BCMB 8020 Exam III April 2 2009 Name 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 C18 BCMB 8020 Exam III Name 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 derivatives 2 BCMB 8020 Exam III Name 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 8 12 20 Using the stick figure method draw the chemical structure of a naturally occurring 16 2 acid 4 points fatty 21 Docosahexaenoic acid is commonly found in what over the counter nutritional supplement 1 point 3 BCMB 8020 Exam III Name 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 4 BCMB 8020 Exam III Name 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 ABtype 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 points total For all questions in this section use sufficient detail to convey your knowledge of the material 29 Use the following table to describe the chemical differences between the typical membrane lipid of an archael species and glycerophospholipids 4 points Category Archae phospholipids Glycerophospholipids Glycerol stereochemistry Glycerol lipid linkage Type of lipid tail Arrangement in membrane 30 You have been asked to perform a fractionation experiment for three proteins Draw the idealized fractionation pattern that you would expect to see after an immunoblot i e draw bands for an integral membrane protein A a peripheral membrane protein that is associated by hydrophobic interactions B and a cytosolic