BCMB 8020 Exam III – 100 points total Name _____________________________ April 1, 2008 True / False (0.5 point each; 10 points total) 1. Regarding integral membrane proteins: ____ they typically have transmembrane segments that are 10 nm in width. ____ they typically constitute 25% of the genes in a typical genome. 2. Regarding naturally occurring fatty acids: ____ they typically have an even number of carbon bonds. ____ they typically have trans double bond configurations when unsaturated. ____ they are relatively insoluble in water. 3. Regarding prokaryotic protein secretion: ____ the Sec-system translocates unfolded proteins. ____ the signal sequence targeting proteins to the Sec-system is retained on secreted proteins. ____ Gram positive prokaryotes make extensive use of Type III systems for infection. 4. Proteins with a PDZ domain: ____ typically bind a phosphorylated target. ____ interact with the N-termini of proteins that are modified by the methionine aminopeptidase. 5. In terms of protease mechanisms: ____ an aspartic protease forms an acyl intermediate with its substrates. ____ the N-terminal product produced by all 4 proteolytic mechanisms would be radiolabeled in the presence of 18O-H2O. 6. Regarding protease inhibitors: ____ PMSF inhibits elastase, chymotrypsin, and trypsin. ____ TLCK inhibits chymotrypsin. 7. GPI-linked proteins: ____ are found in single celled parasites on the extracellular face of the plasmamembrane. ____ are anchored in plasma membranes because of their conjugation with a sphingolipid. 8. On the topic of protein channels: ____ they can be either gated or ungated. ____ the aquaporin channel is 5.8 Å in diameter at its narrowest. 9. Regarding the 4 types of transport ATPases discussed in class: ____ they can all be manipulated to hydrolyze ATP. ____ the P-type ATPases represent the largest transporter gene family. Multiple Choice (2 points each; 28 points total; one correct answer per question) 10. Which of the following biological membranes does not actively restrict ion movement across it? A) endoplasmic reticulum B) nucleus C) peroxisome D) plasma membraneBCMB 8020 Exam III Name _____________________________ 2 11. Which of the following amino acids is not a part of glutathione? A) cysteine B) glutamate C) glycine D) serine 12. Which of the following is the best source of dietary docoahexanoeic acid? A) beef B) fish C) leafy vegetables D) nuts and seeds 13. The polar head group on cholesterol is derived from which functional group? A) an amine B) a hydroxyl group C) a phosphate group D) a sulfhydryl group 14. Cholesterol is similar in size to a fatty acid of which length? A) C12 B) C14 C) C16 D) C18 15. What is the relative abundance of docosahexaenoic acid in the plasma membranes of neurons (by weight relative to other lipid components)? A) 50% B) 33% C) 25% D) 10% 16. Approximately, what percentage of medically relevant drugs target membrane proteins? A) 50% B) 33% C) 25% D) 10% 17. Which of the following is the binding target of the FYVE domain: A) PI(3)P B) PI(3,4)P2 C) PI(4,5)P2 D) PI(1,4,5)P3 – more commonly known as IP3 18. The FYVE domain requires which ion cofactor: A) Ca2+ B) Fe2+ C) Mg2+ D) Zn2+BCMB 8020 Exam III Name _____________________________ 3 19. Which of the following is not known to be nucleophile in proteolytic mechanisms? A) cysteine B) histidine C) serine D) water 20. Which of the following eukaryotic organelle membranes is not known to have an associated ABC transporter? A) endoplasmic reticulum B) lysosome C) nucleus D) plasma membrane 21. Which of the following typically exists in monomeric form in biological membranes? A) ABC-type ATPase B) aquaporin channel C) OmpF general porin D) P-type Ca2+ ATPase 22. Based on class discussion, which of the following amino acids is least likely to be at the interfacial region of a porin or channel ionophore? A) His B) Phe C) Trp D) Tyr 23. Which of the following does not contribute to the selectivity of the aquaporin channel? A) desolvation filter B) dipole filter C) proton filter D) size filter Short Answer - These can be answered using one or two keywords, lists, diagrams, and/or a few sentences (1-4 points each; 31 points total) 24. Using the stick figure method, draw the chemical structure of a naturally occurring 18:2(∆9,12) fatty acid. (4 points)BCMB 8020 Exam III Name _____________________________ 4 25. Transmembrane segments of which type of secondary structure are not readily identified by existing computer algorithms? (1 point) 26. What is the common over-the-counter name for dietary docoahexanoeic acid? (2 points) 27. List the predominant sequence features and/or protein domains of a prokaryotic protein that is destined for secretion via the autotransporter mechanism? (3 points) 28. List two protein interaction domains that were discussed in class that function similarly to the FYVE domain. (2 points) 29. What two types of proteases are generally required for production of peptide hormones such as adreno corticoprophin horomone (ACTH) and β-endorphin? (2 points) 30. Why is palmitoylation not an accurate descriptor for this type of lipid-based protein modification? (2 points)BCMB 8020 Exam III Name _____________________________ 5 31. List the types of lipid-modified proteins that do not have a free carboxylic acid at the C-terminus? (3 points) 32. Which lipid is typically found conjugated to mammalian retroviral Gag polypeptides such as HIV Gag? (2 points) 33. What new paradigm (i.e. pathway) did Dr. Schmidt describe that expands the known paradigms for mediating signal transduction across biological membranes. (2 points) 34. List any four of the six domains that make up the Ca2+ P-type ATPase? (4 points) 35. List the two types of energy potential used to drive ATP synthesis? (2 points) 36. What bacterially derived reagent was essential for the experiments used in determining that the translocon channel was open and continuous with the exit channel of translocating ribosomes? (2 points)BCMB 8020 Exam III Name _____________________________ 6 Long Answer - answer the following questions using several sentences, highly descriptive diagrams, and/or highly descriptive lists; in the case of the experimental diagram, just fill in the appropriate banding pattern