BIOCHEMISTRY

Chemical basis of life: Miller-Urey experiment, abiotic formation of amino acid oligomers, composition of living matter; Water – properties of water, essential role of water for life on earth pH, buffer, maintenance of blood pH and pH of gastric juice, pH optima of different enzymes (pepsin, trypsin and alkaline phosphatase), 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, Ramachandran plot, evolution of protein structure, protein degradation and introduction to molecular pathways controlling protein degradation, structure-function relationships in model proteins like ribonuclease A, myoglobin, hemoglobin, chymotrypsin etc.; basic principles of protein purification; tools to characterize expressed proteins; Protein folding: Anfinsen’s Dogma, Levinthal paradox, cooperativity in protein folding, free energy landscape of protein folding and pathways of protein folding, molten globule state, chaperons, diseases associated with protein folding, introduction to molecular dynamic simulation.

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; concept of catalytic antibodies; catalytic strategies with specific examples of proteases, carbonic anhydrases, restriction enzymes and nucleoside monophosphate kinase; regulatory strategies with specific example of hemoglobin; isozymes; role of covalent modification in enzymatic activity; zymogens.

Sugars - mono, di, and polysaccharides with specific reference to glycogen, amylose and cellulose, glycosylation of other biomolecules - glycoproteins and glycolipids; lipids - structure and properties of important members of storage and membrane lipids; lipoproteins.
Self-assembly of lipids, micelle, biomembrane organization - sidedness and function; membrane bound proteins - structure, properties and function; transport phenomena; nucleosides, nucleotides, nucleic acids - structure, a historical perspective leading up to the proposition of DNA double helical structure; difference in RNA and DNA structure and their importance in evolution of DNA as the genetic material.

Bioenergetics-basic principles; equilibria and concept of free energy; coupled interconnecting reactions in metabolism; oxidation of carbon fuels; recurring motifs in metabolism; Introduction to GPCR, Inositol/DAG//PKC and Ca++ signaling pathways; glycolysis and gluconeogenesis; reciprocal regulations and non-carbohydrate sources of glucose; Citric acid cycle, entry to citric acid cycle, citric acid cycle as a source of biosynthetic precursors; Oxidative phosphorylation; importance of electron transfer in oxidative phosphorylation; F1-F0 ATP Synthase; shuttles across mitochondria; regulation of oxidative phosphorylation; Photosynthesis – chloroplasts and two photosystems; proton gradient across thylakoid membrane; Calvin cycle and pentose phosphate pathway; glycogen metabolism, reciprocal control of glycogen synthesis and breakdown, roles of epinephrine and glucagon and insulin in glycogen metabolism; Fatty acid metabolism; protein turnover and amino acid catabolism; nucleotide biosynthesis; biosynthesis of membrane lipids and sterols with specific emphasis on cholesterol metabolism and mevalonate pathway; elucidation of metabolic pathways; logic and integration of central metabolism; entry/ exit of various biomolecules from central pathways; principles of metabolic regulation; steps for regulation. target of rapamycin (TOR) & Autophagy regulation in relation to C & N metabolism, starvation responses and insulin signaling.