Paper Iv : Basic Physiology (Bc & Mbt)

Department of Biochemistry Faculty of Science The M. S. University of Baroda

Papers for M. Sc. (Biochemistry) Semester syllabus

THEORY SEMESTER - I CREDITS Course Code Basic Biochemistry 03 BC701 Protein Structure and Function & Basic Enzymology 03 BC 702 Cell Biology 03 BC 703 Basic Physiology 03 BC 704 Molecular Biology-I 03 BC 705 Practical I 09 BC 706 Seminar 01 BC 707 TOTAL CREDITS 25

THEORY SEMESTER - II CREDITS Course Code Metabolism - I 03 BC 801 Enzyme Mechanism & Regulation 03 BC 802 Biophysical Techniques 03 BC 803 Endocrinology 03 BC 804 Recombinant DNA Techniques 03 BC 805 Practical II 10 BC 806 Seminar 01 BC 807 TOTAL CREDITS 26

THEORY SEMESTER - III CREDITS Course Code Basic Immunology 03 BC 901 Metabolism - II 03 BC 902 Molecular Biology - II 03 BC 903 Biostatistics & Bioinformatics 03 BC 904 1. Basic Pharmacology (Optional Paper- I) 03 BC905 2. Structural Biology (Optional Paper – I) 03 BC 906 3. Biochemical Toxicology (Optional Paper – I) 03 BC 907 Practical III 07 BC 908 Project Work I 03 BC 909 Seminar 01 BC 910 TOTAL CREDITS 26

THEORY SEMESTER - IV CREDITS Course Code Genetics 03 BC 001 Genetic Engineering & Genomics 03 BC 002 Molecular Medicine 03 BC 003 Plant & Microbial Biochemistry (Optional Paper – II) 03 BC 004 Neurochemistry (Optional Paper – II) 03 BC 005 Advanced Plant Biochemistry (Optional Paper - II) 03 BC 006 Microbial Adaptive Biology (Optional Paper - II) 03 BC 007 Project Work II 10 BC 008 Viva ( External ) 01 BC 009 TOTAL CREDITS 23 Total Credits = 100

Biochemistry 1 SEMESTER I

BC 701 BASIC BIOCHEMISTRY Credit-1 Relevance of properties of water for life. Diffusion rates, viscosity; Thermodynamic principles in metabolism; techniques to study metabolic pathways. Carbohydrate Chemistry: Monomers. Structure-function correlation and diversity in various organisms. Credit-2 Carbohydrate Chemistry: Polymers & Modifications and their structure- function correlation; diversity in various organisms; Amino acids Chemistry: structure-function correlation. Credit-3 Chemistry of Lipids & Nucleotides: structure-function correlation. & Modifications; Chemistry of Vitamin functions.

Books 1. D. Voet (2010) Biochemistry, 4th edition, John Wiley & Sons (ISBN: 978-0-470- 57095-1). 2. D. L. Nelson and M. M. Cox (2007) Lehninger Principles of Biochemistry, Fourth Edition. 3. R. H. Garrett and C. M. Grisham (2008) Biochemistry 4th Edn., Brooks/cole Cengage Learning. 4. Voet, D., Voet, J. G., and Pratt, C. W. (2011) Fundamentals of Biochemistry, 4th Edn., John Wiley & Sons. 5. Haynie, D. T. (2008) Biological Thermodynamics, 2nd Edn., Cambridge Univ. Press. 6. R. R. Crichton (2008) Biological Inorganic Chemistry : An Introduction, Elsevier. 7. G. G. Hammes (2007) Physical chemistry for biological sciences, Wiley-Interscience. 8. Nelson P. (2004) Biological Physics, W. H. Freeman & Co., NY, USA. 9. D. E. Metzler, (2003) Biochemistry, Vol. 1 & II, 2nd Edn., Academic Press.

BC 702 PROTEIN STRUCTURE AND FUNCTION & BASIC ENZYMOLOGY

Credit-1 Proteins: Primary structure and determination; artificial peptide synthesis; restrictions on primary structure (recognition sequences for protein modifications and targeting); Chemical modification of side chains of amino acid residues Credit-2 Forces and interactions responsible for protein structure; Secondary and tertiary structure including prediction; quaternary structure. Scope of enzymology, classification and nomenclature. Kinetics: chemical kinetics; Variations of velocity with [E], [S]. Credit-3 Variations of velocity with pH and temperature; enzyme inhibition; bi- substrate reaction kinetics; uses of kinetic studies in determining enzyme mechanism; scope for increasing enzyme efficiency; enzyme specificity.

Books

1. Gray (2010) Enzymes Biotechnology, Cbs. 2. C. Koehrer & U. L. RajBhandari (2010) Protein Engineering., Springer, NY. 3. Michael, G. M. (2010) Protein Bioinformatics, Elsevier. 4. D. L. Purich (2009) Contemporary Enzyme Kinetics and Mechanism, 3rd Edn., AP. 5. J. Poliana and A. P MacCabe (2007) Industrial Enzymes – Structure, Function and Applications, Springer. 6. W. Aehle (2007) Enzymes in Industry, Wiley-VCH. 7. P. F. Cook and W. W. Cleland (2007) Enzyme Kinetics and Mechanism. Garland Science. 8. D. Whitford (2005) Proteins: Structure and Function. Wiley Publication. 9. A. Carnish Bowden (2004) Fundamental of Enzyme Kinetics, 3rd Edn., Portland Press. 10. G. A. Petsko and D. Ringe (2003) Protein Structure and Function, New Science Press, Ltd. 11. Metzler, D. E. (2003) Biochemistry, Vol. 1 & II, 2nd Edn., Academic Press. 12. S. P. Trevor (2001) Enzymes, Harwood. 13. Voet, D., Voet, J. and Pratt, C. W. (1999) Fundamentals of Biochemistry.

Biochemistry 2 14. Price, N. C. & L. Stevens, (1999) Fundamentals of Enzymology, 3rd Edn., Oxford University Press. 15. H. Uhlig, E. M L. Bednar (1998) Industrial Enzymes and their Applications, Wiley. 16. Creighton, T. E. (1995) Proteins : Structure and Molecular Properties. 17. Fersht, A. R. (1985) Enzyme structure and function, 2nd Edition, W. H. Freeman & Co. NY. 18. Dixon and Webb, (1979) Enzymes. 19. Bayer, Lardy and Myrback, The Enzymes, Academic Press.

BC 703 CELL BIOLOGY

Credit-1 Introduction to cell; evolution of cell; comparative aspects of prokaryotes and eukaryote, Structure and function of Biomembranes, Types of membrane transport. Cytoskeleton, Cell-cell and Cell-Extracellular matrix interactions. Credit-2 Cellular organelles like Endoplasmic reticulum, Golgi, Mitochondria. Lysosomes. Mechanism of protein translocation, Membrane trafficking, Vesicular transport Credit-3 Eukaryotic Cell signaling- Types of receptors, signal transduction by membrane bound, cytosolic and nuclear receptors via various pathways

Books 1. B. Alberts et al. (2010) Essential Cell Biology, 3rd Edn., Garland Science. 2. S. Tompkins (2010) Cell Biology, Appleacademics. 3. T. D. Pollard & W. C. Earnshaw (2008) Cell Biology 2nd Edn., Saunders Elsevier. 4. H. Lodish et al., (2008) Molecular Cell Biology, 6th Edn., W. H. Freeman & Co. NY. USA. 5. K. Roberts, J. Lewis, B. Alberts, P. Walter, A. Johnson and M. Raff. (2008) Molecular Biology of the Cell, 5th Edn., Garland Publishing Inc. New York. 6. Kreitzer, G., F. Jaulin and C. Espenel (2009) Cell Biology Assays: Essential Methods, Academic Press. 7. K. Gerald (2007) Cell and Molecular Biology, Concept and Experiment, 5th Edn., Wiley.

BC 704 BASIC PHYSIOLOGY

Credit-1 Blood Chemistry & blood clotting, function of respiratory system and regulation of respiration, Structure & function of digestive system, digestion and absorption, Credit-2 Structure and function of excretory system and role of kidney in urine formation; fluid electrolyte balance. Neurochemistry – Organization of the nervous system in brief:cellular, organ level, organ-system level; Cells of the nervous system, their structure and function Credit-3 Neurochemistry - special biochemical features (structural and metabolic). Ion Channels and electrical properties of membranes; EPSPs & IPSPs; molecular mechanism of generation of membrane potential and action potential & its propagation;synaptic transmission

1. Guyton, Text book of Medical Physiology, 1998 2. Kelly, Hormones, 1994 3. Ganong, Review of medical physiology, 1997 4. Tortora, G. J. Principles of anatomy and physiology, 2000 5. Devlin, T. M. Text of biochemistry with clinical correlations, 1997 6. Harper, Biochemistry, 1997 7. Aidley. 8. Kuffler and Nichols. From Neuron to Brain. 9. Zigmond. 10. Kandel and Schwartz 11. Siegel. Basic Neurochemistry 12. Nerve, Muscle & Synapse. Katz, B. (1964?). 13. Neuroscience_Bear_Connors_Paradiso_3ed_2007.—added 26thSept.’10. 14. Molecular Biology of the Cell. Alberts B et al.(for ALL basics).

Biochemistry 3 BC 705 MOLECULAR BIOLOGY- I

Credit-1 Nucleic acids and Genome: The central dogma, evidence that DNA is the genetic material. Structure of DNA and RNA, physical properties of DNA- cot plot, kinetic and chemical complexity, Tm, buoyant density, satellite DNA. Organization of the human genome. Chromosome, structure of chromatin- nucleosomes, solenoids, scaffolds.

Credit-2 Chromatin domains and isochores, structure and functional organization of centromeres and telomeres. Transcription : Structure of genes, promoters, enhancers. Structure and mode of action of E. coli RNA polymerase and eukaryotic RNA polymerase I.

Credit-3 Structure and mode of action of RNA polymerases II and III. Co- and -post transcriptional modifications in prokaryotes and eukaryotes. Regulation of transcription in prokaryotes and eukaryotes.

Books

1. B. Lewin, J. E. Krebs, E. S. Goldstein and S. T. Kilpatrick (2009) Lewin’s Essential Genes, 2nd Edn., Jones & Barlett Pub., USA. 2. R. Weaver (2007) Molecular Biology, 4th Edn., McGraw-Hill. 3. J. D. Watson, T. A. Baker, S. P. Bell, A. Gann, M. Levine, R. Losik and Inglis, CSHLP (2007) Molecular Biology of the Gene, 6th Edition, Benjamin Cummings. 4. D. Clark (2009) Molecular Biology: Academic Cell, Academic Press. 5. J. E. Krebs, E. S. Goldstein and S. T. Kilpatrick (2009) Lewin’s Genes X, 10th Edn., Jones & Barlett Pub., USA. 6. Twyman, R. M. (1998) Advanced Molecular Biology, Bioscientific Publ.

BC 706 Practical I (9 Credits)

1. Orientation 2. Tissue Analysis 3. Protein purification 4. Basic Enzymology 5. Immunology

Biochemistry 4 Semester II

BC 801 METABOLISM I (3 Credits) Credit-1 Carbohydrate Metabolism (organization, reactions, regulation etc.)- Glycolysis, Glycogenolysis, Glycogenesis & Gluconeogenesis; HMP, Entner-Doudoroff, Glyoxylate and Poylol pathways. Credit-2 TCA cycle, it’s central role, interactions, organization, reactions, regulation etc. Credit-3 Lipid metabolism: Triglyceride, cholesterol, phospholipid, lipoproteins and eicosanoids.

Books 1. D. Voet (2010) Biochemistry, 4th edition, John Wiley & Sons (ISBN: 978-0-470- 57095-1). 2. D. L. Nelson and M. M. Cox (2007) Lehninger Principles of Biochemistry, Fourth Edition. 3. R. H. Garrett and C. M. Grisham (2008) Biochemistry 4th Edn., Brooks/cole Cengage Learning. 4. Voet, D., Voet, J. G., and Pratt, C. W. (2011) Fundamentals of Biochemistry, 4th Edn., John Wiley & Sons. 5. Haynie, D. T. (2008) Biological Thermodynamics, 2nd Edn., Cambridge Univ. Press. 6. G. G. Hammes (2007) Physical chemistry for biological sciences, Wiley-Interscience. 7. Nelson P. (2004) Biological Physics, W. H. Freeman & Co., NY, USA. 8. D. E. Metzler, (2003) Biochemistry, Vol. 1 & II, 2nd Edn., Academic Press.

BC 802 ENZYME MECHANISM & REGULATION

Credit-1 Enzyme mechanism (acid, base, electrostatic, metal ion, free radical, transition state binding and covalent; proximity and orientation effects, contributions of strain; cofactors function; Credit-2 Experimental approaches to determine mechanism, along with illustration with eg.: chymotrypsin, lysozyme. Rationale for modification of enzyme function(s) for application. Credit-3 Allostery: cooperativity in hemoglobin; various equations & models of allostery; Regulation of individual enzyme activity and a single metabolic step. Logic / strategies of pathway regulation; multienzyme complexes and polyfunctional proteins, their importance for cell physiology; enzyme function in vivo & in vivo kinetics. Enzyme applications.

Books 1. P. F. Cook and W. W. Cleland (2007) Enzyme Kinetics and Mechanism. Garland Science. A. Carnish Bowden (2004) Fundamental of Enzyme Kinetics, 3rd Edn., Portland Press. 2. N. Price and J. Nairn (2009) Exploring Proteins: a student's guide to experimental skills and methods, Oxford Univ. Press. 3. D. L. Purich (2009) Contemporary Enzyme Kinetics and Mechanism, 3rd Edn., AP. 4. R. R. Burgess & M. P. Deutscher (2009) Methods in Enzymology - Guide to Protein purification. 2nd Edn. Vol. 463, Academic Press. 5. Fersht, A. R. (1985) Enzyme structure and function, 2nd Edition, W. H. Freeman & Co. NY. 6. Creighton, T. E. (1995) Proteins : Structure and Molecular Properties. 7. Price, N. L. and Stevens (1989) Fundamentals of Enzymology. 8. Metzler, D. E. Biochemistry, Vol. 1 & II, 2nd Edn., Academic Press, 2003. 9. Dixon and Webb, (1979) Enzymes. 10. Polaina, J. MacCabe, A. P. (2007) Industrial Enzymes - Structure, Function and Applications, Springer.

Biochemistry 5 BC 803 BIOPHYSICAL TECHNIQUES Credit-1 Intermolecular and Intramolecular interactions and their role in determining the structure and function of macromolecules. Radioactive tracer techniques : Radioactive decay, half life, , ,  emitters, decay of radioactivity (scintillation counters and gamma counters etc.), Centrifugation. Credit-2 Methods employed for the separation, characterization and molecular weight determination of macromolecules, such as ultrafiltration, equilibrium dialysis, solvent extraction, ultracentrifugation, precipitation, electrophoresis and chromatography (partition, gel permeation, ion exchange, affinity, GC, HPLC, and FPLC) their principles and applications. Credit-3 Spectroscopy : UV-visible spectroscopy, Infrared, Raman, Resonance Raman, Circular dichroism (CD) and Optical Rotatory dispersion (ORD), Fluorescence, NMR, ESR, Mass, Atomic absorption spectroscopies and X-ray diffraction. Their principles, instrumentation, applications in quantitation, understanding of structure and function, and structural transitions in Biomolecules.

Books 1. R. R. Bergethon (2010) The Physical Basis of Biochemistry : The Foundations of Molecular Biophysics, 2nd Edn., Springer, NY. 2. P. J. Walla (2009) Modern Biophysical Chemistry, Wiley-VCH. 3. D. Sheeham (2009) Physical Biochemistry 2nd Edn., Wiley-Blackwell. 4. Wilson, K and Walker, J.M (2005) Principles and techniques of biochemistry and molecular biology, 6th ed., Cambridge University Press 5. J. A. Goodrich and J. F. Kugel (2006) Binding and Kinetics for Molecular Biologists. Cold Spring Harbor Press. 6. van Holde, K. E. (1998) Principles of Physical Biochemistry, Prentice Hall. 7. Freifelder, D., 1982, Physical biochemistry: applications to biochemistry and molecular biology

BC 804 ENDOCRINOLOGY

Credit-1 General principles of endocrinology; Neuro-endocrinology- Neuro- immuno endocrinology, Chemistry, synthesis, catabolism and physiological action and mechanism of action Hypothalamus and Pituitary. Credit-2 Chemistry, synthesis, catabolism and physiological action and mechanism of action, Thyroid, parathyroid (calcium homeostasis hormones). GIT hormones, pancreatic Hormones and their disorders. Credit-3 Chemistry, synthesis, catabolism and physiological action and mechanism of action of adrenals, Gonads and their disorders. Extra endocrine hormones- ANP, Erythropoietin, Melatonin, etc.

Books

1. Kronenberg, H., Williams, R. H. (2008) Textbook of endocrinology 2. Nussey,S. Whitehead, S. A. (2001) Endocrinology: an integrated approach 3. Baulieu,E. E. and Paul A. Kelly, P. A. (1990) Hormones: from molecules to disease 4. Jonsen, A. R., Siegler, M. and Winslade, W. J. (2002) Clinical ethics: a practical approach to ethical decisions in clinical medicine 5. Christopher Meyers, C. (2007) A practical guide to clinical ethics consulting: expertise, ethos, and power.

Biochemistry 6 BC 805 RECOMBINANT DNA TECHNIQUES

Credit-1 Physical and chemical properties of nucleic acids, purification and analysis of Nucleic acids. Enzymes used in recombinant DNA technology – Principles and applications of DNA polymerases; Restriction endonucleases; DNA modifying enzymes. Principles and uses of nucleic acid hybridizations. Credit-2 Properties and applications of plasmids, phagemids, phage vectors, cosmids, YAC, BAC, etc; Oligonucleotide synthesis and their uses. Credit-3 Principles and methods of nucleic acid sequencing; Characteristics of bacterial strains used for genetic manipulations, Principles and applications of Polymerase chain reaction.

Books 1. Primrose, S., Twyman R. & Old B. (2009) Principles of Gene manipulation & Genomics, 8th Edn., Blackwell Science. 2. Glick B. R., Pasternak J. J. and Patten, C. L. (2010) Molecular Biotechnology - Principles and applications of recombinant DNA, 4th Edn., ASM Press. 3. Hardin, C. et al. (2008) Cloning, Gene Expression and Protein purification Oxford University Press. 4. D. T. Nicholl (2008) .An Introduction to Genetic Engineering, 3rd Edition Cambridge University Press, 5. G. Lipps (2008) Plasmids: Current Research and Future Trends. Caister Academic Press. 6. Metzenberg, S. (2007) Working with DNA. Taylor & Francis. 7. Howe, C. (2007) Gene cloning and manipulation, Cambridge University Press. 8. Wink, M. (2006) An Introduction to Molecular Biotechnology, Wiley-VCH. 9. J. D. Watson, R. M. Myers, A. A. Caudy, & J. A. (2006) Recombinant DNA : Genes & Genomes, 3 Edition, W. H. Freeman Publ. 10. J. Lodge, P. Lund, S. Minchin (2006) Gene Cloning: Principles and Applications, Taylor & Francis Group. 11. T. A. Brown (2010) Gene Cloning and DNA Analysis: An Introduction, 6th Edn., Wiley- Blackwell. 12. D. W. S. Wong (2005) The ABCs of Gene Cloning, Springer. 13. Molecular Cloning: A Laboratory Manual, J. Sambrook, E. F. Fritsch and T. Maniatis, Cold Spring Harbor Laboratory Press, New York, 2000.

BC 806 Practical II (9 Credits)

1. Enzyme kinetics 2. Microbiology 3. Animal Experiments 4. Protein Folding 5. Molecular Biology

Biochemistry 7 SEMESTER III

BC 901 BASIC IMMUNOLOGY (3 Credits)

Credit-1 Nature of Immunity; Cells and tissues of Immune system; Innate Immunity – Role of Microbial Associated Molecular Patterns (Toll-like receptors & Noll Like Receptors); Phagocytes, NK cells, MALT system; Mechanisms of Migration of immune cells into primary and secondary lymphoid organs. Credit-2 Nature of Antigens; Structure and function of antibodies; Structure and function of T cell receptors. Complement System. Histocompatibility antigens - HLA and Disease Credit-3 Generation of Diversity. T cell differentiation – Positive and Negative selection, Antigen Presentation, Activation of T and B cells.

Books 1. B. M. Hannigan, C. B. T. Moore and D. G. Quinn (2010) Immunology 2nd Edn., Viva Books. 2. K. D. Elgert (2009) Immunology, 2nd Edn., Wiley Blackwell. 3. K. M. Murphy, P. Travers, M. Walport (2011) Janeway’s Immunobiology, 8th Edition, Garland Science. 4. W. E. Paul (2008) Fundamental Immunology, 6th Edition, Lippincott Williams & Wilkins. 5. A. K. Abbas, A. H. Lichtman & S. Pillai (2007) Cellular and Molecular Immunology, 6th Edition, Saunders. 6. Kindt, T. J., Osborne, B. A. & Goldsby, R. A. (2006) Kuby Immunology, 6th edition, W. H. Freeman. 7. P. J. Delves, S. J. Martin, D. R. Burton and I. M. Roitt (2006) Roitt’s Essential Immunology 11th Edn., Blackwell Publ.. 8. D. Male, J. Brostoff, D. B. Roth & I. Roitt (2006) Immunology, 7th Edn., Mosby- Elsevier. 9. T. W. Mak and M. E. Saunders (2006) The Immune Response – Basic and Clinical Principles, Academic Press. 10. R. Coico, G. Sunshine and E. Benjamini (2003) Immunology - A Short Course, 5th edition, John Wiley & Sons. 11. M. Wilson (2005) Microbial inhabitants of humans, Cambridge Univ. Press.

BC 902 METABOLISM II (3 Credits) Credit-1 Bioenergetics: Thermodynamic Considerations of the operation of Electron Transport Chain and energy generation (Animals, Plants, and Bacteria). Chemiosmotic theory of Energy Coupling; BAT; Regulation of body temperature; Credit-2 Integration of intermediary metabolism, Biochemical correlates of altered metabolism(diseased states),organ specialization; Mechanisms of 1-electron & 2- electron transfers, Fe-S clusters, cytochromes; In brief: generation of ROS and Mechanism of oxidative damage (Fenton reaction) & targets. Anti-oxidant defenses (SOD, Catalases etc.). Ageing. Credit-3 Nucleotide metabolism & disorders. Cancer cell metabolism. Metabolic specializations in Microorganisms.

Books 1. D. Voet (2010) Biochemistry, 4th edition, John Wiley & Sons (ISBN: 978-0-470- 57095-1). 2. David L. Nelson Michael M. Cox (2007) Lehninger Principles of Biochemistry. 3. Metzler, D. E. Biochemistry, Vol. 1 & II, 2nd Edn., Academic Press, 2003. 4. D. Voet, (2008) Fundamentals of Biochemistry, J. Wiley. 5. Voet, D. and Voet, J. G. Biochemistry, 3rd Edn., John Wiley & Sons, 2004. 6. R. K. Murray, D. K. Granner, P. A. Mayes, V. W. Rodwell Harper's Biochemistry, 27th Edition, McGraw Hill, 2006.

Biochemistry 8 BC 903 MOLECULAR BIOLOGY II (3 Credits) Credit-1 Replication: prokaryotes and eukaryotes, models, DNA dependent and RNA dependent polymerases, mode of action, DNA amplification and polytenization. DNA damage and repair. Credit-2 Recombination: homologous, site specific and nonhomologous or illegitimate recombination. Translation : Structure of tRNA, rRNA and mRNA, ribosomes. Genetic code. Credit-3 Mechanism of translation in prokaryotes and eukaryotes, regulation and post translational modifications, inhibitors of protein synthesis in prokaryotes and eukaryotes.

Books

1. J. E. Krebs, E. S. Goldstein and S. T. Kilpatrick (2009) Lewin’s Genes X, 10th Edn., Jones & Barlett Pub., USA. 2. B. Lewin, J. E. Krebs, E. S. Goldstein and S. T. Kilpatrick (2009) Lewin’s Essential Genes, 2nd Edn., Jones & Barlett Pub., USA. 3. R. Weaver (2007) Molecular Biology, 4th Edn., McGraw-Hill. 4. J. D. Watson, T. A. Baker, S. P. Bell, A. Gann, M. Levine, R. Losik and Inglis, CSHLP (2007) Molecular Biology of the Gene, 6th Edition, Benjamin Cummings. 5. Twyman, R. M. (1998) Advanced Molecular Biology, Bioscientific Publ. 6. D. Clark (2009) Molecular Biology: Academic Cell, Academic Press.

BC 904 BIOSTATISTICS & BIOINFORMATICS

Credit-1 Biostatistics: Measures of central tendency and dispersion, correlation, regression, sampling, probability distribution. Credit-2 Testing of Hypothesis, t-test and 2-test; Analysis of variance. Bioinformatics: Storing of sequences, bioinformatics databases, database searching for similar sequences. Credit-3 Alignment of pairs of sequences Multiple sequence alignment, prediction of RNA secondary structure, phylogenetic prediction, gene prediction. Books 1. Zar, J. H. (2009) Biostatistical analysis. 2. Mahajan, B. K. (2002) Methods in Biostatistics for medical students. 3. Davies, O. L. and Goldsmith, P. L., (1986) Statistical Methods in Research and Production 4. Ferguso, G. (1976) Statistical analysis in physiology and education. 5. David W. Mount. (2001) Bioinformatics: Sequence and Genome Analysis. 6. Christine Orengo, David Jones and Janet Thornton. (2003) Bioinformatics: Genes, proteins and computers.

OPTIONAL PAPER I

BC 905 BASIC PHARMACOLOGY

Credit-1 Types of Drugs, Drug absorption, distribution and metabolism, excretion. Phase I & Phase II Biotransformation Credit-2 Pharmacodynamics- Mechanism of action of drug at different target level. Receptor-ligand interactions. Theories of Receptor- ligand interactions. Credit-3 Basic aspects of drug development, Screening of Drugs, Lead identification & optimization. Preclinical development.

Books

1. Rang & Dale's Pharmacology. 6th Edition. H.P. Rang James M. Ritter Maureen M. Dale Philip Moore

Biochemistry 9 2. Goodman & Gilman's The Pharmacological Basis of Therapeutics ed. Laurence Brunton, John Lazo, Keith Parker 3. Pharmacology and Pharmacotherapeutics, RS Satoskar, SD Bhandarkar

OPTIONAL PAPER I

BC 906 STRUCTURAL BIOLOGY

Credit-1 Protein structure, folding in vitro, Protein stability – thermodynamics and kinetics; Effect of various factors on folding; Solvent engineering for protein folding; Folding intermediates- kinetic, equilibrium and molten globule intermediates; Techniques for studying the structure and folding of proteins. Single molecule studies. Credit-2 Protein folding in vivo, chaperones, peptidyl prolyl isomerase (PPI), Protein disulfide isomerase (PDI) and bacterial disulfide bond forming proteins (Dsb’s); Membrane proteins and quality control; Cotranslational and post-translational modifications; Protein engineering - Recombinant proteins and domains; Prediction of secondary and tertiary structure of proteins; Protein evolution – divergent and convergent, gene regulation with protein structural changes; Comparison of the structure and stability of proteins of mesophilic and extremophilic origin. Credit-3 Protein loss, misfolding, aggregation, context dependence of protein secondary structure, Protein misfolding diseases, therapeutic approaches; Protein degradation, exo- and endo-proteases, mechanisms to escape digestion by exopeptidases, Proteasomes, Ubiquitin dependent and independent mechanisms of protein degradation, Clps.

Books 1. T. E. Creighton Proteins: Structures and Molecular Properties 2. Introduction to Protein Science: Architecture, Function, and Genomics by Arthur M. Lesk (2004) 3. Biochemistry an approach based on chemical logic. (online) by H. Jakuvowski. 4. M. Luckey Membrane Structural Biology Cambridge University Press Hardback (ISBN-13: 9780521856553) 5. Reinhard K. Grisshammer, Susan K. Buchanan (2006) Structural Biology of Membrane proteins –Royal Society of Chemistry. 6. P. A. Rice & C. C. Correl (2008) Protein-Nucleic Acid Interactions: Structural Biology. RSC Publishing. 7. G. M. Blackburn, M. J. Gait, D. Loakes and D. M Williams (2006) Nucleic Acids in Chemistry and Biology, RSC Publishing.

OPTIONAL PAPER I

BC 907 BIOCHEMICAL TOXICOLOGY

Credit-1 Xenobiotic metabolism : Adsorption & Distribution. Phase I Reactions. Oxidation, reduction, hydrolysis and hydration. Phase II Reactions/Conjugation : Methylation, Glutathione and amino acid conjugations. Detoxification Credit-2 Biochemical basis of Toxicology : Mechanism of Toxicity : Disturbance of excitable membrane function, Altered calcium homeostasis. Covalent binding to cellular macromolecules and Genotoxicity. Tissue specificity of toxicity. Credit-3 Acute and chronic Toxicity. Principles and procedures of testing acute toxic effects: Regulatory guidelines, mammalian systems affected and clinical symptoms of systemic toxicity. Factors affecting acute toxicity studies.

Biochemistry 10

Books 1. 1. Rang & Dale's Pharmacology. 6th Edition. H.P. Rang James M. Ritter Maureen M. Dale Philip Moore 2. 2. Goodman & Gilman's The Pharmacological Basis of Therapeutics ed. Laurence Brunton, John Lazo, Keith Parker 3. 3. Pharmacology and Pharmacotherapeutics,RS Satoskar, SD Bhandarkar

BC 908 Practical III (4 Credits)

1. Clinical Chemistry 2. Genetics

Biochemistry 11 SEMESTER IV

BC 001 GENETICS

Classical Genetics (Eukaryotic). Scope and value of the classical genetic approach; model systems; their advantages and shortcomings. Molecular Credit-1 correlates of dominance & recessivity; tests of single gene mutations. Pleiotropy-uses; Penetrance and Expressivity. Mapping using deficiencies & duplication in Drosophila. Diagnosis of a-, hypo-, hyper-, neo- and anti-morphs and uses; ts mutations Credit-2 & uses; uses of mosaics: sexual/mitotic. Bacterial Genetics: Frequency of mutations; the fluctuation test and spontaneous and adaptive mutations. Methods of gene transfer and their uses; conjugation, transduction and transformation; lambda, P1; complementation testing and fine structure mapping of a gene. Yeast genetics. Mapping function and recombination Credit-3 frequency, Mapping by recombination in yeast and Neurospora crassa: tetrad analysis. Basics of human genome mapping: Essential genetic techniques used as a prerequisite to cloning of human genes.

Books 1. J. F. Griffiths, S. R. Wessler, R. C. Lewontin & S. B. Carroll (2011) Introduction to Genetic Analysis, 10th Edn., W. H. Freeman & Co. NY. 7. N. Trun & J. Trempy (2004) Fundamental Bacterial Genetics, Blackwell Publ. 8. Freidberg, E. C., Walker, G. C., Siede, W., Wood, R. W., Schultz, R. A. and Ellenberger, T (2006) DNA repair and Mutagenesis, 2nd Edn., ASM Press. 9. T.A. Brown Gene cloning and DNA analysis An Introduction, 5th Edition. 10. Molecular Cloning: A Laboratory Manual (Third Edition) By Joseph Sambrook, David Russell, 11. Hartl, D. L. & E. W. Jones (2005) Genetics: Analysis of Genes and Genomes. 6th Edn., Jones & Bartlett Publishers. 12. A. Gardener & T. Davies (2009) Human Genetics, 2nd Edn., Scion Publ., UK.

BC 002 GENETIC ENGINEERING & GENOMICS

Credit-1 Cloning of genes – Construction of genomic and cDNA libraries; Molecular genetic and reverse genetic strategies. Analysis of cloned genes: identification of promoters and enhancers, determination of transcriptional start site, intron-exon organization. Credit-2 Gene confirmation by gene disruption, gene knock outs. Protein engineering: site directed mutagenesis, PCR-mediated mutations. Applications of RFLP, AFLP, RAPDs and DNA finger printing. Heterologous gene expression systems in E.coli, yeast, insect cell and mammalian cells. Credit-3 Techniques used for controlled gene expression: antisense oligonucleotides, RNA interference. Techniques used to study protein- protein interactions including principles and applications of two hybrid systems. Gene arrays. Cell cycle and its regulation. Cell death and cancer.

Biochemistry 12 8. Wink, M. (2006) An Introduction to Molecular Biotechnology, Wiley-VCH. 9. J. D. Watson, R. M. Myers, A. A. Caudy, & J. A. (2006) Recombinant DNA : Genes & Genomes, 3 Edition, W. H. Freeman Publ. 10. J. Lodge, P. Lund, S. Minchin (2006) Gene Cloning: Principles and Applications, Taylor & Francis Group. 11. T. A. Brown (2006) Gene Cloning and DNA Analysis: An Introduction, Blackwell Publishing Professional. 12. D. W. S. Wong (2005) The ABCs of Gene Cloning, Springer. 13. Molecular Cloning: A Laboratory Manual, J. Sambrook, E. F. Fritsch and T. Maniatis, Cold Spring Harbor Laboratory Press, New York, 2000.

BC 003 MOLECULAR MEDICINE

Credit-1 Biochemical and molecular basis of pathogenesis, clinical course, diagnosis and treatment of GIT disorders, Liver diseases like jaundice, hepatitis, fibrosis, necrosis and cirrhosis. Acute and chronic renal failure Glomerular and tubular renal diseases. Credit-2 Biochemical and molecular basis of Haemoglobinopathies and other blood disorders. Myocardial infarction, Heart Failure, Hypertension. Credit-3 Biochemical and molecular basis of metabolic disorders and life style disorders - Diabetes, Atherosclerosis, PCOD, Obesity, Parkinson Disease, and Alzheimer’s Disease, OCD, Depression.

Books

1. Tietz Textbook of Clinical Chemistry, Third Edition. Carl A. Burtis and Edward R. Ashwood, eds. 2. Clinical chemistry. William J. Marshall, William J. Marshall (Ph. D.), S. K. Bangert 3. Clinical Chemistry: Principles, Procedures, Correlations, 5th ed. Michael L. Bishop, Edward P. Fody, & Larry Schoeff. Baltimore, MD: Lippincott Williams & Wilkins, 2005. 4. Robbins: Pathol Basis of Disease.7ed.(Cotran R., Kumar F., Collins T. WBSaunders). 5. C. A. Burtis, Edward R. Ashwood and D. E. Bruns (2007) Tietz Fundamentals of Clinical Chemistry. 6th Edn., Saunders. 6. Marshall WJ, Bangert SK. (2008) Clinical Chemistry, 6th Edition. Edinburgh, London: Mosby Elsevier. 7. Kumar, V., Abbas, A. K., Fausto, N. & Aster, J. C. (2010) Robin & Cotron Pathologic basis of Disease. 8th Edn., Saunders-Elsevier. 8. J. Vijg (2007) Aging of the Genome, Oxford Univ. Press. 9. B. S. Weeks & I. E. Alcamo (2010) AIDS : The Biological Basis. 5th Edn., Jones & Bartlett Publ., USA. 10. J. J. Berman (2009) Neoplasms : Principles of development and diversity. Jones & Bartlett Publ., USA.

Optional Paper II

BC 004 PLANT & MICROBIAL BIOCHEMISTRY (3 Credits)

Credit-1 Pathways and regulation of sugar metabolism in E. coli, Pseudomonas, etc.; Mechanism and regulation of fermentation and anaerobic respiration.

Credit-2 Photosynthesis: Photochemistry, Energy Considerations, CO2 fixation, Calvin cycle, C3, C4 and CAM; Photorespiration. Credit-3 Chemistry and Action of Phytohormones and Plant Growth Regulators.

Books 1. Plant Biochemistry by P. M. Dey (Editor), J. B. Harborne 2. Plant Physiology, Fourth Edition by Lincoln Taiz and Eduardo Zeiger 3. Microbiology: Concepts and Applications Michael Joseph Pelczar, E. C. S. Chan, Noel R. Krieg

Biochemistry 13 4. Prescott/Harley/Klein's Microbiology, Joanne Willey, Linda Sherwood, Chris Woolverton 5. Microbiology: An Introduction, Eighth Edition by Gerard J. Tortora 6. Atlas, R. M. (2001) Principles of Microbiology 3rd Edition, Wm. C. Brown Pub., Iowa, USA. 7. M. T. Madigan J. M. Martinko, & J. Parker Brock biology of microorganisms 9th Edn., Prentice Hall Int. Inc. 8. Prescott & Klein Microbiology 5th Edn., Mc Graw Hill. 9. G. J. Tortora Microbiology: An Introduction. 9thEdn, Benjamin Cummings, 2006. 10. Aharon Oren and R. Thane Papke Molecular Phylogeny of Microorganisms Caister Academic Press July 2010, ISBN: 978-1-904455-67-7

BC 005 NEUROCHEMISTRY (Optional Paper II)

Credit-1 CNS, PNS, ANS; Myelination, Blood Brain Barrier, Spatial segregation of cellular functions and axonal transport; Types of synapses and their advantages/functions. Credit-2 Neurotransmitter synthesis, storage, release (general treatment); Metabotropic and Ionotropic receptors (ACh, Glutamate). Neurochemistry of sensory system Credit-3 Various reflexes, adaptation, conditioning, facilitation, augmentation; Post-tetanic potentiation, sensitization; potentiation, desensitization, synaptic plasticity, learning and memory; Neurobiology of circadian rhythms – cellular rhythms, organismal rhythms-central and peripheral.

Books

1. Eric Kandel, James Schwartz, Thomas Jessell. (2000) Principles of Neural Science. 4thed McGraw-Hill, Health Professions Division. 2. Mark F. Bear, Barry W. Connors, Michael A. Paradiso (2007) Neuroscience 3ed., Lippincott Williams & Wilkins. 3. John G. Nicholls, A. Robert Martin, Paul A. Fuchs, David A. Brown, Mathew E. Diamond, and David A. Weisblat (2012). From Neuron to Brain. 5th Edn., Sinauer Publ. 4. Eric Kandel, James Schwartz and Thomas Jessell, Essentials of Neural Science & Behaviour, 2003. 5. Irvin Leritan and Leonard K Acznarck, (2001) The Neuron, Cell and Molecular Biology, 3rd Edn., Oxford University Press, USA. 6. W. Wang (2008) Molecular Mechanisms of Neurotransmitter release. Humana Press. 7. Dale Purves, George J. Augustine, David Fitzpatrick, William C. Hall, Anthony-Samuel LaMantia, Leonard E. White (2011)Neuroscience, Fifth Edition Sinauer Associates, Inc. 8. Larry R. Squire, Darwin Berg, Floyd Bloom, Sascha du Lac, Anirvan Ghosh (2008) Fundamental Neuroscience, Third Edition by Academic Press.

BC 006: ADVANCED PLANT BIOCHEMISTRY (Optional Paper II)

Credit-1 Advances in Phytohormones and its Mechanism.

Credit-2 Light Responses – Red, Far red and Blue light responses.

Credit-3 Phenolic Metabolism - Shikimate, Phenylalanine and Phenylpropanoid pathways, Flavanoids, Lignins and Anthocyanin. Isoprenoid Metabolism - Terpenoids and Carotenoids; Alkaloids, Cyanogenic glycosides and Non- protein amino acids.

1. Plant Biochemistry by P. M. Dey (Editor), J. B. Harborne 2. Plant Physiology, Fourth Edition by Lincoln Taiz and Eduardo Zeiger 3. Biochemistry & Molecular Biology of Plants. Bob Buchanan, Wilhelm Gruissem, Russell Jones

Biochemistry 14 4. Plant biochemistry by Lee and Ceopold.

BC 007: MICROBIAL ADAPTIVE BIOLOGY (Optional Paper II)

CREDIT -1 Structure of bacterial cell, Structure and Biosynthesis of bacterial cell wall; unique targets of cell wall for antimicrobial therapy.

CREDIT -2 Flagellar structure and Biosynthesis; Mechanism of bacterial motility. Adaptation to stationary phase, heat and cold shock, osmolarity and salinity

CREDIT- 3 Adaptation to oxidative stress; Genetics of Pathogenesis: Model organisms, genetic approaches to pathogenesis.

Books

1. Epstein S. S. (2009) Uncultured Microorganisms. Microbiology Monographs Vol. 10 Springer-Verlag. 2. Wen-Tso Liu and Janet K. Jansson (2010) Environmental Molecular Microbiology Caister Academic Press. 3. Xu, J. (2010) Microbial Population Genetics, Caister Academic Press. 4. G. Storz and R. Hennigge (2010) Bacterial Stress Responses, 2nd Edn. ASM Press.

Biochemistry 15