BCH 4054 FINAL EXAM NAME _____________________ December 14, 1995 This exam consists of seven pages. Make sure you have one of each. Several questions involve a choice. Answer only one of the choice. (If you answer both, you need to indicate which answer is to be graded). The last page contains some reduction potentials, some constants, and the genetic code. You may tear this sheet off and use it for scratch work. Good luck on the exam, and have a nice holiday! Points (16) 1. Isolated mitochondria can catalyze a reversal of electron flow through complex I, in which the following overall path of electron flow is followed at the expense of ATP hydrolysis: succinate ---> complex II ---> CoQ ---> complex I ---> NAD+ This electron flow is driven by ATP hydrolysis, so the overall process amounts to the coupling of the following two reactions: succinate + NAD+ ----> fumarate + NADH ATP + H20 ----> ADP + Pi (a) Assuming a 1:1 stoichiometry for the two coupled reactions (reasonable, since each involves movement of four protons), then calculate the delta Go' for the overall coupled reaction. (delta Go' for ATP hydrolysis is -30 kJ/mol in case you have forgotten.) Assume a temperature of 37 oC. (b) Describe the composition of complex I and complex II and their orientation in the mitochondrial membrane. What is another name for complex II? Answer Question 2 or 3 (12) 2. Give the pathway by which palmitic acid (C16:0) is released from triglyceride in adipose tissue, transported to and taken up by the liver, and then converted to acetoacetate which is secreted as a fuel source for peripheral tissues. Don't forget to describe the steps involving transport across membranes. How many ATPs would be made in the liver from the conversion of one mole of palmitic acid to four moles of acetoacetate? (Identify the steps involving CoQH2 and NADH production, assume they yield 1.5 and 2.5 moles of ATP respectively, and show how you calculate the ATP yield). (12) 3. Give the pathway by which glutamate, produced by the breakdown of muscle protein during starvation, can be converted to glucose and urea by the liver. Indicate which reactions take place in the liver cytoplasm and which in the liver mitochondria. Calculate the stoichiometry of the overall reaction: i.e., it takes two moles of glutamate to produce one mole of urea; those two moles of glutamate will produce how many moles of glucose, CO2, and ATP? (Assume oxidative phosphorylation is active, that CoQH2 and NADH yield 1.5 and 2.5 moles of ATP respectively, and show how you calculate the overall ATP yield.) Answer 4 or 5 (6) 4. There are two HMG-CoA synthase enzymes, one in mitochondria and one in the cytoplasm. Give the reaction catalyzed by HMG-CoA synthase, including all reactants and products, and the function of each of the two enzymes. (6) 5. There are two carbamoyl phosphate synthases, one in mitochondria and one in the cytoplasm. Give the reaction catalyzed by each of them, including all reactants and products, and the function of each of the two enzymes. Answer 6 or 7 (8) 6. Identify the component protein domains of fatty acid synthase either by name or reaction catalyzed. Two types of sulfhydryl groups are attached covalently to intermediates of the pathway. Describe the location and function of each sulfhydryl group. (8) 7. Propionyl-CoA is a product of catabolism of both odd chain fatty acids and several amino acids. Explain how it is converted to a TCA cycle intermediate, showing all the intermediates in the conversion, and identifying the enzymes involved and their prosthetic groups. Answer 8 or 9 (10) 8. Elevated blood triglyceride can come from one of two different lipoproteins. One case is classified as Type I hyperlipoproteinemia, the other as Type IV hyperlipoproteinemia. Which protein is involved in each case, what is the cause, and what is the recommended treatment? (10) 9. Both HDL and LDL contribute to blood cholesterol levels. Contrast these two lipoproteins with respect to: (a) apoprotein content; (b) density; (c) electrophoretic mobility; (d) function; and (e) effect on health. (10) 10. Identify five of the following: (a) C1 donor for position 8 of purines (b) Activated ribose involved in nucleotide biosynthesis (c) Covalent modification inactivating glutamine synthetase (d) Allosteric inhibitor of aspartate transcarbamoylase (e) Target enzyme for aminopterin inhibition of cancer cell growth (f) Essential dietary C18 fatty acid which is a precursor of PGE2 (g) Purine nucleotide precursor of both AMP and GMP (h) Amino acid precursor of the pyrimidine ring Answer 11 or 12 (8) 11. The Calvin-Benson cycle constitutes the "dark reaction" of photosynthesis. Identify for this pathway: (a) the first radioactive product that can be isolated from 14CO2 (b) products of photorespiration (c) two substrates for transketolase (d) two substrates for aldolase (e) the cellular location of the pathway (f) the ATP and NADPH stoichiometry of the overall reaction: CO2 ------> "CH2O" (8) 12. Diagram a chloroplast including the thylakoid membrane. Indicate on the diagram the location and orientation of: (a) pigment system I (b) pigment system II (c) ATPase (d) Rubisco (e) cytochrome b/f complex (6) 13. Codons for which of the following amino acids could be converted to a stop codon by a single base substitution? (Circle the appropriate amino acids. The genetic code table is on the last page.) Glu Asp Val Lys Arg Met (6) 14. The following sequence from the middle of a m-RNA could encode three different polypeptides sequences. What are they? 5'-CUCAAAUGAGGACC-3' Answer 15 or 16 (8) 15. Replication of DNA is remarkably error-free. Explain the mechanisms by which the error rate is reduced so much. When an error is detected, how does the cell know which strand to correct? (8) 16. Protein synthesis need not be as error free as DNA synthesis, yet there are some mechanisms that serve to proof read the two recognition steps in translation, (a) attachment of the correct amino acid to the tRNA and (b) insertion of the correct tRNA on the A site of the ribosome. Explain how they work. Answer Question 17 or 18 (10) 17. Explain how the starting point for transcription of a gene is recognized in (a) prokaryotes and (b) eukaryotes. (10) 18. Explain how the starting point for translation of a message is recognized in (a) prokaryotes and (b) eukaryotes. Answer 19 or 20 (6) 19. Explain how GTP is involved in protein synthesis. (6) 20. Describe the post-transcriptional modification of eucaryotic mRNA. Selected Standard Reduction Potentials Reduction Half Reaction Eo' (V) 2 H+ + 2 e- -----> H2 -0.42 NAD+ + H+ + 2 e- -----> NADH -0.32 FAD + 2 H+ + 2 e- -----> FADH2 -0.22 Acetaldehyde + 2 H+ + 2 e- -----> Ethanol -0.20 Pyruvate + 2 H+ + 2 e- -----> Lactate -0.18 Oxaloacetate + 2 H+ + 2 e- -----> Malate -0.17 Fumarate + 2 H+ + 2 e- -----> Succinate +0.03 CoQ + 2 H+ + 2 e- -----> CoQH2 +0.04 Cyt b(ox) + e- -----> Cyt b(red) +0.08 Cyt c1(ox) + e- -----> Cyt c1(red) +0.22 Cyt c(ox) + e- -----> Cyt c(red) +0.23 Cyt a(ox) + e- -----> Cyt a(red) +0.29 1/2 O2 + 2 H+ + 2 e- -----> H20 +0.82 Use the following constants: R = 8.315 x 10-3 kJ mol-1 deg-1; T = 37oC (310 K); ln x = 2.3 log x F = 96.48 kJV-1mol-1 GENETIC CODE (T in the DNA becomes U in the RNA) Second position | T | C | A | G | ----+--------------+--------------+--------------+--------------+---- | TTT Phe (F) | TCT Ser (S) | TAT Tyr (Y) | TGT Cys (C) | T T | TTC " | TCC " | TAC | TGC | C F | TTA Leu (L) | TCA " | TAA Ter | TGA Ter | A T i | TTG " | TCG " | TAG Ter | TGG Trp (W) | G h r --+--------------+--------------+--------------+--------------+-- i s | CTT Leu (L) | CCT Pro (P) | CAT His (H) | CGT Arg (R) | T r t C | CTC " | CCC " | CAC " | CGC " | C d | CTA " | CCA " | CAA Gln (Q) | CGA " | A P | CTG " | CCG " | CAG " | CGG " | G P o --+--------------+--------------+--------------+--------------+-- o s | ATT Ile (I) | ACT Thr (T) | AAT Asn (N) | AGT Ser (S) | T s i A | ATC " | ACC " | AAC " | AGC " | C i t | ATA " | ACA " | AAA Lys (K) | AGA Arg (R) | A t i | ATG Met (M) | ACG " | AAG " | AGG " | G i o --+--------------+--------------+--------------+--------------+-- o n | GTT Val (V) | GCT Ala (A) | GAT Asp (D) | GGT Gly (G) | T n G | GTC " | GCC " | GAC " | GGC " | C | GTA " | GCA " | GAA Glu (E) | GGA " | A | GTG " | GCG " | GAG " | GGG " | G ----+--------------+--------------+--------------+--------------+----