Course BI 201- Structural Biology & Molecular Modeling
Unit I: Macromolecular Structures: Protein - Primary, Secondary, Supersecondary, Tertiary and Quaternary structure, Enzymes- Introduction, Michaelis Menton Kineteis, Enzyme regulation; Classification, Structure and function of Carbohydrates and lipids; 3D Viral structures.
Unit II: Methods to study 3D structure, Principles of crystallography, Co-ordinate systems, Fitting and refinement, Validation, Analysis of 3D structures, Methods for 3D structure prediction, Knowledge based & Fold recognition; Principles of protein folding and methods to study protein folding.
Unit III: Basic concept of Bioenergetics; Thermodynamics principle in biology; energy rich bonds, Computational approaches in structural biology; Macromolecular interactions, Protein - Protein, Protein – Nucleic acids, Protein – carbohydrates.
Unit IV: Overview of molecular modelling - Introduction and challenges, Molecular modelling methods, Conformational searching, Potential energy maps, Ramachandran maps, Ab-initio methods, Semi-empirical methods, Empirical methods- Conformational analysis, Introduction and Methods, Molecular fitting, Energy Minimization, Non-derivative and derivative methods.
Unit V: Global optimization (simulated annealing, Tabu search, genetic algorithms), Applications of energy minimization, Molecular Mechanics, Conformations: global vs. local, Force fields: expressions for stretch, bond, torsion, etc., Description of various force fields: MM3, Dreiding, AMBER, CHARMM, Mechanics of Bio-macromolecules, Molecular Dynamics- Newton's equations for many particles, Verlet and related algorithms, Types of dynamics simulations: adiabatic, constant T, annealed, etc., Conformational searching using MD and other methods, Free energy calculations, Dynamics of Bio-macromolecules
Course BI 202- Statistical Analysis and Optimization Techniques
Unit I: Frequency distribution. Measures of central tendency and measures of dispersion. Correlation and regression: Scatter Diagram, Coefficient of Correlation, Rank correlation. Lines of Regression.
Unit II : Probability theory: Classical and Statistical definitions, conditional probability, Bayes’ Theorem. Random variable, mathematical expectation. Probability Distributions: Binomial, Multinomial, Poisson and Normal Distribution. Introduction and Properties of ‘t’, Chi-square and F distribution.
Unit III : Estimation: Population and sample, Different kinds of sampling. Fundamental concepts of estimation, Maximum Likelihood Estimation, Interval Estimation. Hypothesis testing: students t-test, Paired t-test, large sample tests, F-test, Chi-square test, Analysis of variance.
Unit IV: Multivariate analysis: Multiple correlation and Regression. Introduction to Principal component analysis, Discriminant analysis and Cluster Analysis. Applications: extracting clusters of functionally related genes from microarray results.
Unit V: Dynamic Programming, Gibbs sampling, Markov chains, Hidden Markov Model, Simulated annealing, Genetic algorithm. Applications of these methods in sequence alignments, Protein classification and structure prediction.
Course BI 203- Genetic Engineering
Unit I: Basic steps of r-DNA technology, Enzymes used in r-DNA technology; Restriction endonucleases and their types (I, II & III); Restriction mapping. Ligation- joining of DNA molecules together: blunt end ligation, joining with linkers, adapters & homopolymer tailing.
Unit II: Cloning vectors: general properties , plasmids, bacteriophages, cosmids, shuttle vectors, bacterial artificial chromosomes. Eukaryotic cloning vectors for yeast, higher plants & animal cells.
Unit III: Introduction of recombinant vectors into bacterial & non-bacterial cells. .Selection of clones: colony hybridization, plaque hybridization, immunochemical methods & southern blotting. Gene libraries: genomic library (Shot gun approach), cDNA library (Different methods for synthesizing c DNA molecules).
Unit IV: Expression vectors for expressing foreign genes in E.coli:problems associated with the production of r- proteins in E.coli, production of r protein by eukaryotic cells. Non-radioactive & radioactive labeling of probes. RFLP, RAPD, northern blotting & western blotting.
Unit V: PCR methods & applications, DNA sequencing methods: dideoxy and chemical methods, automated sequencing, sequence assembly.DNA finger printing, Applications of gene techonology: production of pharmaceuticals- humulin, somatotropin, somatostatin, recombinant vaccines.
Course BI 204- Molecular Biology
Unit I: Nucleic acids as genetic information carriers: experimental evidence. DNA structure: historical aspects & current concepts, melting of DNA, types of DNA. DNA replication in prokaryotes: types of polymerases, steps: initiation, elongation (Asymmetric & dimeric nature of DNA Polymerase III & simultaneous synthesis of leadind & lagging Strands), termination. DNA replication in eukaryotes: types of polymerases, replication origins & initiation, steps involved, synthesis of telomeric DNA.Various modes of replication. Superhelicity in DNA, linking number, topological properties, mechanism of action of topoisomerases.
Unit II: Mutation; Spontanaous Mutation and Induced Mutagenesis. Mutagens (Physical Mutagens: non-ionizing radiation & ionizing radiation. Chemical Mutagens; Base analogs, Alkylating Agents, Deaminating Agents, Intercalating Agents and others). Molecular Mechanism of Mutagens. Suppressor Mutation: Intragenic and Intergenic Mutation. DNA Repair Mechanism; Repair by Direct Reversal, Excision Repair, Recombination Repair & SOS Repair.
Unit III: Structural features of RNA (mRNA, tRNA, rRNA). Transcription in prokaryotes: RNA polymerase, promoter, steps: initiation, elongation & termination, antitermination. Trancription in eukaryotes: types of RNA polymerases ( I, II & III), promoter, enhancer & silencer sites for initiation, transcription factors, steps: initiation, elongation & termination. Inhibitors of RNA synthesis. Post trancriptional modification of mRNA: capping, polyadenylation & splicing (group I introns, group II introns, hn RNA using spliceosome/snurposome). Ribozymes.
Unit IV: Basic features of the genetic code. Protein synthesis in prokaryotes and eukaryotes; Structure of ribosomes, steps-details of initiation, elongation & termination, roles of various factors in the above steps, inhibitors of protein synthesis. Synthesis of exported proteins on membrane bound ribosomes: signal hypothesis. Post translational modification of proteins.
Unit V: Regulation of gene expression : operon concept, negatve & positive regulation, instability of bacterial mRNA, inducers and corepressors, catabolite repression. Negative regulation-E. coli. lac operon; positive regulation- E. coli. ara operon; regulation by attenuation- his and trp operons; anti-termination-N protein and nut sites in lambda. Global regulatory responses; heat shock response, stringent response and regulation by small molecules such as cAMP and ppGpp. Regulation of rRNA and tRNA synthesis.
Note : The examiner is expected to set the question paper based on the entire course content. In Section A, the question paper shall include 5 long question (10 marks each) out of which the candidate is required to attempt 3 questions. Section B shall be based on short answers 100-200 words and shall include 4 questions of which the candidate is required to attempt 2 questions of 5 marks each. Section C shall include 10 to 20 questions of half / one mark each and shall be based on objective type / true-false / very short answers like definitions.
Course BI 205- Practical 1 (Course BI 201 & Course BI 202)
Course BI 206-Practical 2 (Course BI 203 & Course BI 204)