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11th December 2020, 08:18 AM
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 Sathyabama Institute of Science and Technology M.Sc - Bioinformatics and Datascience SBIA5101 Structural and Functional Genomics Syllabus SATHYABAMA INSTITUTE OF SCIENCE AND TECHNOLOGY SCHOOL OF BIO AND CHEMICAL ENGINEERING SBIA5101 STRUCTURAL AND FUNCTIONAL GENOMICS L T P Credits Total Marks 3 0 0 3 100 UNIT I INTRODUCTION Structure & Organization of Prokaryotic & Eukaryotic genome - Nucleotide and protein sequencing methods –Chemical, Enzymatic, high through put method – Automated sequencing methods – shotgun – chromosome walking, Contig assembly - Levels of structures in Biological macromolecules. UNIT II CONFORMATIONAL ANALYSIS Biomolecules and their interactions - Forces that determine protein and nucleic acid structure, basic problems, polypeptide chains geometrics, potential energy calculations, observed values for rotation angles, hydrogen bonding, hydrophobic interactions and ionic interactions, disulphide bonds - Prediction of proteins structure - Nucleic acids, general characteristics of nucleic acid structure, geometrics, glycosidic bond rotational isomers - Ribose puckering - forces stabilizing ordered forms, base pairing, base stacking- tertiary structure of nucleic acids. UNIT III STRUCTURAL ANALYSIS OF MACROMOLECULES Size and shape of macromolecules - methods of direct visualization - X-ray crystallography – X–ray diffraction, determination of molecular structures, electron microscopy, NMR. Protein structure databases - Protein Data Bank - SCOP - CATH - structure superposition - RMSD - TM-score- structure alignment - Different structure alignment algorithms - DALI, CE, VAST, TM-align - protein folds in PDB. UNIT IV STRUCTURE-FUNCTIONS RELATIONSHIP DNA binding proteins, Prokaryotic and Eukaryotic transcription factors - DNA polymerases, Helix-turn-Helix motif in DNA binding, Trp repressor, Zn fingers, helix-turn helix motifs in homeodomain, Leucine zippers - DNA polymerases,Membrane proteins and receptors, Trans-membrane segments, bacterio rhodopsin, photosynthetic centres, epidermal growth factor, insullin and PGDGF receptors and their interaction with effectors, protein phosphorylation, immunoglobulins, Serine proteases, ribonuclease, lysozyme. UNIT V FUNCTIONAL GENOMICS Introduction to Functional Genomics - cytological maps - Hap Map - SNPs and variation- Genotyping, microarray- analysis and applications. Microarray oligo sets and fabrication - integrative genomics and Meta genomics. Quantitative Proteomics. Fluorescent imaging techniques. Quantitative RT-PCR analysis. High-throughput cloning and expression strategies. Next Generation Sequencing applications. COURSE OUTCOMES: On completion of the course the student will be able to CO1: The student will acquire a basic knowledge on the basics of genomics. CO2: They will be able to appreciate the influence of conformational parameters on the structure of the macromolecule. CO3: Will be able to select the particular method of structural analysis methodology, given the protein. CO4: Assess the structure and activity relationship of the macromolecule. CO5: Acquire knowledge on the functional aspects of genomics. CO6: Explore the strategies used in highthroghput screening of biological data TEXT / REFERENCE BOOKS 1. Cantor R., Schimmel P.R.,Biophysical Chemistry, Vol. I, II, W.H. Freeman & Co., 1985. 2. Kensal E. van Holde, W. Curtis Johnson and P. Shing Ho, Principle of Physical Biochemistry, Prentice Hall, New York, 1998. 3. Pennington SR, Dunn MJ, Proteomics from Protein Sequence to Function, Viva Books Ltd, 2002. 4. G. Gibson and M. V. Muse. A primer of Genome Science. Sinauer Associates Inc; 2 edition, December 2004. END SEMESTER EXAM QUESTION PAPER PATTERN Max. Marks : 100 Exam Duration : 3 Hrs. PART A : Questions of 6 marks each-out of eight 40 Marks PART B : 2 Questions from each unit with internal choice, each carrying 14 marks 60 Marks   |
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