MS (April-September semester)

Curricula for MS in Biochemistry and Molecular Biology

(April-September semester)

 

                                                             April-September Semester

Credits

Compulsory courses                                                                       ( 9 credits)

 

BMB 507

Advanced Chemistry of Carbohydrates, Lipids and Nucleic acids

2

2

2

3

BMB 509

Advanced Molecular Biology

BMB 511

Protein Structure and Function

BMB 513

Principles of Biochemical Techniques

Elective courses                                                                               (4 credits)

 

BMB 525

Biochemistry of Plant Hormones and Biocides

2

2

2

2

2

BMB 527

Special Topics in Biochemistry

BMB 529

Animal Hormones

BMB 531

Environmental Biochemistry

BMB 504

Design of Biochemical Experiment

BMB 506 Research work                                                                (3 credits)

 

3 (S/U)

Total Credits

16

 

 BMB 507: Advanced Chemistry of Carbohydrates, Lipids and Nucleic acids

 

Carbohydrates: Chemistry of naturally occurring monosaccharides and their biochemically important derivatives: Deoxy and amino sugars, sugar acids and alcohols. Determination of complete structure of glucose.

Chemistry of oligosaccharides.

Chemistry of polysaccharides: Storage and structural polysaccharides; Plant and bacterial cell wall polysaccharides.

Chemistry and biological significance of naturally occurring glycosides and glycosaminoglycans.

Chemistry and function of glycolipids and glycoproteins.

Lipids: Chemistry and function of saturated and unsaturated fatty acids, triacylglycerols, glycerophospholipids and sphingolipids, terpenoids, sterols, carotenoids, tocopherols; Prostaglandins and thromboxanes. Principles of extraction, separation and purification of various lipid fractions.

Chemistry of lipid rancidity. Lipoproteins and membrane lipids. Comparative distribution of lipids in prokaryotes and eukaryotes.

Nucleic acids: Eukaryotic and prokaryotic DNA and their structural features. Circular DNA structure Watson-crick Model. Structural deviation from the model: A and Z DNA; Satellite DNA and their significance. DNA as genetic material: experimental evidence. Physicochemical properties of DNA including optical properties, denaturation, annealing and supercoiling. Histones in DNA staking. Effects of UV light and chemical mutagens on base composition.

Types, structure and function of RNA. Sedimentation characteristics of different RNAs. Catalytic and other functions of RNA. Plasmids. Viral nucleic acids.

Enzymic cleavage of nucleic acids. Maxam-Gilbert and Sanger’s method of sequencing of nucleotides. Southern, Northern and Western blotting. Restriction Fragment Length Polymorphism (RELP) and Polymerase Chain Reactions (PCR).

Books Recommended:

  1. E. Dynamic aspeft of Biochemistry, Oxford University Press, 1973.
  2. Bonner J. and J.E. Varner. Plant Biochemistry. Academic Press 1975.
  3. Davis, D.D. Plant Biochemistry. Black Well Sc. Pub. Oxford, 1975.
  4. Biochemistry by Donald Voet, 1995. 2nd edition, John Wiley and Sons, New York.
  5. Biochemistry by Lubert Stryer, 1995. 4th W. H. freeman and company. New York.
  6. Elliot, W.H. and D.C. Elliot, Biochemistry and Molecular Biology. Oxford University Press, 1997.
  7. Lehninger Principles of Biochemistry by David L. Nelson, 2008. 5th W. H. freeman and company. New York.
  8. Harper’s Biochemistry by Robert K Murray, 2002. 25th McGraw Hill. Printed in Singapore.
  9. Outlines of Biochemistry by Eric E. Conn and Paul K. Stumpf, 1987. 5th John Wiley and Sons, New York.

 

BMB 509: Advanced Molecular Biology

 

A review of concept of chromosome, chromatin and gene. Central dogma for the flow of information.

II. Replication of DNA

Semiconservative DNA, Meselson- stahl experiment, autoradiographic demonstration; applicability to single stranded DNA and RNA.

Geometric problems in semiconservative replication. Theta replication. Eukaryotic chromosomal DNA, Double Stranded DNA replication.

Major enzymic activities involved in DNA replication: DNA polymerases (prokaryotic and eukaryotic), DNA gyrase, ligase, primase, helicase and binding proteins.

Replication process in E. coli: Initiation point, unwinding of parental DNA, polymerization, synthesis of primer, okazaki fragments, joining of precursor strand. Events at replication fork.

Replication of DNA in eukaryotes: Multiple replication forks, histone separation.

DNA repair, fidelity of replication.

III. Transcription:

Definition, classes of RNA molecules. Features of prokaryotic and eukaryotic mRNA, tRNA and rRNA.

Prokaryotic transcription: Stages of transcription-Binding of RNA polymerase to the DNA template, initiation of polymerization, chain elongation and termination of synthesis. Initiation and termination signals.

Eukaryotic trasnscription; eukaryotic RNA polymerases. Difference between prokaryotic and eukaryotic transcripts; promotors, caps and tails; Introns and exons; post transcriptional processing.

Reverse transcription. RNA self replication.

IV. Translation:

Essential components of protein biosynthesis. The Genetic code: Characteristics; deciphering the genetic code, condon assignments. Activation of amino acids: Codon- Anticodon recognition. Structure of Ribosome: Prokaryotic ribosome, eukaryotic ribosome, Stage of protein synthesis: Initiation, elongation and termination. Energy requirement for protein synthesis; fidelity of translation. Difference between prokaryotic and eukaryotic translation. Protein localization in eukaryotes: Synthesis on membrane- bound ribosomes. Endoplasmic reticulum. Signal hypothesis; Glycoprotein. Inhibitors of protein synthesis.

V. Regulation of Gene expression:

The operon model: Lac operon (inducible system), Catabolic repression, Trp operon (repressible system). Transposable genetic elements, mechanism of transposition.

Translation control: Post translational processing, Feedback inhibition; protein degradation.

 

Books Recommended:

  1. Albert L. Lehninger. Principles of Biochemistry. Worth Publishers Inc. 1984.
  2. Donald Voet and Judith G. Voet. Biochemistry. John Wiley and Sons, 1990.
  3. Eric E. Conn, Paul K. Stumpf, George Brunening, Roy, H. Doi. Outlines of Biochemistry. John Wiley and Sons, 1987.
  4. W. Old and S.B. Primose. Principles of Gene manipulation. An introduction to genetic engineering. Blackwell publications 1989.
  5. Bruce Alberts, Dennis Bray, Julian Lewis, Martin Raff, Keith Roberts & James D. Watson Molecular Biology of the cells. 2nd edition, Garland Publishing Inc. N.Y. 1989.
  6. Watson, J.D., Hopkins M.H. and others. Molecular Biology of Genes. 4th The Benjamin/Cummings. Publishing co. 1987.

 

 

BMB 511: Protein Structure and Functions

 

Overview: Protein Function and Architecture.

Amino Acids: Chemical structure/characters, physical properties, way of participation in the folding, forces in protein folding, bonds that stabilize folded proteins, determination of folded structure of a protein and function of proteins.

Properties of the α-helix and β-sheet

Membrane protein structure: Structures of integral membrane proteins.

Protein stability: Bonds add stability to protein structure, properties of folded protein, agents disrupted protein structure.

Protein domain: Classification according to their secondary structural elements, Structural domains of globular proteins, hydrophobic cores, multi-domain proteins, α- and β-Domains.

Protein motifs: Definition based on primary sequence, identification of motifs from sequence.

Structural basis of protein function: Levels of protein function, fundamental biochemical functions, molecular recognition and catalysis, microenvironments, protein flexibility and biochemical function.

Functional properties of structural proteins: Proteins as frameworks, connectors and scaffolds, catalysis, active-site geometry, active-site chemistry, multifunctional enzymes with tunnels.

Control of protein function: Overview of regulation, protein interaction domains, regulation by location, control by pH and redox environment, effector ligand, protein switches based on nucleotide hydrolysis, regulation by degradation, control by phosphorylation, proteolysis, glycosylation, methylation, N-acetylation, sumoylation and nitrosylation.

Characteristics and functions of specialized proteins: Hemoglobin, myoglobins, cytochromes, actinomycin, interferons, seed storage proteins, lectins and other proteins of interest.

 

Recommended Books:

  1. Buxbaum, E. Fundamentals of Protein Structure and Function. Springer Science and Business Media Ltd. New York, NY 10013, USA. 2007.
  2. Creighton, T.E.  Protein function: a practical approach, 2nd Edn. Oxford University Press. 1997.
  3. Darby N.J. and Creighton, T.E.  Protein structure. IRL Press at Oxford University Press. 1993.
  4. Dobson, C.M. Protein Folding. Cambridge University Press, USA. 1996.
  5. Fersht, A. Structure and mechanism in protein science:a guide to enzyme catalysis and protein folding. H. Freeman. San Francisco, USA.  1999.
  6. Petsko, G.A. and Ringe, D. Protein structure and function. New Science Press. 2004.
  7. Obalinsky, T.R. Protein folding: new research. Nova Publishers. Inc. New York. 2006.

 

BMB 513: Principles of Biochemical Techniques

I. General Principles of Biochemical Investigations:

Whole animal studies, Perfusion of isolated organs, Use of plant material; Tissue and cell culture techniques, Preparation of tissue and cell homogenates; Method of cell fractionation.

II. Separation methods:

Centrifugation Techniques, Preparative centrifugation, - Isopycnic, Rate-zonal, Differential and Equilibrium isodensity centrifugation, Analytical ultracentrifugation.

Chromatographic techniques- Adsorption chromatography; Partition chromatography, Ion-exchange chromatography, Gas-liquid chromatography, Permeation chromatography, Affinity chromatography, High Performance liquid chromatography (HPLC).

Electrophoretic techniques: General techniques, Special electrophoresis - Disc electrophoresis, Imminoelectrophoresis, Isoelectric focusing. High voltage paper electrophoresis.

III. Analytical Methods:

Spectroscopic techniques-Basic laws of light absorption, Visible and ultraviolet spectrophotometry, Spectroflourimetry. Flame Spectrophotometry, Mass spectrometry, Nuclear Magnetic  Resonance (NMR).

Radioisotope techniques: Atomic Stability and radiation, Types of radioactive decay, Detection and measurement of radioactivity and safety aspects. Radioisotopes in biological Sciences.

Manometric techniques; Dialysis, Freeze- drying; Polarimetry.

IV. Biotechniques:

Bioassay techniques, Recombinant DNA technology- Biophysical and biochemical techniques used in recombinant DNA work. Restriction enzymes. Gene probes, preparation of chimeric DNA molecules, cloning; Blotting and Hybridation, DNA sequencing. Gene mapping.

Books Recommended: 

  1. Pollister, A. W. Ed. Physical Techniques in Biological Research 2nd Edition, New York, Academic Press, 1966.
  2. Albanese, A. A. Ed. Newer methods of nutritional biochemistry with applications and interpretations. New York, Academic press, 1972.
  3. J. R. Ed. Interacting macromolecules, the theory and practice of their electrophoreresis, ultracentrifugation and chromatography, 1970.
  4. Goodwin, T. W. Ed. Instrumentation in Biochemistry. London, Academic press, 1966.
  5. Draper, S. R. Ed. Biochemical analysis in Crop Science. Oxford University press, London 1976.
  6. Morris J. G. A Biologists Physical chemistry. 2nd Ed. Edward Arnold, London, 1974.
  7. Williams, B. L. and Wilson, K. Ed. A Biologist’s Guide to Principles and Techniques of Practical Biochemistry. William Clowes sons Ltd. London, 1975.
  8. Primrose, S. B. Modern Biotechnology, Blackwell Scientific publications, 1989.
  9. Chopra, V. L. and Nasim, A. Ed. Genetic Engineering and Biotechnology, Oxford and IBH Publishing Co Pvt. Ltd. 1993.
  10. Sambrook, J. E.F. Fritsch and Maniatis. Molecular cloning A laboratory Manual 2nd Cold Spring Harbor Laboratory Press.

 

 BMB 525: Biochemistry of Plant Hormones and Biocides

Phytohormones:

Physiology, importance, mode of action and bioassay of auxins, cytokinins, gibberellins, abscisic acid, methyl jasmonate, ethylene, brassinsteroids and polyamines. Basic concepts of plant cell signaling and stress physiology. Involvement of abscisic acid, methyl jasmonate and salicylic acid in plant cell signaling. Application of synthetic growth regulators in Agriculture.

Biocides:

Biochemistry and mode of action of herbicides. Biochemistry, mode of action and toxicity of organophosphorous insecticides, some important fungicides, bacteriocides, nematocides and acaricides. Biofungicide and Bioinsecticide. Biochemical analysis and bioassay of pesticide residues. Risk of biocides and alternatives. Environmental impact of biocide use.

 

Books Recommended: 

  1. M. Chadwick and D. R. Garrod (ed). Hormones. Recptors and cellular Interactions. Gambride University Press, 1986.
  2. Fox, J. E. and Jacobs, M. (ed.). Molecular Biology of Plant Growth Control. Proc. UCLA Symp. Molecular and Cellular Biology, New York, 1987.
  3. Hassall, K. A. The Biochemistry and Uses of Pesticides: Structure, Metabolism, Mode of Action and Uses in Crop Protection. MacMillan, 2nd Edn. 1990.
  4. Singh and S.K. Sawhney (ed.). Advances in Frontier Areas of Plant Biochemistry. Prentice Hall of India Pvt. Ltd., 1988.
  5. Venis, M.A. Hormone Binding Sites in Plants. Kongman, New York, 1985.

 

BMB 527: Special Topics in Biochemistry

Biological membrane

Membrane transport system

Excitable membrane and sensory systems

Oxygen transporters: Haemoglobin and Myoglobin

Biochemistry of cell differentiation

Cell communication

The complement system

Biochemistry of nitrogen fixation

Cell cytoskeleton

Molecular basis of cancer

Biochemistry of aging and senescence

Biochemistry of fruit ripening

Biochemistry of vision

Biochemistry of contractile elements

Bioluminescence

Acquired Immune Deficiency Syndrome (AIDS)

Inborn error of metabolism

Biochemistry of memory

 

Books Recommended:

  1. Albert Lehninger. Biochemistry. Worth Publishers, Inc. 1984.
  2. Beridge, M.J. The molecular basis of communication within the cell. Sci. An. 253(4), 142-152, 1985.
  3. Charles C. Richardson. Annual Review of Biochemistry. Annual Reviews Inc. 1992.
  4. Donal Voet and Jidith G. Voet. Biochemistry. John Wiley and Sons. N.Y. 1990.
  5. P. Talwar. Text Book of Biochemistry and Human Biology. Prentice Hall of India. New Delhi, 1988.
  6. Orme-Johnson, W.H. Molecular basis of nitrogen fixation. An. Rev. Biophys. Biophys. Chem. 14, 419-459, 1985.
  7. Weinberg, R.A.A. Molecular Basis of Cancer. Sci. Am. 249(5), 126-142, 1983.

 

 BMB 529: Animal Hormones

Organization of mammalian endocrine system. Relationship messengers. Mechanism of hormone action. General features of hormone classes based on action mechanism. Chemical nature, regulation of secretion, physiological and biochemical action of the following hormones: Pituitary hormone, prolactin and gonodotrophins, oxytocin and vassopressin; thyroxine and triodothyronine, epinephrine and norepinephrine, insulin and glucagon, testosterone, estrogen and progresterone; gastrin, cholecystokinin, endorphins, secretin etc.  Parathyroid hormone and calcium metabolism. Pheromones – their chemistry and biological importance.

 

Books Recommended:

  1. Albert L. Lehinger. Principles of Biochemistry Worth. Publishers Inc. 1984.
  2. L. Smith, Robert L. Hill. I. Robert Lehman, Robert J. Lotkowitz, Philip Handler and Abraham White. Biochemistry (Mammalin Biochemistry) Seventh Edition.
  3. Lubert Stryer. Biochemistry. Freeman International Edition, 1981.
  4. K. Murray, D.K. Grannes, P.A. Mays and V.W. Rodwell. Harpers Biochemistry, Appleton and Lange, A Publishing Division of Prentic Hall, 1988.

 

BMB 531: Environmental Biochemistry

Introduction to ecology and ecosystem

Environmental (water, soil and air) pollution: Their sources, effects and bioremediations.

Environmental genetics: Environmentally friendly biofertilizers & biopesticides; Biofuels & Biogas; Bioengineered foods: regulation and safety

Biochemistry of Plant defense systems and plant-pathogen interactions, Control of plant pathogen by genetic engineering

Biochemistry of Abiotic Stresses: Drought and salinity, Freezing stress, Flooding and oxygen deficit, Oxidative and heat stress.

New edible uses of novel plant products:

Uses and modifications of fatty acids & lipids, plants as sources of biodegradable plastics, plants as factories for chemical drug.

 

Books Recommended:

  1. Marquita, K Hill. Understanding Environmental Pollution. 3rd Edition, 2010.

  2.  Stanley E. Manahan. Environmental Chemistry. 8th Edition. 2005.

  3. Gary W. VanLoon, Stephen J. Duffy. Environmental chemistry: a global perspective. 2005. Oxford University Press.

  4. James E. Girard. Principles of Environmental Chemistry. 2004.

 

BMB 504: Design of Biochemical Experiment

 Preliminaries: Nature of experiments, Basic issues of experimental design, Ethical issues of biochemical experimentations.

Data Transformation: square-root transformation, logarithmic transformation and angular transformation, The Box-Cox method.

Regression and Correlation: Simple regression and correlation, method of least squares. Multiple regression and correlation analysis. Tests of significance: t, Chi-square (χ2) and F tests. Concept of sampling techniques.

Basic Experimental Designs: Layout of basic designs and analysis of variance of data in completely randomized design, randomized block design and Latin square design. Multiple comparisons Test, Missing value estimation: Estimation of 1 or 2 missing values in randomized block design and Latin square design and technique of analysis of variance.

Factorial Experiments: Definition, advantages and disadvantages of factorial experiments. Factorial experiments conducted in completely randomized design and randomized block design. Split-plot design and split-split-plot design. Response surface method, Nested design, Analysis of covariance.

 

Texts:

  1. Montgomery, D.C. (2003): Design and Analysis of Experiments, 5th ed, Wiley, N.Y.
  2. Ahmed A.R., M.A.A. Bhuiyan, and M. Z. Hossain (2003). Experimental Designs: Theory and Application. Rokeya Sultana Mili, Dhaka.
  3. Meed, R. R.N. Cornow and A.M. Hasted (1993): Statistical Methods in Agriculture and Experimental Biology. Chapman and Hall.

References:

  1. Gomez, K.A. and A.A. Gomez (1984): Statistical Proceedings for Agricultural Research. John Wiley and Sons.
  2. Federer, M.T. (1977): Experimental Design. Indian ed. Oxford and IBH Publishing Co., N.Y.
  3. John, P.W. M. (1971): Statistical Analysis of Experimental Design. Collier McMilan, N.Y.
  4. Kempthorne, O. (1952): Design and Analysis of Experiments. Wiley and Sons, N.Y.
  5. Scheffe, H. (1961): Analysis of variance. Wiley and Sons, N.Y
  6. Mead, R. (1988): The Design of Experiments: Statistical Principles for Practical Applications. Cambridge University Press.
  7. Das, M.N. and Giri, N.C. (1998): Design and Analysis of Experiments 2nd New Delhi: Wiley Eastern.