STUDY GUIDE FOR FINAL (153A-2 Summer 2006)• The FINAL exam is cumulative. • Buyer beware! This is just an overview and I may have inadvertently missed a topic. Ask me if you have any questions. • You will not need to use a calculator on the exam. • Bring a PhotoID to the exam • I will provide formulas describing competitive, mixed and uncompetitive enzyme inhibition. PROTEINS AND AMINO ACIDS • Amino Acids (structure, properties, hydropathy) • Acid-base properties of amino acids and simple calculations (titration curves) • R/S and D/L descriptions of chirality (enantiomers and diastereomers) • Anabolic/catabolic • Properties of polypeptides/proteins (peptide bond, dihedral angles, ramachandran plot etc..) • Levels of protein structure (primary, secondary etc..) • Helices and beta sheets (structure and properties) • Stabilizing interactions in water soluble globular proteins and their role in folding (hydrogen bonds, salt-bridges etc..) • Fibrous proteins (examples covered in class) • Anfinsen experiment • Hemoglobin and Myoglobin at the level of detail covered in class and the text. • Molecular basis of the Bohr effect • Mathematical description of oxygen binding to Mb (a ligand binding to a single site) • Sickle cell anemia and Prions SUGARS • Carbohydrates (basic structure, role in cell, aldose versus ketoses, L vs D, epimers and anomers). • Structures of relevant sugars (glucose, fructose and ribose) • Chemistry of sugars (formation of furanose and pyranose rings, glycosidic bond formation, reducing sugars) • Glucose polymers (cellulose, starch, glycogen) • Glycoproteins (types, function) LIPIDS • Types of Lipids (triacylglycerols, phospholipids, glycolipids and sterols) (function, properties and general structure) • Fatty acids (structure, properties, saturated vs unsaturated, Number based nomenclature) • Bilayers, liposomes and micelles • Fluid mosaic model (role of cholesterol and fatty acids in modulating fluidity) • Transporters versus pumps. • How GluT1 works. GENERAL PROPERTIES OF ENZYMES • Kinetics of uncatalyzed-unimolecular and –bimolecular reactions • Rates of reactions and their relationship to the activation energy. • What the standard free energy of a reaction means. • Substrate-enzyme binding (induced fit versus ‘lock and key’ concept). • The ways enzymes catalyze reactions (covalent catalysis, transition state stabilization, acid-base catalysis an so forth) • Michaelis Menten Kinetics (Km, kcat, catalytic efficiency and so forth) • Lineweaver-burk plot (be able to abstract relevant kinetic parameters) • Reversible inhibition: competitive, uncompetitive and mixed inhibition (formulas will be provided) • Concept of an irreversible inhibitor • Mechanism of Serine proteases • Enzyme regulation: • Allosteric regulation• Reversible covalent modification (phosphorylation of E1 in the pyruvate dehydrogenase and glycogen phosphorylase given as specific examples.) • Know what Cofactors and Coenzymes are • Feedback inhibition METABOLISM (Glycolysis, fermentation and pyruvate dehydrogenase complex) • Metabolism (anabolism versus catabolism) • Basic thermodynamics of phosphate hydrolysis (simple calculations) • ATP, Acyl phosphates, Enol phosphates, thio-esters • Know that ATP is kinetically stable and why. • Basic thermodynamics!! (The relationship between the standard state free energy change and free energy change of a reaction. What they mean!) • Glycolysis (at the level of detail covered in class; Know Mechanisms) Detailed mechanisms discussed: (i) Kinase reactions (#1,3,7,10) (ii) Aldose <> Ketose (#2,5) (iii) Aldolase enzyme with Schiffs base (iv) Dehydrogenase (#6, fermentation) • Fermentation (lactic acid and alcohol) (at the level of detail covered in class) • Know how NAD, TPP and ATP work. Do not memorize the entire structure of these cofactors, just know how they work. • Know what the pentose phosphate and gluconeogenesis pathways do (how they are related to glycolysis) • Know generally how glycogen is degraded to glucose-1P (phosphorylase and transferase) • Know which enzymes in glycolysis are regulated and why. (Do not memorize the specific regulators). • Know the general functions of insulin, glucagons and epinephrine. • Know how glucagon controls glycolysis and gluconeogenesis (the F2,6P connection) • Diabetes • Pyruvate dehydrogenase complex (up to what we cover in class) • Citric Acid Cycle (be able to draw the structures of intermediates and track carbon flow; know where NADH/FADH2/GTP/CO2 are produced; Know the mechanism of alpha-ketoglutarate dehydrogenase complex; know the reactions that are regulated). • Concept of prochirality and importance • Know what a amphibolic pathway • Know what a anaplerotic reaction is (pyruvate to oxaloacetate in matrix) • Gluconeogenesis (know the three bypass steps, enzyme names not needed). • Know what is meant by a glucogenic amino acid and generally how they can be converted to glucose. • Generally know how dietary fatty acids are transferred from the intestine to cells • Generally know how fatty acids in adipose cells are transferred to other cells • Generally know how fatty acids are brought into the mitochondrion from outside the cell. • The general process of beta oxidation for even numbered saturated fatty acids (no mechanisms just what and how much is produced) • Know what ketone bodies are (their purpose, where they are made, where they are consumed) • Glyoxylate cycle (where it is used and why, structures of intermediates and how this pathway is integrated into the citric acid cycle and gluconeogenesis pathways) • Reduction potential and standard reduction potentials (what they are, simple calculations, relationship to free-energy) • Electron Transport chain (Do not need to know names, just numbers; Know how cytochromes, Fe-S, Cu, FMN,FAD, and Q carry electrons and protons; know how electrons from FADH2 and NADH flow through the complexes, know the Q-cycle, know the general order of redox centers within and between the complexes I to IV; Be able to predict behavior of ET chain of inhibitors discussed in class, Chemiosmotic model) • Bind and change mechanism of complex V • Why 2.5 and 1.5 ATP are made from the oxidation of NADH and FADH2, respectively. •
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