Comprehensive Exam Syll Rev 2010 IITD

Syllabus for Comprehensive Examination
PAPER – I
Part – A : Fundamentals of Biochemical Engineering
- Units and dimensions.

- Stoichiometry and energetics of cell growth and product formation: Elemental
material balance for growth; Concepts of degree of reductance, Ys, Y∆ and YATP.
- Requirements of a fermentation media (qualitative treatment only).
- Monod growth kinetics; growth cycle phases for batch cultivation; Leudeking
and Piret model for product formation kinetics. Concept of maintenance energy.
- Deindoerfer’s classification of fermentations (qualitative treatment only).
- Thermal death kinetics of cells and spores
- Media sterilization: Concept of degree of sterility and decimal reduction time.
Batch sterilization.
Continuous sterilization (qualitative treatment only).
- Air sterilization (qualitative treatment only).
- Oxygen transfer in fermentations: dynamic gassing-out method for kLa
determination.
- Kinetics of enzyme catalyzed reactions: Michaelis-Menten equation; Lineweaver-
Burk plots; Eadie-Hofstee plots; Limitations of quasi-steady state assumption;
substrate inhibition kinetics; competitive, non-competitive and uncompetitive
inhibitions; effect of pH and temperature.
- Bioreactors:
Batch, fed-batch and continuous (CSTR and PFR) reactors.
Immobilized cell and immobilized enzyme reactors (qualitative treatment only).
Conditions for “wash-out” and maximum cell production in chemostat cultures.

- Principles of recovery operations:
Filtrations, centrifugation, solvent extraction, precipitation, adsorption,
chromatography, electrophoresis, membrane separations (qualitative treatment only).
Suggested references
1. “Biochemical Engineering Fundamentals” (second edition), J.E. Bailey and D.F.

Ollis, McGraw Hill Book Co, 1986.
2. “Biochemical Engineering” (second edition), S. Aiba, A.E. Humphrey and N.F.

Milles, Academic Press, 1971.
3. “Bioprocess Engineering: Basic Concepts”, M.L. Schuler and F. Kargi, Prentice

Hall, 1992.
Part B: Principles of Microbiology and Biochemistry
- Organization of procaryotic and eucaryotic cells.
- Structure and function of organelles (mitochondria, endoplasmic reticulum, golgi

bodies) of eucaryotic cells.
- Characteristic features of eubacteria, molds and yeasts.
- Energy transduction in microbes (fermentation, aerobic respiration and anaerobic

respiration).
- Basic metabolic pathways (Glycolysis, TCA cycle, Glyoxalate cycle, Pentose

Phosphate pathway).
- Mutations: Types of mutations, Isolation of mutants, auxotrophic mutants.
- Nutrition of microorganisms – C, N and S compounds, growth factors.
- Microbial Growth – Measurement techniques; growth cycle; effect of environment

on microbial growth.
- Control of microorganisms : heat sterilization, filter sterilization, antiseptics &

chemotherapeutic agents.
- Non-covalent interactions in biomolecular assembly
- Carbohydrates: structure and function (monosaccharides, disaccharides and common

polysaccharides – starch and cellulose).
- Proteins – primary, secondary, tertiary & quaternary structures; glycoproteins.
- Structure and function of nucleotides, DNA and RNAs.
Suggested Books:
1. Brock Biology of Microorganism, 10th Ed. by M.T. Madigan, J.M. Martinko and J.
Parker, Printice Hall, 2003
2. Biochemistry, 5th Ed., by J.M. Berg, J.L. Tymoczko and L. Stryer, W.H. Freeman &
Company, 2002.
3. Microbiology, 4th Ed., by L.M. Prescott, J.P. Harley and D.A. Klein, McGraw-Hill,
1999.
Paper – II
Biochemical Engineering
- Stoichiometry and energetics of cell growth and product formation
- Principles of fermentation media design
- Microbial growth models (structured and unstructured)
- Classification of fermentations
- Media and air sterilization
- Oxygen transfer in fermentations
- Kinetics of enzyme catalyzed reactions
- Bioreactors: Batch, fed-batch and continuous reactors; Immobilized cell and

immobilized enzyme reactors.
- Bioreactor scale-up
- Filtration: constant rate and constant pressure filtration
- Centrifugation: batch and continuous; “Σ” concept; types of centrifuges; scale-up.
- Batch and multistage solvent extraction; Craig extraction; differential extraction.
- Protein precipitation; scale-up.
- Adsorption and elution chromatography
- Electrophoresis and electrodialysis
- Ultrafiltration and its applications
Suggested references
1. “Biochemical Engineering Fundamentals” (second edition), J.E. Bailey and D.F.

Ollis, McGraw Hill Book Co, 1986.
2. “Biochemical Engineering” (second edition), S. Aiba, A.E. Humphrey and N.F.

Milles, Academic Press, 1971.
3. “Bioprocess Engineering: Basic Concepts”, M.L. Schuler and F. Kargi, Prentice

Hall, 1992.
4. “Bioseparations – Downstream Processing for Biotechnology” Belter,
P.A., Cussler, E.L., and Hu W.S., , John Wiley and Sons, New York
Paper-II: Advanced Biochemistry and Molecular Biology
- Structure and function of biological membranes; transport of nutrients.
- Mechanism of enzyme action (Lysozyme, carboxypeptidase A)
- Enzyme kinetics (Michaelis Menten Model)
- Allosteric regulation of enzyme function; Hemoglobin, Phosphofructokinase,

Aspartate transcarbomylase.
- Covalently regulated enzymes (Glycogen metabolism)
- Common regulatory mechanisms in the biosynthesis of amino acids.
- DNA: Replication and its control (with special emphasis on E.coli)
- RNA: Synthesis and gene control in prokaryotes (lac, ara and trp operons)
- RNA: Synthesis and processing in eukaryotes
- Prokaryotic translation and its control; attenuation phenomenon.
- Genetic recombination; basic features of transformation, transduction and

conjugation.
- Enzymes used in molecular cloning and their applications
- DNA sequencing: chemical and enzymatic methods
- Vectors: types and characteristic features
- Site- directed mutagenesis (phosphorothioate method, uracil containing DNA, PCR-

based method)
Suggested Books:
1. Biochemistry, 5th Ed. by J.M. Berg, J.L. Tymoczko and L. Stryer, W.H. Freeman and
Company, 2002
2. Principles of Biochemistry, 3rd Ed. by Cox, Dixon and Lehninger, CBS Publisher
3. Molecular Cell Biology, 5th Ed., H. Lodish, A. Berk, P. Matsudaira, C.A. Kaiser, M.
Krieger, M.P. Sott, S.L. Zipursky and J. Darnell, W.H. Freeman and Company, 2003.
4. Molecular Cloning- A laboratory mannual, 2nd and 3rd Ed. Sambrook, Fritsch and
Maniatis, Cold Spring Harbour Press, New York.
(These books are available only as Reference books in Documentation Unit)

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Syllabus for Comprehensive Examination

- Units and dimensions.

Immobilized cell and immobilized enzyme reactors (qualitative treatment only).

Conditions for “wash-out” and maximum cell production in chemostat cultures.

1. “Biochemical Engineering Fundamentals” (second edition), J.E. Bailey and D.F.

2. “Biochemical Engineering” (second edition), S. Aiba, A.E. Humphrey and N.F.

3. “Bioprocess Engineering: Basic Concepts”, M.L. Schuler and F. Kargi, Prentice

- Organization of procaryotic and eucaryotic cells.

- Structure and function of organelles (mitochondria, endoplasmic reticulum, golgi

- Characteristic features of eubacteria, molds and yeasts.

- Energy transduction in microbes (fermentation, aerobic respiration and anaerobic

- Basic metabolic pathways (Glycolysis, TCA cycle, Glyoxalate cycle, Pentose

- Mutations: Types of mutations, Isolation of mutants, auxotrophic mutants.

- Nutrition of microorganisms – C, N and S compounds, growth factors.

- Microbial Growth – Measurement techniques; growth cycle; effect of environment

- Control of microorganisms : heat sterilization, filter sterilization, antiseptics &

- Non-covalent interactions in biomolecular assembly

- Carbohydrates: structure and function (monosaccharides, disaccharides and common

- Proteins – primary, secondary, tertiary & quaternary structures; glycoproteins.

- Structure and function of nucleotides, DNA and RNAs.

- Stoichiometry and energetics of cell growth and product formation

- Principles of fermentation media design

- Microbial growth models (structured and unstructured)

- Media and air sterilization

- Oxygen transfer in fermentations

- Kinetics of enzyme catalyzed reactions

- Bioreactors: Batch, fed-batch and continuous reactors; Immobilized cell and

- Filtration: constant rate and constant pressure filtration

- Centrifugation: batch and continuous; “Σ” concept; types of centrifuges; scale-up.

- Batch and multistage solvent extraction; Craig extraction; differential extraction.

- Protein precipitation; scale-up.

- Adsorption and elution chromatography

- Electrophoresis and electrodialysis

- Ultrafiltration and its applications

1. “Biochemical Engineering Fundamentals” (second edition), J.E. Bailey and D.F.

2. “Biochemical Engineering” (second edition), S. Aiba, A.E. Humphrey and N.F.

3. “Bioprocess Engineering: Basic Concepts”, M.L. Schuler and F. Kargi, Prentice

Syllabus for Comprehensive Examination

Paper-II: Advanced Biochemistry and Molecular Biology

- Structure and function of biological membranes; transport of nutrients.

- Mechanism of enzyme action (Lysozyme, carboxypeptidase A)

- Enzyme kinetics (Michaelis Menten Model)

- Allosteric regulation of enzyme function; Hemoglobin, Phosphofructokinase,

- Covalently regulated enzymes (Glycogen metabolism)

- Common regulatory mechanisms in the biosynthesis of amino acids.

- DNA: Replication and its control (with special emphasis on E.coli)

- RNA: Synthesis and processing in eukaryotes

- Prokaryotic translation and its control; attenuation phenomenon.

- Genetic recombination; basic features of transformation, transduction and

- Enzymes used in molecular cloning and their applications

- DNA sequencing: chemical and enzymatic methods

- Vectors: types and characteristic features

- Site- directed mutagenesis (phosphorothioate method, uracil containing DNA, PCR-

(These books are available only as Reference books in Documentation Unit)

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