MB 101: Taxonomy, Virology and Cytology

Objective: The main aspects of this paper includes Taxonomy and classification of Bacteria &
Virus, fundamentals of virology along with concepts of new emergent virus, it also includes
molecular aspects of phage and different organelle studies.

No. of Lectures.

UNIT 1: Taxonomy and classification of bacteria and viruses. 12

UNIT 2: Fundamentals of virology 13

UNIT 3: Bacteriophages 09

UNIT 4: Cytology 12

UNIT: 1 Taxonomy and classification of bacteria and virus.

1. Taxonomy and classification of bacteria. Ref. Bergey’s manual, 2nd ed., Vol 1.
1.1 Procaryotic domains
1.2 Classification of Procaryotic organisms and the concept of bacterial species
1.3 Identification of procaryotes
1.4 Numeric Taxonomy
1.5 Polyphasic Taxonomy
1.6 Bacterial nomenclature
1.7 Etymology in nomenclature of procaryotes
1.8 Culture Collections
1.9 Intellectual Property of Procaryotes
1.10 Virus taxonomy Ref. Fields
1.11 The Baltimore scheme of virus classification Ref. Wagner
1.12 Banking diverse data in ICTVdB Ref. Murray

UNIT: 2 Fundamentals of Virology

1. Particles Ref. Cann

2. Genomes Ref. Cann
3. Molecular biology of prion proteins Ref. Fields
4. Prion replication Ref. Fields
5. New and emergent viruses Ref. Cann
6. General features of virus induced cell transformation and oncogenesis Ref. Fields
UNIT: 3 Bacteriophages Ref. Fields

1. Temperate phages
1.1 Phage λ.
1.2 Phage Mu-1 as a Model Transposon.
1.3 Phage P 1 as a Model plasmid.
2. Phage – borne genes for bacterial toxins and other proteins affecting host phenotype.
2.1 Gene acquisition.
2.2 Selection value for the phage.
2.3 Relation to phage biology.
3. Virulent phage.
3.1 Large DNA phage.
3.2 Small DNA phage.
3.3 RNA phage.

UNIT: 4 Cytology

1. The nucleus Ref: Cooper

2. Protein sorting
2.1 The endoplasmic reticulum
2.2 The Golgi apparatus
2.3 Lysosomes
3. Bioenergetics and metabolism
3.1 mitochondria
3.2 Chloroplast and other plastids
3.3 Peroxisomes
4. The cytoskeleton
4.1 Actin filaments
4.2 Intermediate filaments
4.3 Microtubules
5. The plasma membrane
6. Cell structure of The Archaea Ref. Schaechter
References:

1. Bergey’s manual of systematic bacteriology, 2nd Edition, Vol. 1, Springer, ISBN: 0-387-
98771-1.
2. Murray et. al.: Manual of clinical microbiology, Vol. 2, ASM Press, 8th Ed.
3. Wagner et. al.: Basic virology, Blackwell publishers, 3rd Ed.
4. Cann A J (2005): Principals of molecular virology, Elservier academic press, 4th Ed.
5. Knipe D M and Howley P M: Fields virology, Vol. 1, 5th Ed.
6. Knipe D M and Howley P M: Fields virology, Vol. 2, 5th Ed.
7. Copper G M and Hausman R E (2007): The cell, ASM press 4th Ed.
8. Schaechter M (2004): Desk encyclopedia of microbiology, Elsevier Academic Press.  
 MB 102: MOLECULAR BIOLOGY
Objective: The paper intends to deal basic reactions of molecular biology at its most
advanced level.
UNIT 1: GENOME ORGANIZATION
1.1 The Content of the Genome
1.2 Genome Sequences and Gene Numbers
1.3 Chromosomes
1.4 Nucleosomes
Key Research / Review Articles:
1. Gall, J.G. (1981). Chromosome Structure and C-value paradox. The Journal of
Cell Biology, 91 (3), 3s to 14s.
2. Luger, K. et al (1997). Crystal structure of the nucleosome core particle at
2.8 A° resolution. Nature, 389, 251-260.
3. Bentley, S. D. and Parkhill, J. (2004). Comparative genomic structure of
Prokaryotes. Annual Reviews of Genetics, 38, 771-91.
4. Sherratt, D. J. (2003). Bacterial Chromosome Dynamics. Science, 301, 780-
785.
UNIT 2: DNA REPLICATION AND TRANSPOSONS
2.1 The Replication of DNA Ref.: Watson
2.2 Transposons
2.3 Retroviruses and Retroposons
Key Research / Review Articles:
1. McInerney, P. et al (2007). Characterization of a Triple DNA Polymerase
Replisome. Molecular Cell, 27, 527-538.
2. Hubscher, U. et al (2002). Eukaryotic DNA Polymerases. Annual Reviews of
Biochemistry, 71, 133-63.
3. Bell, S. P. and Dutta, A. (2002). DNA Replication in Eukaryotic Cells. Annual
Reviews of Biochemistry, 71, 333-74
4. Ostertag, E. M. and Kazazian, H. H. (2001). Biology of Mammalian L1
Retrotransposons. Annual Reviews of Genetics, 35, 501-38.
UNIT 3: GENE EXPRESSION
3.1 Messenger RNA
3.2 Transcription
3.3 Promoters and Enhancers
3.4 Using the genetic code
3.5 Protein synthesis
Key Research / Review Articles:
1. Noller, H. F. (2005). RNA Structure: Reading the Ribosome. Science, 309,
1508-1514.
2. McClure, W. R. (1985). Mechanism and Control of Transcription Initiation in
Prokaryotes. Annual Reviews of Biochemistry, 54, 171-204.
 3. Shilatifard, A. et al (2003). The RNA Polymerase II Elongation Complex.
Annual Reviews of Biochemistry, 72, 693-715.
4. Woychik, N. A. et al (2002). RNA Polymerase II Machinery: Structure
Illuminates Function. Cell, 108, 453-463.
5. Smale, S. T. and Kadonaga, J. T. (2003). The RNA Polymerase II Core
Promoter. Annual Reviews of Biochemistry, 72, 449-479.
6. Ramakrishnan, V. (2002). Ribosome Structure and the Mechanism of
Translation. Cell, 108, 557-572.

UNIT 4: GENE REGULATION

4.1 The Operon
4.2 Activating Transcription
4.3 Regulatory RNA
Key Research / Review Articles:
1. Harrison, S. C. (1991). A Structural Taxonomy of DNA Binding Domains.
Nature, 353, 715-719.
2. Botsford, J. L. and Harman, J. G. (1992). Cyclic AMP in Prokaryotes.
Microbiological Reviews, 56(1), 100-122.
3. Gottesman, S. (2002). Stealth Regulation: Biological Circuits with Small RNA
Switches. Genes and Development, 16, 2829-2842.
4. Yanofsky, C. et al (1979). Attenuation in the Escherichia coli Tryptophan
Operon: Role of RNA Secondary Structure Involving Tryptophan Codon
Region. Proceedings of the National Academy of Sciences of the USA, 76(11),
5524-5528.
5. Sharp, P. A. (2001). RNA Interference-2001. Genes and Development, 15,
485-490.

Text Reference:
Lewin, B., (2008). Genes IX. Jones and Bartlett Publishers, Sudbury.

Supplementary Reference:
Watson, J. D. et al (2004). Molecular Biology of the Gene. 5th Edition, Benjamin
Cummings, San Francisco.
 MB 103: Microbial Physiology
Objective: The main aspect of this paper includes Inorganic metabolism of nitrogen and sulfur,
electron transport and C1 metabolism, Photosynthesis in prokaryotes. This also includes Carbon
dioxide fixations systems and Cell wall and capsule biosynthesis.

No. of Lectures.

UNIT-1: Inorganic Nitrogen and Sulfur Metabolism. 13

UNIT- 2: Energy Production. 10

UNIT-3: Photosynthesis 09

UNIT-4: Biosynthesis 09

UNIT-1: Inorganic Nitrogen and Sulfur Metabolism. Ref. Albert G. Moat

1.1 Biological Nitrogen fixation.
1.2 The Nitrogen Fixation process
1.3 Symbiotic Nitrogen Fixation.
1.4. Inorganic Nitrogen Metabolism.
1.5 Assimilation of Inorganic Nitrogen.
1.6. General Reactions of Amino Acids.
1.6.1. Amino Acid Decarboxylases.
1.6.2. Amino Acid Deaminases.
1.6.3. Amino Acid Transaminases (Aminotransferases)
1.6.4. Amino Acid Racemases.
1.6.5. Role of pyridoxal-5’-Phosphate in Enzymatic Reactions with Amino Acids.
1.7. The Stickland Reaction
1.8. Sulfate assimilation
1.9. Dissilmilatory sulfate reduction

UNIT- 2: Energy Production. Ref. David White and Moat

2.1 Membrane bioenergetics: the proton potential

2.2 Electron transport
2.3 Metabolism of substrates other than glucose
2.3 Catabolism of Aliphatic hydrocarbons
2.4 Growth on C1 compounds other than CO2: The methylotrophs.

UNIT-3: Photosynthesis Ref. David White

3.1 The phototrophic prokaryotes

3.2 The purple photosynthetic bacteria
 3.3 The green sulfur bacteria
3.4 Cyanobacteria and chloroplast
3.5 Efficiency of photosynthesis
3.6 Photosynthetic pigments
3.7 The transfer of energy from light harvesting pigments to the reaction centre
3.8 The structure of photosynthetic membranes in bacteria

UNIT-4: Biosynthesis Ref. David White

4.1 Carbon dioxide fixations systems

4.2 Cell wall and capsule biosynthesis

References:

1. White D (2003) : The Physiology and Biochemistry of Prokaryotes, Oxford University

Press 2nd Ed.
2. Moat A G et. al (2009).: Microbial Physiology, Wiley-Liss, Inc, New york 4th Ed.
 MB 104: Applied Environmental Microbiology

Objective: This paper is devoted to study of diversity of microbial habitats, processes taking
place in environment and its application in solving environmental problems. It also involves
exploiting these principles for economic purpose.

Unit 1: Biodiversity, Microbial ecology and it’ s tools

1.1 What is Biodiversity? Ref: Hawksworth

1.2 Measurement of Biodiversity Ref: Hawksworth
1.2.1 Taxic measures
1.2.2 Molecular measures
1.2.3 Phylogenetic measures
1.3 Biodiversity at the molecular level: the domains, kingdoms and phyla of life
Ref: Hawksworth
1.4 Theoretical and practical aspects of the quantification of biodiversity among
microorganisms Ref: Hawksworth
1.5 Microbial ecology – New Directions, new importance Ref: BMSB Ed. 2 Vol 1
1.6 Nucleic acid probes and their application in environmental microbiology
Ref: BMSB Ed. 2 Vol 1
1.7 Metagenomic libraries from uncultured microorganisms Ref: Osborn

Unit 2: Waste water engineering

2.1 Waste water Ref: Metcalf and Eddy

2.1.1 Physical characteristics of waste water
2.1.2 Inorganic non metallic constituents
2.1.3 Aggregate organic constituents
2.1.4 Microbial growth kinetics
2.2 Biotreatment of waste Ref: Doble & Anilkumar
2.2.1 Textile effluent
2.2.2 Food and Dairy industry
2.2.3 Sugar and Distillery waste
2.2.4 Pharmaceuticals
2.2.5 Hospital waste
2.2.6 Waste from nuclear plants
Unit 3: Biodegradation and Bioremediation

3.1 Fundamentals of Biodegradation Ref: M. Alexander

3.1.1 Growth linked biodegradation
3.1.2 Acclimation
3.1.3 Detoxication
3.1.4 Activation
3.1.5 Kinetics
3.1.6 Bioavailability
3.1.7 Cometabolism
3.1.8 Inoculation
3.2 Biodegradation of pesticides Ref: Doble & Anilkumar
3.3 Biodegradation of polymers Ref: Doble & Anilkumar
3.4 Biodegradation of dyes Ref: Doble & Anilkumar
3.5 Bioremediation technologies Ref: M. Alexander

Unit 4 : Environmental Biotechnology

4.1 Oil field microbiology Ref: Hurst

4.2 Bioreporter, Biosensor and microprobes Ref: Hurst
4.3 Biodesulfurization Ref: Doble & Anilkumar
4.4 Colonization, adhesion, aggregation and Biofilms Ref: Hurst
4.5 Bioprospecting
4.6 Investigative Biodeterioration Ref: Allsopp
4.7 The control of Biodeterioration Ref: Allsopp

References:

1. Hawksworth, D. L. (1995) Biodiversity: Measurement and Estimation. Chapman & Hall 1

Ed - The royal society.
2. Garrity, G. M. and Boone, D. R. (2001) Bergey's Manual of Systematic Bacteriology
Volume 1: The Archaea and the Deeply Branching and Phototrophic Bacteria; 2 Ed.
Springer.
3. Metcalf & Eddy Inc. (2002) Wastewater Engineering: Treatment and Reuse 4 Ed. McGraw
Hill Higher Education.
4. Doble, M. & Anil kumar (2005) Biotreatment of Industrial Effluents. Butterworth-
Heinemann – An imprint of Elsevier.
5. Alexander, M. (1999) Biodegradation and Bioremediation, 2Ed. Academic Press.
6. Osborn, A. & Smith, C.(2005) Molecular Microbial Ecology (Advanced methods)1Ed.
BIOS Scientific Publisher, Taylor & Francis group.
7. Hurst, C. (2007) Manual of Environmental Microbiology, 3Ed. ASM Press.
8. Allsopp, D.et al(2004) Introduction to Biodeterioration, 2Ed. Cambridge University Press
 M.Sc. MICROBIOLOGY PRACTICALS

SEMESTER 1

1. One step growth curve of phage.

2. Extraction, characterization and quantification of genomic DNA from bacterial cell
3. Extraction of plasmid DNA from bacterial cell
4. Extraction of bacterial DNA using spin column technique
5. Detection siderophore production by Pseudomonas.
6. Study of nodulation of legumes by rhizobia.
7. Analysis of domestic water and waste water
7.1 Physical
• Acidity
• Alkalinity
• Hardness –EDTA titrimetric method
• Chlorine demand
• Solids : TDS and TSS
7.2 Inorganic non-metallic constituents
• Residual chlorine
• Chloride
• pH value
• Oxygen (Dissolved)
7.3 Agregate organic constituents
• Biological oxygen demand
• Chemical oxygen demand
8. Bioremediation of heavy metals : Biosorption
9. Biodegradation of dyes