Biochemistry

Unit I: General and Organic Chemistry for Biochemistry; Functional groups; Groups at the ends of molecules; Groups within molecules; Applications; Spectroscopic identification of functional groups ; Protons and electrons; Acid-base chemistry; Hydrogen bonding; Resonance and tautomerism; Radicals; Nucleophilic reactions; Heteroatoms; Nucleophilic carbon; Application: Synthesis of aspirin; Transition states and high-energy intermediates; Proton transfer; sp2 - sp3 transition; Trigonal bipyramidal TS; Thermodynamics of chemical reactions; Kinetics and thermodynamics; Energy-rich compounds Unit II: Biological molecules: Building blocks and their assemblies; Amino acids, peptides and proteins; The amino acids that constitute proteins; Primary structure: peptide bonds and side chains; Secondary structure; Tertiary structure and forces that stabilize; Application: Chemical synthesis of polypeptides; Carbohydrates and polysaccharides; Chirality; Equilibrium of open chain and cyclic sugars and anomeric carbons; Glycosidic bonds; Survey of important polysaccharides; Application: Industrial conversion of sucrose to glucose and fructose; Nucleotides and nucleic acids; Purines and pyrimidines; Nucleotides comprising DNA vs. RNA; Nucleic acid structure; Interstrand base-pairing Application: DNA hybridization with radiolabeled oligonucleotide; Lipids and membranes Unit III: Biochemical reactions; A compendium of biochemical reactions; Hydrolysis; Group transfer; Isomerizations/racemizations; Oxidations/reductions; Additions/eliminations; Carbon-carbon bond making and breaking; Ligases; Glycolysis: A strategic series of reactions for production of energy-rich compounds; Glucose Fru-1,6-DiPO4: Formation of symmetric hexose diphosphate; Fru-1,6-DiPO4 2 GAP: Splitting the hexose; GAP 3PG: Oxidation and substrate-level phosphorylation; 3PG Pyr: Finessing the phosphate for more ATP; Overall energy gain from glucose 2 Pyr; Citric Acid Cycle: A cyclical series of reactions for oxidation of pyruvate; Overview of the strategy of the citric acid cycle; Input of two carbons from acetyl-CoA: oxaloacetate citrate; Rearrangement: citrate isocitrate; Two oxidative decarboxylations succinate; Oxidation of succinate oxaloacetate, the starting material; Isotope tracing experiments in the citric acid cycle; Unit IV: Quantitative aspects of Enzyme Action; Michaelis-Menten kinetics; Effects of temperature, pH, and salt on enzyme activity; Enzyme inhibition; Factors that contribute to enzyme catalysis; Acid-base reactions; Covalent (nucleophilic) reactions; Proximity; Hydrophobic effects and removal of solvent water; Transition state stabilization; Classics in enzyme mechanisms; Unit V: Metabolic pathways and cycles; Pentose phosphate pathway; Nitrogen metabolism: Urea cycle, and purine and pyrimidine biosynthesis