INTRODUCTION & PROTEIN STRUCTURE:
Levels of molecular organization, Brief discussions on: Amino acids, Nucleic acids, Adenylates, Carbohydrates, Lipids, Cofactors, Vitamins, and Hormones. Composition and primary structures of proteins, Conformational analysis and forces that determine protein structures, geometries, phi, psi, omega angles, Ramachandran or steric contour diagram, allowed chi angles of side chains in proteins, hydrogen bonding, disulphide bonds, hydrophobic interactions, vanderwaals forces, potential energy calculations, alpha helices, beta sheets, helix to coil transition, general features and thermodynamic aspects of protein folding, folding kinetics, protein-ligand interactions, Scatchard plot, cooperative interactions, allosteric effects, Hill constant; Relationship between the primary, secondary, and tertiary structure of proteins. Structure of IgG, fibrous proteins (structure of collagen, keratin). Quaternary structures - dimers, homo & hetero dimers, trimers, tetramers; Protein folds, structural families and classes, multifunctional domains (qualitative examples).
STRUCTURE OF NUCLEIC ACIDS AND BIOMEMBRANES:
General characteristics of nucleic acid structures (A, T, G, C, U), forces and stabilizing geometries, glycosidic bond, rotational isomers. Stabilizing ordered forms of DNA (A, B and Z), base pairing types, base stacking, tertiary structure of DNA (Supercoiled DNA), Melting of the DNA double helix (Hyperchromicity), Interaction with small ions and small molecules. Ribose puckering and Tertiary structure of tRNA. Structure and conformational properties of cell membranes, Singer and Nicholson model, integral proteins in membranes, conformational variations during ion transport, Signal transduction and molecular reception (qualitative).
BIOPHYSICAL TECHNIQUES:
Rayleigh scattering, ultra-centrifugation, viscometry. Electron microscopy (SEM-TEM, AFM), luminescence (fluorescence & phosphorescence), Calorimetry, DSC, Mass spectrometry, LCMS, MALDI-TOF, Voltage Clamp and Patch Clamp (measurements of membrane potentials).
SPECTROSCOPIC TECHNIQUES:
X-ray diffraction: structure determination via single crystal diffraction, fibre diffraction; Neutron diffraction. XAFS. NMR spectroscopy (structure determination). ORD/CD, UV, IR, Laser Raman, ESR/EPR.
BIOMOLECULAR INTERACTIONS & MOLECULAR DYNAMICS:
Association of macromolecules, molecular conjugates, supramolecular interactions, protein-protein interactions, protein-nucleic acid interactions, lipid/membrane-protein interactions. Molecular mechanics and dynamics (Newtonian and Monte Carlo simulations), theoretical principles and its importance towards insilico simulations, results of molecular dynamics calculations and their implications to biological function.
Course outcomes:
After studying this course, students will be able to:
REFERENCE BOOKS
1. Biophysics – An Introduction by Cotterill, Wiley Student Edition.
2. Foundations of Biophysics by A.L. Stanford, Academic Press.
3. Principles of protein structure by G Schulz and R H Schrimer, Springer Verlag.
4. Principles of nucleic acid structure by Sanger, Springer Verlag.
5. Introduction to Protein Science by Arthur M Lesk, Oxford University Press.
6. Biological Spectroscopy by J. D. Campbell and R. A.Dwek, Plenum Press.
7. A Textbook of Biochemistry and Biophysics by S.M Gopinath, Archers & Elevators International Publishing House, India. 1st Edition, 2014.
TEXT BOOKS
1. Biophysical Chemistry by Cantor R. and Schimmel P.R, W. H. Freeman.
2. Physical Biochemistry by David Freifelder, W H Freeman and Company.
3. Biophysical Principles of Structure & Function by Fred M. Snell & Sidney Shulman.
4. Introduction to Protein Structure by Carl Branden and John Tooze, Garland Publishing.
5. Proteins Structure – A Practical Approach by Creighton, Oxford University Press.
6. Physical Chemistry: Principles and Applications in Biological Sciences by Tinoco and others, Prentice Hall.