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? How do the the ETS of choroplasts and Mitochondria compare? Which components/mechanisms are shared or close homologs? 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?
What are chemical reactions? What is reducing agent? Why? (2 reasons) What are sources of reducing equivalents? -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 -oxidation, ketogenesis and F.A. synthesis coordinated?
Modification of fatty acids: Know desaturase reaction. Mixed function oxidases, know mini-electron chain and why needed. How are chains with > 16C made? Saturated vs. unsaturated long chain FA's - why the difference? How are short chain FA's made?
What steps are involved in the synthesis of a triglyceride? How are the fatty acids activated. What is the source of the glycerol? Be able to write the reactions for this process. How does the synthesis of phospholipids (say phosphatidylcholine) compare to the previous? What is cholesterol derived from? What is the strategy of cholesterol biosynthesis? Where does it take place in the cell? which tissue? How is HMG involved? Be able to write the reactions for the synthesis of lanosterol from squalene. What is lanosterol's relation to cholesterol?
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).
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, DH complex, main-line sequence - note deviations!); ala, glu, asp (T); asn, gln (hydrolytic deam, T); arg (orn - glu); ser, thr (dehydratase). 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 O2/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?
You may bring a data/information sheet to the exam, however you must not exceed one side of a single sheet of 8.5" x 11" paper for this sheet. GOOD LUCK!
Last modified 4 March 2009