MS (October-March semester)

Curricula for MS in Biochemistry and Molecular Biology

(October-March semester)

 

                                                         October-March Semester

Credits

Compulsory courses                                                                       (9 credits)

 

     BMB 501

Enzymes and Enzyme Technology

2

     BMB 502

Bioinformatics

2

     BMB 503

Metabolism and Nutritional Biochemistry

3

     BMB 505

Principles of  Recombinant DNA Technology

2

Elective courses                                                                               (4 credits)

 

     BMB 515

Biochemistry of Plant and Microbes

2

     BMB 517

Animal Biochemistry

2

     BMB 519

Biochemistry of Fishes

2

     BMB 521

Molecular Diagnostics and DNA forensic sciences

2

     BMB 523

Clinical Biochemistry and Immunochemistry

2

BMB 506 Research work                                                               (3 credits)

3 (S/U)

Total Credits

16

 

BMB 501: Enzymes and Enzyme Technology

Introduction to enzyme. Measurement and expression of enzyme activity.  Enzyme stability and denaturation. Properties of enzymes with special reference to specificity, mode of action, activation and inhibition. Activation of zymogens. Factors contributing to catalytic efficiency of enzymes. Dependence of enzymatic velocity on substrate and enzyme concentrations. Kinetic treatment of the effect of inhibitors, pH, temperature, pressure and ionic strength. Mechanisms of action of lysozyme and carboxypeptidase. Allosteric enzymes and the models of their action mechanisms. Activity inducer. Mechanism of bisubstrate reactions. Concept of active site and its determination.

Enzyme kinetics and modeling of enzymatic system. Regeneration of cofactors for enzyme biocatalysis. Industrial enzymes: amylase, lipase, protease, glucose isomerase, cellulase, pectinase, inulinase, peroxidases and pectin methyl esterase. Isolation and purification of enzymes. Immobilization of enzymes. Protein engineering of industrial enzymes. Specific enzymes and their application: cold-adapted enzyme, ribozymes, hybrid enzymes, diagnostic enzymes, therapeutic enzymes, isozymes and restriction enzymes. Enzyme-based analytical reagents and biosensors.

 

Books Recommended:

  1. Lehninger Principles of Biochemistry by David L. Nelson, 2008. 5th W. H. freeman and company. New York.
  2. Textbook of Biochemistry by Thomas M. Devlin, 2002. 5th John Wiley and Sons, Inc. Printed in USA
  3. Biochemistry by Donald Voet, 1995. 2nd edition, John Wiley and Sons, New York
  4. Outlines of Biochemistry by Eric E. Conn and Paul K. Stumpf, 1987. 5th John Wiley and Sons, New York
  5. Biochemistry by Albert L Lehninger, 1982. 2nd edition Kalyani Publishers. Ludhiana, New Delhi.
  6. Harper’s Biochemistry by Robert K Murray, 2002. 25th McGraw Hill. Printed in Singapore.
  7. Biochemistry by Lubert Stryer, 1995. 4th W. H. freeman and company. New York.
  8. Biochemistry by Mary K Campbell, 1999. 3rd J/B Woolsey Associates. Printed in USA.

 

BMB 502: Bioinformatics

Introduction to bioinformatics and database: Bioinformatics analyses and its application. Sequence and structure of databases.  Different biological database. Familiarization with databases (NCBI, ENSEMBL etc). Information retrieval from biological database. Access to distributed data.

Sequence alignment and database searching: Different sequence alignment and their significant.  Application and interpretation of BLAST. Application of Multiple sequence alignment via clustalW program. Codon optimization.

Phylogenetic analysis:  Phylogenetic data analysis and tree building method.

Plasmid mapping and Primer design: Restriction mapping. Primer design program and software.

Introduction to Proteomics and Genomics: DNA microarray. Techniques involved in proteomics and genomic.

Bioinformatics software and its application

 

Books Recommended: 

  1. Harisha and Harisha S. Fundamentals of Bioinformatics. I. K. International Publishing House Pvt. Lit. Mumbai-110 016 (India).
  2. Jenny Gu, Philip E. Bourne (edit). Structural Bioinformatics (2nd edition). John Wiley & Sons, Sep 20, 2011.
  3. Jonathan Pevsner. Bioinformatics and Functional Genomics (2nd edition). John Wiley & Sons, May 4, 2009.
  4. David W. Mount. Bioinformatics: Sequence and Genome Analysis. CSHL Press, 2004.
  5. N. Gautham. Bioinformatics: Databases and Algorithms. Alpha Science, 2006.
  6. S. Ignacimuthu. Basic Bioinformatics. Alpha Science International, 2005.

  

BMB 503: Metabolism and Nutritional Biochemistry

Introduction to bioenergetics and energy transformation in biological systems.

General aspects of metabolic processes and their regulation: Glycolysis, glycogenesis, glycogenolysis, gluconeogenesis, citric acid cycle, hexose monophosphate shunt, glyoxylate cycle and uronic acid pathway. Metabolic transformations of amino acids. Urea and uric acid synthesis. Biosynthesis of essential amino acids. Catabolic and anabolic pathways of fatty acids. Biosynthesis of cholesterol.

Hormonal control of metabolism.

Nutrition and Genomics: Nutrient composition of foods. Food quality evaluation. Nutrients in gene expression and regulation. Malnutrition and immunity. Poverty and nutrition. Nutrition in emergencies: famine, war, flood and natural disasters. International nutrition: Nutrition in developing economics. Globalization and Nutrition. Nutritional enhancement of plant foods. Nutrition and HIV/AIDS. Nutritional management of diabetes mellitus and cardiovascular disease. Micronutrients (Vitamins and minerals) in energy transformation system. Obesity and its implication for health. Food and Nutrition Security in developing countries. Street food as meal of millions. Nutrition Interventions Programmes in Bangladesh.

 

Books Recommended:

  1. Lehninger Principles of Biochemistry by David L. Nelson, 2008. 5th W. H. freeman and company. New York.
  2. Textbook of Biochemistry by Thomas M. Devlin, 2002. 5th John Wiley and Sons, Inc. Printed in USA
  3. Biochemistry by Donald Voet, 1995. 2nd edition, John Wiley and Sons, New York
  4. Outlines of Biochemistry by Eric E. Conn and Paul K. Stumpf, 1987. 5th John Wiley and Sons, New York
  5. Biochemistry by Albert L Lehninger, 1982. 2nd edition Kalyani Publishers. Ludhiana, New Delhi.
  6. Harper’s Biochemistry by Robert K Murray, 2002. 25th McGraw Hill. Printed in Singapore.
  7. Biochemistry by Lubert Stryer, 1995. 4th W. H. freeman and company. New York.
  8. Biochemistry by Mary K Campbell, 1999. 3rd J/B Woolsey Associates. Printed in USA.
  9. Nutritional Biochemistry by Tom Brody. 2nd 1998.

 

BMB 505: Principles of Recombinant DNA Technology

I: Rearrangement of Genes:

Mutation: Types and causes. DNA repair mechanisms.

Sexual reproduction: Fusion, Meiosis, Diploidy, Haploidy

Gene Transfer in Bacteria: Transformation, Transduction and conjugation.

Mobile genetic element: Lysogenic phage, plasmids, transposones.

Recombination mechanisms: Site-specific recombination, Homologous recombination, transposition (Holliday mechanism). Illegitimate recombination.

II: Creation of Recombinant DNA molecules.

Recombinant DNA cloning procedure, Restriction endonucleases, Plasmids, Vectors, Synthesis of complementary DNA, integration of cDNA with vector DNA, preparation of genetically pure, clonal population of recipient cells.

Construction of chromosomal clones: Genomic libraries. Fragmentation of DNA.

Cloning of DNA fragment- using plasmids, phage lambda, cosmids.

Chromosome Walking

Identification of specific clones by hybridization: With mRNA, with the cloned cDNA, with synthetic oligonucleotides.

III: Analysis of DNA and RNA

Analysis of chromosomal and extrachromosomal DNA

Analysis of RNA

Determination of base sequence.

IV: Manipulating DNA in Plants and Animals 

Strategies for gene transfer to plant and animal cells. Gene silencing. Biosafety and ethical issues related to genetically modified organism.

V: Practical Benefits from Gene Cloning:

In agriculture, medicine, and industry.

 

Books Recommended:

  1. Jocelyn E. Krebs, Elliott S. Goldstein and Stephen T. Kilpatrick 2011. Lewin’s Genes X. Jones and Bartlett Publishers, Sudbury, MA 01776.
  2. S.B. Primrose and R.M. Twyman 2006. Principles of gene manipulation and genomics 7th ed.Blackwell publishing, USA.
  3. Robert H. Tamarin 1996. Principles of Genetics 5th edition, W.M.C. Brood Publishers.
  4. Watson, J.D, M. Gilman, J. Witowski and M. Zoller 1992. Recombinant DNA 2nd ed. New York  Freeman.
  5. Wu, R.L. Grossman and K. Moldave eds. 1989. Recombinant DNA Methodology, San Diego, Academic Press.
  6. Karl Drlica understanding DNA and Gene Cloning: A Guide for the Curious John Wiley and Sons 1984.
  7. Hardy, K.G. Plasmid- A Practical Approach 1987. IRL Press Ltd.
  8. Kerby, L.T. 1990. DNA Fingerprinting. An introduction New York Stockton Press.

 

 BMB 515: Biochemistry of Plants and Microbes

Cellular and sub-cellular compartmentation. Plant cell and organelle structure, role of compartmentation in regulation of metabolism. Photosynthesis: Light reaction, electron transport, dark reactions, Calvin Cycle and regulation, Photorespiration, C3, C4 and CAM metabolism and their comparison. Role of carbohydrate metabolism in plants in normal and stress conditions. Glyoxylate cycle. Nitrogen and sulfur assimilation and metabolism. Physiology, importance and mode of action of plant hormones. Production and commercial application of secondary metabolites. Medicinal plants and their uses.

Basic concepts of microbes: Properties and classification of microorganisms. Characteristics and functions of microbes. Physical and chemical differences in the structural organization of different microbes. Bacterial cell structure. Classification of bacteria. Nutritional aspects of bacterial cultivation media, composition, growth and reproduction. Environmental factors affecting bacterial growth: temperature, pH and osmotic pressure. Characteristics of viruses. Differences between bacteria and viruses. Classification of viruses. Physical and chemical structures of different Viruses. Bacteriophage. Beneficial and harmful microbial interaction with human. Antibiotics. Microbes in soil. Industrial use of microbes.

 

Recommended books: 

  1. Lehninger Principles of Biochemistry by David L. Nelson, 2008. 5th W. H. freeman and company. New York.
  2. Textbook of Biochemistry by Thomas M. Devlin, 2002. 5th John Wiley and Sons, Inc. Printed in USA
  3. Biochemistry by Donald Voet, 1995. 2nd edition, John Wiley and Sons, New York
  4. Outlines of Biochemistry by Eric E. Conn and Paul K. Stumpf, 1987. 5th John Wiley and Sons, New York
  5. Biochemistry by Albert L Lehninger, 1982. 2nd edition Kalyani Publishers. Ludhiana, New Delhi.
  6. Harper’s Biochemistry by Robert K Murray, 2002. 25th McGraw Hill. Printed in Singapore.
  7. Biochemistry by Lubert Stryer, 1995. 4th W. H. freeman and company. New York.
  8. Biochemistry by Mary K Campbell, 1999. 3rd J/B Woolsey Associates. Printed in USA
  9. Microbial Biochemistry. G.N. Cohen. 2010. 2nd Springer.

 

BMB 517: Animal Biochemistry

Advanced Chemistry of animal cellular biomolecules with reference to protein, nucleic acid, lipid and carbohydrate. Physico-chemical properties of membrane lipids and lipoproteins. Structural and chemical properties of cellulose glycogen and glycosaminoglycans. Physico-chemical properties of enzymes. Enzymes in dairy industries. Biochemistry of digestion and absorption of feedstuffs in ruminants and non-ruminants. Biosynthesis of volatile fatty acids VFA and their metabolic fate. Principles of Bioenergetics. Urea cycle and utilization of urea for microbial protein biosynthesis. Metabolic transformation of amino acids. Metabolic regulation and biological function of glycolysis, Pentose phosphate pathway and citric acid cycle. Differential role of NADH and NADPH.

 

Books Recommended:

  1. Lehninger Principles of Biochemistry by David L. Nelson, 2008. 5th W. H. freeman and company. New York.
  2. Textbook of Biochemistry by Thomas M. Devlin, 2002. 5th John Wiley and Sons, Inc. Printed in USA
  3. Biochemistry by Donald Voet, 1995. 2nd edition, John Wiley and Sons, New York
  4. Outlines of Biochemistry by Eric E. Conn and Paul K. Stumpf, 1987. 5th John Wiley and Sons, New York
  5. Biochemistry by Albert L Lehninger, 1982. 2nd edition Kalyani Publishers. Ludhiana, New Delhi.
  6. Harper’s Biochemistry by Robert K Murray, 2002. 25th McGraw Hill. Printed in Singapore.
  7. Biochemistry by Lubert Stryer, 1995. 4th W. H. freeman and company. New York.
  8. Biochemistry by Mary K Campbell, 1999. 3rd J/B Woolsey Associates. Printed in USA.
  9. Text Book of Biochemistry and Human Biology. G.P. Talwar, 1998. Prentice Hall of India, New Delhi.
  10. Animal Nutrition and feeding Practices in India. S. K. Ranjhan. 1998. 2nd revised edition. Vikas Publishing House Private Ltd. (India).

 

 BMB 519: Biochemistry of Fishes

A brief overview of carbohydrate, fat and protein in fish.

Energy requirement of fishes.

Digestion and absorption of carbohydrate, fat and protein.

Metabolism: Concept of Maintenance metabolism, Basal metabolism, Weight-metabolism relationship.

Metabolism of carbohydrates: Regulation of carbohydrate metabolism, Role of carbohydrate in energy supply. Role of gluconeogenesis.

Metabolism of protein: Metabolic energy of protein. Qualitative and quantitative requirement of amino acids and protein. Evaluation of nutritional value of protein.

Metabolism of lipids: Requirements of fat and fatty acids, Biological oxidation of fatty acids, epoxidation, hydroxylation, oxidative fusion, Oxidation by oxygen and lipoxygenase. Biosynthesis of essential fatty acids, polyenes, triglycerides and prostaglandin’s.

Toxic constituents of oxidized lipid and its effect on fish.

Antioxidant: Types, biochemical mechanism of antioxidant action, synergists.

Concept of free radicals and their reaction mechanism

Vitamins and minerals in fish nutrition.  

Toxins: Types and biochemical effects on fish.

Hormonal control of fish metabolism.

 

Books Recommended: 

  1. Lehninger Principles of Biochemistry by David L. Nelson, 2008. 5th W. H. freeman and company. New York.
  2. Biochemistry by Donald Voet, 1995. 2nd edition, John Wiley and Sons, New York.
  3. Biochemistry by Lubert Stryer, 1995. 4th W. H. freeman and company. New York.
  4. Biological Chemistry. Mahler, H.R. and E.H. Cordes. 1971. Harper and Harper.
  5. The Biochemistry of Fishes. Williams, R.T. (ed.). 1951. London, Cambridge University Press.
  6. Nutrition of Pond Fishes. Harper, B.1990. Cambridge University Press.
  7. Lipids in Foods, Chemistry, Biochemistry and Technology. Gunstone, F.D. and Norris, F. A.1983 Pergamon Press.
  8. Food Antioxidant. Hudson, B.J.F. 1990. Elsevier Science Publishers Ltd.
  9. Fish Nutrition. Halver, J.E. 2nd Edition. 1988. Academic Press.

 

BMB 521: Molecular Diagnostics and DNA Forensic Sciences

Introduction to Molecular Diagnostics. Isolation and characterization of DNA/RNA from different clinical specimens. Molecular methods for diagnosis of genetic disorders, infectious diseases and cancer.

PCR in molecular diagnostics: Conventional PCR and real time PCR, qualitative and quantitative PCR, PCR-ELISA.

DNA technology in forensic sciences: DNA Polymorphism, Minisatellite sequences or Variable Number of Tandem Repeats (VNTRs), Microsatellite sequences or Short Tandem Repeats (STRs), Biology and nomenclature of STR markers, Single Nucleotide Polymorphism (SNPs), SINEs and LINEs.

DNA typing methods: DNA fingerprinting, Restriction Fragment Length polymorphism (RFLP), Single locus and multi-locus DNA typing, Allele specific oligonucleotides (ASO). DNA detection methods: Silver staining, Fluorescent dyes and gel electrophoresis. 

DNA Extraction and quantitation from forensic samples: DNA Extraction from liquid blood, soft tissues, bone, teeth, buccal cells, semen, blood stains, and semen stains etc.  DNA quantitation: Spectrophotometry, Fluorometry, Slot-blot, Real-time PCR. 

Applications of DNA Profiling

Identity test, Parentage test, Sib ship analysis, Kinship analysis. Identification of dead bodies.

 

Books Recommended:

  1. Mousumi Debnath, Prakash S. Bisen, Godavarthi B. K. S. Prasad. Molecular Diagnostics: Promises and Possibilities. Springer, 2010.
  2. Wayne W. Grody, M.D., Robert M. Nakamura, M.D., Frederick L. Kiechle. Molecular Diagnostics: Techniques and Applications for the Clinical Laboratory. Academic press. 2010.
  3. Harald Kessler. Molecular Diagnostics of Infectious Diseases. 2010.

 

BMB 523: Clinical Biochemistry and Immunochemistry

Abnormalities of carbohydrate, protein and fat metabolism with special reference to metabolic diseases.

Disorder and test of gastrointestinal functions.

Disorder and test for renal, hepatic and cardiac functions.

Clinical syndromes associated with disturbance of water, electrolytic and acid-base balance.

Clinical enzymology with special reference to serum enzymes.

Antigens and haptens; immunoglobulins and cellular basis of their formation. Antigen-antibody reactions.

 

Books Recommended: 

  1. Bach, J.F. Editor. Immunology. John Wiley and Sons, 1980.
  2. Kane, KO, J. J. (Editor). Clinical Biochemistry of Domestic Animals. 3rd Edition, Academic Press Inc. 1980.
  3. Newsholme, E.A. and Leech, A.R. Biochemistry for Medical Sciences. John Wiley and Sons, 1985.
  4. Qunn, L.Y. Immunological concepts. Iowa State University Press, 1968.
  5. Soyd, C. Fundamentals of Immunology. 4th Edition, New York, Interscience Publishers, 1966.
  6. Talwar, G.P. Editor. Text Book of Biochemistry and Human Biology, New delhi, Prentice Hall Pvt. Ltd. , 1980.
  7. Whithy, L.G.; Perly-Robb, I.W. and Smith, A.F. Lecture Notes on Clinical chemistry, 3rd Oxford. Blackwell Scientific Publication, 1984.