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UGA BCMB 8020 - 2009examIII

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BCMB 8020 Exam III Name _____________________________ April 2, 2009 True / False (1/2 point each; 12 points total) 1. Fatty acid biosynthesis requires: ___ biotin ___ NADPH ___ ATP ___ GTP 2. Gram positive prokaryotes: ___ include organisms such as E. coli ___ have an extensive peptidoglycan layer ___ make extensive use of Type III secretion systems for infection ___ often use porins for small molecule transport 3. The Bromo domain: ___ contains 5 alpha helical bundles ___ makes extensive use of electrostatic intermolecular interactions ___ is the only interaction domain that interacts with acetylated lysines ___ is found on histones 4. Regarding proteolysis: ___ serine proteases have the same molecular mechanism regardless of substrate ___ cysteine proteases release the C-terminal portion of a polypeptide prior to the N-terminal portion ___ aspartic proteases rely on phosphorylation of aspartic amino acids as part of their mechanism ___ the four established protease classes each form acyl intermediates with their substrates 5. Regarding lipid-linked proteins: ___ GPI is a type of sphingolipid ___ GPI utilizes its amino group as a nucleophile in GPI protein formation ___ isoprenylation can be mediated by three distinct isoprenoid transferases ___ phospholipases can release the isoprenoid moiety of isoprenylated proteins 6. Regarding ABC-type transporters: ___ they have a modular design ___ their nucleotide binding domains (NBD) are structurally similar regardless of transport substrate ___ each ABC transporter is designed to transport a unique substrate ___ their transport mechanism was substantially elucidated by the first X-ray crystal structure of an ABC transporter (MsbA) Multiple Choice (2 points each; 24 points total; one correct answer per question) 7. The Fatty Acid Synthase primarily produces fatty acids of what length? A) C12 B) C14 C) C16 D) C18BCMB 8020 Exam III Name _____________________________ 2 8. Fatty acids are released from the Fatty Acid Synthase through the action of: A) ATP hydrolysis B) carboxylation C) reduction D) a thioesterase 9. The most recent hypothesis that attempts to explain the nature of the signal sequence associated with type III bacterial secretion systems suggests that the signal is: A) dependent on a lipid modification B) dependent on mRNA C) dependent on N and C-terminal polypeptide sequences D) tripartite in nature 10. The typical width of the lipid portion of a biological membrane is: A) 1.5 nm B) 5 nm C) 8 nm D) 15 nm 11. Which of the following amino acid is least likely to be found within a TM segment according to guidelines outlined in the article titled “Border Crossing” by Bowie. A) glutamine B) leucine C) methionine D) phenylalanine 12. Sphingomyelin synthesis depends on: A) glycerophosphatidylcholine B) glycerophosphatidylethanolamine C) glycerophosphatidylinositol D) glycerophosphatidylserine 13. Which of the following agents should you add to get the broadest target specificity against serine proteases that might be present in a crude cellular lysate? A) EDTA B) PMSF C) TPCK D) TLCK 14. As discussed in class, which of the following have not been co-opted into secondary messengers systems: A) amino acids B) fatty acid conjugates C) inorganic ions D) nucleotide derivativesBCMB 8020 Exam III Name _____________________________ 3 15. Which of the following is not a selectivity filter utilized by aquaporins? A) dipole filter B) osmotic filter C) proton filter D) size filter 16. Which of the following is the largest gene family of transport ATPases? A) ABC-type B) F-type C) P-type D) V-type 17. What does the P stand for in P-type ATPases? A) peripheral B) phosphate C) PKA activated D) proline 18. Which of the following is likely to be found at the interfacial region of porins? A) phenylalanine B) tryptophan C) tyrosine D) all of the above Short Answer - These can be answered using keywords, lists, diagrams, and/or 1-2 sentences (1-5 points each; 28 points total) 19. Two specific examples were provided in class in which methionine residues were described as being good for maintaining protein-peptide interactions with diverse substrates. List the two examples AND their interactors. (3 points) 20. Using the stick figure method, draw the chemical structure of a naturally occurring 16:2(∆8,12) fatty acid. (4 points) 21. Docosahexaenoic acid is commonly found in what over-the-counter nutritional supplement? (1 point)BCMB 8020 Exam III Name _____________________________ 4 22. What are the immediate energy requirements needed for glycerophosphatidylcholine synthesis? (2 points) 23. Answer the following regarding serpins. (5 points total; 1 point each) What type of molecule is a serpin (i.e. carbohydrate, lipid, nucleic acid, protein)? What does the acronym serpin stand for? Where are human serpins generally found? Name a specific serpin. What is the primary function of serpins? 24. Answer the following regarding protein lipid modifications. (4 points total; 1 point each) What modification does the term palmitoylation refer to? Why is the term palmitoylation misleading? Provide an example of a myristoylated protein. Provide an example of an isoprenylated protein. 25. Answer the following regarding taxol analogs and/or the multi-drug resistance (MDR/Pgp) channel. (3 points total; 1 point each) What fatty acid is being linked to taxol analogs as a means to improve its potency? Is MDR/Pgp affinity for the fatty acid modified analog improved, decreased, or unchanged relative to unmodified analog? MDR/Pgp belongs to what class of transport ATPases? 26. What two filters do cationic channels (e.g. the potassium) possess that allow for selectivity of cargo? (2 points)BCMB 8020 Exam III Name _____________________________ 5 27. In terms of their neurotoxicity, what is the target of botulinum and clostridial neurotoxins AND what specific effect do these toxins have on cellular function. (3 points) 28. What chemical reaction facilitates intracellular release of the A domain ‘warhead’ from many AB-type protein toxins? (1 point) Long Answer - answer the following questions using several sentences, highly descriptive diagrams, and/or highly descriptive list (4-9 points each; 36


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UGA BCMB 8020 - 2009examIII

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