| Schedule |
 |
| Chem431 |
|
F 2001 |
|
|
Review: Study Guide I material, particularly on enzymes and enzyme catalysis, as it pertains to metabolism.
Vitamins and Cofactors: What are vitamins? What cofactors correspond to the five vitamins we studied in detail (niacin, riboflavin, pantothenate, lipoate, and biotin). In what portion (specifically) does the chemistry take place in each of these cofactors? What are the major metabolic functions of NAD+ and FAD? What distinguishes NAP+ from NADP+? What is the metabolic consequence of this difference? What do we mean by metabolic compartmentation? What distinguishes FAD from FMN? What is the function of the "ADP" portion of NAD+, NADP+, and FAD? What common theme connects NAD+, FAD, and Coenzyme A? What are the specific major metabolic functions of Coenzyme A, lipoic acid, and biotin? What common themes connect these three cofactors? How long is the acyl (pentanoate) plus lysine "arm" for lipoate and biotin (measure in "atoms")? How does this compare to the "arm" in coenzyme A?
What is an enzyme? (define) Turnover number. velocity.
Specificity: Lock and Key model and its failure. Induced fit model - explain. How do substrates bind? Chemical specificity. Why are enzymes big (<5% of surface is active site)?
Catalysis: Know major types we discussed: general acid/base (as opposed to specific), covalent, proximity/orientation, distortion/transition state binding, charge stabilization, metal ion. What is meant by a "concerted" mechanism? Be able to explain an enzyme mechanism in terms of the catalytic types we have discussed. Be familiar with mechanism of lysozyme. Be familiar with the shared mechanism of the serine proteases and the "catalytic triad" used by them. Zymogens.
Enzyme Kinetics: Review: 1st, 2nd, 3rd and zero orders: linear plots vs. time, rate ( =velocity) versus [S]. What does reaction order tell you about mechanism? vi vs. [S] or Michaelis-Menten plot. Be able to identify order, find Vmax and Kmwith this plot. What are main assumptions in steady-state derivation of M-M eqn? Consequences of M-M eqn at [S] >> Km, [S] << Km, [S] = Km. Be able to interpret Lineweaver-Burke and M-M plots and find Vmax and Km values for normal and inhibited reactions. Be able to draw plots and interpret plots relating rate to temperature and to pH.
Inhibition: competitive: model mechanism, kinetics, plots; non-competitive: model (mechanism), kinetics, plots; un-competitive: model (mechanism), kinetics, plots.
Multisubstrate enzymes: be able to distinguish between Ping-Pong, Ordered Sequential and Random Sequential mechanisms and diagrams. Be able to distinguish these mechanisms using product inhibition data and logic ("binding same enzyme form").
Allosteric Enzymes: define. Heterotropic. Homotropic. Cooperativity. What do V vs. [S] plots look like? How are these plots affected by (+) and (-) effectors? Consider an enzyme exhibiting a sigmoidal kinetic plot (a negative effector is present, and the enzyme is acting cooperativity): how would a competitive inhibitor affect this plot? a non-competitive inhibitor?
Concerted (symmetry) model for homotropic allosteric enzymes. Be able to explain model (shifting equil.) for substrates and effectors - correlate to kinetics. Sequential Model - explain.
Overview of Metabolism: Phototroph. Chemotroph. Thermodynamics.
DG = DH- T DS. What is DG (in words)? What does it indicate about energy availability? What does DG tell you about a system? DG° '(definition). DG = DG° '+ RT lnQ. DG° ' = -RT lnKeq. Know how to solve simple problems using thermo relationships. How do you find DG for a series of reactions? Keq? E° ' (reduction potential)? Driving reactions by coupling: sequentially, in parallel. Note special function of enzymes in latter case. Anabolic. Catabolic.Why ATP? "Hi Energy". What do we mean by "hi energy?" Be able to explain "hi energy" in various compounds we have discussed. What is Energy charge? How is it maintained? Why is it of interest? Be able to calculate E.C.; Shifting Equilibria (DG) with ATP.
NAD(P)+ and Flavins as "universal" carriers for electrons. Note chemically active vs. recognition portions of these molecules. CoA as carrier of acyl groups (activated).What are vitamins? Why are they vitamins? Know relationship between vitamins and cofactors we have discussed. What are the fat soluble vitamins and their major functions?
Know the Stages of Metabolism and what major processes occur in each. Memorize the following structures: ATP, ADP, AMP, NAD+, NADP+, NADH, NADPH, glucose, fructose, mannose, G-6-P, F-6-P; starch, cellulose, glyceraldehyde, glycerate, pyruvate and phosphorylated derivatives; citrate, succinyl CoA, oxalacetate.
Glycolysis: This is a central pathway of metabolism, and one we will refer back to repeatably, you may find it useful to memorize it in your learning strategy. What is the overall process (reactant and products). 3 stages : I, preparatory (Glu Æ F-1,6-bisP); II, oxidative (F-1,6-bisP Æ 2 x 3-PGA); III energy generation (2 x 3-PGA Æ 2 x Pyr). Need to regenerate NAD+: aerobic vs. anaerobic. What reactions are irreversible? Which enzymes are involved in control? What are the regulatory effectors of these enzymes? How are regulatory steps determined? (Keq. vs. measured Q or DG). Which steps consume ATP? Which produce ATP? Where are NAD+/NADH involved? Understand this pathway (you may find memorizing it useful to your understanding): What kinds of chemical reactions are involved? How are they catalyzed? Correlation of enzyme names and chemical reactions. Strategy of reactions in pathway: Why split into three carbon pieces? Why oxidize? Why is PFK main regulatory step? Why not first step of pathway? Know detailed catalytic mechanisms for Aldolase and Glyceraldehyde-3-P DH. Be able to correlate with kinetic mechanisms. Know cofactors used by various enzymes.Why is 2,3-BPG necessary?
Glycogen: Know reactions for incorporating Glu-6-P into glycogen. What is the function of UDPG? Why is PPi released in Transferase reaction? Why do organisms have synthase and phosphorylase? (why not just phosphorylase?) How much energy is required to incorporate one Glu. into glycogen (in ATP units)? Glycogen synthesis requires a primer. Know phosphorylase reaction.How many ATP's result from glycolysis starting with glycogen? glucose? Why difference? How is glycogen debranched? (What activities are required?) How is glycogen metabolism controlled? (Hormone mediated enzyme phosphorylations; cascade amplification; allosteric effectors to match local needs; note "futile cycles" in phosphorylation/dephosphorylation of proteins - what effect do they have on control? response?) Doesn't this stuff (control) seem ideal for a short essay?
Pyruvate & the Kreb's Cycle: What are various fates of pyruvate? Know overview and mechanism of Pyruvate DH complex, including: all cofactors and structures of chemically active portions of TPP, FAD and Lipoamide. How is pyruvate involved in filling the TCA cycle (anapleurosis)? How is it involved in gluconeogenesis? How is complex regulated? Covalent regulation. Know quaternary structure of complex (qualitative).
Gluconeogenesis and Glycolytic Control: Know the major branch points and entry points for sugars in carbohydrate metabolism (´ glycogen, ´glycerol-P, ´ Pentose-P shunt,´ Kreb's Cycle, ¨fructose, ¨ galactose, ´glycerol) - see metabolism handouts. Know the "bypass" reactions of gluconeogenesis. How is glycolysis/gluconeogenesis linked to Kreb's Cycle? What is a futile cycle? Is a futile cycle always futile or can it be useful? Know how glycolysis/gluconeogenesis controlled. Note the hierarchy of control. In what senses does PFK function as the main and most important control enzyme in glycolysis. Know what substances act as effectors for PFK and how they work. Know how PFK activity indirectly affects the activities of the other control enzymes of glycolysis/gluconeogenesis. Be able to discuss in detail the regulation of carbohydrate metabolism and, in particular, the regulation of PFK.
Pentose Phosphate Shunt: What are the two portions of this pathway? What is the net result of each? Which intermediates are common to glycolysis and pentose-P? How can this pathway be used to completely oxidize glucose? Does it? Always? In which tissues are the different portions elaborated? How is pentose-P controlled? How does control integrate it to biosynthesis? Know oxidation steps. Know flow diagram. Know mechanisms for Transketolase and Transaldolase (be able to figure out).
