Biochemistry
Unit - I
Chemical basis of life; Composition of living matter; Water – properties, pH, ionization and hydrophobicity;
Emergent properties of biomolecules in water; Biomolecular hierarchy; Macromolecules; Molecular assemblies;Structure-function relationships
Amino acids – structure and functional group properties; Peptides and covalent structure of proteins;
Elucidation of primary and higher order structures; Evolution of protein structure; Structure-function
relationships in model proteins like ribonuclease A, myoglobin, hemoglobin, chymotrypsin etc.; Tools to
characterize expressed proteins.
Unit - II
Enzyme catalysis – general principles of catalysis; Quantitation of enzyme activity and efficiency; Enzyme
characterization and Michaelis-Menten kinetics; Relevance of enzymes in metabolic regulation, activation,
inhibition and covalent modification; Single substrate enzymes
Unit - III
Sugars - mono, di, and polysaccharides; Suitability in the context of their different functions- cellular structure,energy storage, signaling; Glycosylation of other biomolecules - glycoproteins and glycolipids; Lipids -structure and properties of important members of storage and membrane lipids; lipoproteins
Unit - IV
Biomembrane organization - sidedness and function; Membrane bound proteins - structure, properties and
function; Transport phenomena Nucleosides, nucleotides, nucleic acids - structure, diversity and function; sequencing; Brief overview of central dogma
Unit - V
Bioenergetics-basic principles; Equilibria and concept of free energy; Coupled processes; Glycolytic pathway; Kreb’s cycle; Oxidative phosphorylation; Photosynthesis; Elucidation of metabolic pathways; Logic and integration of central metabolism; entry/ exit of various biomolecules from central pathways; Principles of metabolic regulation; Regulatory steps; Signals and second messengers.
Texts/References
1. V.Voet and J.G.Voet, Biochemistry, 3rd edition, John Wiley, New York, 2004.
2. A.L. Lehninger, Principles of Biochemistry, 4th edition, W.H Freeman and Company, 2004.
3. L. Stryer, Biochemistry, 5th edition, W.H. Freeman and Company, 2002.
Unit I
Cell Theory & Methods of Study
Microscope and its modifications – Light, phase contrast and interference, Fluorescence, Confocal, Electron
(TEM and SEM), Electron tunneling and Atomic Force Microscopy, etc.
Membrane Structure and Function
Structural models; Composition and dynamics; Transport of ions and macromolecules; Pumps,
carriers and channels; Endo- and Exocytosis; Membrane carbohydrates and their significance
in cellular recognition; Cellular junctions and adhesions; Structure and functional significance
of plasmodesmata.
Unit II
Organelles
Nucleus – Structure and function of nuclear envelope, lamina and nucleolus; Macromolecular
trafficking; Chromatin organization and packaging; Cell cycle and control mechanisms;
Mitochondria – structure, organization of respiratory chain complexes, ATP synthase, Structure- function
relationship; Mitochondrial DNA and male sterility; Origin and evolution; Chloroplast– Structure-function
relationship; Chloroplast DNA and its significance; Chloroplast biogenesis; Origin and evolution.
Unit III
Endo-membrane System and Cellular Motility
Structure and function of microbodies, Golgi apparatus, Lysosomes and Endoplasmic Reticulum; Organization
and role of microtubules and microfilaments; Cell shape and motility; Actin-binding proteins and their
significance; Muscle organization and function; Molecular motors; Intermediate filaments; Extracellular
matrix in plants and animals.
Unit IV
Cellular Movements and Pattern Formation
Laying of body axis planes; Differentiation of germ layers; Cellular polarity; Model plants like Fucus and
Volvox; Maternal gene effects; Zygotic gene effects; Homeotic gene effects in Drosophila; Embryogenesis and
early pattern formation in plants; Cell lineages and developmental control genes in Caenorhabditis.
Unit V
Differentiation of Specialized Cells
Stem cell differentiation; Blood cell formation; Fibroblasts and their differentiation; Cellular basis of immunity;
Differentiation of cancerous cells and role of proto-oncogenes; Phase changes in Salmonella; Mating cell
types in yeast; Surface antigen changes in Trypanosomes; Heterocyst differentiation in Anabaena; Sex
determination in Drosophila.
Plant Meristem Organization and Differentiation
Organization of Shoot Apical Meristem(SAM); Organization of Root Apical Meristem(RAM); Pollen
germination and pollen tube guidance; Phloem differentiation; Self-incompatibility and its genetic control;
Embryo and endosperm development; Heterosis and apomixis.3
Texts/References
1. Lodish et al., Molecular cell Biology, 4th Edition, W.H. Freeman & Company, 2000.
2. Smith & Wood, Cell Biology, 2nd Edition, Chapman & Hall, London, 1996.
3. Watson et al., Molecular Biology of the gene, 5th Edition, Pearson Prentice Hall. USA, 2003.
4. B. M. Turner, Chromatin & Gene regulation, 1st Edition, Wiley-Blackwell, 2002.
5. Benjamin Lewin, Gene IX, 9th Edition, Jones and Barlett Publishers, 2007.
Molecular Biology - 3 Credits
Unit I
Genome organization
Organization of bacterial genome; Structure of eukaryotic chromosomes; Role of nuclear matrix
in chromosome organization and function; Matrix binding proteins; Heterochromatin and Euchromatin; DNA
reassociation kinetics (Cot curve analysis); Repetitive and unique sequences; Satellite DNA;
DNA melting and buoyant density; Nucleosome phasing; DNase I hypersensitive regions; DNA methylation & Imprinting.
Unit II
DNA Structure; Replication; Repair & Recombination
Structure of DNA - A-,B-, Z- and triplex DNA; Measurement of properties-Spectrophotometric, CD, AFM
and Electron microscope analysis of DNA structure; Replication initiation, elongation and termination in
prokaryotes and eukaryotes; Enzymes and accessory proteins; Fidelity; Replication of single stranded circular
DNA; Gene stability and DNA repair- enzymes; Photoreactivation; Nucleotide excision repair; Mismatch
correction; SOS repair; Recombination: Homologous and non-homologous; Site specific recombination;
Chi sequences in prokaryotes; Gene targeting; Gene disruption; FLP/FRT and Cre/Lox recombination.
Unit III
Prokaryotic & Eukaryotic Transcription
Prokaryotic Transcription; Transcription unit; Promoters- Constitutive and Inducible; Operators;
Regulatory elements; Initiation; Attenuation; Termination-Rho-dependent and independent;
Anti-termination; Transcriptional regulation-Positive and negative; Operon concept-lac, trp, ara, his,
and gal operons; Transcriptional control in lambda phage; Transcript processing; Processing of
tRNA and rRNA
Eukaryotic transcription and regulation; RNA polymerase structure and assembly; RNA polymerase
I, II, III; Eukaryotic promoters and enhancers; General Transcription factors; TATA binding proteins
(TBP) and TBP associated factors (TAF); Activators and repressors; Transcriptional and post-transcriptional
gene silencing
Unit IV
Post Transcriptional Modifications
Processing of hnRNA, tRNA, rRNA; 5'-Cap formation; 3'-end processing and polyadenylation; Splicing;
RNA editing; Nuclear export of mRNA; mRNA stability; Catalytic RNA.
Translation & Transport
Translation machinery; Ribosomes; Composition and assembly; Universal genetic code; Degeneracy of codons;4
M.Sc (General Biotechnology)
Termination codons; Isoaccepting tRNA; Wobble hypothesis; Mechanism of initiation, elongation and
termination; Co- and post-translational modifications; Genetic code in mitochondria; Transport of proteins
and molecular chaperones; Protein stability; Protein turnover and degradation
Unit V
Mutations; Oncogenes and Tumor suppressor genes
Nonsense, missense and point mutations; Intragenic and Intergenic suppression; Frameshift mutations;
Physical, chemical and biological mutagens; Transposition - Transposable genetic elements in prokaryotes
and eukaryotes; Mechanisms of transposition; Role of transposons in mutation; Viral and cellular oncogenes;
Tumor suppressor genes from humans; Structure, function and mechanism of action of pRB and p53 tumor
suppressor proteins; Activation of oncogenes and dominant negative effect; Suppression of tumor suppressor
genes; Oncogenes as transcriptional activators.
Text/References
1. Benjamin Lewin, Gene IX, 9th Edition, Jones and Barlett Publishers, 2007.
2. J.D. Watson, N.H. Hopkins, J.W Roberts, J. A. Seitz & A.M. Weiner; Molecular Biology of the Gene, 6th Edition,
Benjamin Cummings Publishing Company Inc, 2007.
3. Alberts et al; Molecular Biology of the Cell, 4th edition, Garland, 2002.
Analytical Techniques - 3 Credits
Unit I
Basic Techniques
Buffers; Methods of cell disintegration; Enzyme assays and controls; Detergents and membrane proteins;
Dialysis, Ultrafiltration and other membrane techniques
Spectroscopy Techniques
UV, Visible and Raman Spectroscopy; Theory and application of Circular Dichroism; Fluorescence; MS,
NMR, PMR, ESR and Plasma Emission spectroscopy
Unit II
Chromatography Techniques
TLC and Paper chromatography; Chromatographic methods for macromolecule separation - Gel permeation,
Ion exchange, Hydrophobic, Reverse-phase and Affinity chromatography; HPLC and FPLC; Criteria of
protein purity
Electrophoretic techniques
Theory and application of Polyacrylamide and Agarose gel electrophoresis; Capillary electrophoresis; 2D
Electrophoresis; Disc gel electrophoresis; Gradient electrophoresis; Pulsed field gel electrophoresis
Unit III
Centrifugation
Basic principles; Mathematics & theory (RCF, Sedimentation coefficient etc); Types of centrifuge -
Microcentrifuge, High speed & Ultracentrifuges; Preparative centrifugation; Differential & density gradient
centrifugation; Applications (Isolation of cell components); Analytical centrifugation; Determination of
molecular weight by sedimentation velocity & sedimentation equilibrium methods5
M.Sc (General Biotechnology)
Unit IV
Radioactivity
Radioactive & stable isotopes; Pattern and rate of radioactive decay; Units of radioactivity; Measurement
of radioactivity; Geiger-Muller counter; Solid & Liquid scintillation counters (Basic principle,
instrumentation & technique); Brief idea of radiation dosimetry; Cerenkov radiation; Autoradiography;
Measurement of stable isotopes; Falling drop method; Applications of isotopes in biochemistry; Radiotracer
techniques; Distribution studies; Isotope dilution technique; Metabolic studies; Clinical application;
Radioimmunoassay
Unit V
Advanced Techniques
Protein crystallization; Theory and methods; API-electrospray and MALDI-TOF; Mass spectrometry; Enzyme
and cell immobilization techniques; DNA & Peptide Synthesis.
Texts/References
1. Freifelder D., Physical Biochemistry, Application to Biochemistry and Molecular Biology, 2nd Edition, W.H.
Freeman & Company, San Fransisco, 1982.
2. Keith Wilson and John Walker, Principles and Techniques of Practical Biochemistry, 5th Edition, Cambridge
University Press, 2000.
3. D. Holme & H. Peck, Analytical Biochemistry, 3rd Edition, Longman, 1998.
4. R. Scopes, Protein Purification - Principles & Practices, 3rd Edition, Springer Verlag, 1994.
5. Selected readings from Methods in Enzymology, Academic Press.
Biostatistics and Computer Applications - 3 Credits
Unit I
Fundamental concepts in applied probability; Exploratory data analysis and statistical inference; Probability
and analysis of one and two way samples; discrete and continuous probability models; Expectation and
variance; Central limit theorem; Inference; Hypothesis; Critical region and error probabilities; Tests for
proportion; Equality of proportions; equality of means of normal populations(variance known, variance
unknown); Chi-square test for independence; P-value of the statistic; Confidence limits; Introduction to one
way and two-way analysis of variance; Data transformations
Unit II
Elements of programming languages - C and PERL; Data base concept; Database management system;
Database browsing and Data retrieval; Sequence database and genome database; Data Structures and
Databases; Databases such as GenBank; EMBL; DDBJ; Swissprot; PIR; MIPS; TIGR; Hovergen; TAIR;
PlasmoDB; ECDC; Searching for sequence database like FASTA and BLAST algorithm.
Unit III
Cluster analysis; Phylogenetic clustering by simple matching coefficients; Sequence Comparison; Sequence
pattern; Regular expression based pattern; Theory of profiles and their use in sequence analysis; Markov
models; Concept of HMMS; Baum-Welch algorithm; Use of profile HMM for protein family classification;
Pattern recognition methods6
Unit IV
Goals of a Microarray experiment; Normalization of Miroarray data; Detecting differential gene expression;
Principal component analysis; Clustering of microarray data; Structure determination by X-ray
crystallography; NMR spectroscopy; PDB (Protein Data Bank) and NDB (Nucleic Acid Data Bank); File
formats for storage and dissemination of molecular structure.
Unit V
Methods for modeling; Homology modeling; Threading and protein structure prediction; Structure-structure
comparison of macromolecules with reference to proteins; Force fields; Molecular energy minimization; Monte
Carlo and molecular dynamics simulation
Texts/References
1. Wayne W. Daniel, Biostatistics : A foundation for Analysis in the Health Sciences, 8th Edition, Wiley, 2004.
2. Prem S. Mann, Introductory Statistics, 6th Edition, Wiley, 2006.
3. John A. Rice, Mathematical Statistics and Data Analysis, 3rd Edition, John A. Rice, Duxbury Press, 2006.
4. Campbell and Heyer, Discovering Genomics, Proteomics, & Bioinformatics, 2nd Edition, Benjamin
Cummings, 2002.
5. Cynthia Gibas and Per Jambeck, Developing Bioinformatics Computer Skill, 1st Edition, O’Reilly
Publication, 2001.
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