in alco-
hol, SCPs, amino acids, and organic acid fermentations. Extraction and purification of the products
is expensive. Sulfite waste liquor is the by-product of the paper industry; it contains carbohydrates
Fermentation 259
and is used in yeast cultivation. Whey is the by-product of the dairy industry. It is used in alcohol,
SCP, gum, vitamins, and lactic acid fermentation.
10.6.1.3 Oils and Fats

Vegetable oils are used as carbon sources. Oils provide more energy per weight compared to sug-
ars. They also have antifoaming properties, but they are generally used as additives rather than as
the sole carbon source. Examples are olive oil, cottonseed oil, soybean oil, linseed oil, and lard
(animal fat).
10.6.1.4 Hydrocarbons
The C12–C18 alkanes can be used as carbon sources. They are cheap and have more carbon and
energy content per weight than sugars. They can be used in organic acids, amino acids, antibiotics,
enzymes, and proteins fermentations.
10.6.1.5 Nitrogen Sources

Ammonia, ammonium salts, and urea are the most commonly used nitrogen sources in the fer-
mentation process. Ammonia also serves the purpose of pH control. Other substances used as
nitrogen sources are corn steep liquor, soya meal, peanut meal, cottonseed meal, amino acids,
and proteins.
10.6.1.6 Minerals
All microorganisms have certain mineral requirements for growth and metabolism. Calcium,
chlorine, magnesium, phosphorous, potassium, and sulfur are the essential minerals for all media.
Other minerals such as copper, cobalt, iron, manganese, molybdenum, and zinc are needed in trace
amounts and are generally present as impurities in other components. The specific concentrations
of these elements required depend on the microorganism being used.
10.6.1.7 Growth Factors

Some microorganisms cannot synthesize the full complement of cell components and therefore
require preformed compounds called growth factors. Vitamins, amino acids, and fatty acids
are used as growth factors in the fermentation process to complement the cell components of
microorganisms.
10.6.1.8 Chelating Agents

Chelating agents prevent the formation of insoluble metal precipitates. They form complexes with
metal ions present in the medium and can be utilized by microorganisms. Chelating agents are not
required in large-scale fermentation processes since some of the other ingredients in such processes,
such as yeast extract, perform the function of forming complexes with metal ions. One example of
a chelating agent is EDTA, which is a versatile chelating agent and is able to form six bonds with a
metal ion. It is frequently used in soaps and detergents because it forms a complex with calcium and
magnesium ions. These ions are present in hard water and interfere with the cleaning action of soaps
and detergents. Other chelating agents are citric acid and pyrophosphates.
10.6.2 Controlling pH
Buffers are used to maintain the pH of a medium as microbial growth is affected by changes in pH.
The optimum pH for most microorganisms is 7.0. Commonly used buffers are calcium carbonate,
ammonia, and sodium hydroxide. The balanced use of carbon and nitrogen sources will also form
a basis for pH control as the buffering capacity can be provided by proteins, peptides, and amino
acids, such as in corn steep liquor. The pH may also be controlled by adding ammonia or sodium
hydroxide and sulfuric acid to the medium.
10.6.3 Antifoaming Agents

Microbial processes produce a large amount of foam in the fermentation vessel. This is caused by
microbial proteins or other components of the media. Foaming causes the removal of cells from the
media and their autolysis; thus, releasing more microbial foam-producing proteins aggravates the
problem. Foam will reduce the working volume of the fermentation vessel, decrease the rate of heat
transfer, and deposit cells on the top of the fermentor. The air filter in the fermentor becomes wet,
allowing the growth of contaminating microorganisms. Antifoaming agents are also called surfac-
tants, that is, they reduce the surface tension in the foam and destabilize foam-producing proteins.
Commonly used antifoaming agents are stearyl alcohol, cottonseed oil, linseed oil, olive oil, castor
oil, soybean oil, cod liver oil, silicones, and sulfonates.
An ideal antifoam should be highly dispersible in foam, fast acting, nontoxic to humans and
microorganisms, long acting in preventing new foam formation, cheap, heat sterilizable, and have
no effect on oxygen transfer. Compounds that meet most of these requirements are alcohols, stearyl,
octyldecanol, esters, and fatty acids and their derivatives, particularly glycerides, which include
cottonseed oil, linseed oil, soybean oil, olive oil, castor oil, sunflower oil, rapeseed oil, cod liver oil,
silicones, sulfonates, alkaterge C, oxazaline, and polypropylene glycol. These antifoams are gener-
ally added when foaming occurs during fermentation. Because many antifoams have low solubility,
they need a carrier such as lard oil, liquid paraffin, or castor oil, which may be metabolized and
affect the fermentation process. Unfortunately, the concentrations of many antifoams required to
control fermentations will reduce the oxygen-transfer rate by as much as 50%; therefore, antifoam
additions must be kept to an absolute minimum. There are also other antifoams that increase the
oxygen-transfer rate. If the oxygen-transfer rate is severely affected by antifoams additions, then
mechanical foam breakers may have to be considered as a possible alternative.
10.6.4 Air
Air is required for aeration and is supplied to the fermentor by means of pumps or compressors. It
is sterilized by passing through filters before being introduced. The amount of air and the extent of
purity required depend on the fermentation process being carried out. The majority of fermentation
processes are aerobic and, therefore, require the provision of oxygen. If stoichiometry of respiration
is considered, then the oxidation of glucose may be r epresented as follows:
C6 H12 O6 + 6O 2 = 6H 2 O + 6CO 2
Oxygen is normally supplied to microbial cultures in the form of air, this being the cheapest
available source of the gas. The method for provision of a culture with a supply of air varies with
the scale of the process. Laboratory-scale cultures may be aerated by means of the shake flask
technique, where the culture is grown in a conical flask shaken on a platform contained in a con-
trolled environment chamber, whereas pilot and industry-scale fermentations are normally carried
out in stirred, aerated vessels. It is often advantageous to culture relatively small volumes (1 dm3) in
stirred, aerated vessels as this enables the cultural conditions to be better monitored and controlled
and facilitates addition of supplements and removal of samples. Some fermentors are so designed
that adequate oxygen transfer is obtained without agitation.
10.6.5 Steam
Steam is used to sterilize fermentors and other equipment and to control temperature. Continuous
dry steam supply is required for the fermentation process and care should be taken to prevent steam
condensation.
Fermentation 261
Agitation system
Feeding pump
System monitor
Medium
Sensors probes
Air
Reactor tank Thermal jacket
Submerged aerator
Effluent
FIGURE 10.10 External view of an ideal fermentor.
Standard shake flask Flying saucer shake flask

or the Erlenmeyer flask
Shake flask with baffles Flatbed Thompson bottle
FIGURE 10.11 Different types of shaker flasks.
10.6.6 Fermentation Vessels

Laboratory-scale fermentations are carried out in shaker flasks and flatbed bottles. Large-scale fer-
mentations are carried out in glass or stainless steel tank fermentors. A fermentation vessel should
be cheap, nontoxic to the microorganism used for the process, easy to sterilize, easy to operate,
robust and reliable, and leak-proof; allow visual monitoring of the fermentation process and sam-
pling; and not allow the contamination of its contents (Figure 10.10).
10.6.7 Shaker Flasks

Shaker flasks are conical vessels made of glass that are available in different sizes. The typical vol-
ume of these flasks is 250 ml. There are different types of shaker flasks, such as baffled, unbaffled,
Erlenmeyer, and flying saucer. Shaker flasks are used for screening microorganisms and cultivat-
ing them for inoculation. Shaker beds or shaker tables are used to allow oxygen transfer by their
continuous rotary motion. Baffled flasks are used to increase oxygen transfer. Shaker flasks need to
be plugged to prevent contamination with other microorganisms. Cotton wool, polyurethane foam,
glass, and synthetic plugs are commonly used. Fernwald shaker flasks and flatbed Thompson bottles
are expensive and are not commonly used (Figure 10.11).
10.7 TYPES OF FERMENTATION

10.7.1 Solid-State Fermentation
Solid-state (substrate) fermentation (SSF) holds tremendous potential in the production of enzymes.
It is of special interest in processes where the crude fermented product may be used directly as the
enzyme source. SSF has been defined as the fermentation process occurring in the absence or near
absence of free water. SSF processes generally use a natural raw material such as carbon and an
energy source. SSF can also use an inert material as the solid matrix, which requires supplementing
a nutrient solution containing necessary nutrients as well as a carbon source. The solid substrate
(matrix), however, must contain enough moisture. Depending on the nature of the substrate, the
amount of water absorbed can be one or several times more than its dry weight, which leads to
relatively high water activity (aw) on the solid/gas interface in order to allow a higher rate of the
biochemical process. Low diffusion of nutrients and metabolites takes place in lower-water-activity
conditions, whereas compaction of the substrate occurs under conditions of higher water activity.
Hence, maintenance of an adequate moisture level in the solid matrix along with suitable water
activity is essential for SSF processes. Solid substrates should generally have a large surface area
per unit volume (say, in the range of 103–106 m2/cm3 for the ready growth on the solid/gas inter-
face). Smaller substrate particles provide larger surface areas for microbial attacks but pose dif-
ficulty in aeration/respiration due to limitations in interparticle space availability. Larger particles
provide better aeration/respiration opportunities but less surface area. In bioprocess optimization,
sometimes it may be necessary to use a compromised size of particles (usually a mixed range) for
cost-effectiveness. For example, wheat bran, which is the most commonly used substrate in SSF, is
obtained in two forms: fine and coarse. The former contains small particles (mostly smaller than
500–600 µ) and the latter contains mostly large particles. Most SSF processes use a mix of these
two forms at different ratios for optimal production.
Solid substrates generally provide a good dwelling environment to microbial flora comprising
bacteria, yeast, and fungi. Among these, filamentous fungi are the best-studied organisms for SSF
due to their hyphal growth; they have the ability to not only grow on the surface of the substrate
particles but also penetrate through them. Several agricultural crops such as cassava and barley and
agro-industrial residues such as wheat bran, rice bran, sugarcane bagasse, cassava bagasse, various
oil cakes (e.g., coconut oil cake, palm kernel cake, soybean cake, and groundnut oil cake), fruit pulps
(e.g., apple pomace), corn cobs, sawdust, seeds (e.g., tamarind, jack fruit), coffee husk and coffee
pulp, tea waste, and spent brewing grains are the most commonly used substrates for SSF processes.
During growth on such substrates, hydrolytic exoenzymes are synthesized by the microorganisms
and excreted outside the cells, which create and help in accessing simple products (carbon sources
and nutrients) by the cells. This in turn promotes biosynthesis and microbial activities.
Based on the type of microorganisms involved, SSF processes can be classified into two main
groups, natural (indigenous) SSF and pure-culture SSF, using individual strains or a mixed culture.
Composting and ensiling are the two best examples of SSF processes, which involve natural micro-
flora. Bioprocesses involving pure-culture SSF have also been known for a long time.
10.7.2 Semicontinuous Fermentation

The semicontinuous fermentation process is based on a continuous feeding rate and discontinuous
medium withdrawal. A semicontinuous culture, once established, can be continued almost indefi-
nitely, requiring relatively brief interruptions for harvesting and resupplying the fermentor with a
fresh medium. To overcome some of the limitations of batch processing, continuous operation in a
plug flow system must be considered. As the contaminated solids travel through the system, specific
conditions develop in the successive reactor. One practical way of achieving a plug flow system is
using a sequence of batch reactors. In an experimental cascade of three stirred batch slurry reactors,
the contaminated solids (oil contamination) are periodically transferred to the next step.
Fermentation 263
10.7.3 Continuous Fermentation

Continuous fermentation process is the process in which cells are maintained in a continuous culture
in the exponential growth phase by the frequent addition of a fresh medium that is exactly balanced
by the removal of cell suspension from the bioreactor for the recovery of cells or fermentation prod-
ucts. On the one hand, there is a continuous addition of nutrients, and on the other hand, there is a
continuous removal of fermented broth. This is in contrast to a batch fermentation process in which
a large volume of nutrient medium is inoculated, and growth and biochemical synthesis are allowed
to proceed only until the maximum yield is obtained. At this point, batch fermentation is stopped
for product recovery, the fermentor is cleaned and resterilized, and a new fermentation is started. At
first glance, continuous fermentation appears to be the better of the two procedures because the fer-
mentation equipment is in constant use with little shutdown time and, theoretically at least, after the
initial inoculation further production of inoculums is not required. However, the inherent problems
associated with the continuous fermentation process often do not allow the achievement of this goal.
Continuous fermentation can be conducted in various ways. It can be carried out as a “single
stage” in which a single fermentor is inoculated and then kept in continuous operation by balancing
the input and output of the nutrient solution and harvested culture, respectively. In “recycle” con-
tinuous fermentation, a portion of the withdrawn culture, or of the residual unused substrate plus the
withdrawn culture, is recycled to the fermentation vessel. For example, the immiscible hydrocarbon
substrate of hydrocarbon fermentation can be recycled for further microbial attack. A portion of
the organisms being produced during a continuous fermentation process also can be recycled in
certain instances in which the actual available substrate level in the nutrient solution for microbial
growth is quite low. An example of this type of substrate is sulfite waste liquor with its low available
carbohydrate content; in this instance, the recycling of cells provides a higher population of cells
in the fermentor and, hence, greater productivity. Multistage ethanol production with the recycling
of yeast is another such example. A third type of continuous fermentation is “multistage” continu-
ous fermentation. It involves two or more stages with the fermentor being operated in sequence.
The multistage continuous fermentation process is particularly applicable to fermentation in which
growth and synthetic activities of the cells are not simultaneous, that is, synthesis is not growth-
related but occurs after the cell multiplication rate slows down.
There are two commonly used, possible means by which microbial activity in a continuous cul-
ture can be controlled: (1) the “turbidostat” and (2) the “chemostat.” In the turbidostat, the total cell
population is held constant by using a device that measures culture turbidity so as to regulate both
the nutrient feed rate to the fermentor and the culture withdrawal rate from the fermentor. If the
population numbers rise above a predetermined level, a greater amount of fresh medium is added
to the fermentor so as to dilute the cell concentration; thus, there is no limiting nutrient consciously
imposed with this process so that the cell growth rate should always be maximal. However, the
growth must be maintained in the logarithmic growth phase or very close to it. This factor is a
disadvantage in that fermentation must be performed at a lower maximum cell population than is
possible with a chemostat, and this causes a greater residue of unused nutrient to be lost from the
fermentation vessel with the withdrawal of the harvested culture.
In contrast to the turbidostat, a chemostat maintains the nutrient feed and culture withdrawal
rates at constant values that are always less than the values that allow a maximum growth rate.
The growth rate is controlled by supplying only a limiting amount of a critical growth nutrient in
the feed solution. Thus, cell multiplication cannot proceed at a rate greater than that allowed by the
availability of this critical nutrient. The controlling factor for growth, however, does not necessar-
ily have to be a limiting nutrient; it can also be a relatively high concentration of a toxic product
of the fermentation process. The chemostat is used more often than the turbidostat, because fewer
mechanical problems are encountered in this process and because of the occurrence of less residual
unused nutrient in the harvested culture. Table 10.1 presents a list of representative microorganisms
investigated for their possible use in continuous fermentations.
TABLE 10.1
Representative Genera of Organisms Grown in Continuous Cultures
Organization Genera
Algae Chlorella, Euglena, Scenedesmus, Spirulina,
Anacystis, Aerobacter
Bacteria Bacillus, Brucella, Clostridium, Salmonella
Fungi Ophiostoma, Penicillium, Aspergillus
Protozoa Tetrahynema
Yeast Saccharomyces
TABLE 10.2
Chemical Products from Continuous Fermentation
Growth Associated Not Growth Associated
Acetic acid Acetone
Butanediol Butanol
Ethanol Glycogen
Gluconic acid Subtilin
Hydrogen sulfide Chloramphenicol
Lactic acid Penicillin, streptomycin
Vitamin B12
From among the aforementioned potential continuous fermentation processes, only the produc-
tion of beer, fodder yeast (from sulfite paper mill waste), vinegar, and baker’s yeast (from molasses)
have found commercial applications. However, the activated sludge system for the processing of
wastewaters also may be considered a commercialized continuous fermentation process, which dif-
fers from the more conventional fermentation only in that it deals with a mixed microbial population
acting on a heterogeneous substrate and that the products of this fermentation do not have as much
commercial importance (Table 10.2).
10.8 TYPES OF FERMENTORS

The main function of a fermentor is to provide a controlled environment for the growth of microor-
ganisms or animal cells to obtain a desired product. Some of the bioreactor types are discussed in
Sections 10.8.1 through 10.8.7.
10.8.1 Stirred-Tank Fermentors

Stirred-tank fermentors are the most commonly used fermentors. They are cylindrical vessels with
a motor-driven agitator to stir the contents in the tank. The top-entry stirrer (agitator) model is most
commonly used because it has many advantages, including ease of operation, reliability, and robust-
ness (Figure 10.12).
The bottom-entry stirrer (agitator) model is rarely used. Stirred-tank reactors have the following func-
tions: homogenization, suspension of solids, dispersion of gas–liquid mixtures, aeration of liquid, and
heat exchange. The stirred-tank reactor is provided with a baffle and a rotating stirrer is attached either at
the top or at the bottom of the bioreactor. The typical decision variables are the type, size, location, and
number of impellers, and sparger size and location. These determine the hydrodynamic pattern in the
reactor, which in turn influences mixing times, mass and heat transfer coefficients, shear rates, and so on.
Fermentation 265
Inoculum
Sight glass
Thermometer
Stimer
Air
FIGURE 10.12 Stirred-tank fermentor.
Conventional fermentation is carried out in a batch mode. Since stirred-tank reactors are com-
monly used for batch processes with slight modifications, these reactors are simple in design and easy
to operate. Even today, many of the industrial bioprocesses are carried out in batch reactors; although
significant developments have taken place in recent years in reactor design, the industry still prefers
stirred tanks because in case of contamination or substandard product formation the loss is minimal.
The batch stirred tanks generally suffer due to their low volumetric productivity. The downtimes are
quite large and unsteady-state fermentation imposes stress on microbial cultures due to nutritional
limitations. The fed batch mode adopted in recent years eliminates this limitation. The stirred-tank
reactor offers excellent mixing and reasonably good mass-transfer rates. The cost of operation is low
and the reactors can be used with a variety of microbial species. Since the stirred-tank reactor is
commonly used in the chemical industry, mixing concepts are well developed. Stirred-tank reactors
with immobilized cells are not favored generally due to attrition problems; however, by separating
the zone of mixing from the zone of cell culturing one can successfully operate such systems.
Laboratory-scale stirred-tank fermentors are made of borosilicate glass with a stainless steel lid
and a top-entry stirrer. The typical volume of such fermentors is 1–100 L. Stirrers consist of a motor
attached to a shaft. The shaft contains impellers. Stainless steel fermentors are also used in labo-
ratories having special requirements. They are made of high-grade stainless steel with an internal
surface that should be polished to reduce the adhesion of contents to the walls of fermentor joints;
the surface must be smooth and free from any pinholes.
10.8.1.1 Fermentation Vessel Additional Equipment

10.8.1.1.1 Agitator
The agitator is required to achieve a number of mixing objectives, for example, bulk fluid and
gas phase mixing, air dispersion, oxygen transfer, heat transfer, suspension of solid particles, and
maintaining a uniform environment throughout the vessel contents. The agitator consists of a shaft,
impellers with 4–6 blades, and a motor to drive it. Shafts should have double seals to prevent
the leakage of contents. The main function of the agitator is mixing the contents, aeration, and
removal of carbon dioxide produced during fermentation process by mixing action. Agitators may
be classified as follows (Figure 10.13):
• Rushton blade or disk turbine: This is the most commonly used impeller because of its
simple design, robustness, and ease of operation. It has 4–6 blades (Figure 10.13).
• Open turbine impellers.
• Marine impellers.
(a) (b)
(c) (d)
FIGURE 10.13 Different types of agitators: (a) and (b) Rushton blade disk turbine, and (c) and (d) marine
impeller.
The disk turbine consists of a disk with a series of rectangular vanes set in a vertical plane around
the circumference, and the vaned disk has a series of rectangular vanes attached vertically to its
under side. Air from the sparger hits the underside of the disk and is displaced toward the vanes,
where the air bubbles are broken up into smaller bubbles. The vanes of a variable pitch open turbine
and the blades of a marine propeller are attached directly to a boss on the agitator shaft. In this case,
the air bubbles do not initially hit any surface before getting dispersed by the vanes or blades.
Since the 1940s, a Rushton disk turbine of one-third the fermentor diameter has been considered
the optimum design for use in many fermentation processes. It was established experimentally that
the disk turbine is most suitable in a fermentor since it can break up a fast air stream without itself
becoming flooded with air bubbles.
10.8.1.1.2 Baffles
Four baffles are fixed on the walls of the fermentor and are used to prevent the formation of a vortex.
Impellers and baffles produce axial or radial flow patterns of the contents in the fermentor. Baffles
are metal strips of roughly one-tenth the vessel diameter and are attached radially to the wall. The
agitation effect is only slightly increased with wider baffles and drops sharply with narrower baffles.
Extra cooling coils may be attached to baffles to improve the cooling capacity of a fermentor with-
out unduly affecting the geometry (Figure 10.14).
10.8.1.1.3 Compressor
Compressors are used to pump air under pressure into a fermentor from the bottom to promote aeration
and mixing. They are used mainly in large fermentors. For laboratory-scale, small fermentors, air pumps
are used. Compressors should be oil-free in order to provide food-grade clean air to the fermentor.
10.8.1.1.4 Filters
A filter is used to filter the air supplied by the compressor before it enters the fermentor to ensure
the air supply is clean. Types of filters are as follows:
• Membrane filters: They are made of cellulose acetate and nitrate with a constant pore size
of 0.2 mm to ensure filtering of particulate matter. They are not cheap, but they are easy
to maintain.
Fermentation 267
FIGURE 10.14 Baffles.
• Packed-bed filters: They contain glass wool or cotton wool packed in a container through
which air is passed. Pore size is not uniform and these filters are susceptible to compaction
and wetting, thereby causing channeling.
• Cartridge filters: The filter element is present in a stainless steel or polycarbonate cartridge
in these filters. They are reliable and durable, but they are also expensive.
10.8.1.1.5 Aeration System (the Sparger)

A sparger may be defined as a device for introducing air into the liquid in a fermentor. Three basic
types of spargers are used: (1) porous sparger, (2) orifice sparger (a perforated pipe), and (3) com-
bined sparger-agitator. A combined sparger-agitator may be used in laboratory fermentors.
10.8.1.1.5.1 Porous Sparger A porous sparger is made of sintered glass of ceramics or metal. It
is used only in laboratory-scale nonagitated vessels. The size of the bubble formed is 10–100 times
larger than the pore size. There is a pressure drop across the sparger and the holes tend to be blocked
by the organism’s growth, which is the limitation of a porous sparger.
10.8.1.1.5.2 Orifice Sparger An orifice sparger is used in small stirred fermentors. It is a perfo-
rated pipe kept below the impeller in the form of crosses or rings. Its size should be approximately
three-quarters of the impeller diameter. Air holes drilled to the undersurfaces of the tubes and the
holes should be at least 6 mm in diameter. This type of sparger is used mostly with agitation. It
is also used without agitation in some cases such as in yeast manufacture, effluent treatment, and
production of SCP.
10.8.1.1.5.3 Nozzle Sparger A nozzle sparger is mostly used in large-scale applications. It is

a single open/partially closed pipe positioned centrally below the impeller. When air is passed
through this pipe, there is lower pressure loss than in a porous sparger and the holes do not get
blocked.
10.8.1.1.5.4 Combined Sparger-Agitator This is air supply through the hollow agitator shaft.
Air is emitted through holes in the disk or blades of the agitator.
10.8.1.1.6 Sensors
Sensors are used to monitor and control various fermentation parameters such as pH, temperature,
and oxygen content.
10.8.1.1.7 Pumps
Liquid/medium is introduced to the fermentor using a pump. Various types of pumps are available,
including
• Peristaltic pumps: They provide a constant flow rate and mild pumping. As liquids do not
backflow, check valves are not required (Figure 10.15).
• Mini or delta pumps: They are used for adding pH control agents such as acid and alkali
and for adding antifoam agents. Mini pumps are fixed-speed pumps and can pump against
pressure (Figure 10.16).
• Larger pumps: They are used to add nutrients to the medium. Speed can be varied by alter-
ing the bore size of tubes.
10.8.1.1.8 Additional Equipment

10.8.1.1.8.1 Feed Ports The addition of nutrients and acid/alkali to small fermentors is nor-
mally made through silicone tubes, which are autoclaved separately and pumped by a peristaltic
FIGURE 10.15 A peristaltic pump.
Discharge
Air-bleed
valve
Relief
Plunger valve
Diaphragm
Reciprocating motion
Hydraulic
fluid
Relief
valve
Suction
FIGURE 10.16 A diaphragm pump.

Fermentation 269
pump after aseptic connection. In large fermentor units, nutrient reservoirs and associated piping
are usually an integrated part which can be sterilized with the vessel. However, there may also be
ports that are used intermittently. These can be sterilized in situ with steam after the connection is
completed and before any conditions are made.
10.8.1.1.8.2 Valves and Steam Traps Valves attached to fermentors and ancillary equipments
are used for controlling the flow of liquids and gases in a variety of ways:
• Simple on/off valves, which are either fully open or fully closed
• Valves that provide coarse control of flow rates
• Valves that may be adjusted very precisely so that flow rates may be accurately controlled
• Safety valves, which are constructed in such a way that liquids or gases flow in only one
direction
There are different models of valves:

1. Opening and closing valves, raising or lowering the blocking unit
• Gate valve: A sliding disk moving in/out of the flow path by a turn of the stem
• Globe valve: A horizontal disk/plug, which is raised or lowered
• Piston valve: Similar to a globe valve except that a piston controls the flow
• Needle valve: Similar to a globe valve except that the disk is replaced with a tapered
plug/needle
2. Drilled sphere/plug
• Plug valve: Parallel/tapered plug with an orifice on a 90° turn closes/opens the flow
path
• Ball valve: Similar to a plug valve except that balls with orifices replace the plug
3. Disk rotating between bearings
• Butterfly valve: A disk rotates about a shaft and closes against the seal to stop the flow
4. Rubber diaphragm/tube pinching
• Diaphragm valve: Similar to a pinch valve except that there is no pinching but pushing
from one side against a diaphragm
• Pinch valve: A flexible sleeve closed by a pair of pinch bars (rubber, neoprene, etc.)
Valves are chosen based on four types of applications:

1. On/off application: Globe valve, butterfly valve
2. Crude flow control: Gate valve
3. Accurate control: Needle valve
4. Very sterile operation: Pinch valve, diaphragm valve
10.8.1.1.8.3 Check Valves Valves used to prevent the accidental reversal of the flow of liquid
or gas due to a break down are called check valves. There are three types of check valves: (1) swing
check, (2) lift check, and (3) combined stop and check valves.
10.8.1.1.8.4 Pressure-Control Valves Pressure-control valves are used for two purposes:
1. Pressure reduction
2. Pressure retaining
10.8.1.1.8.5 Safety Valves There are various types of safety valves by which the increase in
pressure is released. They are
• A spindle lifted from its seating against the pressure, which releases pressure
• Bursting/rupturing of disks to release pressure
In case of releasing a gas, the escaping gas must be treated before release.
10.8.1.1.8.6 Steam Traps A steam trap is important in removing any steam condensate. There
are two components to a steam trap: (1) a valve and seat assembly and (2) an open/close device. The
operation of the components is based on the following:
• Density of fluid: A float (ball/bucket) floats in water but sinks in steam. When it floats the
valve closes, and when it sinks the valve opens.
• Temperature of fluid: The steam trap has a water/alcohol mixture, which senses any change
in temperature. This mixture expands in hot steam and closes the valve. When it contracts
in cool water, the valve is opened.
• Kinetic effect of fluid in motion: Low-density steam flows with a high velocity. Similarly,
high-density steam flows with a low velocity. The conversion of pressure energy into
kinetic energy controls the opening and closing of the valve.
10.8.2 ALF
ALFs do not have mechanical agitation systems (e.g., motor, shaft, impeller blades); the contents are
agitated by injecting air from the bottom. Sterile atmospheric air is used if the microorganisms are
aerobic and inert gas is used if the microorganisms are anaerobic. This is a gentle method of mixing
the contents and is most suitable for fermentation of animal and plant cell cultures, since mechani-
cal agitation produces high shearing stress that may damage the cells. ALFs are most widely used
for large-scale production of monoclonal antibodies (Figure 10.17).
An ALF is generally classified as a pneumatic reactor without any mechanical stirring arrange-
ments for mixing. The turbulence caused by the fluid flow ensures adequate mixing of the liquid. A
draft tube is provided in the central section of the reactor. The introduction of the fluid (air/liquid)
causes an upward motion and results in circulatory flow in the entire reactor. The air/liquid veloci-
ties will be low and, hence, energy consumption is also low. ALFs can be used for both free and
immobilized cells. There are very few reports on ALFs for metabolite production. The advantage of
air-lift reactors is the elimination of attrition effects generally encountered in mechanically agitated
reactors. It is ideally suited for aerobic cultures since its oxygen mass transfer coefficient is quite
Gas flow outlet
Gas-lift
bioreactor Bubble
Internal
tube
Inoculated
gel bead
Gas
Flowmeter distributor
Gas flow inlet
FIGURE 10.17 Air-lift fermentor.

Fermentation 271
high in comparison with stirred-tank reactors. This is ideal for SCP production from methanol as
carbon substrate. This is used mainly to avoid the production of excess heat during mechanical
agitation.
10.8.3 Fixed-Bed Fermentors

Packed-bed or fixed-bed bioreactors are commonly used with attached biofilms, especially in
wastewater engineering. The use of packed-bed reactors gained importance after the potential of
the whole-cell immobilization technique was demonstrated. The immobilized biocatalyst is packed
in the column and fed with nutrients from either the top or bottom.
One of the disadvantages of packed beds is the change in flow characteristics resulting from
alterations in bed porosity during the operation. While working with soft gels such as alginates and
carrageenan, the bed compaction that generally occurs during fermentation results in a high pres-
sure drop across the bed. In many cases, the bed compaction is so severe that gel integrity is severely
hampered. In addition, channeling may occur due to turbulence in the bed. Although packed beds
belong to the class of plug flow reactors in which back mixing is absent, in many packed beds a
slight amount of back mixing occurs, which changes the characteristics of fermentation.
Packed beds are generally used in cases where substrate inhibition governs the rate of reaction.
Packed-bed reactors are widely used with immobilized cells. Several modifications such as tapered
beds to reduce the pressure drop across the length of the reactor, inclined bed, horizontal bed, and
rotary horizontal reactors have been tried with limited success (Figure 10.18).
10.8.4 Tower Fermentors

Tower fermentors are simple in design and easy to construct. They consist of a long cylindrical ves-
sel with an inlet at the bottom, an exhaust at the top, and a jacket to control temperature. They do
not require agitation; hence, they do not have shafts, impellers, or blades. Tower fermentors are used
for the continuous fermentation of beer, yeast, and SCPs (Figure 10.19).
A bubble column fermentor is the simplest type of tower fermentor; it consists of a tube that is
air sparged at the base. It is an elongated, nonmechanically stirred fermentor with an aspect ratio of
6:1. This type of fermentor is used in citric acid production.
10.8.5 Batch Culture Fermentation

Batch culture is a closed culture system, which contains an initial limited amount of a medium. As
the growth of the microorganism proceeds, the medium availability changes and the organism goes
through a number of phases as described in Section 10.3.
Gel beads
Large
nonmoving
particles
Cells are trapped

in the gel matrix
FIGURE 10.18 Fixed-bed fermentor.

Motor The prepared

The yeast
medium
starter
(mash)
Fermentation tank
Foam jets (fermenter)
Foam breaker
Cooling water Distillation

Foam tube
Thermostat
Purification
Cooling coil
Aeration disk
Sampling tube Storage
Air/oxygen
inlet
(a) (b)
FIGURE 10.19 Tower fermentor: (a) Diagrammatic view of tower fermentation, and (b) a flow chart of tower
fermentation.
10.8.6 Fed-Batch Culture

Two basic approaches to fed-batch fermentation are possible: (1) constant-volume fed-batch culture
or fixed-volume fed-batch and (2) variable-volume fed-batch.
10.8.6.1 Fixed-Volume Fed-Batch

In this type of fed-batch fermentation, the limiting substrate is fed without diluting the culture. The
culture volume can be maintained practically constant by feeding the growth-limiting substrate in
its undiluted form, for example, as a very concentrated liquid or gas (e.g., oxygen). Alternatively,
the substrate can be added by dialysis or, in a photosynthetic culture, radiation can be the growth-
limiting factor without affecting the culture volume. A certain type of extended fed-batch culture,
that is, the cyclic fed-batch culture for fixed-volume systems, refers to periodic withdrawal of a por-
tion of the culture and use of the residual culture as the starting point for a further fed-batch process.
Basically, once the fermentation reaches a certain stage (e.g., when aerobic conditions cannot be
maintained anymore), the culture is removed and the biomass is diluted to the original volume using
sterile water or a medium containing the feed substrate. Dilution decreases the biomass concentra-
tion and results in an increase in the specific growth rate. Subsequently, as feeding continues the
growth rate will decline gradually as biomass once more increases and approaches the maximum
amount sustainable in the vessel, at which point the culture may be diluted again.
10.8.6.2 Variable-Volume Fed-Batch

As the name implies, a variable-volume fed-batch is one in which the volume changes with the fer-
mentation time. The way in which the volume changes depends on the requirements, limitations, and
objectives of the operator. The feed can be provided according to one of the following three options:
1. The same medium used in the batch mode is added.

2. A solution of the limiting substrate at the same concentration as that in the initial medium
is added.
3. A very concentrated solution of the limiting substrate is added at a rate less than that in
options 1 and 2.
This type of fed-batch can be further classified into repeated fed-batch processes or cyclic fed-
batch cultures, and single fed-batch processes. In the former, once fermentation reaches a certain
Fermentation 273
stage after which the culture is not effective anymore, a quantity of the culture is removed from the
vessel and replaced by a fresh nutrient medium. The decrease in volume results in an increase in the
specific growth rate, which is followed by a gradual decrease in volume as the quasi-steady state is
established. The latter type refers to a type of fed-batch in which supplementary growth medium is
added during fermentation but no culture is removed until the end of the batch. This system presents
a disadvantage over the fixed-volume fed-batch and the repeated fed-batch processes. Much of the
fermentor volume is not utilized until the end of the batch is reached and, consequently, the duration
of the batch is limited by the fermentor volume.
10.8.6.3 Advantages and Disadvantages of Fed-Batch Reactors

Fed-batch fermentation is an intermediary technique between batch and continuous fermentation. A
proper feed rate with the right component constitution is required during the process. Fed-batch offers
many advantages over batch and continuous cultures. It can be easily concluded that under controllable
conditions and with the requisite knowledge of the microorganism involved in the fermentation process,
the feed of the required components for growth and/or other substrates required for the production of the
product can never be depleted and the nutritional environment can be maintained approximately constant
during the course of the batch. The production of by-products that are generally related to the presence
of high concentrations of the substrate can also be avoided by limiting its quantity to amounts that are
required solely for the production of the biochemical. When high concentrations of the substrate are pres-
ent, cells get overloaded, that is, their oxidative capacity is exceeded, and due to the Crabtree effect prod-
ucts other than the one of interest are produced, reducing the efficacy of the carbon flux. Moreover, these
by-products have even proved to “contaminate” the product of interest, as ethanol does in the production
of baker’s yeast, and to impair cell growth, thereby reducing fermentation time and related productivity.
Sometimes, controlling the substrate is also important due to catabolic repression. Since this method
usually permits the extension of operating time, high cell concentrations, and thereby improved pro-
ductivity [mass of product/(volume × time)] can be achieved. This aspect is greatly favored in the
production of growth-associated products. Additionally, this method allows the replacement of water
loss by evaporation and decrease in the viscosity of the broth, such as in the production of dextran
and xanthan gum, by the addition of a water-based feed. As previously mentioned, fed-batch might be
the only option for fermentations dealing with toxic or low-solubility substrates. When dealing with
recombinant strains, fed-batch mode can guarantee the presence of an antibiotic throughout the course
of the fermentation process with the intent of keeping the presence of an antibiotic-marked plasmid.
Since growth can be regulated by the feed, and knowing that in many cases a high growth rate
can decrease the expression of encoded products in recombinant products, the possibility of having
different feeds and feed modes makes fed-batch an extremely flexible tool for control in such cases.
Because the feed can also be a multisubstrate, the fermentation environment can still be provided
with required protease inhibitors that might degrade the product of interest, metabolites, and pre-
cursors that increase the productivity of the fermentation process.
Finally, in fed-batch fermentation no special piece of equipment is required in addition to the
one required by batch fermentation, even when the operating procedures for sterilization and pre-
vention of contamination are considered. A cyclic fed-batch culture has an additional advantage:
The productive phase of a process may be extended under controlled conditions. Such controlled
periodic shifts in growth rate provide an opportunity to optimize product synthesis, particularly if
the product of interest is a secondary metabolite whose maximum production takes place during
the deceleration in growth.
10.8.6.4 Equipment
10.8.6.4.1 Vessels
Laboratory-scale fermentations are carried out in shaker flasks and flatbed bottles. Large-scale
fermentations are carried out in glass or stainless steel tank fermentors. A fermentation vessel
should be cheap, not allow contamination of its contents, be nontoxic to the microorganism used
e
b
a
f
c
a
d
g b b
(a) (b)
FIGURE 10.20 Fermentation vessels. (a) A holding vessel: A screw-neck borosilicate glass vessel with
medium/inoculum addition assembly is shown. In the figure, a denotes a stainless steel rod, b denotes silicon
tubing, c denotes a silicon disk, d a hypodermic needle, e an air vent, f a screw cap, and g a magnetic bar. (b)
An aspirator-type vessel for introducing an inoculum of filamentous fungi into the fermentor is shown. In this
figure, a denotes a cottonwool plug and b denotes a magnetic stirrer bar.
for the process, be easy to sterilize, be easy to operate, be robust and reliable, allow visual moni-
toring of the fermentation process, allow sampling, and be leak proof (Figure 10.20).
10.8.6.4.1.1 Shaker Flasks

Shaker flasks are conical vessels made of glass and are available in different sizes. The typical vol-
ume of these flasks is 250 mL. There are different types of shaker flasks, such as baffled, unbaffled
or Erlenmeyer, and flying saucer flasks. Shaker flasks are used for screening of microorganisms
as well as their cultivation for inoculation. Shaker beds or shaker tables are used to allow oxygen
transfer by their continuous rotary motion. Baffled flasks are used to increase oxygen transfer.
Shaker flasks need to be plugged to prevent contamination with other microorganisms. Cottonwool,
polyurethane foam, glass, and synthetic plugs are commonly used to make shaker flasks. Fernwald
shaker flasks and flatbed Thompson bottles are expensive and are not commonly used (Figure 10.11).
10.8.6.4.2 Pumps
A syringe pump is useful in the case of fed-batch for controlling liquid flow rate. A syringe is filled
with liquid and secured onto the pump. Syringe plungers link to movable pistons to firmly secure to
the main body of the pump. Regulated piston movement controls the flow rate. This pump is ideal
for use with low flow rates.
Peristaltic pumps are also used to control flow rate (Figure 10.15). They control flow rate by
squeezing and releasing pulse flow. The tubing through which the liquid flows is housed on a roller.
The circular motion (speed) pinches and releases the tubing. The flow is smoother with more rollers.
This pump can be controlled by a process controller with inputs of respiratory quotient and optical
density. Peristaltic pumps are mostly used for adding acids and bases.
Another type of controlling device is a diaphragm pump (Figure 10.16). The liquid is allowed
to flow through a flexible tube that utilizes a piston, and a pump controls the flow. The ball valves
present in the flow prevent leakages and control the direction of the flow.
10.8.6.5 Control Techniques for Fed-Batch Fermentations

10.8.6.5.1 Proportional-Integral-Derivative Control Systems
The process parameters measured using probes may be controlled using control loops. A control
loop consists of four components: (1) a measuring element, (2) a controller, (3) a final control ele-
ment, and (4) the process to be controlled. A simple type of control is feedback control, in which
the measuring element senses a process property and generates a corresponding output signal. The
Fermentation 275
Mathematical Fermentation
model
Sensors
Parameters
Reading
Controllers
FIGURE 10.21 Control techniques for fed-batch fermentations.
controller compares the measurement signal with a predetermined desired value (setpoint) and pro-
duces an output signal to counteract any differences between the two. The final control element
receives the control signal and adjusts the process by changing a valve opening or pump speed and
causing the controlled process property to return to the set point. In manual control systems, a plant
operative is instructed to monitor data throughout the time of operation and take appropriate action
if there is any change from the set point (Figure 10.21).
10.8.6.5.2 The Proportional-Integral-Derivative Controller

A proportional-integral-derivative controller (PID controller) is a generic control loop feedback
mechanism widely used in industrial control systems. A PID controller attempts to correct the error
between a measured process variable and a desired set point by calculating and then outputting a
corrective action that can adjust the process accordingly.
The PID controller calculation (algorithm) involves three separate parameters: (1) proportional,
(2) integral, and (3) derivative values. The proportional value determines the reaction to the cur-
rent error, the integral determines the reaction based on the sum of recent errors, and the derivative
determines the reaction to the rate at which the error is changing. The weighted sum of these three
actions is used to adjust the process through a control element such as the position of a control valve
or the power supply of a heating element. By “tuning” the three constants in the PID controller algo-
rithm, the PID can provide the control action designed for specific process requirements.
The response of the controller can be described in terms of the responsiveness of the controller to an
error, the degree to which the controller overshoots the setpoint, and the degree of system oscillation.
Note that the use of the PID algorithm for control does not guarantee optimal control over the system.
Some applications may require the use of only one or two modes to provide appropriate system control.
This is achieved by setting the gain of undesired control outputs to zero. A PID controller will be called
a PI, PD, P, or I controller in the absence of the respective control actions. PI controllers are particularly
common, since derivative action is very sensitive to measurement noise, and the absence of an integral
value prevents the system from reaching its target value due to the control action. The PID control scheme
is named after its three correcting terms, whose sum constitutes the manipulated variable (MV). Hence,
MV (t ) = Pout + I out + Dout
where Pout, Iout, and Dout are contributions to the output from the PID controller from each of the
three terms, as defined next.
The proportional term makes a change to the output that is proportional to the current error
value. The proportional response can be adjusted by multiplying the error by a constant Kp, which
is called proportional gain. The proportional term is given as follows:
Pout = K p e(t )
where SP is the substrate product ratio in the fermenter and PV is the product volume ratio in the fer-
menter; where Pout denotes proportional output; Kp denotes proportional gain, a tuning parameter; e
is given by error = SP − PV; and t is time or instantaneous time (the present).
A high proportional gain results in a large change in the output for a given change in the error. If
the proportional gain is too high, the system can become unstable. In contrast, a small gain results
in a small output response to a large input error and a less responsive (or sensitive) controller. If the
proportional gain is too low, the control action may be too small when responding to system distur-
bances. In the absence of disturbances, pure proportional control will not settle at its target value
but will retain a steady-state error that is a function of proportional gain and process gain. Despite
the steady-state offset, both tuning theory and industrial practice indicate that it is the proportional
term that should contribute to the bulk of output change.
The contribution from the integral term is proportional to both the magnitude of the error and
the duration of the error. Summing the instantaneous error over time (integrating the error) gives
the accumulated offset that should have been corrected previously. The accumulated error is then
multiplied by integral gain and added to the controller output. The magnitude of the contribution
of the integral term to the overall control action is determined by the integral gain, Ki. The integral
term is given by
τ
I out = K i ∫ ( τ )dτ
0
where Iout denotes integral output; Ki is integral gain, a tuning parameter; e is given by error =
SP – PV; and τ denotes time in the past contributing to the integral response. The integral term
(when added to the proportional term) accelerates the movement of the process toward the set-
point and eliminates the residual steady-state error that occurs with a proportional only controller.
However, since the integral term is responding to accumulated errors from the past, it can cause the
present value to overshoot the set point value (cross over the setpoint and then create a deviation in
the other direction).
The derivative term is the rate of change of the process error calculated by determining the slope
of the error over time (i.e., its first derivative with respect to time) and multiplying this rate of change
by the “derivative gain,” Kd. The magnitude of the contribution of the derivative term to the overall
control action is termed the derivative gain, Kd.
The derivative term is given by
de
Dout = K d
dt
where Dout denotes derivative output; Kd denotes derivative gain, a tuning parameter; e is given by
error = SP −PV; and t is time or instantaneous time (the present).
The derivative term slows down the rate of change of the controller output, an effect that is most
noticeable close to the controller setpoint. Hence, derivative control is used to reduce the magnitude
of the overshoot produced by the integral component and improve the combined controller-process
stability. However, differentiation of a signal amplifies noise in the signal and, thus, this term in the
controller is highly sensitive to noise in the error term and can cause a process to become unstable if
the noise and the derivative gain are sufficiently large. Outputs from the three terms, proportional,
integral, and derivative, are summed to calculate the output of the PID controller. Defining u(t) as
the controller output, the final form of the PID algorithm is as follows:
τ de
MV (t ) = K p e(t ) + K i ∫ e(τ)dτ + K d
0 dt
Fermentation 277
The tuning parameters are as follows:
• Proportional gain (Kp): A large value of Kp typically means a faster response, since the
larger the error the larger the feedback to compensate. An excessively large proportional
gain will lead to process instability.
• Integral gain (Ki): A large value of Ki implies that steady-state errors are eliminated quicker.
The trade-off is larger overshoot: Any negative error integrated during transient response
must be integrated away by positive error before reaching steady state.
• Derivative gain (Kd): A large Kd value decreases overshoot, but slows down transient
response and may lead to instability.
10.8.7 Continuous Culture Fermentation

In continuous culture fermentation, the exponential growth phase of an organism may be prolonged
by the addition of a fresh medium to the vessel. The vessel should be designed in such a way that
the added volume displaces an equal volume of culture from the vessel. If a medium is fed continu-
ously to such a vessel at a suitable rate, a steady state is achieved eventually. During steady state, the
formation of a new biomass in the vessel is equivalent to the loss of cells from the vessel. The flow
of medium into the vessel is related to the total volume of the medium in the vessel; it is expressed
as the dilution rate, D, which can be expressed in the form of a mathematical equation:
D = F /V
where F is the flow rate (in cubic decimeters per hour) and V is the total volume. The net change in
cell concentration over a time period may be expressed as follows:
dx /dt = growth − output or x − Dx
Under steady-state conditions, the cell concentration remains constant; thus, dx/dt = 0 and the
equation becomes
μx = Dx
and μ = D.
10.8.7.1 Chemostat
Under steady-state conditions, the specific growth rate is controlled by the dilution rate, which
is a controllable variable. An important objective of continuous culture operation is to control
cell growth at a level at which productivity is optimum. There are several ways this can be
achieved. One way is to maintain a constant fermentor volume and to use a flow rate that gives
appropriate productivity. In this mode of operation, the fermentor system is known as a chemo-
stat. The chemostat is by far the simplest and most common mode of operation of a continuous
culture. Cell growth in chemostat cultures is maintained steady by a constant inflow of a fresh
medium consisting of nutrients (nitrogen, phosphorous, glucose) at a concentration that makes it
growth limiting. Other constituents of such a medium are present at concentrations higher than
the required values. Increases or decreases in the concentration of the growth-limiting factor are
correspondingly expressed by increases or decreases in the growth rate of cells.
The volume of the chemostat can be controlled by using either a pump or, where contamina-
tion can be a significant problem, a pump-based control system. This setup is commonly used in
laboratory investigations and animal cell culture systems. An overflow system has the advantage
that only one pump is required. However, as the effluent flow rate is determined by gravity alone,
there is a greater possibility of contaminants moving up the effluent tube into the reactor. Overflow
systems are widely used in wastewater treatment and have been used in the large-scale continuous
culture of bacteria. In other techniques, a fermentor variable, for example, turbidity or pH, will be
monitored using an appropriate detector and the liquid flow rate will be automatically adjusted so
as to maintain the variable at a constant level. Examples of these types of continuous fermentors are
pH-stat, turbidostat, and nutristat. However, apart from the pH-stat, these reactors are rarely used
as the necessary measurement-control systems are generally unreliable over long periods of time.
10.8.7.2 Turbidostat
A turbidostat is a continuous culturing method in which the turbidity of the culture is held constant
by manipulating the rate at which the medium is fed. If turbidity tends to increase, the feed rate is
increased to dilute the turbidity back to its set point. When turbidity tends to fall, the feed rate is
lowered so that growth can restore the turbidity to its set point. The most widespread large-scale
application of continuous culture reactors is in wastewater treatment. Activated sludge plants, trickle
bed filters, anaerobic digester, and ponds all operate in a continuous manner. Cell immobilization is
also often used to improve the efficiency of the process. Continuous cultures are well established in
the wastewater treatment industry for several reasons:
• Unlike pure-culture microbial and animal cell systems, contamination is not a consider-
ation as the wastewater feed always contains microorganisms.
• Continuous reactors have long been used in waste treatment and their use is not considered
a risk.
• Finally, using batch cultures is simply not economically feasible. Wastewater flows are
often measured in mega liters per hour and batch reactors simply cannot cope with the
load.
10.9 STERILIZATION IN FERMENTATION

It is essential for all fermentation processes to ensure a yield of the desired product as this allows
the growth of the desired microorganisms. All the components of fermentation need to be sterilized,
including the nutrient medium and other ingredients. The fermentation vessel and other accessory
equipment must also be sterilized to ensure pristine conditions and virtually no contamination.
Different techniques for sterilization are available based on the properties of the component being
sterilized. The most commonly used techniques include sterilization by heat, such as heat steriliza-
tion, moist heat sterilization, dry heat sterilization, incineration, and boiling; sterilization by chemi-
cals; sterilization by filtration; and sterilization by radiation. The specific technique of sterilization
applied in a fermentation process depends on the following:
• The type of microorganism present: Some microorganisms are more resistant than others
and it is very difficult to kill them compared to others.
• The number of microorganisms present: It is much easier to kill a small number of organ-
isms compared to a large number of organisms.
• The amount and type of organic material that protects the microorganisms: Blood or tissue
remaining on poorly cleaned instruments acts as a shield to microorganisms during the
sterilization process.
• The number of cracks and crevices on an instrument that might harbor microorganisms:
Microorganisms collect in and are protected by scratches, cracks, and crevices such as the
serrated jaws of tissue forceps.
Sterilization can be achieved in a number of ways, such as moist heat sterilization, dry heat
sterilization, incineration, boiling, sterilization by chemicals, filtration, and radiation, as shown
in Figure 10.22. The application of heat is considered the most reliable method for sterilization of
Fermentation 279
Methods of
sterilization
Physical Chemical
Heat Radiation Filtration Liquid Gaseous

Earthenware Alcohols Formaldehyde
Asbestos Aldehyde Ethylene oxide
Sintered Phenolices Plasma
Glass membrane Halogens
Dry Moist Nonionizing Ionizing Heavy metals
heat heat Surface active
Electromagnetic
Red heat Below 100°C particulate agents
Flaming At 100°C Dyes
Incineration Above 100°C
Hot air oven
Infrared
FIGURE 10.22 Various methods of sterilization.
articles that can withstand high temperatures. Heat acts by oxidative effects as well as the dena-
turation and coagulation of proteins. Articles that cannot withstand high temperatures can still be
sterilized at lower temperatures by prolonging the duration of exposure. Factors affecting steriliza-
tion by heat are as follows:
• Nature of heat: Moist heat is more effective than dry heat.

• Temperature and time: Temperature and time are inversely proportional to each other. As
temperature increases, the time required decreases.
• Number of microorganisms: The higher the number of microorganisms the higher the
temperature or longer the duration of exposure required.
• Nature of the microorganisms: The effectiveness of sterilization depends on the species
and strain of the microorganism; sensitivity to heat may vary among microorganisms.
Spores are highly resistant to heat.
• Type of material: Articles that are heavily contaminated require high temperatures or pro-
longed exposure. Certain heat-sensitive articles must be sterilized at lower temperatures.
• Presence of organic material: Organic materials such as protein, sugars, oils, and fats
increase the time of exposure required.
10.9.1 Moist Heat Sterilization

This is the most commonly used technique for sterilization of a wide variety of fermentation com-
ponents. Steam is used at high pressure and temperature at 121°C for 15 minutes, causing denatur-
ation of enzymes and degradation of nucleic acids, resulting in the death of the microorganisms
present. This process is carried out by using an autoclave in which the components to be sterilized
are placed in water and heated (Figure 10.23). Steam is produced and high pressure is developed
inside the autoclave. Most of the fermentation components such as the culture medium, small fer-
mentors, and glassware are sterilized by this technique.
Lid handle
Pressure Air exhaust

gauge valve
Main safety
valve
Pressure-
type weight
Locking nuts
safety valve
Water-level
mark Vacuum release
knob
Immersion
heater Inner vessel
Stand
FIGURE 10.23 An autoclave.
Steam sterilization requires four conditions: (1) adequate contact, (2) sufficiently high tempera-
ture, (3) correct time, and (4) sufficient moisture. Although all conditions are necessary for steril-
ization to take place, sterilization failures in clinics and hospitals are most often caused by lack of
steam contact or failure to attain adequate temperature. Moist heat acts by coagulation and dena-
turation of proteins.
10.9.1.1 Moist Heat Sterilization at Temperatures below 100°C

Moist heat sterilization at temperatures below 100°C can occur in the following ways:
• Pasteurization: This process was originally used by Louis Pasteur. Currently, this proce-
dure is used in the food and dairy industry. There are two methods of pasteurization: (1)
the holder method (heated at 63°C for 30 minutes) and (2) the flash method (heated at 72°C
for 15 seconds followed by quickly cooling to 13°C). Other pasteurization methods include
the use of ultra-high temperature (UHT), that is, heating at 140°C for 15 seconds and
at 149°C for 0.5 seconds. This method is suitable to destroy most milk-borne pathogens
such as Salmonella, Mycobacteria, Streptococci, Staphylococci, and Brucella; however,
Coxiella may survive pasteurization. Efficacy is tested by the phosphatase test and the
methylene blue test.
• Vaccine bath: The contaminating bacteria in a vaccine preparation can be inactivated by
heating the preparation in a water bath at 60°C for 1 hour. Only vegetative bacteria are
killed and spores survive.
• Serum bath: The contaminating bacteria in a serum preparation can be inactivated by heat-
ing the preparation in a water bath at 56°C for 1 hour on several successive days. Proteins
in the serum will coagulate at higher temperatures. Only vegetative bacteria are killed and
spores survive.
• Inspissation: This is a technique to solidify as well as disinfect egg- and serum-containing
media. The medium containing serum or egg are placed on the slopes of an inspissator
and heated at 80°C–85°C for 30 minutes on three successive days. On the first day, the
Fermentation 281
vegetative bacteria die; spores that germinate by the next day are killed on the following
day. The efficacy of the process depends on germination of spores in between inspissation
sessions. If the spores fail to germinate, then this technique cannot be considered a steril-
ization technique.
10.9.1.2 Moist Heat Sterilization at 100°C

Moist heat sterilization at 100°C can occur in the following ways:
• Boiling water: Boiling water (100°C) kills most vegetative bacteria and viruses imme-
diately. Certain bacterial toxins such as staphylococcal enterotoxin are resistant to heat.
Some bacterial spores are resistant to boiling and survive; hence, boiling is not a substitute
for sterilization. The killing activity can be enhanced by the addition of 2% sodium bicar-
bonate. When absolute sterility is not required, certain metal articles and glassware can be
disinfected by placing them in boiling water for 10–20 minutes. The lid of the boiler must
not be opened during the period of exposure.
• Steam at 100°C: Instead of keeping articles in boiling water, they are subjected to free
steam at 100°C. Traditionally, Arnold’s and Koch’s steamers were used. An autoclave
(with the discharge tap kept open) can also serve the same purpose. A steamer is a metal
cabinet with perforated trays to hold the articles and a conical lid. The bottom of the
steamer is filled with water and heated. The steam generated sterilizes the articles when
they are exposed for a period of 90 minutes. Media such as TCBS, DCA, and selenite
broth are sterilized by steaming. Sugar and gelatin in the medium may get decomposed
on autoclaving; hence, they are exposed to free steaming for 20 minutes for three suc-
cessive days. This process is known as tyndallization (after John Tyndall), fractional
sterilization, or intermittent sterilization. The vegetative bacteria in the exposed arti-
cles are killed in the first exposure and the spores that germinate by the following day
are killed on subsequent days. The success of the process depends on the germination
of spores.
10.9.1.3 Moist Heat Sterilization at Temperatures above 100°C

Sterilization can be effectively achieved at a temperature above 100°C using an autoclave. Water
boils at 100°C at atmospheric pressure, but if the pressure is raised, the temperature at which water
boils also increases. In an autoclave, water is boiled in a closed chamber. As the pressure rises, the
boiling point of water increases. At a pressure of 15 lbs inside the autoclave, the temperature is
121°C. Exposure of articles to this temperature for 15 minutes sterilizes them. To destroy the infec-
tive agents associated with spongiform encephalopathies (prions), higher temperatures or longer
times are used; for this purpose, an application temperature of 135°C or 121°C for at least 1 hour is
recommended (Figure 10.23).
Advantages of steam sterilization are as follows: Steam has more penetrative power than dry air,
it moistens the spores (moisture is essential for coagulation of proteins), condensation of steam on
cooler surfaces releases latent heat, and condensation of steam draws in fresh steam. Exposure to
steam is a very effective method of sterilization; it is quicker than using a hot air oven.
Disadvantages of steam sterilization are as follows: Drenching and wetting of articles may occur
when they are exposed to steam. The presence of trapped air may reduce the efficacy of steriliza-
tion, and articles take a long time to cool down after exposure to steam.
Methods for sterilization control include the following: Physical methods include automatic pro-
cess control, use of a thermocouple, and use of a temperature chart recorder. Chemical methods
include use of Browne’s tube No. 1 (black spot) and succinic acid (whose melting point is 121°C)
and use of Bowie Dick tape. Bowie Dick tape is applied to articles being autoclaved. If the process
is satisfactory, dark brown stripes appear across the tape. Biological methods include using a paper
strip containing 106 spores of Geobacillus stearothermophilus.
10.9.2 Dry Heat Sterilization

Dry heat acts by protein denaturation, oxidative damage, and toxic effects of elevated levels of
electrolytes, whereas moist heat acts by coagulation and denaturation of proteins. Moist heat is
superior to dry heat in action. The temperature required to kill microbes by dry heat is more than
that required by moist heat. Thermal death time is the minimum time required to kill a suspension
of organisms at a predetermined temperature in a specified environment. Dry heat sterilization is
performed in the following ways:
• Red heat: Articles such as bacteriological loops, straight wires, tips of forceps, and searing
spatulas are sterilized by holding them in a Bunsen flame until they become red hot. This is
a simple method for effective sterilization of such articles, but it is limited to those articles
that can be heated to redness in flame.
• Flaming: Flaming is the method of passing an article over a Bunsen flame without heating
it to redness. Articles such as scalpels, mouths of test tubes, flasks, glass slides, and cover-
slips are passed through the flame a few times. Even though most vegetative cells are killed
by this method, there is no guarantee that spores would die on such short exposures. This
method too is limited to articles that can be exposed to a flame. Cracking of glassware may
occur as a result of exposure to flame.
• Hot air oven: This method was introduced by Louis Pasteur. Articles to be sterilized are
exposed to a high temperature (160°C) for the duration of 1 hour in an electrically heated
oven. Since air is a poor conductor of heat, the even distribution of heat throughout the
chamber is achieved by using a fan. The heat is transferred to the article by radiation, con-
duction, and convection. The oven should be fitted with a thermostat control, a temperature
indicator, and meshed shelves, and it must have adequate insulation.
Articles such as metallic instruments (e.g., forceps, scalpels, and scissors), glassware (e.g., petri
dishes, pipettes, flasks, and all-glass syringes), swabs, oils, grease, petroleum jelly, and some phar-
maceutical products are sterilized.
The sterilization process is as follows: Articles to be sterilized must be perfectly dry before plac-
ing them inside a hot air oven to avoid breakage. Articles must be placed at sufficient distance from
each other so as to allow free circulation of air between them. The mouths of flasks, test tubes, and
both ends of pipettes must be plugged with cotton wool. Articles such as petri dishes and pipettes
may be arranged inside metal canisters and then placed in the oven. Individual glass articles must
be wrapped in kraft paper or aluminum foils.
The sterilization cycle takes into consideration the time taken for articles to reach the sterilizing
temperature, the defined period for which the sterilizing temperature is maintained (holding time),
and the time taken for the articles to cool down. Different temperature-time relations for holding
time are 60 minutes at 160°C, 40 minutes at 170°C, and 20 minutes at 180°C. Increasing the tem-
perature by 10°C shortens the sterilizing time by 50%. The hot air oven must not be opened until the
temperature inside falls below 60°C in order to prevent breakage of glassware.
10.9.3 Incineration
Incineration is a method of destroying contaminated materials by burning them in an incinerator.
Articles such as soiled dressings, animal carcasses, pathological material, and bedding should be
subjected to incineration. This technique results in the loss of the article; hence, it is suitable only
for those articles that have to be disposed of. Polystyrene materials emit dense smoke when burned,
and should not be incinerated.
Incineration is a waste treatment process that involves the combustion of organic substances
contained in waste materials. Incineration and other high-temperature waste treatment systems are
Fermentation 283
described as “thermal treatment.” The incineration of waste materials converts the waste into ash,
flue gas, and heat. The ash is mostly formed by the inorganic constituents of the waste and may
take the form of solid lumps or particulates carried by the flue gas. The flue gases must be cleaned
of gaseous and particulate pollutants before they are dispersed into the atmosphere. In some cases,
heat produced by incineration can be used to generate electric power.
Incineration with energy recovery is one of several waste-to-energy (WtE) technologies, includ-
ing gasification, plasma arc gasification, pyrolysis, and anaerobic digestion. Incineration may also
be implemented without energy and material recovery. In several countries, there are still con-
cerns from experts and local communities about the environmental impact of incinerators. In some
countries, incinerators built just a few decades ago often did not include a materials separation
mechanism to remove hazardous, bulky, or recyclable materials before combustion. These facili-
ties tended to risk the health of their workers and the local environment by facilitating inadequate
levels of gas cleaning and combustion process control. Most of these facilities did not generate
electricity.
Incinerators reduce the solid mass of original waste by 80%–85% and the volume (already
compressed somewhat in garbage trucks) by 95%–96%, depending on composition and degree of
recovery of materials such as metals from the ash for recycling. This means that although incin-
eration does not completely replace land filling, it significantly reduces the necessary volume for
disposal. Garbage trucks often reduce the volume of waste using a built-in compressor before
delivering it to the incinerator. Alternatively, the volume of uncompressed garbage is reduced
at landfills by approximately 70% using a stationary steel compressor, albeit with significant
energy cost. In many countries, simple waste compaction is a common practice for compaction
at landfills.
10.9.4 Chemicals
Disinfectants are chemicals that destroy pathogenic bacteria from inanimate surfaces. Some chemi-
cals have a very narrow spectra of activity, whereas some have very wide spectra. Chemicals that
can sterilize articles are called chemisterilants. Chemicals that can be safely applied over skin and
mucus membranes are called antiseptics. An ideal antiseptic or disinfectant should have the follow-
ing properties:
• Wide spectrum of activity

• Ability to destroy microbes within practical periods of time
• Active in the presence of organic matter
• Ability to make effective contact and be wettable
• Active in any pH
• Stability
• Long shelf life
• Speed
• High penetrating power
• Nontoxic, nonallergenic, nonirritative, and noncorrosive
• No bad odor
• No nonvolatile residue or stain
• Able to retain efficacy on reasonable dilution
• Inexpensive and easily available
An ideal disinfectant with all the aforementioned properties is not yet available. The level of
disinfection achieved depends on contact time, temperature, type and concentration of the active
ingredient, presence of organic matter, and type and quantum of microbial load. The chemical dis-
infectants at working concentrations rapidly lose their strength on standing.
10.9.4.1 Alcohols
Alcohols have the following properties:
• Mode of action: Alcohols dehydrate cells, disrupt membranes, and cause coagulation of
proteins.
• Examples: Ethyl alcohol, isopropyl alcohol, and methyl alcohol.
• Application: A 70% aqueous solution is more effective at killing microbes than absolute
alcohols. Note that 70% ethyl alcohol (spirit) is used as an antiseptic on skin. Isopropyl
alcohol is preferred to ethanol. Isopropyl alcohol can also be used to disinfect surfaces, and
is used to disinfect clinical thermometers. Methyl alcohol kills fungal spores; hence, it is
useful in disinfecting inoculation hoods.
• Disadvantages: Alcohols are skin irritants, volatile (evaporates rapidly), and inflammable.
10.9.4.2 Aldehydes
Aldehydes have the following properties:
• Mode of action: Aldehydes act through the alkylation of the amino group, carboxyl group,
or hydroxyl group and probably damage nucleic acids. They kill all microorganisms,
including spores.
• Examples: Formaldehyde and glutaraldehyde.
• Application: Note that 40% formaldehyde (formalin) is used for surface disinfection and
fumigation of rooms, chambers, operation theaters, biological safety cabinets, hospital
wards, sickrooms, and so on. Fumigation is achieved by boiling formalin, heating parafor-
maldehyde, or treating formalin with potassium permanganate. Formaldehyde also steril-
izes bedding, furniture, and books. Note that 10% formalin with 0.5% tetraborate sterilizes
clean metal instruments. Further, 2% gluteraldehyde is used to sterilize thermometers,
cystoscopes, bronchoscopes, centrifuges, anesthetic equipments, and so on. An exposure
of at least 3 hours at alkaline pH is required for action by gluteraldehyde. Note that 2%
formaldehyde at 40°C for 20 minutes is used to disinfect wool and 0.25% at 60°C for 6
hours is used to disinfect animal hair and bristles.
• Disadvantages: Vapors are irritating (they must be neutralized by ammonia). Aldehydes
have poor penetration and leave nonvolatile residue. Their activity is reduced in the pres-
ence of protein. Glutaraldehyde requires alkaline pH and only those articles that are wet-
table can be sterilized using gluteraldehyde.
10.9.4.3 Phenol
Phenols have the following properties:
• Mode of action: Phenol acts by disruption of membranes, precipitation of proteins, and

inactivation of enzymes.
• Examples: 5% phenol, 1%–5% cresol, 5% lysol (a saponified cresol), hexachlorophene,
chlorhexidine, and chloroxylenol (Dettol).
• Applications: Joseph Lister used phenol to prevent infection of surgical wounds. Phenols
are coal-tar derivatives. They act as disinfectants at high concentrations and as antiseptics
at low concentrations. They are bactericidal, fungicidal, and mycobactericidal, but they
are inactive against spores and most viruses. They are not readily inactivated by organic
matter. Corrosive phenolics are used for disinfection of ward floors, in discarding jars in
laboratories, and for disinfection of bedpans. Chlorhexidine can be used in an isopropanol
solution for skin disinfection or as an aqueous solution for wound irrigation. It is often used
as an antiseptic hand wash. A 20% chlorhexidinegluconate solution is used for preoperative
Fermentation 285
hand and skin preparation and for general skin disinfection. Chlorhexidinegluconate is
also mixed with quaternary ammonium compounds such as cetrimide to obtain stronger
and broader antimicrobial effects (e.g., Savlon). Chloroxylenols are less irritating on skin,
can be used for topical purposes, and are more effective against gram-positive bacteria
than gram-negative bacteria. Hexachlorophene is chlorinated diphenyl and is much less
irritating on skin than chloroxylenols. It has a marked effect on gram-positive bacteria but
a poor effect on gram-negative bacteria, mycobacteria, fungi, and viruses. Triclosan is an
organic phenyl ether with good activity against gram-positive bacteria, and is effective to
some extent against many gram-negative bacteria including Pseudomonas. It also has fair
activity against fungi and viruses.
• Disadvantages: Phenol is toxic and corrosive and a skin irritant. Chlorhexidine is inacti-
vated by anionic soaps. Chloroxylenol is inactivated by hard water.
10.9.4.4 Halogens
Halogens have the following properties:
• Mode of action: Halogens are oxidizing agents and cause damage by oxidation of the
essential sulfhydryl groups of enzymes. Chlorine reacts with water to form hypochlorous
acid, which is microbicidal.
• Examples: Chlorine compounds (chlorine, bleach, hypochlorite) and iodine compounds
(tincture of iodine, iodophores).
• Applications: Tincture of iodine (2% iodine in 70% alcohol) is an antiseptic. Iodine can
be combined with neutral carrier polymers such as polyvinylpyrrolidone to prepare iodo-
phores such as povidone-iodine. Iodophores permit slow release and reduce irritation of
the antiseptic. For hand washing, iodophores are diluted in 50% alcohol. Note that 10%
povidone-iodine is used in its undiluted form in pre- and postoperative skin disinfection.
Chlorine gas is used to bleach water. Household bleach can be used to disinfect floors.
In higher concentrations, chlorine is used to disinfect swimming pools. Note that 0.5%
sodium hypochlorite is used in serology and virology. It is used at a dilution of 1:10
in decontamination of spillage of infectious material. Mercuric chloride is used as a
disinfectant.
• Disadvantages: Halogens are rapidly inactivated in the presence of organic matter. Iodine
is corrosive and staining. Bleach solution is corrosive and will corrode stainless steel
surfaces.
10.9.4.5 Heavy Metals

Heavy metals have the following properties:
• Mode of action: Heavy metals act by precipitation of proteins and oxidation of the sulfhy-
dryl groups. They are bacteriostatic.
• Examples: Mercuric chloride, silver nitrate, copper sulfate, and organic mercury salts (e.g.,
mercurochrome and merthiolate).
• Applications: Note that 1% silver nitrate solution can be applied on the eyes as treatment
for ophthalmianeonatorum (Crede’s method). This procedure is no longer followed. Silver
sulfadiazine is used topically to help prevent colonization and infection of burn tissues.
Mercurials are active against viruses at dilutions of 1:500 to 1:1000. Merthiolate at a con-
centration of 1:10,000 is used in the preservation of serum. Copper salts are used as a
fungicide.
• Disadvantages: Mercuric chloride is highly toxic; heavy metals are readily inactivated by
organic matter.
10.9.4.6 Surface Active Agents

Surface active agents have the following properties:
• Mode of action: Surface active agents concentrate at interfaces between the lipid-contain-
ing membrane of a bacterial cell and the surrounding aqueous medium. These compounds
have long-chain hydrocarbons that are soluble in fat and charged ions that are soluble in
water. Since they contain both hydrocarbons and charged ions, they concentrate on the sur-
face of membranes. They disrupt cell membranes, resulting in leakage of cell constituents.
• Examples: Surface active agents are soaps or detergents. Detergents can be “anionic” or
“cationic.” Detergents containing negatively charged long-chain hydrocarbons are called
anionic detergents. These include soaps and bile salts. If the fat-soluble part is made to
have a positive charge by combining it with a quaternary nitrogen atom, it is called a cat-
ionic detergent. Cationic detergents are known as quaternary ammonium compounds (or
quat). Cetrimide and benzalkonium chloride act as cationic detergents.
• Applications: They are active against vegetative cells, mycobacteria, and enveloped viruses.
They are widely used as disinfectants at dilutions of 1%–2% for domestic and hospital uses.
• Disadvantages: Their activity is reduced by hard water, anionic detergents, and organic mat-
ter. Pseudomonas can metabolize cetrimide, using it as a carbon, nitrogen, and energy source.
10.9.4.7 Dyes
Dyes have the following properties:
• Mode of action: Acridine dyes are bactericidal because of their interaction with bacterial
nucleic acids.
• Examples: Examples include aniline dyes such as crystal violet, malachite green, and bril-
liant green, and acridine dyes such as acriflavine and aminacrine. Acriflavine is a mix-
ture of proflavine and euflavine. Only euflavine has effective antimicrobial properties.
The related dye ethidium bromide is also germicidal. It intercalates between base pairs in
DNA. Dyes are more effective against gram-positive bacteria than gram-negative bacteria
and are more bacteriostatic in action.
• Applications: They may be used topically as antiseptics to treat mild burns. They are used
as paint on the skin to treat bacterial skin infections. Dyes are used as selective agents in
certain selective media.
10.9.4.8 Hydrogen Peroxide
Hydrogen peroxide has the following properties:
• Mode of action: Hydrogen peroxide acts on microorganisms by releasing nascent oxygen.

It produces a hydroxyl-free radical that damages proteins and DNA.
• Applications: It is used at 6% concentration to decontaminate instruments and equipment
such as ventilators. A 3% hydrogen peroxide solution is used for skin disinfection and
deodorizing wounds and ulcers. Strong solutions are sporicidal.
• Disadvantages: Hydrogen peroxide decomposes in the presence of light and is broken
down by catalase; proteinaceous organic matter drastically reduces its activity.
10.9.4.9 Ethylene Oxide
Ethylene oxide (EO) has the following properties:
• Mode of action: EO is an alkylating agent. It acts by alkylating sulfhydryl, amino, car-

boxyl, and hydroxyl groups.
• Properties: It is a cyclic molecule, which is a colorless liquid at room temperature. It has a
sweet ethereal odor, readily polymerizes, and is flammable.
Fermentation 287
• Application: It is a highly effective chemisterilant capable of killing spores rapidly.

Because it is highly flammable, it is usually combined with CO2 (10% CO2 + 90% EO) or
used as dichlorodifluoromethane. It requires the presence of humidity to be active. EO has
good penetration and is well absorbed by porous materials. It is used to sterilize heat-labile
articles such as bedding, textiles, rubber, plastics, syringes, disposable petri dishes, and
complex apparatus such as the heart-lung machine and respiratory and dental equipment.
Efficiency testing is done using Bacillus subtilis var. niger.
• Disadvantages: EO is highly toxic, irritating to eyes and skin, highly flammable, muta-
genic, and carcinogenic.
10.9.4.10 β-Propiolactone
β-Propiolactone (BPL) has the following properties:
• Mode of action: BPL is an alkylating agent and acts through the alkylation of carboxyl and
hydroxyl groups.
• Properties: It is a colorless liquid with a pungen, slightly sweetish smell. It is a condensa-
tion product of ketone with formaldehyde.
• Application: It is an effective sporicidal agent and has broad-spectrum activity. Note that
0.2% is used to sterilize biological products. It is more efficient in fumigation than form-
aldehyde. It is used to sterilize vaccines, tissue grafts, surgical instruments, and enzymes.
• Disadvantages: BPL has poor penetrating power and is a carcinogen.
10.9.5 Sterilization Using Filtration

Filtration does not kill microbes; it merely separates them. Membrane filters with pore sizes of
0.2–0.45 μm are commonly used to remove particles from solutions that cannot be autoclaved.
Filtration is used to remove microbes from heat-labile liquids such as serum, antibiotic solutions,
sugar solutions, and urea solution. Various applications of filtration include removing bacteria from
ingredients of culture media, preparing suspensions of viruses and phages free of bacteria, measur-
ing sizes of viruses, separating toxins from culture filtrates, counting bacteria, clarifying fluids, and
purifying hydatid fluid. Filtration is aided by the use of either positive or negative pressure provided
by vacuum pumps. Older filters made of earthenware or asbestos are called depth filters. Different
types of filters are as follows:
• Earthenware filters: These filters are made up of diatomaceous earth or porcelain. They
are usually baked into the shape of a candle. Different types of earthenware filters are as
follows:
• Pasteur–Chamberland filter: These candle filters are from France and are made of
porcelain (sand and kaolin). A similar filter from Great Britain is a Doulton filter.
Chamberland filters are made with various porosities, which are graded as L1, L1a,
L2, L3, L5, L7, L9, and L11. Doulton filter porosities are graded as P2, P5, and P11.
• Berkefeld filter: These filters are made of kieselguhr, a fossilized diatomaceous earth
found in Germany. They are available in three grades depending on their porosity
(pore size): V (veil), N (normal), and W (wenig). The quality of a V-grade filter is
checked using a culture suspension of Serrtiamarcescens (0.75 μm).
• Mandler filter: This filter comes from the United States and is made of kieselguhr,
asbestos, and plaster of Paris.
• Asbestos filters: These filters are made from the chrysotile type of asbestos; they chemi-
cally comprise magnesium silicate. They are pressed to form disks, which are to be used
only once. A disk is held inside a metal mount, which is sterilized by autoclaving. Asbestos
filters are available in the following grades: HP/PYR (for removal of pyrogens), HP/EKS
(for absolute sterility), and HP/EK (for clarifying).
• Sintered glass filters: These are made from finely ground glass that is fused sufficiently
to make small particles of glass adhere to one another. They are usually available in the
form of a disk fused into a glass funnel. Grade 5 filters have average pore diameters of
1–1.5 μm. They are washed in running water in the reverse direction, cleaned with warm
concentrated H2SO4, and sterilized by autoclaving.
• Membrane filters: These filters are made from a variety of polymeric materials such as
cellulose nitrate, cellulose diacetate, polycarbonate, and polyester. The older type of mem-
brane, called “gradocol” (graded colloid ion) membrane, comprised cellulose nitrate.
Gradocol membranes have average pore diameters of 3–10 μm. The newer ones comprise
cellulose diacetate. These membranes have a pore diameter ranging from 0.015 to 12
μm. These filters are sterilized by autoclaving. Membrane filters are made in two ways:
Capillary pore membranes have pores produced by radiation, whereas labyrinthine pore
membranes are produced by forced evaporation of solvents from cellulose esters.
• Air filters: Air can be filtered using high-efficiency particle air (HEPA) filters, which are
usually used in biological safety cabinets. HEPA filters are at least 99.97% efficient for
removing particles greater than 0.3 μm in diameter. Examples of areas where HEPA filters
are used include rooms housing severely neutropenic patients and operating rooms des-
ignated for orthopedic implant procedures. HEPA filter efficiency is monitored using the
dioctylphthalate (DOP) particle test using particles that are 0.3 μm in diameter.
The disadvantages of depth filters are possibility of migration of filter material into the filtrate,
absorption or retention of certain volumes of liquid by the filters, pore sizes that are not definite,
and the possibility of viruses and mycoplasma passing through the filters. The advantages of mem-
brane filters are known porosity, absence of retention of fluids, ability to reuse after autoclaving, and
compatibility with many chemicals. However, membrane filters have little loading capacity and are
fragile.
10.9.6 Sterilization Using Radiation

Two types of radiation are used: (1) ionizing and (2) nonionizing. Nonionizing rays are low-
energy rays with poor penetrative power, whereas ionizing rays are high-energy rays with good
penetrative power. Since radiation does not generate heat, it is termed “cold sterilization.” In
some parts of Europe, fruits and vegetables are irradiated to increase their shelf life up to 500%.
Rays that are longer than the wavelength of visible light are nonionizing. The microbicidal
wavelength of UV rays lies in the range 200–280 nm, with 260 nm being the most effective. UV
rays are generated using a high-pressure mercury vapor lamp. It is at 260 nm of wavelength that
absorption by microorganisms is at its maximum, which results in the germicidal effect of rays.
UV rays induce formation of thymine-thymine dimers, which ultimately inhibit DNA replication.
UV rays readily induce mutations in cells irradiated with a nonlethal dose. Microorganisms such
as bacteria, viruses, and yeast that are exposed to effective UV radiation are inactivated within
seconds. Since UV rays do not kill spores, they are considered to be of use in surface disinfec-
tion. UV rays are used to disinfect hospital wards, operation theaters, virus laboratories, cor-
ridors, and so on. Disadvantages of using UV rays include the low penetrative power of the rays
and the limited life of UV bulbs. Some bacteria have DNA repair enzymes that can overcome
the damage caused by UV rays. The presence of organic matter and dust prevents UV rays from
reaching their destination; UV rays are harmful to skin and eyes. Further, they do not penetrate
glass, paper, or plastic.
Ionizing rays are of two types: (1) particulate and (2) electromagnetic rays. They are described
as follows:
Fermentation 289
• Electron beams are particulate in nature, whereas gamma rays are electromagnetic in
nature. High-speed electrons are produced by a linear accelerator from a heated cathode.
Electron beams are used to sterilize articles such as syringes, gloves, dressing packs, foods,
and pharmaceuticals. When using electron beams, sterilization is accomplished in a few
seconds. Unlike electromagnetic rays, the instruments can be switched off. Disadvantages
of using electron beams include poor penetrative power and the requirement of sophisti-
cated equipment.
• Electromagnetic rays such as gamma rays emanate from the nuclear disintegration of cer-
tain radioactive isotopes (Co60, Cs137). They have more penetrative power than electron
beams, but they require a longer exposure time. These high-energy radiations damage the
nucleic acids of microorganisms. A dosage of 2.5 Mrad kills all bacteria, fungi, viruses,
and spores. It is used commercially to sterilize disposable petri dishes, plastic syringes,
antibiotics, vitamins, hormones, glassware, and fabrics. Disadvantages of using electro-
magnetic rays include the following: Unlike electron beams, they cannot be switched off.
Glassware tends to become brownish, and there is loss of tensile strength in fabric. Gamma
irradiation impairs the flavor of certain foods. Bacillus pumilus E601 is used to evaluate
the sterilization process.
10.10 PRODUCT RECOVERY

The extraction and purification of fermentation products may be difficult and costly. Ideally, one
is trying to obtain a high-quality product as quickly as possible at an efficient recovery rate using
minimum plant investment and operation at minimal costs. Unfortunately, the recovery costs of
microbial products may vary from as low as 15% to as high as 70% of the total manufacturing costs.
Obviously, the chosen process, and therefore its relative cost, will depend on the specific product.
The reported percentages of cost are 15% for industrial ethanol, 20%–30% for bulk penicillin G,
and up to 70% for enzymes (Figure 10.24). The high cost of downstream processing will affect the
overall objective in some fermentation processes. The choice of recovery process is based on the
following six criteria:
1. Intracellular or extracellular location of the product

2. Concentration of the product in the fermentation broth
Fermentation process
Foam separation
Primary separation: removal of insoluble products/cell (centrifugation,

filtration, and sedimentation)
Cell disruption (mechanical, enzymatic, and chemical) product isolation: solvent extraction,
adsorption, aqueous two-phase system, and precipitation
Purification techniques: (a) chromatography (ion exchange, gel permeation, and affinity),
(b) membrane separation (microfiltration, ultrafiltration, and reverse-phase electrophoresis)
Product polishing (crystallization, drying, and filtration)
FIGURE 10.24 Flowchart of downstream processing.

3. Physical and chemical properties of the desired product (as an aid to selecting separation
procedures)
4. Intended use of the product
5. Minimal acceptable standard of purity
6. Marketable price for the product
The main objective of the first stage in the recovery of an extracellular product is the removal of
large solid particles and microbial cells, which is usually done by centrifugation or filtration (Figure
10.24). In the next stage, the broth is fractionated or extracted into major fractions using ultrafiltra-
tion, reverse osmosis, adsorption/ion exchange/gel filtration, affinity chromatography, liquid–liquid
extraction, two-phase aqueous extraction, or precipitation.
10.10.1 Precipitation
Precipitation may be conducted at various stages of the product recovery process. It is a particularly
useful process in that it allows enrichment and concentration in one step, thereby reducing the vol-
ume of material for further processing. It is possible to obtain some products (or to remove certain
impurities) directly from the broth by precipitation or to use the technique after a crude cell lysate is
obtained. Typical agents used in precipitation render the compound of interest insoluble and include
the following:
• Acids and bases to change the pH of a solution until the isoelectric point (pI) of the com-
pound is reached and pH equals pI, when there is no overall charge on the molecule and
its solubility is decreased.
• Salts such as ammonium and sodium sulfates are used for the recovery and fractionation
of proteins. The salts remove water from the surface of a protein, revealing hydrophobic
patches that come together and cause the protein to precipitate. The most hydrophobic
proteins will precipitate first, allowing fractionation to take place.
• Organic solvents, such as dextrans, can be precipitated out of a broth by the addition of
methanol. Chilled ethanol and acetone can be used in the precipitation of proteins mainly
because they cause changes in the dielectric properties of the solution.
• Nonionic polymers such as polyethylene glycol (PEG) can be used in the precipitation of
proteins and are similar in behavior to organic solvents.
• Polyelectrolytes can be used in the precipitation of a range of compounds, in addition to
their use in cell aggregation.
• Protein-binding dyes (triazine dyes) bind to and precipitate certain classes of proteins.
• Affinity precipitation is an area of much current interest in that precipitants are able to bind
to, and precipitate, compounds selectively.
10.10.2 Product Recovery by Solvent Extraction

Solvent extraction is a classical method of recovery in addition to the concentration of various products.
Solvent extraction has several advantages, such as the selectivity of extraction directly from broth or reac-
tion medium, reduction in product loss as the product is just transferred to a second phase, and easy scale-
up. Solvent extraction involves extraction of a compound in a liquid phase to another liquid. The solute
originally present in the aqueous phase gets partitioned in both the phases. The distribution between the
two immiscible liquids and solubility in the two liquids decide the efficacy of extraction. The choice of
solvent selection is based on the dielectric point. The dielectric constant is a measure of the degree of the
molar polarization of a compound. An increase in the dielectric pole increases the polarity of the solute:
D = C /C0
Fermentation 291
where D is the dielectric constant, C is electrostatic capacity of a condenser containing the sub-
stance between the plates, and C0 is electrostatic capacity of the same condenser when it is com-
pletely evacuated. The final choice of solvent is influenced by the “partition coefficient” (K):
K = concentration of solute in the extract/concentration of solute in the raffinate
A high value of k requires single-stage extraction and a low value of k requires multistage extrac-
tion. In single-stage batch extraction, the aqueous feed is mixed with the organic solvent, and after
equilibration the extract phase containing the desired solute is separated out for further process-
ing. In some cases, single-stage extraction may not be enough and a multistage process is required
wherein a fresh volume of solvent is contacted with the raffinate. Continuous extraction can be car-
ried out by cocurrent or countercurrent methods. In cocurrent extraction, there are n mixer vessels
in line and the raffinate goes from vessel 1 to vessel n. Fresh solvent is added in each stage and the
extracting solvent passes through the cascade of vessels in the same direction. At every stage, the
extract is recovered.
In countercurrent extraction, the extracted raffinate passes from vessel 1 to vessel n while the
product-enriched solvent flows from vessel n to vessel 1. This is the most efficient method of extrac-
tion. Solvent recovery following the extraction process is essential; it is usually done by distilla-
tion. Distillation is performed in three stages: (1) evaporation of the solvent into its vapor phase,
(2) vapor–liquid separation, and (3) condensation to collect the solvent. The stages are described
as follows:
1. Evaporation is the removal of solvent as a vapor from the solution

2. Vapor–liquid separation is performed in a column to separate the lower-boiling (more vola-
tile) component from other less volatile components
3. Condensation of the vapor recovers the more volatile solvent fraction
Evaporation is the removal of a solvent from a solution by the application of heat to the solution.
A wide range of evaporators are available. Some are operated on a batch basis, whereas others are
operated continuously. Most industrial evaporators use tubular heating surfaces. Circulation of the
liquid past the heating surfaces may be induced by boiling or by mechanical agitation. In batch
distillation, vapor from the boiler passes up the column and is condensed. Part of the condensate
will be returned as the reflux for countercurrent contact; with rising vapor in the column, the dis-
tillation is continued until a satisfactory recovery of lower-boiling (more volatile) components is
accomplished. The ratio of condensate returned to the column as reflux to condensate withdrawn as
product is, along with the number of plates or stages in the column, the major parameter for control-
ling product purity.
Continuous distillation is started in a similar way as batch distillation, but no condensate is with-
drawn initially. There is total reflux of the condensate until ideal operating conditions are established
throughout the column. At this stage, the liquid feed is fed into the column at an intermediate level.
The more volatile components move upward as vapor and are condensed, followed by partial reflux
of the condensate. Meanwhile, the less volatile fractions move down the column to the evaporator. At
this part of the bottoms, a fraction is continuously withdrawn and the part is reboiled and returned
to the column. Countercurrent contacting of the vapor and liquid streams is achieved by causing the
vapor to be dispersed in the liquid phase and the liquid to be dispersed in a continuous vapor phase.
10.10.2.1 Distribution Coefficient

In the typical example of solvent (liquid–liquid) extraction described in Section 10.10.2, the product
is a fairly large organic molecule, which one would predict would not be very soluble in water. On
the other hand, if the product is a lower-molecular-weight or “small” molecule, one would predict
that it might be at least partially soluble in water. Therefore, it might not completely “move” into
the organic layer; it might also partially dissolve in the aqueous layer. For water-soluble organic
materials, such as acetic acid or sugar, most of the solute will reside in the water phase. A quantita-
tive measure of how an organic compound will distribute itself between aqueous and organic phases
is called the “distribution coefficient” or partition coefficient. It is the ratio, K, of the solubility of
solute dissolved in the organic layer to the solubility of material dissolved in the aqueous layer (note
that K is independent of the actual amounts of the two solvents mixed):
K = Distribution coefficient
Solubility of organic (g/100 mL)

K=
Solubility of water (g/100 mL)
The constant K is essentially the ratio of the concentrations of the solute in the two different
solvents once the system reaches equilibrium. At equilibrium, the molecules naturally distribute
themselves in the solvent where they are more soluble. Inorganic and water-soluble materials will
stay in the water layer and more organic molecules will remain in the organic layer. By using the
correct solvent system, a molecule can be specifically selected and extracted from another solvent.
Since the distribution coefficient is a ratio, unless K is very large not all molecules of a solute
will reside in the organic layer in a single extraction. Usually two, three, or four extractions of the
aqueous layer with an organic solvent are carried out in sequence in order to remove as much of
the desired product as possible from the aqueous layer. The effectiveness of multiple small-volume
extractions versus one large-volume extraction can be demonstrated using a simple calculation.
Imagine that one extraction can recover 90% of the compound. A second extraction with the same
solvent may be able to pull out 90% of the remaining material. Effectively, 99% of the compound
is recovered with two extractions. One large extraction can obtain only the initial 90% of the com-
pound. Many smaller extractions are more efficient than one large extraction. This phenomenon can
be proved mathematically, using the following equation:
⎛ ⎞
⎜ 1 ⎟
Fraction extracted into solvent B = ⎜
VB ⎟
⎜1+ ⎟
⎝ VA nK ⎠
This equation provides the fraction of material extracted by solvent B, where n is the number of
extractions performed, K is the distribution coefficient, VA is the volume of solvent A, and VB is the
volume of solvent B. Distribution coefficients play a large role in the efficacy of a drug. In order for a
drug to be absorbed into a brain cell, it must pass through what is called the blood–brain barrier into
the brain cell. The drug must have enough water solubility to dissolve in the blood and be carried
to the brain. However, to pass through the cell wall, which consists largely of water-insoluble fatty
lipids with solubility properties similar to that of an organic solvent, the drug must have reasonable
organic solvent solubility. Cell membranes use the same fundamental solubility principles as the
extraction process. The cell membrane shown in Figure 10.25 consists of an ionic head and a very
nonpolar or hydrophobic center.
The ionic head of the lipid orients itself in aqueous environments, creating a very nonpolar inte-
rior. Ions such as K+ and Ca++ cannot traverse the interior of the cell readily because the interior is
very nonpolar and does not support these ions. Extraction uses the same partitioning effect to isolate
organic compounds. Just as in this biological example, in the extraction process organic compounds
choose where to dwell according to the distribution coefficient. Synthetic drug design must take
Fermentation 293
Ionic head
Nonpolar interior
Ionic head
FIGURE 10.25 Simple schematic of a cell membrane.
into account the importance of having a distribution coefficient that allows drug transport both in
aqueous blood and through organic membranes.
10.10.2.2 Solvent Selection

One important aspect when choosing a solvent system for extraction is to pick two immiscible
solvents. Some common liquid–liquid extraction solvent pairs are water–dichloromethane, water–
ether, and water–hexane. Notice that all the combinations include water. Most extractions involve
water because it is highly polar and immiscible with most organic solvents. In addition, the com-
pound you are attempting to extract must be soluble in the organic solvent but insoluble in the water
layer. An organic compound such as benzene is simple to extract from water, because its solubility
in water is very low. However, solvents such as ethanol and methanol will not separate using liquid–
liquid extraction techniques, because they are soluble in both organic solvents and water.
There are also practical concerns when choosing extraction solvents. As mentioned previously,
the two solvents must be immiscible. The cost, toxicity, and flammability of solvents should be con-
sidered. The volatility of the organic solvent is important. Solvents with low boiling points, such as
ether, are often used to make isolating and drying the isolate material easier. If ether is used (boiling
point = 35°C), then evaporation to collect the solid is fast.
One common mistake when performing an extraction is to mix up the layers and discard the
wrong one. The densities of the solvents will predict which solvent is the top or bottom layer. In
general, the densities of nonhalogenated organic solvents are less than 1.0 g/mL and the densi-
ties of halogenated solvents are greater than 1.0 g/mL. One common solvent pair is dichlorometh-
ane and water. The density of dichloromethane is 1.325 g/mL and that of water is 1.000 g/mL.
Dichloromethane is more dense that water; therefore, dichloromethane will be the bottom layer
and water will be the top layer. Table 10.3 lists the densities of some extraction organic solvents.
Although density is the physical property that determines which layer is the top and which is the
bottom, a very concentrated solute dissolved in either layer can reverse the order. The best method
to avoid making a mistake is a drop test. Add a few drops of water to the layer in question and watch
the drop very carefully. If the layer is water, then the drop will mix with the solution. If the solvent
TABLE 10.3
Common Extraction Solvents Listed by Density
Solvent Density (g/mL)
Hexane 0.695
Ether 0.708
Toluene 0.867
Water 1.000
Dichloromethane 1.325
Chloroform 1.492
is the mistaken organic layer, then the water drop will create a second layer. In general, this method
can help to determine the identity of the layer. However, it is still best to keep all the layers until the
extraction is complete and the desired product has been isolated.
One significant problem with solvent extraction is that no solvent is completely insoluble in
another solvent. In practice, one additional step is usually carried out before evaporating the organic
solvent, that is, drying over anhydrous sodium sulfate or some other drying agent. Drying a liquid
might seem a peculiar concept, since we normally think of all liquids as being wet; drying an
organic liquid in the organic laboratory has a special meaning to chemists. It means to remove all
traces of water from the liquid. Even water and hexane are slightly soluble in each other (Table 10.3).
After separating the two solvents, residual water remains in the hexane or ether organic layer.
This will remain and stick to the solid product when we remove the more volatile solvent. Therefore,
chemists remove the water from the organic layer by adding an insoluble inorganic solid to the solu-
tion that absorbs the water, thereby “drying” it. Granular anhydrous sodium sulfate is the drying
agent most often used, although other drying agents are also available. All inorganic solids work by
reacting with the water to form hydrates, which is their preferred form if water is available:
Na 2 SO 4 + H 2 O → Na 2 SO 4 .5H 2 O
MgSO 4 +H 2 O → MgSO 4 .7H 2 O
CaCl 2 +H 2 O → CaCl 2 .6H 2 O
2CaSO 4 +H 2 O → (CaSO 4 )2 .H 2 O
The aforementioned compounds will associate or hydrate themselves with water. Table 10.4 lists
some common drying agents along with their speed, capacity, and hydration. These drying agents
do not dissolve in the solvent they are drying. They may change somewhat, for example, sodium
sulfate will clump together as it reacts with water, but they will remain solids in normal extraction
solvents. This makes them easy to remove by decantation (pouring off of the liquid) or by gravity
filtration. Usually, the organic solvent will go from cloudy to clear in the process of being dried.
You should be careful to remove all these solid drying agents before solvent evaporation takes place
or you might confuse them with your product. When you take a melting point and the product does
not melt by 300°C, you have probably isolated your drying agent. It is recommended that the drying
agent chosen is in a granular form. After the drying agent has removed the residual water, it is easier
to remove large granular particles. Drying a solvent, however, is not an exact science. An excess
of drying agent should be used to ensure that all the water is removed. If water remains after the
materials are collected, it could interfere with the analysis. Keep adding the drying agent until there
are no more clumps of drying agent stuck to the sides or bottom of the flask. Drying agents should
float freely in the beaker, similar to snow.
TABLE 10.4
Hydrated Complexes for Some Common Drying Agents
Drying Agent Formula Speed Capacitya Hydrationb
Sodium sulfate Na2SO4 Medium High 7–10
Magnesium sulfate MgSO4 Fast High 7
Calcium chloride CaCl2 Fast Low 2
Calcium sulfate (Drierite) CaCl2 Fast Low ½–2
a Capacity refers to the amount of water removed per given weight of the drying agent.
b Hydration is the number of water molecules removed per molecule of the drying agent.
Fermentation 295
10.10.2.3 Acid–Base Extraction

There are three special cases of liquid–liquid extraction that are extremely useful for isolating and
purifying amines, carboxylic acids, and phenols. All three of these functional groups can be inter-
converted from nonionic organic solvent–soluble forms to water-soluble ionic forms by changing
the pH:
Amines: RNH 2 + H+ ⇔ RNH 3+
Phenols: PhOH + OH ⇔ PhO − +
−
H2O
Carboxylic acids: RCOOH + OH ⇔ RCOO + H 2 O
− −
Solid–liquid or liquid–liquid extractions rely on the solubility of the solute to be extracted. In

acid–base extraction, the molecule to be extracted is transformed so that we impose a new solubil-
ity on the molecule. One specific example is benzoic acid, which is an organic acid. Benzoic acid
is soluble in most organic solvents, including dichloromethane and ether. However, this acid can
be easily deprotonated with a base to give a charged ionic species that is readily soluble in water:
COOH COO—Na+
Base
+ H2O
(NaOH

By converting benzoic acid to its sodium salt, the solubility is changed drastically. Now the
sodium salt is soluble in water and will migrate to the water layer. Because the solvents chosen are
immiscible in each other, the layers can be easily separated. Although the separation is complete,
we no longer have benzoic acid. To obtain the original compound, the salt must be protonated with
a strong inorganic acid. Once benzoic acid is recovered by adding the inorganic acid, it will precipi-
tate in the water to provide a pure compound. This method works very well with mixtures of strong
organic acids, weak organic acids, bases, and neutral compounds. We can use the acid–base func-
tionality to our advantage. By changing the pH of the aqueous phase in a liquid–liquid extraction,
the distribution coefficient is drastically changed, pulling the molecules into either an organic layer
or an aqueous layer at will. Carboxylic acids, phenols, and amines can be easily separated from
neutral components. However, all other common functional groups remain unaffected by changes
in aqueous pH, so they will always distribute between layers in the same way because their distribu-
tion coefficients are unaffected by pH. Figure 10.26 details the reagents needed to separate benzoic
acid, aniline, and phenol.
Whether you use acid–base, solid–liquid, or liquid–liquid, extraction is a useful organic tool to
separate a mixture of compounds. From the early drugs that were extracted from trees and plants to
modern day pharmacology, extraction is used to separate and purify organic molecules.
10.10.3 Ion Exchange

Ion exchange chromatography is based on synthetic resins of an aromatic nature and were suitable
for the separation and purification of inorganic ions and small molecules.
Ion exchange is a reversible chemical reaction in which an ion (an atom or molecule that has lost
or gained an electron and has thus acquired an electrical charge) from a solution is exchanged for a
similarly charged ion attached to an immobile solid particle. These solid ion-exchange particles are
either naturally occurring inorganic zeolites or synthetically produced organic resins. The synthetic
organic resins are the predominant type used today because their characteristics can be tailored to
specific applications. An organic ion-exchange resin comprises high-molecular-weight polyelectro-
lytes that can exchange their mobile ions for ions of similar charge from the surrounding medium.
Each resin has a distinct number of mobile ion sites that set the maximum quantity of exchanges per
COOH COO–Na+ COOH

Weak base Acid
(Na2HCO3) (HCl)
Benzoic acid Sodium salt of benzoic acid Benzoic acid
NH2 NH3+Cl– NH2

Acid Base
(HCl) (K2CO3)
Aniline Protonated aniline Aniline
OH O–Na+ OH
Strong base Acid
(NaOH) (HCl)
Phenol Sodium salt of phenol Phenol
FIGURE 10.26 Acid–base extraction equations.
unit of resin. In most plating processes, water is used to cleanse the surface of the parts after each
process bath. To maintain quality standards, the level of dissolved solids in the rinse water must be
regulated. Fresh water added to the rinse tank accomplishes this purpose, and the overflow water is
treated to remove pollutants and then discharged. As the metal salts, acids, and bases used in metal
finishing are primarily inorganic compounds, they are ionized in water and can be removed by
contact with ion-exchange resins. In the water-deionization process, the resins exchange hydrogen
ions (H+) for positively charged ions (such as nickel, copper, and sodium ions) and hydroxyl ions
(OH−) for negatively charged sulfates, chromates, and chlorides. Because the quantities of H+ and
OH− ions are balanced, the result of the ion-exchange treatment is relatively pure, neutral water.
To ensure efficient, reproducible purification that gives the required degree of purity, it is ben-
eficial to develop a multistep process using the purification strategy of capture, intermediate puri-
fication, and polishing (CIPP). IEX plays a significant and highly flexible role in most multistep
purification schemes. If a specific affinity medium is not available or if little is known about the
target molecule, IEX is recommended as the first step to be considered in any purification scheme.
The technique can be used for capture, intermediate purification, or polishing, according to the
demands of the specific application. Since IEX offers different selectivities (using anion or cation
exchangers) and since the pH of the purification can be modified to alter the charge characteristics
of the sample components, it is possible to use the technique more than once in the same purification
scheme. In addition, IEX can be used with stepwise elution for a rapid capture step or with gradient
elution to achieve the highest resolution in a polishing step (Figure 10.27).
Ion-exchange reactions are stoichiometric and reversible, and as such they are similar to other
solution phase reactions. For example,
NiSO 4 + Ca ( OH )2 = Ni ( OH )2 + CaSO 4
In this reaction, the nickel ions of nickel sulfate (NiSO4) are exchanged for the calcium ions of the
calcium hydroxide [Ca(OH)2] molecule. Similarly, a resin with hydrogen ions available for exchange
will exchange those ions for nickel ions from solution. The reaction can be written as follows:
2 ( R − SO3 H ) + NiSO 4 = ( R − SO3 ) 2Ni + H 2 SO 4
Fermentation 297
Polishing
Intermediate
purification Achieve final
high-level purity
Purity
Preparation, Capture
extraction, Remove bulk
clarification impurities
Isolate, concentrate,
and stabilize
Steps
FIGURE 10.27 Various steps involved in ion-exchange purification.
R indicates the organic portion of the resin and SO3 is the immobile portion of the ion-active
group. Two resin sites are needed for nickel ions with a +2 valence (Ni+2). Trivalent ferric ions
require three resin sites. As shown, the ion-exchange reaction is reversible. The degree to which
the reaction proceeds to the right will depend on the resin’s preference or selectivity for nickel ions
compared with its preference for hydrogen ions. The selectivity of a resin for a given ion is measured
by the selectivity coefficient K, which in its simplest form for the reaction
R − A + + B+ = R − B+ + A +
is expressed as
K = (Concentration of B+ in resin/concentration of A + in resin) ×

(concentration of A + in solution/concentration of B+ in solution)
The selectivity coefficient expresses the relative distribution of ions when a resin in the A+ form
is placed in a solution containing B+ ions. Table 10.5 gives the selectivities of strong acid and strong
base ion-exchange resins for various ionic compounds. The selectivity coefficient is not constant
but varies with changes in solution conditions. It does provide a means to determine what to expect
when various ions are involved in a reaction. As indicated in Table 10.5, strong acid resins have a
preference for nickel over hydrogen. Despite this preference, the resin can be converted back to the
hydrogen form by contact with a concentrated solution of sulfuric acid (H2SO4):
( R--SO4 ) 2Ni + H 2SO4 → 2 ( R − SO3 H ) + NiSO 4
This step is known as regeneration. In general terms, the higher the preference a resin exhibits for
a particular ion, the greater the exchange efficiency in terms of resin capacity for removal of that ion
from solution. Greater preference for a particular ion, however, will result in increased consumption
of chemicals for regeneration. Resins currently available exhibit a range of selectivities and thus
have broad application. The relative preference for divalent calcium ions (Ca++) over divalent copper
ions (Cu++) is approximately 1.5–1. For a heavy metal–selective resin, this preference is reversed
and favors copper by a ratio of 2300 to 1.
10.10.3.1 Resin Types

Ion-exchange resins are classified as cation exchangers, having positively charged mobile ions avail-
able for exchange, and anion exchangers, whose exchangeable ions are negatively charged. Both
anion and cation resins are produced from the same basic organic polymers. They differ in the
ionizable group attached to their hydrocarbon networks. It is this functional group that determines
TABLE 10.5
Selectivity of Ion-Exchange Resins in Order of Decreasing Preference
Strong Acid Cation Exchanger Strong Base Anion Exchanger
Barium Iodide
Lead Nitrate
Calcium Bisulfate
Nickel Chloride
Cadmium Cyanide
Copper Bicarbonate
Zinc Hydroxide
Magnesium Fluoride
Potassium Sulfate
Ammonia–sodium
the chemical behavior of the resin. Resins can be broadly classified into strong or weak acid cation
exchangers and strong or weak base anion exchangers (Table 10.5).
Strong acid cation resins are so named because their chemical behavior is similar to that of a
strong acid. The resins are highly ionized in both acid (R–SO3H) and salt (R–SO3Na) forms. They
can convert a metal salt to its corresponding acid by the following reaction:
2 ( R − SO3 H ) + NiCl 2 → ( R − SO 4 )2 Ni + 2HCl
The hydrogen and sodium forms of strong acid resins are highly dissociated and the exchange-
able Na+ and H+ are readily available for exchange over the entire pH range. Consequently, the
exchange capacity of strong acid resins is independent of the pH of the solution. These resins are
used in the hydrogen form for complete deionization; they are used in the sodium form for water
softening (removal of calcium and magnesium). After exhaustion, the resin is converted back to the
hydrogen form (regenerated) by contact with a strong acid solution, or the resin can be converted
to the sodium form with a sodium chloride solution. Hydrochloric acid (HCl) regeneration would
result in a concentrated nickel chloride (NiCl) solution.
In a weak acid cation resin, the ionizable group is a carboxylic acid group (COOH) as opposed
to the sulfonic acid group (SO3H) used in strong acid resins. These resins behave similarly to weak
organic acids that are weakly dissociated. Weak acid resins exhibit a much higher affinity for hydro-
gen ions than do strong acid resins. This characteristic allows regeneration to the hydrogen form
with significantly less acid consumption than is required for strong acid resins. Almost complete
regeneration can be accomplished with stoichiometric amounts of acid. The degree of dissocia-
tion of a weak acid resin is strongly influenced by the solution’s pH. Consequently, resin capacity
depends in part on the pH of the solution. A typical weak acid resin has limited capacity below a pH
of 6.0, making it unsuitable for deionizing acidic metal finishing wastewater.
Similar to strong acid resins, strong base anion resins are highly ionized and can be used over
the entire pH range. These resins are used in the hydroxide (OH) form for water deionization. They
react with anions in solution and can convert an acid solution to pure water:
R − NH 3 OH + HCl → R − NH 3 Cl + HOH
Regeneration with concentrated sodium hydroxide (NaOH) converts the exhausted resin to the
hydroxide form.
Weak base anion resins are similar to weak acid resins in that the degree of ionization is strongly
influenced by the pH of the solution. Consequently, weak base resins exhibit minimum exchange
capacity above a pH of 7.0. These resins merely sorb strong acids; they cannot split salts.
Fermentation 299
In an ion-exchange wastewater deionization unit, the wastewater passes through a bed of strong
acid resin first. Replacement of the metal cations (Ni++, Cu++) with hydrogen ions lowers the pH of
the solution. The anions (SO4−2, Cl−) can then be removed with a weak base resin because the enter-
ing wastewater will normally be acidic and weak base resins adsorb acids. Weak base resins are
preferred over strong base resins because they require less regenerant chemical. A reaction between
the resin in the free base form and Cl proceeds as follows:
R − NH 2 + HCl → R − NH 3 Cl
The weak base resin does not have a hydroxide ion form as does the strong base resin. Consequently,
regeneration needs to only neutralize the absorbed acid; it need not provide hydroxide ions. Weakly
basic reagents such as ammonia (NH3) or sodium carbonate that are not so expensive can be used.
Heavy metal–selective chelating resins behave similarly to weak acid cation resins but exhibit a
high degree of selectivity for heavy metal cations. Chelating resins are analogous to the chelating
compounds found in metal finishing wastewater, that is, they tend to form stable complexes with
the heavy metals. In fact, the functional group used in these resins is an EDTA–Na compound. The
resin structure in the sodium form is expressed as R–EDTA–Na. The high degree of selectivity for
heavy metals permits separation of these ionic compounds from solutions containing high back-
ground levels of calcium, magnesium, and sodium ions. A chelating resin exhibits greater selectivity
for heavy metals in its sodium form than in its hydrogen form. Regeneration properties are similar
to those of a weak acid resin; the chelating resin can be converted to the hydrogen form with doses
slightly greater than stoichiometric doses of acid because of the fortunate tendency of the heavy
metal complex to become less stable under low pH conditions.
Potential applications of chelating resins include polishing to lower the heavy metal concentra-
tion in the effluent from a hydroxide treatment process and directly removing toxic heavy metal cat-
ions from wastewaters containing a high concentration of nontoxic, multivalent cations. Table 10.6
shows the preference of a commercially available chelating resin for heavy metal cations over cal-
cium ions. (Chelating resins exhibit a similar magnitude of selectivity for heavy metals over sodium
or magnesium ions.) The selectivity coefficient defines the relative preference exhibited by the resin
for different ions. The preference for copper (Table 10.6) is 2300 times that for calcium. Therefore,
when a solution that contains equal molar concentrations of copper and calcium ions is treated, at
equilibrium the molar concentration of copper ions in the resin will be 2300 times the concentration
of calcium ions. When a solution that contains calcium ions with a molar concentration 2300 times
more than that of the copper ion concentration is treated, at equilibrium the resin would hold an
equal concentration of the copper and calcium.
TABLE 10.6
Chelating Cation Resin Selectivity for Metal Ions
Metal KM/Caa
Hg +2 2800
Cu+2 2300
Pb+2 1200
Ni+2 57
Zn+2 17
Cd+2 15
Co+2 6.7
Fe+2 4.7
Mn+2 1.2
Ca+2 1
Experiment: Study Fermentation Process for Lactic Acid Production by

Streptococcus thermophilus and Cell Biomass
Principle
Fermentation is a biological and enzymatic process of conversion of carbohydrates into lactic acid,
alcohols, carbon dioxide, and so on, by some bacteria and fungi. These organisms use fermentation as
a method of obtaining energy in the form of ATP. It is a cellular process that transfers the energy in
glucose bonds to bonds in ATP.
The energy in ATP can then be used to perform cellular work. Fermentation is an anaerobic (without
utilizing oxygen) process; cellular respiration is an aerobic (utilizing oxygen) process. All living organ-
isms, including bacteria, protists, plants, and animals, produce ATP by fermentation or cellular respi-
ration and then use ATP in their metabolism. The process of fermentation followed by Streptococcus
thermophilus is homolactic fermentation; in this process, one mole of glucose gets converted into two
moles of lactic acid:
C6 H12 O 6 → 2 CH 3 CHOHCOOH
Before the fermentation starts, a molecule of glucose must split into two moles of pyruvate; this
process is known as glycolysis. Fermentation and cellular respiration involve oxidation-reduction reac-
tions (redox reactions). Redox reactions are always defined in terms of electron transfers, with oxidation
being the loss of electrons and reduction the gain of electrons. In cellular respiration, two hydrogen
atoms are removed from glucose (oxidation) and transferred to a coenzyme called NAD+, reducing this
compound to NADH (Figure 10.28).
Requirements
A small laboratory-grade fermentor, balance, autoclave, cooling centrifuge, pH meter, hot plate.
Glucose
Glycolysis
NAD+
ATP
Glucose NADH Cytoplasm
Pyruvate
–O2 +O2 Mitochondrion

ATP
s
NADH tron
Elec ed via
Electron
ion
i transport chain
carr
tat
en
NAD+ Kreb's DH
NA H 2
rm
FAD
Fe
CO2 cycle
ATP
Ethanol + CO2
2 Ethanol
or
lactate
FIGURE 10.28 Stages of cellular respiration and fermentation.

Fermentation 301
Media Composition
Gram per
Ingredients Liter
Universal peptone 10
Meat extract 5
Yeast extract 5
Glucose 20
Dipotassium hydrogen phosphate 2
Diammonium hydrogen citrate 2
Sodium acetate 5
Magnesium sulfate 0.1
Manganous sulfate 0.05
Final pH = 6.5 ± 0.2 at 37°C.
Procedure
1. Prepare 1 LMRS broth and pour it into a fermentor vessel.
2. Autoclave media at 121 psi for 20 minutes in the vessel and allow it to cool overnight.
3. Inoculate an actively growing culture of S. thermophilus to the fermentor vessel and initiate
the fermentation process.
4. Allow the process to run for 24 hours.
5. Harvest the culture from the fermentor by centrifugation at 4000 rpm.
Fermentation Process
The inoculation of S. thermophilus should always be done carefully under total aseptic conditions
through the inoculation port on the top plate of the fermentor with the help of an inoculation syringe.
After inoculation, the pH should be adjusted to 7; allow the fermentation process to run for 24 hours for
complete cell multiplication, leading to high cell density or mass production. The conditions required
for S. thermophilus to grow in a uniform manner are as follows:
• Temperature should be not less than 36°C and not more than 41°C.
• The pH of the media should be between 6.5 and 7.2.
• A very low amount of oxygen can be supplied as the organism is a facultative anaerobe.
The pH of the medium starts dropping as the microbe enters the log phase of the bacterial growth
curve because of the production of lactic acid, which is an end product of the homofermentative process
of the microbe to gain energy for survival (Figures 10.29 and 10.30).
Experiment: Sugar Fermentation by Yeast (Saccharomyces cerevisiae) for

Production of Ethanol and Cell Biomass
Principle
Yeast can metabolize sugar in two ways: (1) aerobically, with the aid of oxygen, and (2) anaerobically,
without the aid of oxygen. When yeasts respire aerobically, oxygen gas is consumed at the same rate that
CO2 is produced; there will be no change in gas pressure in the test tube. However, when yeasts ferment
the sugars anaerobically, CO2 production will cause a change in the pressure of a closed test tube since no
oxygen is being consumed. This pressure change monitors the fermentation rate and metabolic activity
of the organism. The fermentation of glucose can be described by the following equation (Figure 10.31):
C6 H12 O 6 → 2 CH 3 CH 2 OH + 2 CO 2 + ENERGY

Glucose Ethanol
Carbon dioxide
Note that alcohol is a by-product of this fermentation.
FIGURE 10.29 (See color insert.) A laboratory-grade fermentor of capacity 2 L containing MRS broth.
FIGURE 10.30 (See color insert.) A fermentor after 24 hours of incubation. The visible color difference in
the media shows a high cell density of S. thermophilus.
Requirements
A 50-mL centrifuge tube, glucose reagent, yeast inoculum, distilled water.
Procedure
1. Take two centrifuge tubes and add glucose to each centrifuge tube. Add 1, 2, 3, and 4 g of
glucose to achieve 5%, 10%, 15%, and 20% w/v glucose concentrations, respectively.
2. Add distilled water to increase the volume to 20 mL.
3. Add 150 µL of yeast inoculum to the glucose solution. Yeast inoculum is prepared by incubat-
ing active dry yeast with distilled water for 20 minutes in a water bath at 32°C at 120 rpm.
4. Weigh the tubes. This is the zero-hour reading.
5. Loosen the caps of the centrifuge tubes. Keep them in a water bath at 32°C with shaking at
100 rpm.
6. Weigh the tubes again and record the time.
Fermentation 303
Glucose
(1G)
G F
Sucrose
(1G; 1F) F
Fructose
(1F)
CH3CO COO–
Pyruvate
CO2 H+
CH3COH
Acetaldehyde
H+
CH3 CO2 OH
Ethanol
FIGURE 10.31 Sugar fermentation process for the production of ethanol and cell biomass.
7. On the next day, weigh the tubes after 24 hours (according to the fermentation start time).
Necessary equations:
Wco = Wt − W0
2
mEtoH = mCO = WCO /M CO

2 2 2

AEtoH = mEtoH × M EtoH
In these equations, WCO2 is mass of CO2 produced at a particular time period, mCO2 denotes
moles of CO2 produced, m EtOH denotes moles of ethanol produced, M CO2 is the molecular
weight of CO2, MEtOH is the molecular weight of ethanol, and AEtOH is amount of ethanol pro-
duced in grams.
Data Analysis Procedure

1. Determine the amount of ethanol produced (in grams) at respective time periods for four dif-
ferent glucose concentrations in the fermentation media.
2. Plot the amount of ethanol produced versus the fermentation time for the four glucose con-
centrations (Table 10.7).
3. Discuss the correlation of total ethanol produced with glucose concentrations.
Yeast Count Exercise

Perform yeast count using hemocytometer technique.
Equipment and Materials

Dry yeast, distilled water, methylene blue solution
TABLE 10.7
Effect of Different Concentration of Glucose on Ethanol Production by Yeast
Glucose
Concentration Time Weight of Centrifuge Tube Calculated Loss in Amount of Ethanol
(% w/v) (hours) (Wtime) Weight (Wt−W0) Produced (g)
5 0 W0=
8 W8=
24 W24=
40 W40=
10 0 W0=
8 W8=
24 W24=
40 W40=
15 0 W0=
8 W8=
24 W24=
40 W40=
20 0 W0=
8 W8=
24 W24=
40 W40=
Procedure
1. Yeast inoculum is prepared by adding 5 g of dry yeast and 25 mL of distilled water.
2. This solution is incubated in a water bath at 32°C at 120 rpm for 20 minutes.
3. After incubation, the yeast solution is diluted 1000 times.
4. To 1000 µL of diluted yeast solution, methylene blue dye is added. Dead yeast cells become
blue in color, whereas live cells retain the original mustard yellow color.
5. Pour 100 µL of the aforementioned solution into the hemocytometer well.
6. Count the yeast cells in the four corner squares of the hemocytometer.
7. Yeast concentration will be determined based on the dimensions of the hemocytometer
square and cells counted.
Calculations
number of live cells × dilution factor
Total live cell concentration in cells per milliliteer =
volume of corner square
number of dead cells × dilution factor

Total dead cell concentration in cells per milliliteer =
volume of corner square
Volume of the corner square per milliliter = 16 × volume of the smallest square
Experimental Procedures
A. Determining Cell Concentration
1. Zeroing the spectrophotometer: Set the wavelength to 630 nm. Using the knob on the left, set
the reading to 0% transmission when the chamber is empty; using the knob on the right, set
the reading to 100% transmission when the chamber contains a test tube with about 4 mL of
pure medium.
Fermentation 305
2. Determining cell concentration: First, flush out the sample tube for your group’s fermentor
by taking an 8–10 mL sample, which you will then discard. Take another 8–10 mL sample
from your group’s fermentor and gently mix it. Take about 4 mL from your sample tube and
transfer it to a glass test tube. Clean the outside of the test tube with ethanol, insert it into the
spectrophotometer, and record the absorbance reading. If the absorbance reading is greater
than 0.25, which is a typical limit of linear correlation between absorbance and cell mass
concentration, dilute the sample with a known amount of pure medium and measure the
absorbance again to check if the absorbance reading is on the linear portion of the calibra-
tion curve. Record time for the sample taken along with the absorbance reading in the linear
range, as well as the dilution factor.
B. Glucose Measurement
Take your undiluted yeast sample tube and insert into it the thin plastic sample tubing from the
glucose analyzer. If the analyzer is in “Standby” mode, hit the “Run” key; after the machine is cali-
brated, hit the “Sample” key. If the analyzer is not in the standby mode, just hit the “Sample” key.
The glucose concentration in the medium from your sample will be printed out in about 1 minute.
Record this value.
C. Ethanol Assay
The ethanol concentration is determined using a simple and quick chemical assay. This assay is based
on the following reaction:
Ethanol + NAD
alcohol dehydrogenase
→ acetaldehyde + NADH
The amount of NADH produced in this reaction is proportional to the amount of ethanol added as a
substrate. This quantity of NADH is determined spectrophotometrically at 340 nm. The ethanol assay
reagent for this assay contains NAD and alcohol dehydrogenase.
1. Take 0.5 mL from your undiluted sample, pipette it into an Eppendorf tube, and spin at 14,000
rpm for 5 minutes.
2. Add 2 mL of ethanol assay reagent to each of three cuvettes.
3. Add 10 µL of pure medium to the first cuvette; this is your blank. Cover with a parafilm and
mix gently.
4. Add 10 µL of the ethanol standard (0.08% w/v) to the second cuvette; this is your standard.
Cover with a parafilm and mix gently.
5. Add 10 µL of sample (from the supernatant from step 4) to the third cuvette; this is your
sample. Cover with a parafilm and mix gently.
6. Incubate the cuvettes at room temperature for 10 minutes.
7. Clean the outside of the cuvettes, and then read the absorbance of each cuvette at 340 nm; use
the blank to zero the spectrophotometer. If the sample absorbance is greater than 1.7, dilute
the supernatant from your sample to 1:4 and perform the assay again using this diluted super-
natant. Do not redo the blank and the standard.
8. Calculate the ethanol concentration for your sample using the following formula:
A(sample)
Ethanol (in grams per liter ) = × 0..8 (for the undiluted samples)
A(standard)
Record this value.
SUGGESTED READING
Bailey, J. E., and D. Ollis. 1986. Biochemical Engineering Fundamentals, 2nd ed. New York: McGraw-Hill.
Casida, L. E. 1968. Industrial Microbiology, 460. Hoboken, NJ: John Wiley & Sons.
Creuger, W., and A. Crueger. 2004. Biotechnology: A Textbook of Industrial Microbiology, 2nd ed., 260.
Sutherland, MA: Sinaur Assoc., Inc.
Doelle, H. W. 1994. Microbial Process Development. Singapore: World Scientific Publ.
Glazer, A. N., and H. Nikaido. 2007. Microbial Biotechnology-Fundamentals of Applied Microbiology, 2nd ed.,
541. Cambridge: Cambridge University Press.
Prescott, S. C. 2007. Industrial Microbiology. India: Agrobios.
Stanbury, P. F., A. Whitaker, and S. J. Hall. 1999. Principles of Fermentation Technology, 376. Oxford, UK:
Butterworth-Heinemann.
IMPORTANT LINKS
1. Fermentor: http://www.gelifesciences.com/aptrix/upp01077.nsf/Content/na_blotting_site~nadetection~na_
autoradiography_cassettes?opendocument&cmpid=ppcaw100
2. ALF: http://www.electrolab.biz/Product_List/FerMac_Air_Lift_Vessel.aspx
3. Fixed-bed fermentor: http://www.environmental-expert.com/products/fixed-bed-fermentor-101742/view-
comments
4. Incinerator: http://www.nikaengg.com/incinerators.htm
11 Conductivity Meter
11.1 INTRODUCTION
Conductivity is the ability of a solution, metal, or gas—in brief, all materials—to pass an electric
current. In solutions, the current is carried by cations and anions, whereas in metals it is carried by
electrons. How well a solution conducts electricity depends on a number of factors, namely concen-
tration, mobility of ions, valence of ions, and temperature. All substances possess some degree of
conductivity. In aqueous solutions, the level of ionic strength varies from the low conductivity of
ultra pure water to the high conductivity of concentrated chemical samples.
11.2 PRINCIPLES
Conductivity is typically measured in aqueous solutions of electrolytes. Electrolytes are substances
containing ions, that is, solutions of ionic salts or of compounds that ionize in a solution. The ions
formed in a solution are responsible for carrying the electric current. Electrolytes include acids,
bases, and salts, and they can be either strong or weak. Most conductive solutions measured are
aqueous solutions, as water has the capability of stabilizing the ions formed by a process called
solvation (see Figure 11.1).
11.2.1 Strong Electrolytes

Strong electrolytes are substances that are fully ionized in a solution. As a result, the concentra-
tion of ions in a solution is proportional to the concentration of the electrolyte added. They include
ionic solids and strong acids, for example, HCl. Solutions of strong electrolytes conduct electricity
because positive and negative ions can migrate largely independently under the influence of an
electric field.
11.2.2 Weak Electrolytes

Weak electrolytes are substances that are not fully ionized in solution. For example, acetic acid
partially dissociates into acetate ions and hydrogen ions, so that an acetic acid solution contains
both molecules and ions. A solution of a weak electrolyte can conduct electricity, but usually not as
well as a strong electrolyte because there are fewer ions to carry the charge from one electrode to
the other.
11.3 COMMON DEFINITIONS

11.3.1 Resistance
This is the reciprocal of the conductivity value and is measured in ohm-cm. It is generally limited
to the measurement of ultrapure water, the conductivity of which is very low. The resistance of the
solution (R) can be calculated using Ohm’s law (V = R × I):
307
Electrical current, I
Voltage, V
‒ +
‒ +
‒ ‒ +
+
‒ ‒ + +
FIGURE 11.1 Migration of ions in a solution.
R = V /I
where
V = voltage (volts)
I = current (amperes)
R = resistance of the solution (ohms)
11.3.2 Conductance
Electricity is the flow of electrons. This indicates that ions in a solution will conduct electricity.
Conductivity is the ability of a solution to pass an electric current. The conductivity reading of a
sample will change with temperature. Conductance (G) is defined as the reciprocal of the electrical
resistance (R) of a solution between two electrodes:
G = 1/R( S )
κ = GiK
where
κ = conductivity (S/cm)
G = conductance (S), where G = 1/R
K = cell constant (cm−1)
The principle by which instruments measure conductivity is simple: two plates are placed in a
sample, a potential is applied across the plates (normally a sine wave voltage), and the current is
measured. Conductivity (G), the inverse of resistivity (R), is determined from the voltage and cur-
rent values according to Ohm’s law:
G = I / R = I (amps)/E (volts)
The conductivity meter measures the conductance and displays the reading converted into con-
ductivity. Since the charge on ions in a solution facilitates the conductance of an electric current,
the conductivity of a solution is proportional to its ionic concentration. In some situations, however,
Conductivity Meter 309
Sodium chloride Sulfuric acid
Conductivity
Conductivity
io
n
tio
ct
ac
a
er
r
te
t
in
in
n
n
io
tio
t
lu
o lu
so
S
o
N Ion concentration Ion concentration
Sodium chloride Sulfuric acid
FIGURE 11.2 Conductivity of sulfuric acid and sodium chloride/ion concentration.
TABLE 11.1
Conductivity of Some Common Solutions
Solution Conductivity
Absolute pure water 0.055 μS/cm
Power plant boiler water 1.0 μS/cm
Good city water 50 μS/cm
Ocean water 53 mS/cm
Reverse osmosis water 50–100 μS/cm
Domestic tap water 500–800 µS/cm
conductivity may not correlate directly to concentration. The graphs in Figure 11.2 illustrate the
relationship between conductivity and ion concentration for two common solutions. Notice that
the graph is linear for sodium chloride solution, but not for highly concentrated sulfuric acid. Ionic
interactions can alter the linear relationship between conductivity and concentration in some highly
concentrated solutions.
The water-softening industry refers to “grains” of hardness and uses TDS (total dissolved solids)
as a measurement scale. While TDS is really a gravimetric measurement, since in a solution the
solids are predominately present in ionic form, they can be approximated with conductivity. The
TDS scale uses 2 μS/cm = 1 ppm (part per million as CaCO3). It is also expressed as 1 mg/L TDS.
While the method of measurement is the same, some conductivity meters can make the conversion
and express the results of a measurement in many different units. This is helpful for users who are
accustomed to one particular unit of measurement (Table 11.1).
11.4 CONDUCTIVITY METER

A typical conductivity meter applies an alternating current (I) at an optimal frequency* to two
active electrodes and measures the potential (V). Both the current and the potential are used to cal-
culate the conductance (I/V). The conductivity meter then uses the conductance and cell constant to
display the conductivity (Figure 11.3):
Conductivity† = cell constant × conductance
Note that the current source is adjusted so that the measured potential (V) is equal to the reference
potential (Er) (approximately ±200 mV).
* The measuring frequencies of a typical conductivity meter are 94 Hz in the 4.000–40.00 μS range and 46.9 kHz in the
400.0 mS–2.000 S range.
† At sample temperature.
Current
measurements
1/V Conductance
Two-pole Four-pole
V
±200 mV Potential
measurements
Reference potential
source Er
Current
source
FIGURE 11.3 Diagram of a simplified conductivity meter.
TABLE 11.2
Optimum Conductivity Range for Cells of Three
Different Constants
Cell Constant Optimum Conductivity Range (μS/cm)
0.1 0.5–400
1.0 10–2000
10.0 1000–200,000
TABLE 11.3
Common Alpha Values of Some Common Solutions
Substance at 25°C Concentration (wt%) α
HCl 10 1.56
KCl 10 1.88
H2SO4 50 1.93
NaCl 10 2.14
HF 1.5 7.20
HNO3 31 31.0
11.4.1 Cell Constant

This is the ratio of the distance (d) between the electrodes to the area (a) of the electrodes (see Table 11.2):
K = d /a
where
K = cell constant (cm−1)

a = effective area of the electrodes (cm2)
d = distance between the electrodes (cm)
Common alphas (α) are listed in Table 11.3. To determine α of other solutions, simply measure
conductivity at a range of temperatures and graph the change in conductivity versus the change in
temperature. Divide the slope of the graph by Gtcal to get α.
11.5 CONDUCTIVITY CELLS

11.5.1 Two-Pole Cell
In a traditional two-pole cell (Figure 11.4), an alternating current is applied between the two poles
and the resulting voltage is measured. The aim is to measure the solution resistance (Rsol) only.
However, the resistance (Rel) caused by the polarization of the electrodes and the field effect inter-
feres with the measurement, and both Rsol and Rel are measured.
11.5.2 Three-Pole Cell

The three-pole cell (Figure 11.5) is not as popular now as it has been replaced by the four-pole cell.
The advantage of this design was that the third pole, which was linked to pole 1, allowed the field
lines to be guided and confined in an optimal manner, limiting dispersion in the measurement and
minimizing influences on the measurement such as beaker volume and the position of the cell in the
beaker (field effect). It guarantees a better reproducibility when determining the cell constant and
therefore more reproducible results.
11.5.3 Four-Pole Cell

In a four-pole cell (Figure 11.5), a current is applied to the outer rings (1 and 4) in such a way that a
constant potential difference is maintained between the inner rings (2 and 3). As this voltage mea-
surement takes place with a negligible current, these two electrodes are not polarized (R2 = R3 =
0). The conductivity will be directly proportional to the applied current. The geometry of four-pole
cells with outer tubes minimizes the beaker field effect, due to the measurement volume being well
defined within the tube. The position of the conductivity cell in the measuring vessel or the sample
volume therefore has no influence on the measurement.
Electrical current
V
Rsol
Rel Rel
(a) (b)
FIGURE 11.4 (a) Two-pole conductivity cell and (b) simplified diagram of a two-pole conductivity cell.
Electrical current
V
1 Rsol 4
Rel Rel
2 3
(a) V (b)
(c)
FIGURE 11.5 (a) Three-pole cell, (b) four-pole cell, and (c) simplified diagram of a four-pole conductivity cell.
11.5.4 Platinized Cells

Covering the cell poles (plates or rings) with a layer of platinum black is another way to minimize
polarization effects and avoid error in measurements. The surface of the pole is increased and the
current density is decreased; therefore, the polarization effect is less. Consequently, the cell constant
is linear over 2–3 decades toward the higher conductivity range. The platinum black must not be
damaged or scratched, as this will modify the surface of the poles and therefore the cell constant.
However, one minor disadvantage of platinized cells is that the cell constant tends to drift faster
than the constant of nonplatinized cells. It is advisable to use platinized cells only in nonviscous
samples, without suspensions and to perform frequent calibrations.
11.5.5 Flow-Through Cell

Flow-through-type conductivity cells (Figure 11.6) are designed for flow measurements and mea-
surements in small sample volumes. These measurements can be performed in a closed liquid sys-
tem protected from the air. If a measurement is to be performed in pure water, it is necessary to use
a flow cell. Contact with air must be avoided. The reason for this is that the carbon dioxide in the air
forms hydrogen carbonate ions in water and leads to a change in the conductivity. A circulation cell
can be used in two ways: (1) circulation, where the solution flows nonstop during the measurement,
and (2) pipette, where a quantity of solution is drawn into the cell. This technique is ideal for small
sample volumes.
11.5.6 Advantages and Disadvantages of Two-Pole and Four-Pole Cells
Two-Pole Cell
Advantages Disadvantages
Easier to maintain Field effects—cell must be positioned in the centre of the
measuring vessel
Use with sample changer (no carryover) Only cells with no bridge between the plates
Economical Polarization in high-conductivity samples
Recommended for viscous media or samples with Calibrate using a standard with a value close to measuring
suspension value accurate over 2 decades
Four-Pole Cell
Advantages Disadvantages
Linear over a very large conductivity range Unsuitable for micro samples; depth of immersion 3–4 cm
Calibration and measurement in different ranges Unsuitable for use with a sample changer
Flow-through- or immersion-type cells
Ideal for high-conductivity measurements
Can be used for low-conductivity measurements if the cell
capacitance compensated
11.5.7 Conductivity Cells and Measurement Ranges

The number of poles and whether they are platinized or not influences the measurement. The mea-
surement range over which the cell stays linear becomes broader as the number of poles increases.
Platinized poles also contribute to increasing the measurement span in which the cell is linear.
Figure 11.7 shows guidelines for choosing a cell corresponding to a measuring range.
FIGURE 11.6 Flow-through cell.
Conductivity μS/cm MS/cm

cells (sample) (sample)
0.1 1 10 100 1 10 100 1000
Two-pole
Nonplatinized
Three-pole
Four-pole
Two-pole
Platinized
Three-pole
Four-pole
Recommended Nonrecommended
FIGURE 11.7 Guidelines for choosing a cell corresponding to a measuring range.
11.5.8 Calibration
Determination of the cell constant is required to convert conductance readings into conductivity
results.
11.5.9 Standard Solution

A standard solution of known conductivity is used to calibrate the conductivity-measuring chain.
11.5.10 Reference Temperature

Conductivity readings are often referenced to a specific temperature, typically 20°C or 25°C, for
comparative purposes.
11.5.11 Automatic Temperature Correction

Algorithms for automatic conversion of sample conductivity to a reference temperature are as
follows:
Conductivity Values at 25°C

Pure water 0.055 μS/cm
Deionized water 1 μS/cm
Rainwater 50 μS/cm
Drinking water 500 μS/cm
Industrial wastewater 5 mS/cm
Seawater 50 mS/cm
1 mol/L NaCl 85 mS/cm
1 mol/L HCl 332 mS/cm
11.6 FACTORS INFLUENCING THE MEASUREMENT

The accuracy of conductivity measurements can be influenced by the following factors:
• Polarization
• Contamination
• Geometry
• Cable resistance
• Cable capacitance
• Frequency change
• Temperature
11.6.1 Polarization
Applying an electric current to electrodes in a solution may cause an accumulation of ionic species
near the electrode surfaces and chemical reactions at the surfaces (Figure 11.8). Thus, a polarization
resistance arises on the electrode surface, which may lead to erroneous results as it is a parasitic
component to the solution resistance.
11.6.1.1 Preventing Polarization

Polarization effects can be reduced or prevented by the following:
• Applying an alternating current: The measuring current will flow through the double layer
capacitance (Cdl) of the electrodes instead of building up a voltage drop across the elec-
trode surface due to the solution resistance (Rsol). Rel is then much smaller than Rsol.
• Adjusting the measuring frequency: The frequency has to be adapted to the conductivity
of the sample. Low frequencies are applied at low conductivities, where polarization is
negligible compared to the solution resistance (Rsol). High frequencies are applied at high
conductivities, where the solution resistance (Rsol) is low in order to minimize the polariza-
tion resistance (Rel) (Figure 11.9).
• Optimizing the electrode areas: Increasing the active surface area of the electrodes with
a layer of platinum black reduces the current density and consequently the polarization
effect.
• Using a four-pole conductivity cell: The polarization resistance has no influence on the
measurement.
‒ +
– +
– +
+
–
+
–
+
+ +
FIGURE 11.8 Accumulation of ionic species at the electrode surface.
Rel Rel
Rsol
Cdl Cdl
If DC
high Rsol high
If AC
low low
FIGURE 11.9 Polarization resistance.
11.6.2 Contamination of Electrode Surfaces

Deposits on the electrode surface of a two-pole cell have an effect similar to polarization errors, that
is, they cause the conductivity reading to be lower than usual. These effects can also be prevented
with a four-pole conductivity cell.
11.6.3 Geometry-Related Errors: Field Effects

Errors are also caused by field effects—the part of the measuring field that falls outside the geo-
metric space of the two-pole cell (Figure 11.10). These field lines can affect the measurement if
something interferes with the field lines, such as the beaker walls. Three- and four-pole conductivity
cells are designed to minimize this effect. If the entire measuring field is contained within the body
of the cell, then field errors cannot be caused by the beaker wall.
11.6.4 Cable Resistance

A cable has a given length, and therefore a given resistance. The cable resistance induces error on
the result and must be taken into account. Compensate the cable resistance when
• Solution resistance is low (below 50 Ω), that is, for high-conductivity measurements
• Performing measurements using two- or three-pole cells
Field lines
+ ‒
FIGURE 11.10 Geometry-related errors field effects.
The cable resistance of a cell is normally specified by the manufacturer. Note that for four-pole cells,
the cable resistance has no influence. If a value is demanded during programming of the conductiv-
ity meter, enter zero.
11.6.5 Cable Capacitance

A shielded cable of a given length has a given capacity. When the measured conductance is low
(below 4 μS), the cable capacitance is not negligible and must be taken into account. Compensate
the cable capacitance when
• Using a four-pole cell

• Measuring low conductivities
• The cable capacitance of the conductivity cell is greater than 350 pF
The cable capacity is normally specified by the manufacturer.
11.6.6 Frequency Change

Low frequencies are applied at low conductivities, where the polarization resistance is negligible
when compared to the resistance of the solution. They also contribute to reducing the cable capaci-
tance effect, which is greater when the conductivity is low (high solution resistance).
High frequencies are applied at high conductivities, where the solution resistance is low. In most
conductivity meters, the frequency is automatically increased with increasing conductance of the
sample, to avoid polarization errors at high conductivity.
11.6.7 Temperature Effect

Conductivity measurements are temperature dependent: if temperature increases, conductivity
increases. For example, the conductivity measured in a 0.01 D KCl solution at 20°C is 1.273 mS/
cm, whereas at 25°C, it is 1.409 mS/cm. The concept of reference temperature was introduced
to allow the comparison of conductivity results obtained at different temperatures. The reference
temperature is usually 20°C or 25°C. The conductivity meter measures the actual conductivity and
temperature and then converts it to the reference temperature using a temperature correction func-
tion and displays the conductivity at the reference temperature. It is mandatory to always associate
the temperature with a conductivity result. If no temperature correction is applied, the conductivity
is the value taken at the measurement temperature. For temperature correction, different options
can be selected:
• Linear function
• Nonlinear function for natural waters according to ISO/DIN7888
• No correction
To perform correct conductivity measurements, use a temperature sensor or a conductivity cell

with a built-in temperature sensor. For high-accuracy measurement, thermostat samples so that the
same temperature is used for the calibration and measurement.
11.6.7.1 Linear Temperature Correction

In moderately and highly conductive solutions, temperature correction can be based on a linear
equation involving a temperature coefficient (θ). The coefficient is usually expressed as a conductiv-
ity variation in %/°C. Linear temperature correction is used, for example, for saline solutions, acids,
and leaching solutions:
100
κ Tref = iκT
100 + θ ( T − Tref )
where
κ Tref = conductivity at Tref

κT = conductivity at T
Tref = reference temperature
T = sample temperature
θ = temperature coefficient
Note that the correction is accurate only within a limited temperature range around T1 and T2.
Figure 11.11 shows T1 = 26°C, T2 = 14°C, and Tref = 25°C. The greater the difference between T and
Tref, the higher the risk of error.
11.6.7.2 Determination of the Temperature Coefficient (θ)

By measuring the conductivity of a sample at temperature T1 close to Tref and another temperature
T2, you can calculate the temperature coefficient by using the following equation:
(κ T2 − κ T1 ) i 100
θ=
(T2 − T1 ) i κ T1
Real-sample conductivity
KT1
0.015
Conductivity (S/cm)
KT2
0.010
T2 T1
0.005
5 15 25 35
Temperature (ºC)
FIGURE 11.11 Conductivity versus temperature.

T2 should be selected as a typical sample temperature and should be approximately 10°C different
from T1. The temperature coefficients of the following electrolytes generally fall into the ranges
shown below
• Acids: 1.0–1.6%/°C
• Bases: 1.8–2.2%/°C
• Salts: 2.2–3.0%/°C
• Drinking water: 2.0%/°C
• Ultrapure water: 5.2%/°C
11.6.7.3 Nonlinear Temperature Correction

Linear temperature correction is not suitable for many aqueous liquids under test, and the tempera-
ture dependency can only be described by nonlinear functions such as the nonlinear function for
natural waters, that is, for ground water, surface water, drinking water, and wastewater. The prin-
ciple of this correction is that the conductivity measured at the sample temperature is corrected to
25°C to give K25:
K 25 = f25 ( T ) i K T
f 25 (T) is the temperature correction factor used for the conversion of the conductivity values of natu-
ral water from T to 25°C. The conductivity meter calculates f 25 (T) from a four-degree polynomial
equation. This equation fits conductivity variations against temperature for natural water stated in
Natural Water Temperature Correction (ISO/DIN 7888). The nonlinear correction is defined by
ISO/DIN 7888 standard and is applicable for measurements between 0°C and 35.9°C.
11.7 MEASURING TECHNIQUES

11.7.1 Determination of the Cell Constant
Calibration is important because the result is the correct value of the cell constant in your work-
ing conditions. The cell constant is a factor that is used to convert the measured conductance to
conductivity:
Conductivity ( S i cm −1 ) = cell constant ( cm −1 ) × conductance ( S)
The cell constant is determined by the geometry of the cell but in practical terms can only be
measured using a standard of known conductivity, for example, KCl 0.01 D solution. The cell con-
stant changes with time. Some modifications can occur due to contamination or due to physical–
chemical modification, in the case of platinized cells. It is therefore recommended to calibrate the
cell at least once a week. However, if you use a platinized cell, it is advisable to perform a daily
conductivity measurement in a standard. If the result obtained is in accordance with the theoreti-
cal value, continue your measurements. If not, your cell needs to be cleaned (if nonplatinized)
or replatinized (if platinized). For high-precision measurements, it is necessary to determine the
cell constant by performing a calibration measurement on a standard thermostat at the desired
temperature.
Note that for two-pole cells, the standard used for the calibration must have a conductivity value
as close as possible to the conductivity of the sample to measure. When using a two-pole cell, the
choice of the cell constant value varies with the linear measurement range of the cell selected.
Typically, a cell with K = 0.1 cm−1 is chosen for pure water measurements, while for environmental
water and industrial solutions a cell with K = 0.4–1 cm−1 is used. Cells with up to K = 10 cm−1 are
best for very-high-conductivity samples. In the case of a four-pole cell, the cell constant value is
generally included in the range 0.5–1.5 cm−1.
11.7.2 Conductivity Measurements

Conductivity measurements can only be performed after calibration, as the cell constant value is
used to calculate the conductivity.
11.7.2.1 Low-Conductivity Measurements (Pure Water)

One of the main applications of low-conductivity measurements is checking the quality of pure
water. Pharmaceutical laboratories are obliged to respect regulations laid down by national phar-
macopoeias; for example, the fifth supplement of the United States Pharmacopoeia (USP) lays down
rules for checking the quality of pure water or fully deionized water used for the production of
injection products.
11.7.2.2 Principle of Pure Water Measurements

11.7.2.2.1 USP Standards
The conductivity partly depends on the pH, the temperature, and the amount of atmospheric carbon
dioxide, which has been dissolved in the water to form ions (intrinsic conductivity). The conduc-
tivity also depends on the chloride, sodium, and ammonium ions considered as water impurities
(extraneous conductivity). The conductivity (intrinsic and extraneous) of the water is measured and
compared to values listed in a table to evaluate if the studied water is suitable for use in pharma-
ceutical applications. If the sample fails stage 1, additional tests have to be performed (stages 2 and
3) in order to determine if the excessive conductivity value is due to intrinsic factors or extraneous
ions. The main requirement is that the cell constant be known with an uncertainty better than ±2%.
11.7.2.2.2 European Pharmacopoeia Standards

The cell consists of two parallel platinum plates at a defined distance. It is confined within a glass
jacket with two pipe connectors enabling measurement in flow mode. This cell is calibrated using
a conductivity standard of 26.6 μS/cm at 20°C, which is traceable to NIST (National Institute of
Standards and Technology). All measurements are made with a precision conductivity meter using
the AC current at a low frequency.
11.7.2.3 High-Conductivity Measurements

High-conductivity measurements are performed when samples are water solutions, highly concen-
trated in dissociated species, that is, salts, acids, and bases. The conductivity method is used to con-
trol the concentration of pure or mixed solutions. For example, the conductivity method is preferred
to pH measurements in production plants of concentrated acids or bases.
11.7.3 Contacting Conductivity

Contacting conductivity uses a cell with two metal or graphite electrodes in contact with the elec-
trolyte solution. An AC current is applied to the electrodes by the conductivity meter, and the
resulting AC voltage is measured. This technique can measure down to pure water conductivity. Its
main drawback is that the cell is susceptible to coating and corrosion, which drastically decreases
the reading. In strongly conductive solutions, there can also be polarization effects, which result in
nonlinearity of measurements.
Induced current dependent

Input AC on the conductivity
voltage of the sample
Drive Pickup
coil coil
Sample
Current field
FIGURE 11.12 Toroidal conductivity AC current passing through a toroidal drive coil.
11.7.4 Toroidal “Inductive” Conductivity

A toroidal conductivity measurement is made by passing an AC current through a toroidal drive
coil, which induces a current in the electrolyte solution (see Figure 11.12). This induced solution
current, in turn, induces a current in a second toroidal coil, called the pickup toroid. The amount of
current induced in the pickup toroid is proportional to the solution conductivity.
The main advantage of toroidal conductivity is that the toroidal coils are not in contact with the
solution. They are either encased in a polymeric material or are external to a flow-through cell. One
of the main disadvantages of toroidal conductivity measurements is that it lacks the sensitivity of
contacting measurement. Toroidal sensors are also typically larger than contacting sensors, and the
solution current induced by the toroid occupies a volume around the sensor. Hence, toroidal sensors
need to be mounted in a larger pipe.
11.8 RELIABLE MEASUREMENTS

Reliable measurement results can be obtained when you follow the simple rules discussed in this
section.
11.8.1 Calibrate Frequently

The cell constant value is an important factor of conductivity measurements. You must be sure
of the cell constant value before starting measurements. It is impossible to recommend a given
calibration interval for conductivity cells because the interval will depend on the application, the
samples, and the operating conditions in use. Check the cell constant regularly, especially when
using a platinized cell, due to increased risk of contamination or physical–chemical modification
of the platinum layer.
11.8.2 Temperature and Stirring Conditions

Thermostat if you want accurate measurements. The temperature and stirring conditions during
calibration must be as close as possible to the conditions used during the measurement. Note that for
conductivity measurements, the conductivity reading can be expressed at the measuring tempera-
ture or at a reference temperature using a temperature correction factor.
11.8.3 Position of Conductivity Cell

Make sure that all the poles of the conductivity cell are completely covered by the sample. Always
position a two-pole cell in the center of the measuring vessel.
11.8.4 Low-Conductivity Measurements

• Use a flow-through cell, to avoid atmospheric contamination from carbon dioxide.
• Use cells with a low cell constant, 1 cm−1 or lower.
• Use nonplatinized cells for easier cleaning and faster response.
• Make sure that your instrument is able to apply an appropriate measuring frequency.
11.8.5 High-Conductivity Measurements

• Use platinized cells to avoid polarization errors, preferably four-pole cells.
• Use cells with a high cell constant (1 cm−1 or higher if possible).
• Do not dilute samples in order to bring them into a measuring range. Conductivity is not
proportional to concentration at high levels.
• Make sure that your instrument is able to apply an appropriate measuring frequency.
11.8.6 Traceability
Using one of Radiometer Analytical’s Demal range of certified conductivity standards to cali-
brate your measuring chain guarantees that your conductivity measurements are traceable to
NIST.
11.9 MAINTENANCE AND STORAGE

11.9.1 Make Sure That Your Cell Is Clean
Between measurements, rinse the cell with deionized water. If the cell has been exposed to a solvent
immiscible with water, clean it with a solvent miscible with water, for example, ethanol or acetone,
and rinse carefully with water. In the event of deposits on the cell, dip the cell in normal cleaning
solution for approximately 1 hour. Rinse thoroughly with distilled water after cleaning.
11.9.2 Store the Conductivity Cell Carefully

Before storing the cell, rinse it carefully in deionized water.
• Short-term storage: in deionized water

• Long-term storage: in deionized water or store dry
• After long-term storage, condition the cell for 8 hours in deionized water, before use
11.9.3 Handle Platinized Cells Carefully

Do not touch the black platinum layer of the platinized cells. To rinse the platinized cells, dip the
cell several times in a beaker of demineralized water. Be careful when rinsing platinized cells using
deionized water from a water bottle. The force of the water could remove some of the platinum layer
and consequently modify the cell constant.
11.10 APPLICATIONS
11.10.1 Conductivity Measurements
Conductivity measurements simply detect the presence of ions in a solution and are therefore non-
specific measurements. Conductivity applications encompass, for instance, the monitoring of water
purity, drinking water, and process water quality. Conductivity measurement is also a rapid and
inexpensive way of determining the ionic strength of a solution. The conductivity κ is calculated
using the conductance G and the cell constant K:
κ = G i K (S / cm)
11.10.2 Resistivity Measurements

Resistivity measurements are used as a reliable indicator of ionic water quality, especially for ultra-
pure water and more generally when a resistivity value is preferred to a conductivity value, for
example, when checking for water contamination in organic solvents. The resistivity of a solution
is calculated on the basis of the conductance G compensated for the cable resistance, cable capaci-
tance, and cell constant of the conductivity cell used. The resistivity ρ is calculated as follows:
1
ρ= Ω i cm -1
κ
11.10.3 TDS Measurements

TDS measurements are the measure of the total concentration of ionic species of a sample. The
magnitude is relative to the standard solution used to calibrate the meter. TDS measurements in the
pulp and paper industry measure accurately and easily the total organic and inorganic dissolved
solids in water.
11.10.3.1 What Is TDS and How Is It Measured?

The TDS corresponds to the total weight of cations, anions, and the undissociated dissolved species
in one liter of water. The standard method (Arnold et al. 1992) to determine TDS is to evaporate
a measured sample of water to dryness at 180°C, under strict laboratory conditions, and carefully
weigh the amount of dry solids remaining. The precision of the standard method depends on the
nature of the dissolved species. The TDS method in a typical conductivity meter offers a quicker
and easier way of determining TDS by measuring the conductiviy than using a conversion factor to
give TDS readings.
11.10.3.2 Determination of the TDS Factor

Conductivity readings are converted to TDS readings by multiplication with a known mathematical
factor. The factor depends on the reference material used to prepare the standard. Perform a calibra-
tion using a standard of known TDS(STD). The TDS factor is calculated as follows:
TDS(STD)
TDS factor =
κ18 (STD)
TDS(STD) is expressed in milligrams per liter. κ18(STD) is the conductivity of the standard cor-
rected to 18°C (in microsiemens per centimeter). The conductivity of the standard measured is cor-
rected to 18°C using the corresponding temperature correction table.
The TDS factor calculated by the conductivity meter also provides information about the quali-
tative ionic composition of the water sample. If the TDS factor is outside the 0.55–0.7 range, the
TDS calibration should be considered suspect and must be repeated. If a TDS factor below 0.55 is
confirmed, the sample probably contains a significant concentration of a constituent that cannot be
measured (e.g., ammonia or nitrite). A TDS factor above 0.8 may indicate the presence of a large
amount of poorly dissociated calcium and sulfate ions.
The sample conductivity is measured at the sample temperature (0°C–99°C) and corrected to
18°C. The sample TDS, TDS (SMP), is calculated from the sample conductivity corrected to 18°C,
κ18 (SMP):
TDS (SMP) (in milligram per liter) = TDS factor × k18 (SMP).
TDS values between 4 and 20,000 mg/L can be displayed. To obtain the most accurate measure-
ments, perform the standard and sample measurements at the same temperature. Such TDS mea-
surements are accurate as long as the composition of the samples varies only slightly.
11.10.4 Concentration Measurements

Since the charge of the ions in solution facilitates the conductance of electric current, the conduc-
tivity of a solution is highly (but not totally) proportional to its ion concentration. As conductivity
is a nonspecific technique, concentration calculation using conductivity measurements is valid for
samples containing only the species of interest. The first step to measuring concentration is to know
the conductivity of the solution as a function of the concentration of the species of interest. This data
can come from published conductivity versus concentration curves for electrolytes, or from labora-
tory measurements. Over large conductivity ranges, conductivity will increase with concentration,
but may reach a maximum and then decrease with increasing concentration. When using conductiv-
ity measurements to determine the concentration, it is important to work at a constant temperature
for calibration and measurements because the shape of the conductivity versus concentration curve
will change with the temperature.
11.10.4.1 Necessary Conditions

With the help of conductivity versus concentration data, the following conditions are necessary to
perform a concentration measurement:
• There must be a measurable change in conductivity over the desired concentration range.
• Conductivity must either increase or decrease with concentration. If a maximum or min-
imum is present in the desired concentration range, concentration cannot be measured
(Figure 11.13).
Conductivity
Measurable Measurable Measurable

0 to A% B to C% D to E%
0 A B C D E
Concentraction (%)
FIGURE 11.13 Conductivity versus concentration.

To calculate a sample concentration, the conductivity meter must be calibrated against 1–3
standards of known concentration. At the end of the calibration, a formula expressing the con-
centration as a function of the conductivity measured is determined. The sample concentration
is calculated from the sample conductivity measured and the coefficients obtained during the
calibration.
11.10.4.2 Determination of Concentration Coefficients

A calibration using 1–3 standards of known concentration is performed. For each standard
• The conductivity of the standard is measured at the standard’s temperature.

• The conductivity of the standard is corrected to a reference temperature Tref (linear correc-
tion or natural water correction as for a conductivity measurement).
At the end of the calibration, the conductivity meter calculates and displays the A0, A1, and A2
coefficients of the following equation:
C = A0 + A1 i κ Tref + A2 i (κ Tref )2
where
C = concentration
κ Tref = conductivity corrected to the Tref reference temperature
In one-point calibration, A1 is calculated, and A0 and A2 are equal to 0. In two-point calibration, A0

and A1 are calculated, and A2 = 0.
All the measurements of the standards must be performed at the same temperature. To obtain
the most accurate measurements, thermostat the standards and the samples at the reference
temperature Tref.
11.10.4.3 Determination of the Sample Concentration

The conductivity of a sample is measured at the sample’s temperature, then corrected to a reference
temperature Tref to give κ Tref (linear correction or “natural water” correction as for a conductivity
measurement). The sample concentration CSMP is then calculated using the following equation:
CSMP = A0 + A1 × κ Tref + A2 × (κ Tref )2
A0, A1, and A2 are the coefficients determined during the calibration.
11.10.4.4 Limitations of the Concentration Method

For some samples with high concentrations, the conductance = f (concentration) curve may show
a maximum. This can lead to major measurement errors as shown in Figure 11.14 for the example
of HCl. For HCl, a maximum around 860 mS is obtained for a concentration of about 19% (see the
curve in Figure 11.14). Two calibrations have been performed using three standards each. The two
calibration curves obtained are represented as dashed lines on the conductance = f (concentration)
curve.
When performing measurements on a 32% HCl sample using calibration no. 1, the conductivity
meter measures a conductance of 720 mS and finds a concentration of 10% instead of 32%. The cor-
rect result (32%) is obtained if sample measurements are performed using calibration no. 2.
40
Concentration in % by weight
32
30 Calibration
no.2
20
Cmax
10
Calibration
no.1
0 120 240 360 480 600 720 840 960

Conductance at 25ºC in mS
FIGURE 11.14 Concentration versus conductance for a HCl solution.
11.10.4.5 Recommendations
To obtain accurate measurements in concentrated samples, some precautions must be taken:
• For the sample analyzed, you must know if the conductance = f (concentration) curve
shows a maximum for the conductance. If this is the case, the concentration value Cmax
must be known.
• A calibration on three standards must be performed with the following recommendation:
the three standard concentrations must be greater or less than the Cmax value.
• Make sure that the change in conductivity is only due to the species of interest. As conduc-
tivity is a nonselective measurement, conductivity change due to any other species would
lead to misinterpretation of the concentration results.
11.10.5 Salinity Measurements

Salinity is a measurement without units that corresponds to the weight of dissolved salts in seawater.
The salinity is calculated from an empirical relationship between the conductivity and salinity of a
seawater sample. Oceanographic tables and standards endorsed by UNESCO/SCOR/ICES/IAPSO
are used for the calculation. Salinity measurements are performed with no direct temperature cor-
rection. The calculation is valid for salinity values in the range 2–42 at a sample temperature of
−2°C to +35°C:
Gt =Gt cal {1+α ( T -Tcal )}
where
G t = conductivity at any temperature T in °C

Gt cal = conductivity at calibration temperature Tcal in °C
α = temperature coefficient of the solution at Tcal in °C
To determine α of other solutions, simply measure the conductivity at a range of temperatures

and graph the change in conductivity versus the change in temperature. Divide the slope of the
graph by Gt cal to get α.
11.10.5.1 Determination of the Sample Salinity

11.10.5.1.1 Calibration
Calibration is carried out using a standard seawater solution κ15 (STD) (salinity = 35, conductivity =
42.896 mS/cm at 15°C). The conductivity of the sample is measured at the sample temperature T.
The conductivity of standard seawater κT (STD) is calculated from the following equation:
k T (STD) = f (T ) κ15 (STD)
The conversion factor f (T) is calculated from a four-degree polynomial formula.
11.10.5.1.2 Salinity of the Sample

At the sample temperature T, the sample conductivity measured is κT (SMP). Salinity is calculated
from the equation below combined with a five-degree polynomial formula:
R = κ T (SMP)/κ T ( STD )
11.10.5.1.3 Ensure Correct Cell Positioning and Reproducible Stirring Conditions

The positioning of a two-pole conductivity cell in the beaker is essential for accurate results due to
the influence of the field lines.
11.10.5.1.4 Select the Appropriate Cell for Application

Different types of conductivity cells exist; the following criteria will help to determine the selection.
Regarding the measuring range (high or low conductivity), a four-pole cell covers a wide measure-
ment range, whereas a platinized cell is recommended for high-conductivity measurements.
11.10.5.1.5 Use Certified Conductivity Standards

No conductivity measurement can be more precise than the standards used for the calibration. To
ensure optimum accuracy time after time, calibrate your system with solutions that are fully traceable
to national standards. Two types of conductivity standards exist, certified or economical. If a labora-
tory is involved in an accreditation, certification, or quality procedure, use the certified standards.
11.10.5.2 Demal Solution

11.10.5.2.1 Definition
In 1940, Jones and Bradshaw determined the demal definition as the weight of KCl/weight of the
solution.
11.10.5.2.2 KCl Demal Solutions

The mass of KCl/1000 g of solution as the molar weight is redefined from time to time; there is
a need to redefine the conductivity for a given molarity of KCl solution. Using a given mass in a
defined mass of water means that the determined conductivity of these solutions will not change
over time (Table 11.4).
TABLE 11.4
Mass of KCl/1000 g of Solution in Demal at 25°C
Solution Type at 25°C Mass of KCl/1000 g of Solution (g) Conductivity
1D 71.1352 111.3 mS/cm
0.1 D 7.4191 12.85 mS/cm
0.01 D 0.745263 1408 μS/cm
The conductivity of the demineralized water used must not exceed 2 μS/cm. Corrections for air
buoyancy must be applied to the weighing. For the preparation of standards, refer to OIML (the
International Organisation of Legal Metrology) Recommendation no. 56 (OIML 1991).
11.10.5.2.3 U.S. Pharmacopoeia and European Pharmacopoeia Standards
USP <645> with stage 1, 2, and 3 compliance is required for purified water and water for injection. Only
a few resistivity/conductivity meters conform to these requirements. Some of these requirements are:
• Resolution of 0.1 μS/cm or greater

• Accuracy at 1.3 μS/cm of 0.1 μS/cm
• Must be able to read with or without automatic temperature compensation
• Verifiable cell constant ±2%
11.10.5.2.4 Correct Reading to a Reference Temperature
Conductivity measurements are strongly temperature dependent. Add a temperature sensor to your
system for automatic temperature measurements and temperature correction of the conductivity to
a reference temperature (Tables 11.5 through 11.8).
TABLE 11.5
Conductivity (in mS/cm) of Demal Concentrations of
1, 0.1, and 0.01 D KCl Solutions
Temperature (°C) KCla 1 D KClb 0.1 D KClb 0.01 D
0 65.14 7.13 0.773
1 66.85 7.34 0.796
2 68.58 7.56 0.82
3 70.32 7.77 0.843
4 72.07 7.98 0.867
5 73.84 8.2 0.891
6 75.62 8.42 0.915
7 77.41 8.64 0.94
8 79.21 8.86 0.965
9 81.03 9.08 0.989
10 82.85 9.31 1.014
11 84.68 9.54 1.039
12 86.54 9.76 1.065
13 88.39 9.99 1.09
14 90.26 10.22 1.116
15 92.13 10.46 1.142
16 94.02 10.69 1.168
17 95.91 10.93 1.194
18 97.81 11.16 1.22
19 99.72 11.4 1.247
20 101.63 11.64 1.273
21 103.56 11.88 1.3
22 105.49 12.12 1.327
23 107.42 12.36 1.354
24 109.36 12.61 1.381
25 111.31 12.85 1.409
26 113.27 13.1 1.436
27 115.22 13.35 1.464
28 13.59 1.491
29 13.84 1.519
(Continued)
TABLE 11.5 (Continued )

Conductivity (in mS/cm) of Demal Concentrations of
1, 0.1, and 0.01 D KCl Solutions
Temperature (°C) KCla 1 D KClb 0.1 D KClb 0.01 D
30 14.09 1.547
31 14.34 1.575
32 14.59 1.603
33 14.85 1.632
34 15.1 1.66
35 15.35 1.688
36 15.61 1.717
37 15.86 1.745
38 16.12 1.774
39 16.37 1.803
40 16.63 1.832
41 16.89 1.861
42 17.15 1.89
43 17.4 1.919
44 17.66 1.948
45 17.92 1.977
46 18.18 2.007
47 18.44 2.036
48 18.7 2.065
49 18.96 2.095
50 19.22 2.124
a For the Demal KCl solution: extrapolation of the NIST results from OIML
conductivity values at 0°C, 18°C and 25°C.
b “Organisation Internationale de Métrologie Légale (OIML)”, Recommendation
no. 56 and “The National Institute of Standards and Technology (NIST)”,
Journal of Solution Chemistry, Vol. 20, no. 4 1991.
TABLE 11.6
Conductivity (in mS/cm) of Various Molar Concentrations of KCl Solutions
Temperature (°C) KCl 1 M KCl 10−1 M KCl 2 × 10−2 M KCl 10−2 M
0 65.41 7.15 1.521 0.776
1 67.13 7.36 1.566 0.8
2 68.86 7.57 1.612 0.824
3 70.61 7.79 1.659 0.848
4 72.37 8 1.705 0.872
5 74.14 8.22 1.752 0.896
6 75.93 8.44 1.8 0.921
7 77.73 8.66 1.848 0.945
8 79.54 8.88 1.896 0.97
9 81.36 9.11 1.945 0.995
10 83.19 9.33 1.994 1.02
11 85.04 9.56 2.043 1.045
12 86.89 9.79 2.093 1.07
13 88.76 10.02 2.142 1.095

Conductivity (in mS/cm) of Various Molar Concentrations of KCl Solutions
Temperature (°C) KCl 1 M KCl 10−1 M KCl 2 × 10−2 M KCl 10−2 M
14 90.63 10.25 2.193 1.121
15 92.52 10.48 2.243 1.147
16 94.41 10.72 2.294 1.173
17 96.31 10.95 2.345 1.199
18 98.22 11.19 2.397 1.225
19 100.14 11.43 2.449 1.251
20 102.07 11.67 2.501 1.278
21 104 11.97 2.553 1.305
22 105.94 12.15 2.606 1.332
23 107.89 12.39 2.659 1.359
24 109.84 12.64 2.712 1.386
25 111.8 12.88 2.765 1.413
26 113.77 13.13 2.819 1.441
27 115.74 13.37 2.873 1.468
28 13.62 2.927 1.496
29 13.87 2.981 1.524
30 14.12 3.036 1.552
31 14.37 3.091 1.581
32 14.62 3.146 1.609
33 14.88 3.201 1.638
34 15.13 3.256 1.667
35 15.39 3.312
36 15.64 3.368
TABLE 11.7
Average Temperature Coefficients of Standard Electrolyte Solutions Expressed as
%/°C of the Conductivity Value at 25°C
Temperature Range °C KCl 1 M KCl 0.1 M KCl 0.01 M Saturated NaCl
15–25 1.725 1.863 1.882 1.981
15–25–35 1.73 (15 °C–27°C) 1.906 1.937 (15°C–34°C) 2.041
25–35 1.762 (25°C–27°C) 1.978 1.997 (25°C–34°C) 2.101
TABLE 11.8
Conductivity (in μS/cm) Values of a 0.05% NaCl Solution
Temperature (°C) Conductivity Temperature (°C) Conductivity
0 540.4 27 1056.53
1 557.73 28 1077.54
2 575.2 29 1098.67
3 592.79 30 1119.92
4 610.53 31 1141.3
5 628.4 32 1162.8
6 646.4 33 1184.41
(Continued)

Conductivity (in μS/cm) Values of a 0.05% NaCl Solution
Temperature (°C) Conductivity Temperature (°C) Conductivity
7 664.55 34 1206.15
8 682.83 35 1228
9 701.26 36 1249.96
10 719.82 37 1272.03
11 738.53 38 1294.21
12 757.37 39 1316.49
13 776.36 40 1338.89
14 795.48 41 1361.38
15 814.74 42 1383.97
16 834.14 43 1406.66
17 853.68 44 1429.44
18 873.36 45 1452.32
19 893.18 46 1475.29
20 913.13 47 1498.34
21 933.22 48 1521.48
22 953.44 49 1544.71
23 973.8 50 1568.01
24 994.28
25 1014.9
26 1035.65
Experiment: Measurement of Soil Electrical Conductivity

Objectives
Define and understand the meanings of the term soil electrical conductivity (EC)
Principles
Salinity affects the physical and chemical characteristics of soil aggregates. These properties may
be influenced by parent materials, rainfall, organic materials, plants, and various manmade soil
amendments.
High salt concentrations, particularly those containing K+ and Na+, that have a weak charge and
large hydrated radii increase the swelling and dispersion of clay particles in soil. This effect decreases
with increased charge and decreased hydrated radii of base cations. Swelling and dispersion (puddling)
both cause a loss of pore space and permeability. This occurs due to clay particles expanding in physical
size and a loss of aggregation. The tendency to cause swelling and dispersion can be shown as follows:
Ca 2+ < Mg2+ < K + < Na +
Salinity may be measured in multiple ways. The EC of soil to determine relative salinity is an easy
and quick method. EC measures the ability of soil to conduct an electric charge across a distance. This
measurement is recorded as decisiemens per meter. Keep in mind that porosity, water content, tem-
perature, and cation exchange capacity also affect the EC of a soil. Specific base cation content, such
as Na+, may also be quantified to determine salinity using an atomic adsorption or mass spectrometer.
Requirements
Beaker, conductivity meter, deionized water, balance, pipette, spatula, soil sample
Method
1. Place five scoops of a soil sample into a beaker.
2. Add five scoops of deionized water to the beaker and stir. Mix the soil and water thoroughly.
About 30 strokes is adequate.
3. Let the solution sit for 5 minutes.
4. Rinse the probes with deionized water.
5. Place the probes into the soil–water paste.
6. Press the measurement button on the conductivity instrument.
7. The measurement is stable when the measure icon stops flashing.
8. Record the results displayed on the screen. The EC has been temperature-corrected by the
instrument.
9. To proceed with measuring another sample, repeat from step 1.
Results
Record the EC for all soil samples and sampling depths. Repeat readings for mulch and roadside soils.
Discussion
1. Compare the change of EC with the depth of your soil. What is the trend and why?
2. How do your EC values compare with mulch and roadside soil collections and with soils of
other groups?
SUGGESTED READING
“Conductivity Theory and Practice.” Radiometer Analytical SOS, 72 rue d’ Alsace, 69627, Villeurbanne Cedex,
France, p. 50.
Greenberg, A E., L S. Clesceri, and A D. Eaton, eds. Standard Methods for the Examination of Water and
Wastewaters, 18th ed., part 2540C, pp. 2–55. Washington, DC: American Public Health Association,
1992.
Hewitt, G. F. Chemical Engineering Division. Harwell, U.K: U.K.A.E.A Research Group Atomic Energy
Research Establishment, 1960.
OIML (Organisation Internationale de Métrologie Légale). “Recommendation No. 56 and The National
Institute of Standards and Technology (NIST).” Journal of Solution Chemistry 20, no.4 (1991).
Wagner, R. “Temperaturkorrekturfaktoren für die elektrische Leitfähigkeit von Wässern.” Zeitschrift für Wasser
und Abwasserforschung 2 (1980).
IMPORTANT LINKS
1. Conductivity meter: http://www.radiometer-analytical.com
2. http://www.eutech.nl
Glossary
α-helix A common motif in the secondary structure of proteins.
β-pleated sheet (β sheet) The second form of regular secondary structure in proteins.
Abbe condenser A lens that is specially designed to mount under the stage of a microscope and typically
moves in a vertical direction.
Absorbance Refers to the mathematical quantity of light.
Absorption Refers to the physical process of absorbing light.
Acid fast stain A staining property of the Mycobacterium species such that cells stained with hot carbol fuch-
sin will not decolorize with acid–alcohol.
Acidity Ability of a substance to react with a base.
Adsorption The process of interaction between a solute and the surface of an adsorbent.
Adsorption chromatography A chromatography technique in which we make one solvent immobile (by
adsorption on a solid support matrix) and another mobile.
Aerobe Microbes growing in the presence of oxygen.
Affinity chromatography A method of separating biochemical mixtures based on a highly specific interac-
tion such as the interaction between antigen and antibody, enzyme and substrate, or receptor and ligand.
Agarose gel electrophoresis Technique used for the separation of DNA fragments ranging from 50 base pairs
to several megabases (millions of bases) using a specialized apparatus.
Aggregate A clustered mass of individual cells that is solid, fluffy, or pelletized, which can clog the pores of
filters or other fermentation apparatus.
Alkalinity Alkalinity is the acid neutralizing capacity of solutes in a water sample, reported in milliequivalents
per liter and consists of the sum of titratable carbonate and noncarbonate chemical species in a filtered
water sample.
Alpha particle A positively charged particle that consists of two protons and two neutrons bound together.
Alternate current A type of current in which the direction of the current flowing in the circuit is constantly
reversed back and forth.
Amino acids A class of 20 hydrocarbon molecules that combine to form proteins in living things.
Amplifier A device for increasing the power of a signal.
Anaerobe Microbes growing in the absence of air or oxygen.
Analog A voltage or current signal that is a continuous function of the measured parameter.
Analog meter A scale and pointer meter capable of indicating a continuous range of values.
Analytical ultracentrifuge An ultracentrifuge that uses one of the three optical systems (schlieren, Rayleigh,
or absorption) for the accurate determination of sedimentation velocity or equilibrium.
Angular aperture The apparent angle of a lens aperture as seen from the focal point.
Angular velocity A vector quantity that specifies the angular speed of an object and the axis about which the
object is rotating.
Anion An ion in which the number of electrons is greater than the number of protons; the particle is a negative
ion, also called an anion.
Anode An electrode through which electric current flows into a polarized electrical device.
Antibodies A protein present in serum or other body fluids that combines specifically with antigens.
Antifoam agent A chemical added to the fermentation broth to reduce surface tension and counteract the
foaming (bubbles) caused by mixing, sparging, or stirring.
Antigen A substance, usually macromolecular, that induces specific antibody formation.
Ascending chromatography A chromatography technique in which the solvent is moving against the gravi-
tational force.
Aseptic Sterile atmosphere free from bacteria, viruses, and contaminants such as foreign DNA.
Atom A basic unit of matter that consists of a dense central nucleus surrounded by a cloud of negatively
charged electrons.
Atomic absorption spectroscopy (AAS) A spectroanalytical procedure for the qualitative and quantitative
determination of chemical elements using the absorption of optical radiation (light) by free atoms in a
gaseous state.
Attenuated Weakened (attenuated) bacteria and viruses are often used as vaccines; they can no longer produce
diseases, but they can still stimulate a strong immune response similar to natural microbes.
333
334 Glossary
Autoradiography A process by which radioactive materials, although not often exclusively incorporated into
cell structures, are located by exposure to a photographic emulsion forming a pattern on a film corre-
sponding to the location of the radioactive compounds within the cell.
Backflushing A column-switching technique in which a four-way valve placed between the injector and the
column allows the mobile phase to flow in either direction.
Bacterial capsule A compact layer of polysaccharide exterior to the cell wall in some bacteria.
Bacteriophage Viruses that infect bacteria; sometimes used as a vector.
Bandwidth Also known as spectral bandwidth or bandpass; relates to the physical size of the slit from which
light passes out from a monochromator.
Base pair Two bases on different strands of a nucleic acid that join together; in DNA, cytosine (C) always
pairs with guanine (G), and adenine (A) always links with thymine (T). In RNA molecules, adenine pairs
with uracil (U).
Baseline The line drawn by a data system when the only signal from the detector is from the mobile phase.
Batch culture Large-scale cell culture in which the cell inoculum is cultured to maximum density in a tank or
air-lift fermentor, harvested, and processed as a batch.
Beer–Lambert law (or Beer’s law) The linear relationship between the absorbance and concentration of an
absorbing species.
Beta particle High-speed electron or positron, especially one emitted in radioactive decay.
Binocular microscope A microscope with a head that has two eyepiece lenses.
Bioactivity Ability of a molecule to function correctly after it has been delivered to the active site of the
body (in vivo).
Bioavailability Measure of the true rate and the total amount of drug that reaches the target tissue after
administration.
Biologic A therapeutic agent derived from living things.
Biopharmaceutical A therapeutic product created through the genetic manipulation of living things, including
(but not limited to) proteins and monoclonal antibodies, peptides, and other molecules that are not chemi-
cally synthesized, along with gene therapies, cell therapies, and engineered tissues.
Bioprocessing Organisms or biologically derived macromolecules that are used to carry out enzymatic reac-
tions or manufacture products
Bioreactor A vessel capable of supporting a cell culture in which a biological transformation takes place (also
called a fermentor or reactor).
Bright field illumination Lighting that shines through a transparent specimen that appears dark against a
bright background; also called transmitted light illumination. It is the opposite of dark field illumination.
Broth The contents of a microbial bioreactor—cells, nutrients, waste, and so on.
Buffer Measure of the ability of a solution to resist pH change when a strong acid or base is added.
Capacitance The ability of a capacitor to store energy in an electric field.
Capillary gel electrophoresis Bundle of extremely narrow gel-filled tubes used to significantly speed up the
electrophoresis process of separating biological materials.
Carrier Term used most often in affinity chromatography, which refers to the support that is used to carry the
active ligand, usually by a covalent bond. It can also refer to the support in other chromatographic modes.
Carrier ampholytes Small, soluble molecules that are capable of acting as an acid or a base in standard 2D
gel electrophoresis.
Cascade effects A series of events that result from one initial cause.
Catabolites Waste products of catabolism by which organisms convert substances into excreted compounds.
Cathode An electrode through which an electric current flows out of a polarized electrical device.
Cation An ion in which the number of electrons is less than the number of protons; the particle is a positive
ion, also called a cation.
Cell constant The ratio of distance between conductance titration electrodes to the area of the electrodes. It is
measured from the determined resistance of a solution of known specific conductance.
Cell culture Cells taken from a living organism and grown under controlled conditions (in culture). It is a
method used to maintain cell lines or strains.
Cell density Measurement of the absorbance (also known as optical density or OD) of a suspension of cells
at 600 nanometers (OD 600 nanometers), which can give an indication of when cells are ready for
harvesting.
Cell line When cells from the first culture (taken from the organism) are used to make subsequent cultures, a
cell line is established.
Cell organelle A specialized subunit within a cell that has a specific function and is usually separately enclosed
within its own lipid bilayer.
Glossary 335
Centrifugal field A space in which centrifugal forces may be detected.

Centrifugation A process that involves the use of centrifugal force for the sedimentation of mixtures using a
centrifuge.
Centrifuge An apparatus, generally driven by an electric motor (some older models were spun by hand), that
puts an object in rotation around a fixed axis by applying a force perpendicular to the axis.
Chemostat A growth chamber that keeps a bacterial culture at a specific volume and rate of growth by limiting
the nutrient medium and removing the spent culture.
Chromatic aberration (CA) A type of distortion in which a lens fails to focus all colors to the same conver-
gence point. It occurs because lenses have different refractive indexes for different wavelengths of light
(dispersion of the lens). The refractive index decreases with increasing wavelength.
Chromatography A separation technique based on the differential distribution of constituents of a mixture
between two phases, one of which moves relative to the other.
Circular dichroism (CD) The differential absorption of left and right circularly polarized light.
Clone To duplicate something exactly, whether a gene or a whole organism; or, an organism that is a geneti-
cally identical copy of another organism.
Cloning vectors Methods of transferring desired genes to organisms that will be used to express them. Cloning
vectors are used to make recombinant organisms.
Column A tube that contains the stationary phase. The stationary phase differentially interacts with the sam-
ple’s constituent compounds as they are carried along in the mobile phase.
Column chromatography Any form of chromatography that uses a column to hold the stationary phase.
Compound microscope A microscope with more than one objective lens.
Concentration using a factor The concentration of a sample is determined by multiplying the absorbance
value by a specific factor.
Condenser A lens that concentrates light on a specimen and increases the resolution.
Conductance An expression of the ease with which an electric current flows through a substance.
Conductivity The ability of a material to conduct an electric current.
Conductivity meter A device to measure conductivity.
Contrast The difference in visual properties that makes an object (or its representation in an image) distin-
guishable from other objects and the background.
Countercurrent chromatography (CCC) or partition chromatography A category of chromatography
techniques.
Counting chamber A device used for counting the cell number.
Coverslip A thin square or circular piece of transparent glass or plastic placed over the specimen on a micro-
scope slide. It flattens out liquid samples and helps single-plane focusing.
cpm Counts per minute; used for measuring radioactivity.
Cryopreservation Maintenance of frozen cells, usually in liquid nitrogen.
Cyanobacteria A phylum of bacteria that obtain their energy through photosynthesis.
Cyclotrons Circular particle accelerators in which charged subatomic particles generated at a central source are
accelerated spirally outward in a plane perpendicular to a fixed magnetic field by an alternating electric field.
Cytoplasm The protoplasm of a cell outside the nucleus.
Dalton The unit of molecular weight equal to the weight of a hydrogen atom.
Dark field microscopy Technique used to enhance the contrast in unstained specimens.
Dark field plate Circular iris that sits on the base of the microscope above the light source and reflects the light
horizontally to the specimen, thereby achieving lateral illumination.
Decay The disintegration of the nucleus of an unstable nuclide by the spontaneous emission of charged par-
ticles, photons, or both.
Degassing Process of removing dissolved gas from the mobile phase before or during use.
Density A physical property of matter; each element or compound has a unique density associated with it.
Density gradient centrifugation Sedimentation based on a spatial variation in density over an area.
Descending chromatography A chromatography technique in which the solvent moves toward the gravita-
tional force.
Detector An electronic device that quantitatively discerns the presence of separated components as they elute
in a separation process.
DGGE (denaturing gradient gel electrophoresis) A technique for screening single nucleotide polymor-
phisms (SNPs).
Differential centrifugation Sedimentation based on differences in the size and density of particles.
Diffraction Various phenomena that occur when a wave encounters an obstacle.
Digital signal An output signal that represents the size of an input in the form of a series of discrete quantities.
336 Glossary
DNA (deoxyribonucleic acid) The nucleic acid based on deoxyribose (a sugar) and the nucleotides G, A, T,
and C. It occurs in a corkscrew-ladder shape; it is the primary component of chromosomes, which thus
carry the inheritable characteristics of life.
DNA fingerprinting Sequences of nucleic acids in specific areas (loci) on a DNA molecule are polymorphic,
which means that the genes in these locations may differ from person to person. The DNA fragments can
be cut from such sequences using restriction enzymes. Fragments from various samples can be analyzed
to determine whether they are from the same person. The technique of analyzing restriction fragment
length polymorphism (RFLP) is called DNA typing or DNA fingerprinting.
DNA vaccine A nucleic acid vaccine; genes coding for specific antigenic proteins are injected to produce those
antigens and trigger an immune response.
Double beam A configuration in which a light source is split in two. One beam illuminates the reference
cell holder and the other illuminates the sample. This configuration enables reference corrections to be
applied continually throughout a measurement and is commonly used when the sample and the reference
change over time, for example, in kinetics measurements.
Downstream processing Bioprocessing steps following fermentation or cell culture or both; a sequence of
separation and purification activities needed to obtain the required product at the necessary level of purity.
dpm Disintegrations per minute of an isotope in terms of efficiency.
Efficacy The ability of a substance (such as a protein therapeutic) to produce a desired clinical effect; its
strength and effectiveness.
Efficiency Measurement of the sharpness of an eluting band or peak; high efficiencies indicate low diffusion
and dispersion, which are major contributors to peak broadening.
Effluent The mobile phase after it has passed through the analytical column.
Electrode An electrical conductor used to make contact with a nonmetallic part of a circuit (e.g., a semicon-
ductor, an electrolyte, or a vacuum).
Electrolyte Substance that dissociates into ions when dissolved in a suitable medium or melted and thus form
conductors of electricity.
Electromagnetic field (EMF) Physical field produced by moving electrically charged objects.
Electromagnetic interference (EMI) Disturbance that affects an electrical circuit due to either electromag-
netic induction or electromagnetic radiation (EMR) emitted from an external source.
Electromagnetic radiation (EMR) Form of energy that exhibits wavelike behavior as it travels through space.
EMR has both electric and magnetic field components, which oscillate in phase perpendicular to each
other and perpendicular to the direction of energy propagation.
Electromagnetic technique Active method that uses an electromagnetic signal to detect variations in subsur-
face conductivity.
Electromotive force (emf) The maximum potential difference between two electrodes of a galvanic or
voltaic cell.
Electron A negatively charged subatomic particle. It can be either free (not attached to any atom) or bound to
the nucleus of an atom.
Electron beam A beam of electrons that illuminates the specimen and produces a magnified image.
Electron capture detector (ECD) A very sensitive detector used in GLC/GC for analysis of halogenated
compounds. As electronegative species pass through the detector, they capture low-energy electrons,
causing a decrease in cell current.
Electron microscope The type of microscope that uses electrons rather than light to create an image of the
target.
Electron spin resonance (ESR) A sophisticated spectroscopic technique that detects free radicals or inorganic
complexes in chemical and biological systems.
Electrophoresis Separation technique based on the motion of colloidal particles in an electric field.
ELISA (enzyme-linked immunosorbent assay) A test to measure the concentration of antigens or antibodies.
Eluant The mobile phase in a chromatographic separation.
Elution order The order in which components pass out of the column in the separation process.
Emission flame spectroscopy A flame photometry technique in which the solution containing the sample to
be analyzed is optically excited in an oxyhydrogen or oxyacetylene flame.
Emission spectrum The spectrum of frequencies of EMRs emitted by an element’s atoms or a compound’s
molecules when they return to a lower energy state.
Endogenous Growing or developing from a cell or organism, or arising from causes within an organism.
Endonuclease A restriction enzyme that breaks up nucleic acid molecules at specific sites along their length;
such enzymes are naturally produced by microorganisms as a defense against foreign nucleic acids.
Endoplasmic reticulum An extensive array of internal membranes in eukaryotes.
Glossary 337
Endotoxin A poison in the form of a fat–sugar complex (lipopolysaccharide) that forms a part of the cell wall
of some types of bacteria; it is released only when the cell is ruptured and can cause septic shock and
tissue damage.
Enzymes Functional proteins that catalyze biochemical reactions by causing or speeding up reactions without
getting changed in the process.
Epithelium (epithelial) The layers of cells between an organism and its tissues or organs and their environ-
ment (skin cells, inner linings of lungs or digestive organs, outer linings of kidneys, etc.).
Eukaryotic Organism whose cells contain complex structures enclosed within membranes.
European Pharmacopoeia (EP) Guidelines for product quality and measurement consistency.
Exclusion chromatography (size-exclusion chromatography) A chromatographic method in which mol-
ecules in a solution are separated by their size and, in some cases, molecular weight.
Exogenous Developing from outside; originating externally.
Express To translate a cell’s genetic information, which is stored in its DNA (gene), to a specific protein.
Expression system Organism chosen to manufacture (by expression) a protein of interest through recombi-
nant DNA technology.
Expression vector A way of delivering foreign genes to a host, creating a recombinant organism that will
express the desired protein.
Eyepiece Referred to as an ocular, the eyepiece is the lens nearest to your eye.
Eyepiece reticles Sometimes also called “eyepiece micrometers”; they are clear circular glass inserts with a
scale inscribed on them.
Fermentation The process by which microorganisms break down complex organic substances, generally in
the absence of oxygen, to produce alcohol and carbon dioxide.
Fermentor A bioreactor used to grow bacteria or yeasts in liquid culture.
Filar eyepiece A micrometer is a combination of a focusing eyepiece and a reticle, but it features a moveable
line rule.
Fine focus A knob used to fine-tune the focus of a specimen in conjunction with coarse focus.
Flame ionization detector (FID) A common type of detector used in gas chromatography (GC) and super-
critical fluid chromatography.
Flame photometer An instrument that uses a flame to evaporate a solvent, sublimate and atomize metal, and
then excite a valence electron to an upper energy state.
Flame photometric detector (FPD) Sulfur- and phosphorus-containing hydrocarbons burn in a flame, pro-
ducing chemiluminescent species that are monitored at selective wavelengths.
Floc A fluffy aggregate that resembles a woolly cloud.
Flow rate (F) The volumetric rate of flow of a mobile phase through an LC column.
Fluorescence The ability of a substance to emit light of a certain wavelength when it is activated by the light
of another wavelength.
Fluorescence detectors Fluorescence detectors project a specified wavelength of light into the sample, caus-
ing the component of interest to fluoresce; thus the emitted light is detected.
Fluorescence illumination A technique that provides cooler and brighter light than tungsten. This is beneficial
when viewing slides for long periods of time or observing live specimens, such as protozoa.
Fluorescence microscope An optical microscope used to study the properties of organic or inorganic sub-
stances using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection
and absorption.
Fluorescence spectroscopy A type of electromagnetic spectroscopy that analyzes fluorescence from a sample.
Fluorescent confocal microscopes Usually laser based; designed to provide high-resolution images without
interference from out-of-focus portions of the sample. They can also view deeper into a specimen when
compared with conventional epifluorescence microscopes.
Focal length A measure of how strongly the system converges (focuses) or diverges (defocuses) light.
Focal planes The plane that is perpendicular to the axis of a lens or mirror and passes through the focal point.
Focus The ability to achieve a clear image, which is typically achieved by moving either the eyepiece tubes
or the stage.
Gamma particle Denoted as γ; EMR of high frequency (very short wavelength) with energies in the range
104–107 eV.
Gas ionization The condition of being dissociated into ions (as by the action of heat, radiation, chemical reac-
tion, or electrical discharge); “the ionization of a gas.”
Gas–liquid chromatography (GLC) The mobile phase (or moving phase) is a carrier gas, usually an inert gas
such as helium or an unreactive gas such as nitrogen. The stationary phase is a microscopic layer of liquid
or polymer on an inert solid support inside a piece of glass or metal tubing called a column (a homage to
338 Glossary
the fractionating column used in distillation). It is also sometimes known as GC, vapor-phase chromatog-
raphy (VPC), or gas–liquid partition chromatography (GLPC). These alternative names, as well as their
respective abbreviations, are frequently found in scientific literature. Strictly speaking, GLPC is the most
correct terminology and is thus preferred by many authors.
Gas–solid chromatography (GSC) A subclassification of GC in which the mobile phase is a gas and the
stationary phase is a solid.
Geiger–Mueller counter An instrument that detects and measures the intensity of radiation, such as particles
from a radioactive material, consisting of a Geiger tube and associated electronic equipment.
Gene The unit of inheritance consisting of a sequence of DNA, occupying a specific position within the
genome. Three types of genes have been identified: (1) structural genes encoding particular proteins,
(2) regulatory genes controlling the expression of other genes, and (3) genes for transfer RNA (tRNA) or
ribosomal RNA (rRNA) instead of proteins.
Genetic engineering Altering the genetic structure of an organism (adding foreign genes, removing native
genes, or both) through technological means rather than traditional breeding.
Genotype The genetic composition of an organism (including expressed and nonexpressed genes), which may
not be readily apparent.
Germ cell The “sex cells” in higher animals and plants that carry only half of the organism’s genetic material
and can combine to develop into new living things.
Glass electrode A type of ion-selective electrode made of a doped glass membrane that is sensitive to a
specific ion. It is an important part of the instrumentation for chemical analysis and physicochemical
studies.
Glass probe Sensors or elements used to measure temperature by correlating the resistance. Mostly they are
consist of a length of fine coiled wire wrapped around a ceramic or glass core.
Glycosylation Adding one or more carbohydrate molecules onto a protein (a glycoprotein) after it has been
built by the ribosome; a posttranslational modification.
GMPs Good manufacturing practices required by FDA regulations.
Golgi body A cell organelle consisting of stacked membranes where posttranslational modifications of pro-
teins are performed; also called a Golgi apparatus.
Gram stain A method of differentiating bacterial species into two large groups (gram-positive and gram-
negative groups).
Growth hormone A protein produced in the pituitary gland to control cell growth.
Guard column A small column placed between the injector and the analytical column. It protects the analyti-
cal column against contamination by sample particulates and strongly retained species.
Hemocytometer A device originally designed for counting blood cells. Today, it is also used to count other
types of cells as well as other microscopic particles.
Hemoglobin The iron-containing oxygen transport metalloprotein in the red blood cells of all vertebrates with
the exception of the fish family Channichthyidae, as well as the tissues of some invertebrates.
Half-life The period of time it takes for the amount of a substance undergoing decay to decrease by half.
Halogen Provides the brightest illumination. The best microscopes have halogen lighting; stereo microscopes
with top lighting also use halogen lighting.
Hanging drop method One of the most common methods for demonstrating bacterial motility.
High-performance liquid chromatography (HPLC) This is sometimes referred to as high-pressure liquid
chromatography. A chromatographic technique that can separate a mixture of compounds and is used
in biochemistry and analytical chemistry to identify, quantify, and purify the individual components
of a mixture.
High-performance thin-layer chromatography (HPTLC) An enhanced form of thin-layer chromatography
(TLC). A number of enhancements can be made to the basic method of TLC to automate the different
steps, increase the resolution achieved, and allow more accurate quantitative measurements.
Hormone A protein released by an endocrine gland to travel in the blood and act on tissues at another location
in the body.
Huygenian eyepiece Eyepiece consisting of two plano-convex lenses positioned with both convex lenses fac-
ing toward the object.
Hybridoma An immortalized cell line (usually derived by fusing β-lymphocyte cells with myeloma tumor
cells) that secretes desirable antibodies.
Illumination system The light source on light microscopes; it is typically mounted under the stage.
Image An artifact, for example, a two-dimensional picture, that has a similar appearance to some subject, usu-
ally a physical object or a person.
Glossary 339
Immersion oil A special oil used with the 100× objective in order to concentrate light rays and increase the
resolution of an image.
Immortalize To alter cells (either chemically or genetically) so that they can reproduce indefinitely.
Immunoelectrophoresis A method for the separation and characterization of proteins based on electrophore-
sis and reaction with antibodies.
Immunofluorescence A technique used for light microscopy with a fluorescence microscope; used primarily
on biological samples.
In vitro Performed in the laboratory rather than in a living organism (in vivo).
In vivo In the body; in a living organism.
Incident ray A ray of light that strikes a surface. The angle between this ray and the perpendicular or normal
to the surface is the angle of incidence.
Infrared (IR) spectroscopy A type of spectroscopy that deals with the IR region of the electromagnetic spec-
trum, that is, light with a longer wavelength and lower frequency than visible light.
Injector A mechanism for accurately injecting a predetermined amount of sample into the mobile phase
stream.
Inlet The initial part of a column where the solvent and the sample enter.
Inoculate To introduce cells into a culture medium.
Inoculum Material (usually cells) introduced into a culture medium.
Interference A phenomenon in which two waves superpose to form a resultant wave of greater or lower
amplitude.
Interference microscope Uses two separate light beams with much greater lateral separation than those used
in phase contrast microscopy or in differential interference microscopy (DIC).
Interferon A cytokine that inhibits virus reproduction.
Ion An atom or a group of atoms in which the number of electrons is different from the number of protons.
Ion chamber A gas-filled enclosure containing positive and negative electrodes that measures the amount of
radiation passing through the enclosure according to the degree of ionization caused by the radiation.
Ion-exchange chromatography (or ion chromatography) A process that allows the separation of ions and
polar molecules based on their charge.
Ionization (or ionizing) radiation Radiation composed of particles that individually have sufficient energy
(or the ability to liberate sufficient energy) to remove an electron from an atom or molecule.
Iris diaphragm A diaphragm found on high-power microscopes under the stage; the diaphragm is typically a
five-hole disk; each hole has a different diameter.
Isoelectric focusing Protein separation technique in which a mixture of protein molecules is resolved into its
components by subjecting the mixture to an electric field in a supporting gel having a previously estab-
lished pH gradient.
Isocratic Constant-composition mobile phase used in liquid chromatography.
Isopycnic centrifugation The word “isopycnic” means “equal density.” It is also known as density gradient
centrifugation or equilibrium sedimentation. It is a technique used to separate molecules on the basis of
buoyant density.
Isotachophoresis (ITP) A nonlinear electrophoretic technique used in the separation of a variety of ionic
compounds ranging from small molecules, like metal ions, to large molecules, like proteins.
Isotope A chemical element with the same atomic number as another element (i.e., the same number of nuclear
protons) but a different atomic mass (i.e., a different number of nuclear neutrons).
Kilodalton (kDA) Unified atomic mass unit (also known as amu; symbol: u) or dalton (symbol: Da) that is
used for indicating mass on an atomic or molecular scale.
Kinetic measurements The absorbance of a sample at a given wavelength is measured over a specified time.
The change in absorbance and slope of this plot provides details about the rate of reaction.
Lens Standard achromatic lenses help to prevent color distortion.
Ligase An enzyme that causes fragments of DNA or RNA to link together; used with restriction enzymes to
create recombinant DNA.
Light-emitting diode (LED) Produces light at a single wavelength without the need for a monochromator.
Lamp life is almost infinite and LED sources are stable with little variation in bandwidth, making them
an attractive, low-cost solution for simple applications.
Light microscopes Any microscope that uses a source of light to create an image of the specimen; essentially
includes all compound and stereo microscopes.
Linear accelerator (LINAC) An apparatus for accelerating charged subatomic particles; used in radiotherapy,
physics research, and the production of radionuclides.
340 Glossary
Linearity A measurement process that ensures accurate quantitation.

London dispersion forces (LDFs) Forces named after the German–American physicist Fritz London; they
are weak intermolecular forces that arise from the interactive forces between instantaneous multipoles in
molecules without permanent multipole moments.
Lymphocytes White blood cells that produce antibodies.
Lysosomes Cell organelles containing enzymes; responsible for degrading proteins and other materials
ingested by the cell.
Macrokinetics Movement of whole cells and their media within a bioreactor.
Magnification The essence of a microscope is its ability to magnify a specimen.
Mechanical stage A flat mechanism that sits on top of the stage and allows the viewer to move a specimen
through small distances, a task that is otherwise difficult at high magnifications.
Media A (usually sterile) preparation made for the growth, storage, maintenance, or transport of microorgan-
isms or other cells.
Membrane Any thin sheet or layer.
Metabolites Chemical by-products of metabolism, which is the chemical process of life.
Microanalysis The chemical identification and quantitative analysis of very small amounts of chemical sub-
stances (generally less than 10 mg or 1 mL) or very small surfaces of materials (generally less than 1 cm2).
Microbiology The study of microscopic life, such as bacteria, viruses, and yeast.
Microbore A column with a smaller-than-usual internal diameter (<2 mm) used in HPLC.
Microcarrier A microscopic particle (often, a 200-μm polymer bead) that supports cell attachment and growth
in a suspension culture.
Microencapsulated Surrounded by a thin, protective layer of biodegradable substance referred to as a microsphere.
Microheterogeneity Slight differences in the amino acid sequence of a protein.
Microinjection Manually using tiny needles to inject microscopic material (such as DNA) directly into cells
or cell nuclei; computer screens provide a magnified view.
Microkinetics Movement of chemicals into, out of, and within a cell.
Micrometer Also called a micron; it is the metric linear measurement used in microscopy. There are 1000
microns in a millimeter.
Microorganism A microbe; a living thing too small to be seen by the naked eye.
Microscope An instrument used to see objects that are too small to be seen by the naked human eye. The sci-
ence of investigating small objects using such an instrument is called microscopy.
Microtubules Cellular organelles common in microorganisms; they are thin tubes that make structures
involved in cellular movement.
Mirror An instrument that allows you to direct ambient light up through the hole in the stage of a microscope
and illuminate a specimen.
Mitochondria Cell organelles; seat of respiration and electron transport. Often referred to as the powerhouse
of a cell.
Mobile phase A solvent that moves the solute through the column.
Molecule The result of two or more atoms combining by chemical bonding.
Monoclonal antibody (MAb) A highly specific, purified antibody that recognizes only a single antigen.
Monocular microscope A compound microscope with a single eyepiece.
Multicellular Organisms comprising more than one cell; they often contain billions of cells, arranged in vari-
ous organs, tissues, and systems.
Multiwavelength measurement Sample absorbance is recorded at multiple wavelengths.
Mutagen An agent (chemicals, radiation) that causes mutations in DNA.
Mutation A permanent change in DNA sequence or chromosomal structure.
Mycoplasma A genus of bacteria that lack a cell wall. Without a cell wall, they are unaffected by many com-
mon antibiotics.
Myeloma Lymphocytic cancer; a malignancy normally found in bone marrow.
Myoglobin An iron- and oxygen-binding protein found in the muscle tissue of vertebrates in general and in
almost all mammals.
Normal-phase chromatography A mode of chromatography carried out with a polar stationary phase and a
nonpolar mobile phase.
Nuclear magnetic resonance (NMR) A physical phenomenon in which magnetic nuclei in a magnetic field
absorb and reemit EMR.
Nuclear reactor A device used to generate power in which nuclear fission takes place as a controlled chain
reaction, producing heat energy that is generally used to drive turbines and provide electric power.
Nuclear reactors are used as a source of power in large power grids and in submarines.
Glossary 341
Nucleic acids DNA or RNA: long, chain-like molecules comprising nucleotides.

Nucleotides Molecules comprising a nitrogen-rich base, phosphoric acid, and a sugar. The bases can be ade-
nine (A), cytosine (C), guanine (G), thymine (T), or uracil (U).
Nucleus A specialized, usually spherical mass of protoplasm encased in a double membrane, and found in
most living eukaryotic cells, directing their growth, metabolism, and reproduction, and functioning in the
transmission of genetic characters.
Numerical aperture (NA) A measure of the diameter of the aperture compared to the focal length of a lens
and, ultimately, of the resolving power of a microscope.
Objective lens The lens closest to the specimen that first receives the rays from the specimen (the object) and
forms the image in the focal plane of the eyepiece.
Ocular meter An ocular micrometer serves as a scale or rule. This is simply a disk of glass on which equally
spaced divisions are etched. The rule may be divided into 50 subdivisions or, more rarely, into 100
subdivisions.
Oncogene A gene that, when expressed as a protein, can lead a cell to become cancerous, usually by removing
the normal constraints on its growth.
Organelle A structurally discrete component that performs a certain function inside a eukaryotic cell.
Organism A single, autonomous living thing. Bacteria and yeasts are organisms, whereas mammalian and
insect cells used in a culture are not.
Oxygen electrode Also referred to as the Clark electrode, it measures oxygen on a catalytic platinum surface
using the net reaction.
Paper chromatography A technique that involves placing a small dot or line of a sample solution on a strip
of chromatography paper. The paper is placed in a jar containing a shallow layer of solvent and the jar is
sealed. As the solvent rises through the paper, it meets the sample mixture, which starts to travel up the
paper with the solvent. This paper is made of cellulose, a polar substance, and the compounds within the
mixture travel farther if they are nonpolar. Substances that are more polar bond with the cellulose paper
more quickly and, therefore, they do not travel as far.
Particle size (dp) The average particle size of the packing in an LC column.
Partition chromatography A method of chromatography using the partition of the solutes between two liquid
phases (the original solvent and the film of solvent on the adsorption column).
Partition coefficient (Kd) A measure of how a compound distributes itself between two immiscible solvent
phases.
Peak When the detector registers the presence of a compound, the normal baseline signal it sends to the data
system changes. This results in a deflection from the baseline called a peak.
Peak identification Performed by comparing the sample chromatogram to a chromatogram of a standard solu-
tion separated under the same conditions.
Peak shape The profile of a chromatographic peak.
Peptides Proteins consisting of fewer than 40 amino acids.
pH meter An electronic instrument used for measuring the pH (acidity or alkalinity) of a liquid (although
special probes are sometimes used to measure the pH of semisolid substances).
Phase contrast A contrast-enhancing microscopic technique that shifts the light phase wavelength, thereby
causing the light deviated by a specimen to appear dark on a light background.
Phenotype The physical appearance of an organism as distinguished from its genetic makeup.
Photocell A resistor whose resistance decreases with increasing incident light intensity; it can also be referred
to as a photoconductor.
Photodiode array (PDA) PDA detectors are UV/Vis detectors that record the absorbance of light at many
different wavelengths simultaneously.
Photomultiplier An electronic sensing device used to detect the electromagnetic energy of a wide range of
frequencies and intensity levels.
Photon An elementary particle, the quantum of an electromagnetic interaction, and the basic unit of light and
all other forms of EMR.
Pilot plant A medium-scale bioprocessing facility used as an intermediate in scaling up processes from the
laboratory to commercial production.
Plasmid Hereditary material that is not part of a chromosome; plasmids are circular and self-replicating and
are found in the cytoplasm of cells (naturally in bacteria and some yeast). They can be used as vectors for
introducing up to 10,000 base pairs of foreign DNA into recipient cells.
Polyacrylamide gel electrophoresis (PAGE or SDS PAGE) Electrophoresis in which a polyacrylamide gel
is used as the diffusion medium.
Polymerase An enzyme that catalyzes the production of nucleic acid molecules.
342 Glossary
Polymerase chain reaction (PCR) A method of duplicating genes exponentially.

Posttranslational modifications Protein processing done by Golgi bodies after proteins are constructed by
ribosomes.
Potentiometer An instrument for measuring the potential (voltage) in a circuit.
Preparative chromatography The process of using liquid chromatography to isolate a sufficient amount of
material for other experimental or functional purposes.
Prions Resembling viruses, these pathogens comprise only protein, with no detectable nucleic acid.
Prokaryotes Simple organisms with no cell organelles.
Proteins Macromolecules whose structures are coded in an organism’s DNA. Each is a chain of more than 40
amino acids folded back upon itself in a particular way.
Proteolytic Capable of lysing (denaturing or breaking down) proteins.
Pulsed-field gel electrophoresis (PGFE) Electrophoresis in which the direction of the electric field is changed
periodically.
Radioactive decay Spontaneous decomposition of the nuclei of atoms of radioactive substances; measured as
the proportion of atoms in a radionuclide that decompose per unit of time, usually stated as the half-life
of that particular isotope.
Radioactive fallout Dissemination of radioactive substances through the atmosphere and deposition on the
environment generally; causes radiation injury.
Radioactive isotope One of two or more atoms with the same number of protons but different number of
neutrons with a nuclear composition.
Radioactive tracer A radioactive isotope that replaces a stable chemical element in a compound and can thus
be followed or tracked through one or more reactions or systems; generally an isotope that is introduced
into and followed through the body.
Radioimmunoassay (RIA) A technique in radiology used to determine the concentration of an antigen, anti-
body, or other protein in the serum. The technique involves the injection of a known amount of a radio-
actively labeled substance that reacts with the protein in question.
Radioisotopes A version of a chemical element that has an unstable nucleus and emits radiation during its
decay to a stable form.
Radiotherapy The treatment of diseases with ionizing radiation.
Ramsden eyepiece Comprises two plano-convex lenses with the same focal length and glass placed less
than one focal length apart; a design created by the astronomical and scientific instrument maker Jesse
Ramsden in 1782.
Recombinant Containing genetic material from another organism. Genetically altered microorganisms are
usually referred to as recombinant, whereas plants and animals so modified are called transgenic.
Reflection The change in direction of a wave front at an interface between two different media so that the wave
front returns into the medium from which it originated.
Refraction The change in direction of a wave due to a change in its speed. It is essentially a surface phenomenon.
Refractive index Expressed as the ratio of the speed of light in a vacuum relative to that in the considered
medium.
Reference electrode An electrode that has a stable and well-known electrode potential.
Relative centrifugal force (RCF) The measurement of force applied to a sample within a centrifuge is tradi-
tionally known as RCF.
Resistance The property of a component that restricts the flow of an electric current.
Resolution The ability of a lens to distinguish the fine details of the specimens being viewed.
Resolving power The ability of an imaging device to separate (i.e., to see as distinct) points of an object that
are located at a small angular distance.
Restriction enzyme Bacterial enzyme that cuts DNA molecules at the location of particular sequences of
base pairs.
Retina A translucent filmy piece of tissue lining the back of the eyeball.
Reversed-phase chromatography (RPC) The most common HPLC mode; uses hydrophobic packings such
as octadecyl or octysilane phases bonded to silica or neutral polymeric beads. The mobile phase used is
usually water and a water-miscible organic solvent such as methanol or acetonitrile.
Rf (value retention factor) Defined as the ratio of the distance traveled by the substance to the distance trav-
eled by the solvent.
Ribosome Cell organelles that translate RNA to build proteins.
RNA Ribonucleic acid; similar to DNA but is based on ribose sugar and has the base uracil (U) in place of thy-
mine (T). Various forms of RNA are found, such as messenger RNA (mRNA), tRNA, and rRNA. Most
RNA molecules are single-stranded molecules, although they can form double-stranded units.
Glossary 343
Roller bottle A container with large growth surfaces in which cells can be grown in a confluent monolayer.
The bottles are rotated or agitated to keep the cells in suspension, but they require extensive handling,
labor, and media.
Rotor Rotating part of a mechanical device.
Sample capacity The amount of sample that can be injected onto an LC column without overloading it.
Sampling rate The frequency with which a detector checks the flow cell. Sampling rate is often called the
time constant.
Saturated calomel electrode (SCE) A reference electrode based on the reaction between elemental mercury
and mercury chloride.
Scale up To take a biopharmaceutical manufacturing process from the laboratory scale to a scale at which it
is commercially feasible.
Scanning electron microscope (SEM) A type of electron microscope that scans the surface of a sample using
a beam of electrons. These systems are characterized by producing high-resolution images with a large
depth of field and are capable of reaching extremely high magnifications.
Scintillation counter A measuring instrument for counting individual ionizing events.
Seed stock The initial inoculum, or the cells placed in growth medium from which other cells will grow.
Sensitivity The sensitivity setting is the line between normal background noise and a true peak.
Sequence The precise order of bases in a nucleic acid or amino acids in a protein.
Serum The watery portion of an animal or plant fluid (such as blood) remaining after coagulation. When
cheese is made, whey is the milk serum that is left behind.
Shorter wavelength Electromagnetic radiation with shorter wavelengths may be called “millimeter waves”,
terahertz radiation or even T-rays.
Single beam All light passes through the sample holder. Measurements are made by placing a reference in the
sample holder, which is measured to standardize the instrument. This reference value is subtracted from
subsequent sample measurements to remove effects from the solvent and the cell.
Single wavelength measurement Also known as a fixed wavelength measurement. This is the simplest appli-
cation of a spectrophotometer and allows the measurement of absorbance or transmittance (percentage
of transmission [%T]) at a specified wavelength.
SIP Steam in place or sterilize in place.
Slide A flat, rectangular glass plate on which a specimen may be placed.
Somatic cell In higher organisms, a cell that (unlike germ cells) carries the full genetic makeup of an organism.
Sparge To spray. A sparger is the component of a fermentor that sprays air into the broth.
Spherical aberration An optical effect observed in an optical device (lens, mirror, etc.) that occurs due to the
increased refraction of light rays when they strike a lens or the reflection of light rays when they strike a
mirror near its edge in comparison with light rays that strike nearer to the center.
Split beam Light from a source is split into two paths with approximately 70% of the energy from the mono-
chromator passing through the sample and the rest going to a separate feedback detector. This corrects
variations in energy and improves measurement stability and reproducibility.
Stable isotope One that does not transmute into another element with emission of corpuscular or EMRs.
Stage The platform on which slides and specimens are placed for viewing.
Stage micrometer Simply a microscope slide with a scale etched on the surface.
Staining An auxiliary technique used in microscopy to enhance contrast in a microscopic image.
Stationary phase A solid, or a liquid supported on a solid.
Strain A population of cells all descended from a single cell.
Substage The part of a microscope below the stage, including the illumination system.
Substrate Reactive material; the substance on which an enzyme acts.
Substratum The solid surface on which cells move or grow.
Supernatant Material floating on the surface of a liquid mixture (often the liquid component that has the low-
est density).
Support The solid particles in a column. The support can be naked, coated, or have a chemically bonded phase
in HPLC.
Surfactant Any substance that changes the nature of a surface, such as lowering the surface tension of water.
Suspension Particles floating in (not necessarily on) a liquid medium, or the mix of particles and the
liquid itself.
Symbiotic Living together for mutual benefit.
Synthesis Creating products through chemical and enzymatic reactions.
Tailing A peak with an asymmetrical factor greater than 1. An asymmetrical peak is the result of a component
that is excessively retarded in eluting.
344 Glossary
Teflon membranes They are chemically stable and inert, and suitable for applications involving aggressive
organic solvents, strong acids, and alkalis.
Thermal conductivity detector (TCD) A filament’s temperature increases as analytes present in the carrier
gas pass over it, causing its resistance to increase.
Thin-layer chromatography (TLC) Involves a stationary phase of a thin layer of an adsorbent, such as silica
gel, alumina, or cellulose, on a flat, inert substrate. Compared to paper chromatography, this technique
has the advantages of faster runs, better separations, and the choice between different adsorbents. For
even better resolution and to allow for quantification, high-performance TLC can be used.
Tissue culture Growing plant or animal tissues outside the body, as in a nutrient medium in a laboratory;
similar to cell culture, but cells are maintained in their structured tissue form.
Titer A measured sample. (Drawing a measured, representative sample from a larger amount is to titrate.)
Total dissolved solids (TDS) A measure of the combined content of all inorganic and organic substances con-
tained in a liquid in molecular, ionized, microgranular (colloidal sol), or suspended form.
Tracer carbon dating A process in which a naturally radioactive carbon isotope with an atomic mass of 14
and a half-life of 5730 years is used in determining the age of ancient organic, geologic, or archeological
specimens.
Transgenics The alteration of plant or animal DNA so that it contains a gene from another organism.
Translation The process by which information transferred from DNA by RNA specifies the sequence of
amino acids in a polypeptide (protein) chain.
Transmission electron microscope (TEM) A microscope in which a beam of electrons is transmitted through
an ultrathin specimen, which interacts with the specimen as it passes through.
Transmittance The fraction of incident light (or other EMR) at a specified wavelength that passes through a
sample.
Trypsin, tryptic digestion Trypsin, from the pancreas, is an enzyme that helps in the digestion of proteins.
A tryptic digest is accomplished simply by taking a pure, whole protein and subjecting it to certain enzy-
matic activity that breaks down the protein into specific peptides and or peptide chains.
Tryptic fragment analysis Quantitating the resultant fragments caused by tryptic digestion.
Tungsten The least expensive source of illumination. It is hotter but less bright than other kinds of illumination.
Turbidostat A variation of a chemostat; a turbidostat is designed to keep organisms at a constant concentra-
tion. A turbidity sensor measures the concentration of organisms in a culture and adds additional medium
when a preset value is exceeded.
Turbulent flow field The state that results from mixing the contents of a fermentor or bioreactor to provide
oxygen to the cells. This must be balanced against the shear that causes cell damage and death.
Two-dimensional chromatography A type of chromatographic technique in which the injected sample is
separated by passing it through two different separation stages.
Two-dimensional difference gel electrophoresis A method of comparing two or more samples on the same
two-dimensional gel electrophoresis gel.
Two-dimensional gel electrophoresis Electrophoresis in which a second perpendicular electrophoretic trans-
port is performed on the separate components resulting from the first electrophoresis. This technique is
usually performed on polyacrylamide gels.
Ultracentrifuge A centrifuge optimized for spinning a rotor at very high speeds; capable of generating accel-
erations as high as 2,000,000 g.
Ultraviolet (UV) Portion of the electromagnetic spectrum below blue light (380 nm).
UV/Vis detector The tunable- or variable-wavelength UV/Vis detector is the most popular form of detector.
For methods involving organic compounds in aqueous mobile phases, the UV/Vis detector takes advan-
tage of compounds’ varying absorptivities of UV and visible light.
Unicellular Composed of only a single cell.
Vaccine Preparation of an antigen from a killed or modified organism that elicits an immune response (the
production of antibodies) to protect a person or animal from a disease-causing agent.
Vacuolation Term used in cell and tissue culture. Excess fluid, debris (aggregates), or gas (from sparging) can
form inside a cell vacuole. A vacuole is a cavity within a cell that can be relatively clear and filled with
fluid, gas (as in a number of blue-green algae), or food (as in protozoa).
Van der Waals forces Refers to forces including attractions between atoms, molecules, and surfaces, as well
as other intermolecular forces.
Vector The plasmid, virus, or some other vehicle used to carry a DNA sequence into the cell of another species.
Velocity Speed in a given direction.
Vessel jacket A temperature control method consisting of a double wall outside the main vessel wall. Liquid
or steam flows through the jacket to heat (or cool) the fluid in the vessel.
Glossary 345
Viability Life and health; the ability to grow and reproduce. A measure of the proportion of live cells in a
population.
Virus The simplest form of life. It comprises RNA or DNA wrapped in a shell of protein; a small infectious
agent that can replicate only inside the living cells of organisms.
Viscosity A measure of the resistance of a fluid, which is being deformed by either shear or tensile stress.
Visible light Electromagnetic radiation that is visible to the human eye and is responsible for the sense
of sight.
Voltage Electric potential energy per unit charge; measured in joules per coulomb (unit is volts).
Water for injection Very pure water that is suitable for medical uses.
Wavelength scanning Also known as spectral scanning or wave scan measurements.
Xenon Xenon flash lamps provide high-energy light sources with short warm-up times and long lamp lives.
They measure in both the UV and visible regions of the electromagnetic spectrum from 190–1100
nanometers.
X-radiation (x-ray) A form of EMR with a wavelength in the range of 0.01–10 nanometers, corresponding
to frequencies in the range of 30 PHz to 30 EHz (3 × 1016 to 3 × 1019 Hz) and energies in the range of
120 eV to 120 keV. They are shorter in wavelength than UV rays and longer than gamma rays.
X-ray diffraction (XRD) A versatile, nondestructive technique that reveals detailed information about the
chemical composition and crystallographic structure of natural and manufactured materials.
Yeast A single-celled fungus that feeds on sugar and is used to make bread rise and for alcoholic fermentation.
FIGURE 1.4 Microscopic view under a compound microscope of the cyanobacterium Anabaena variabilis,
showing cell differentiation.
FIGURE 1.7 Microscopic observation of a mutant A. variabilis under high resolution.

(a) (b)
FIGURE 1.10 Photomicrograph of A. cylindrica showing the position of heterocysts in between the vegetative cells: (a) bright field and (b) fluorescent photomicrographs.
(a)
(b)
(c)
FIGURE 1.13 Figure showing (a) sporangium and sporangiospore in a slime mold viewed under a com-
pound microscope, (b) fungal conidia of Fusarium and Alternaria under oil immersion, and (c) electron
micrograph of phycovirus attached to cyanobacteria and different types of phycoviruses.
Control S1P S1P+Et-OH
Lyso-tracker
Auramine
Merged
FIGURE 1.16 Figure showing (a) fluorescence in situ hybridization of Betaproteobacteria and (b) immunofluorescence detection of sphingosine 1-phosphate (S1P) in
tuberculosis. (Courtesy of Pernthaler et al., 2008, Proceedings of the National Academy of Sciences 105, 7052–7057 10.1073/pnas.0711303105.)
Frequency (Hz)
Wavelength
0.1 Å
Gamma rays
1019
{10.1Ånm
1018
X-rays
1 nm
400 nm
1017
10 nm
Electromagnetic
1016
Ultraviolet
spectrum
500 nm
100 nm
1015
Visible
Near IR {1000
1 μm
nm
600 nm
1014
Infrared 10 μm
1013
700 nm
Thermal IR 100 μm
1012
Far IR μm
1000 MHz {1000
1 mm
1011
UHF Microwaves 1 cm
500 MHz 1010 Radar
10 cm
109
1m
VHF
7-13 108 Radio, TV
100 MHz FM 10 m
VHF 107
2-6 100 m
50 MHz
106 AM
1000 m
Long waves
FIGURE 5.1 EM spectrum.

1 2 3 4 5 6 1 2 3 4 5 6 7
(a) (b)
M 1 2 3 4 5 6
M 1 2 3 4 5 6 kDa
kDa
205 205
116
116 97.4
97.4
46
46
43
43
29
29
(c) (d)
FIGURE 7.6 Top: Protein profile of different fractions of metabolic antigens of Aspergillus fumi-
gates obtained by size-exclusion chromatography on 12% SDS-PAGE stained with Coomassie blue:
(a) Arrow shows 70–72 kDa protein doublet bands and (b) arrow shows 18 kDa purified protein.
(c) Protein profile of metabolic antigens of Aspergillus fumigates precipitated by graded saturation of ammo-

nium sulfate. (d) Identification of immunogenic proteins by Western blotting. Lane M, molecular weight
marker; 1-, 2-, 3-, 4-, and 5-proteins precipitated at 20%, 40%, 60%, 80%, and 100% saturation of ammonium
sulfate in culture filtrate, respectively.
M 1 2 3 4 5 6
kDa
205
116
70 kDa
97.4
66
45
29
A 18 kDa
FIGURE 7.15 (b) Electrophoretic protein profile of a fungus Aspergillus fumigates with known-molecular-
weight marker protein.
FIGURE 8.12 Computer-generated tertiary structures of crystallographic data of ferredoxin proteins FdxH1
and FDxH2 from the cyanobacterium Anabaena variabilis.
FIGURE 10.29 A laboratory-grade fermentor of capacity 2 L containing MRS broth.
FIGURE 10.30 A fermentor after 24 hours of incubation. The visible color difference in the media shows a
high cell density of S. thermophilus.
Biotechnology
Introduction to Instrumentation
in Life Sciences
Instrumentation is central to the study of physiology and genetics in living organisms,
especially at the molecular level. Numerous techniques have been developed to address
this in various biological disciplines, creating a need to understand the physical
principles involved in the operation of research instruments and the parameters required
in using them. Introduction to Instrumentation in Life Sciences fills this need
by addressing different aspects of tools that hold the keys to cutting-edge research and
innovative applications, from basic techniques to advanced instrumentation. The text
describes all topics so even beginners can easily understand the theoretical and
practical aspects.
Comprehensive chapters encompass well-defined methodology that describes the

instruments and their corresponding applications in different scientific fields. The book
covers optical and electron microscopy; micrometry, especially in microbial taxonomy;
pH meters and oxygen electrodes; chromatography for separation and purification of
products from complex mixtures; spectroscopic and spectrophotometric techniques to
determine structure and function of biomolecules; preparative and analytical centrifuga-
tion; electrophoretic techniques; x-ray microanalysis including crystallography;
applications of radioactivity, including autoradiography and radioimmunoassays;
and fermentation technology and subsequent separation of products of interest.
The book is designed to serve a wide range of students and researchers in diversified
fields of life sciences: pharmacy, biotechnology, microbiology, biochemistry, and environ-
mental sciences. It introduces different aspects of basic experimental methods and
instrumentation. The book is unique in its broad subject coverage, incorporating funda-
mental techniques as well as applications of modern molecular and proteomic tools that
are the basis for state-of-the-art research. The text emphasizes techniques encountered
both in practical classes and in high-throughput environments used in modern industry.
As a further aid to students, the authors provide well-illustrated diagrams to explain
the principles and theories behind the instruments described.
K14893
ISBN: 978-1-4665-1240-5
90000
9 781466 512405

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Introduction to

Boca Raton London New York

CRC Press is an imprint of the

© 2013 by Taylor & Francis Group, LLC

No claim to original U.S. Government works

International Standard Book Number-13: 978-1-4665-1241-2 (eBook - PDF)

and the CRC Press Web site at

Chapter 2 Micrometry ................................................................................................................ 37

2.4 Eyepiece Designs.............................................................................................. 39

Chapter 3 Electrochemical Techniques....................................................................................... 45

4.4 Paper Chromatography and Thin-Layer

4.13 Affinity Chromatography.................................................................................94

Chapter 5 Spectroscopy............................................................................................................. 115

5.7.3 Chemical Shifts................................................................................. 141

Chapter 6 Centrifugation........................................................................................................... 163

Chapter 7 Electrophoresis.......................................................................................................... 185

7.3 Working with the Electrophoresis Apparatus................................................ 189

Chapter 8 X-Ray Microanalysis.................................................................................................209

Chapter 9 Techniques with Radioisotopes................................................................................. 225

Chapter 10 Fermentation.............................................................................................................. 249

10.5.2 Anaerobic Fermentation.................................................................... 255

10.9.4 Chemicals........................................................................................... 283

Chapter 11 Conductivity Meters..................................................................................................307

1.2 MAGNIFICATION, RESOLUTION, AND CONTRAST

FIGURE 1.1 Image formation on the retina of the eye.

h´ F = Focal length of lens

F = Focal length of lens

1.3 LIGHT (BRIGHT FIELD) MICROSCOPY

Single lenses have two inherent defects:

Aperture iris Illumination

FIGURE 1.3 The student microscope.

Lens of the eye

Real image formed by

FIGURE 1.5 Schematic representation of the optical system of a compound microscope.

Unresolved Partially resolved Resolved

Dry objective Oil immersion

1.3.2 Contrast of a Microscope

Condenser Immersion oil

1.3.3 Uses of the Light (Bright Field) Microscope

1.3.4 Care of the Microscope

180° out of phase

1.4 DARK FIELD MICROSCOPE

FIGURE 1.15 Schematic representation of a phase microscope.

1.5 PHASE CONTRAST MICROSCOPE

1.6 INTERFERENCE MICROSCOPE

1.7 UV AND FLUORESCENCE MICROSCOPES

Control S1P S1P+Et-OH

Light source Reflector

350 400 450 500 550

Bacterial cell Fluorescent dye coated Bacterial cell combined with

FIGURE 1.18 Fluorescence staining technique and microscopy.

1.7.1 Uses of UV and Fluorescence Microscopes

1.8 ELECTRON MICROSCOPY

Light source Electron beam

Field condenser Condenser magnet

Substage condenser Condenser magnet

Eyepiece Project lens

1.8.1 Operation of TEM

a. Condenser lens coil system