| Schedule |
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| Chem431 |
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F 2001 |
Review study guides I and II with particular emphasis on the overall processes and pathways. Be able to make energy calculations,etc. Learn overall pathways, etc. first - memorize details later!!! The final will probably be approximately 30:70 old and new material.
Kreb's Cycle: In what way can the cycle be considered catalytic for AcCoA breakdown? Why is this elaborate system required to oxidize an acetyl group? Can any other molecules be completely oxidized by the cycle? Why not? Know chemistry of reactions in cycle. What is strategy here? What is the "main line" sequence? Where is NADH produced? FADH2? GTP? Which reaction is irreversible? How is the cycle controlled? Be able to follow a label through the cycle. How can citrate behave as an asymmetric molecule? Be able to use the Kreb's Cycle and associated reactions to oxidize any of the intermediates of the cycle. Know reactions interconverting Pyruvate, oxaloacetate and PEP. Which of these reactions is regulated? How? Where do glutamate, alanine and aspartate enter the TCA Cycle?
Electron Transport System: Know localization. What kinds of evidence do we have for ordering of components. Where is ATP production associated? What are: cytochromes, flavoproteins, Non Heme Iron proteins, CoQ? Know what functional groups or cofactors are used by various conponents. Know order of major components in ETS starting with NADH, Succinate, Glycerol-P, or Fatty acyl CoA and how many ATP's are normally produced. Be able to explain and/or diagram the model we discussed for the coupling of electron transport and ox. phos. (chemiosmotic). Be able to calculate P/O ratios for any compounds oxidized via the ETS. Be able to calculate P/O ratios for the aerobic catabolism of any compound given, or for which you know, its pathway of metabolism. Be able to trace the electron shuttle systems (malate-aspartate and glycerol phosphate shuttles). How is ATP/ADP transported across the inner mitochodrial membrane.
Photosynthesis:What is the stoichiometry of the light reactions? What is the light used for? What is the "Z" scheme? Be able to outline Photosystem I and Photosystem II and be able to explain what happens in each. Where do the various parts of photosynthesis occur in the chloroplast? What is the reaction center in the light reactions? "Antenna?"
Know Ribulose-1,5-bis P carboxylase (RuBisCo) reaction. How is RuBisCo regulated? What is the stoichiometry of the Calvin Cycle? What pathways are represented in this cycle's reactions? How does this pathway change between light and dark (day and night)? Why? What is the difference between C4 and C3 plants? Do C4 plants still use the Calvin cycle? What is the rationale for plants to have the C4 cycles?
b-Oxidation of Fatty Acids: Where do these reactions take place? What is the first step? Which step controls the rate? Would you say that the breakdown of short chain fatty acids is uncontrolled? Explain. Carnitine shuttle. "Mainline Sequence." What are oxidizing agents? How are AcCoA groups cleaved off? (Claisen cleavage.) Be able to calculate energy yield from the complete or partial oxidation of a given fatty acid. Compare to glucose. How many turns of beta-oxidation to convert a fatty acid to AcCoA? Under what conditions will "ketone bodies" be formed (instead of complete oxidation). (High [ATP] with continued breakdown of FA's, therefore need to form ketone bodies to recycle CoA.)
Ketogenesis: Know reactions by which ketone bodies are synthesized and degraded. What are "ketone bodies?" Are they all ketones? In which tissues do these reactions occur? b-hydroxybutyrate vs. acetoacetate. What do we mean by the statement: "ketone bodies give the liver overall control of fatty acid metabolism?" What is the source of CoA in acetoacetate degradation? Does this cost energy?
Fatty Acid Biosynthesis: What are chemical reactions?
What is reducing agent? Why? (2 reasons) What are sources of reducing
equivalents? b-oxidation is a thermo
favorable process; so is fatty acid biosynthesis. How is this
apparent paradox resolved? How is AcCoA "activated?"
Compare the enzyme involved to Pyruvate Carboxylase. How is AcCoA
carboxylase regulated? Rationalize the use of citrate and palmitoyl
CoA as regulatory substances. What are the activities of the FattyAcid
synthase complex? What is ACP1? ACP2? How
do they differ in function? In regards to binding? What is the
Pyruvate Malate Shuttle? Be able to outline this series of reactions.
Integrate FA biosynthesis with the production of reducing equivalents
assuming glucose as the ultimate precursor. Don't forget compartmentation.
How is the control of b-oxidation,
ketogenesis and F.A. synthesis coordinated?
Metabolism of Amino Acid Nitrogen: Rationalize the different
forms of excreted nitrogen. What is the major reaction for NH3
production? Know Glutamate D.H.: reaction catalyzed, function,
compartmentation, control. What are the major transaminases?
What are their functions? What is the reaction catalyzed? Explain
why this is a redox reaction. Know the mechanism of action of
this family of enzymes: details of pyridoxal-P involvement (including
structures) formation of Shiff base; "electron sink;"
electrophilic attack; bond labilized. Aldimine? Ketimine? What
other bonds in amino acids may be labilized by Pyridoxal-P? Write
a kinetic mechanism diagram for transaminase. How are serine and
threonine deaminated? GluNH3 and AspNH3?
D-amino acids? Urea Cycle: What is the first committed
reaction? What is the function of ornithine? Compare to oxalacetate
in TCA. Note ATP energy equivalents with and without fumerate
oxidation and glutamate DH. Note net results as on Flow diagram.What
are nitrogen inputs? Integrate these inputs with your knowledge
of transaminases and glutamate DH. Why is arginine an essential
amino acid? Note compartmentation of Urea cycle and interaction
with TCA (tricycle).
Amino Acid Catabolism, the carbon skeletons: Be able
to write out pathways for the complete degradation of the following
amino acids (including structures, but given a.a. formulas): val,
leu, and ilu, (T, D.H. complex, main-line sequence - note deviations!);
ala, glu, asp (T): asn, gln; arg (orn - glu); ser, thr (deaminase).
Know where others feed into major pathways, and what portions
go where. Be able to calculate P/O ratios for any a.a. you can
break down as above. Of course, this calculation implies you can
calculate ATP's/aa and Oxygen's/aa! Be able to compare these P/O
ratios to those of Glucose and Palmitate. Which amino acids are
preferentially metabolized in the intestinal mucosa, the skeletal
muscle, the liver? How is nitrogen transported from muscle and
brain to the liver? What is the alanine cycle?
Amino Acid Biosynthesis: Be able to trace the biosynthesis of ala, asp, and glu from glucose (or any other glucogenic carbon source).
You may bring a data/information sheet to the final exam, however you must not exceed one side of a single sheet of 8.5" x11" paper for this sheet! GOOD LUCK!
