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; LineweaverBurk 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.

Syllabus for Comprehensive Examination 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

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, 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, PCRbased 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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