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sp07 final exam notes final

sp07 final exam notes final - BIOCHEMISTRY 102 FINAL EXAM...

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BIOCHEMISTRY 102 FINAL EXAM NOTES 6/6/07 FINAL VERSION The final exam will be approximately 300 points, and will be divided into roughly 200 points from weeks 7-10 and 100 points from weeks 1-6. The following list gives you a specific description of the areas that will be covered in the final from weeks 7 to 10 of the class, and identifies the relevant portions of the 1 st and 2 nd midterm exam notes that will be covered in the final. 1 . Some problems from Problem Sets 7-10, or slight variations on these problems, may be on the exam. 2 . A number of questions will be based on the concepts, explanations, and important facts presented in lecture during weeks 7-10. Some (but not all) of these concepts, explanations, and facts are mentioned below. 3 . Know the sequence of reactions, structure of each molecule, use of ATP, NAD , FAD, NADPH, etc., and subcellular localization (cytosol, inner mitochondrial membrane, mitochondrial matrix, etc.) for the following: (a) For the oxidative branch of the pentose phosphate pathway (= the phosphogluconate pathway; see lecture handout 33 ) you should know either the name or the structure of each molecule, the use of NADP + and any other products/reactants at each step. You do not need to memorize the non-oxidative branch of the pentose phosphate pathway, but you should know that the general function of the non-oxidative branch is to return the carbons of the 5 carbon sugar ribose-5-P to intermediates in the glycolytic reaction sequence. You should also know that the non-oxidative branch requires transaldolase and transketolase, and that the transketolase requires a thiamine pyrophosphate prosthetic group. (b) Fatty acid biosynthesis starting with 2 acetyl CoA in the cytosol and ending with the formation of CH 3 CH 2 CH 2 C(O)-S-ACP. (see handout #36 ). (c) The pathway for the transport of acetyl CoA from the mitochondrial matrix to the cytosol; the pathway for the return of oxaloacetate to the mitochondria via malic enzyme and pyruvate (see handout #38 ). Know that the transfer of acetyl CoA from matrix to cytosol is driven by 1 ATP hydrolysis and that, in the return of oxaloacetate to the matrix, one NADH is converted to NADPH at the expense of 1 ATP hydrolysis. (d) Amino Acid Catabolism: Be able to reproduce the reactions which convert a dietary amino acid to an α keto acid (transamination with production of glutamate from α KG) and the oxidative deamination reaction which converts glutamate to α KG plus NH 4 + (glutamate dehydrogenase) (that is, know the reactions at the top of handout #25 ). Be able to reproduce the carbamoyl P synthetase reaction and all reactions of the urea cycle (see lecture handout # 27 ). Know that 18 of the α keto acids from the 20 common amino acids either already are, or can be converted to, a TCA cycle intermediate or pyruvate. Know the overall cost of excreting nitrogen as urea rather than as NH 4 + (4 ATP equivalents per urea) and why terrestrial vertebrates needed to evolve the energetically expensive urea synthesis pathway for nitrogen disposal while fish excrete NH 4 + directly through their gills.
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