In this course the students learn the theoretical basis of the analysis performed by different bioinformatics softwares/databases and how to use those tools effectively to solve biological problems. The course has both lecture and practical components. The topics taught in this course are: Databases - sequence, structure, non-redundant; Sequence alignment - pairwise and multiple; phylogenetics; Structure prediction methods − high-accuracy, template based, free modeling (new folds); Secondary structure prediction; Pattern recognition − PSSMs, weight matrices; Docking, Structure analysis.
The theoretical and experimental aspeects of protein crystal structure determination is taught in this course. The basic theory behind every step and the computer program/software used in protein crystal structure determination process is explained in this course. The students get the opportunity to setp crystallization screens, mound the protein crystal, collect and process diffraction data, solve and refine structure. The course contents are:Protein production for crystallization, Protein crystallization, Crystal geometry, X-ray diffraction, Statistics and probability in crystallography, Instrumentation and diffraction data collection, Diffraction data to electron density, Solving phase problem, Isomorphous replacement method, Anomalous scattering method, Phase combination and improvement, Molecular replacement, Model building and refinement, Structure validation and deposition, Judging a crystallographic model, Computer program for analyzing protein structures.
This course covers the detailed aspects of enzyme kinetics and understanding the structural as well as chemical basis of catalytic reaction mechanism. The primary topics taught in this course are: Rate accelerations in biological systems; Catalysis and historical perspective on enzymes; Overview of applied enzymology and enzyme technology; Enzyme nomenclature; Origins of enzyme catalytic power; Structural basis of enzyme action and characterization of active site residues; Kinetic approaches to understand enzyme action; Michaelis-Menten kinetics; Evaluation of Km, kcat and enzyme inhibition analysis; Concept of an efficient catalyst; Elucidation of kinetic mechanism through initial velocity, product inhibition, pH and isotopic analysis; Role of metal ions in enzyme catalysis; Integration of kinetic, chemical and structural data to describe enzyme action; Control of enzyme activity and its role inn regulating metabolism − in vivo enzymology; Frontiers in enzymology: Rational design of an enzyme catalyst, directed evolution, abzymes, non-protein catalysts.
Basic biochemistry, cell and molecular biology are taught in this course. The topics covered in the course are: Biochemical unity and biological diversity, Relationship between structure and function, Separation techniques: basis and importance, Microbial kingdom (Prokaryotes, eukaryotes, archaea) Microbial growth. Hemoglobin: portrait of an allosteric protein. Enzymes. Catalytic and regulatory strategies. Carbohydrates, lipids, membranes. Signal transduction. Metabolism: basic concepts and design. Oxidative and photo-phosphorylation. Integration of metabolism. Flow of genetic information. Recombinant DNA technology. Genomes. Concept of homology.