BCMB 8020 Exam III Name: _________________________________Dr. Schmidt - Lectures 5-16 March 4, 2003100 2 2 11 00-1-1-2-215050amino acid positionK&Dindex1. Lipids can be classified into two broad groups. List them. (2 points)2. Draw the general structure (i.e., a cartoon) of a generic membrane phospholipid AND identifythe key parts of the structure. (4 points).3. Which molecule (larger than an atom) is used as a precursor in the synthesis of all lipids? (1 point)4. Which nucleotide triphosphate (NTP) is required for glycerophospholipid synthesis ANDwhich of the NTP phosphate groups is specifically incorporated into the lipid? (2 points)5. List the lipid(s) that specifically incoporate phosphatidic acid? (2 points)6. Identify the predicted membrane spans in the following Kyte and Doolittle hydropathy plotusing shading and numerical identifiers (I, II, etc.) AND depict the possible topology/topologiesfor this protein. (4 points)7. What are the features of the targeting signal that directs a protein to the general Sec-dependent secretion system in prokaryotic organisms? Describe OR depict with descriptivelabels (4 points)BCMB 8020 Exam III Name: _____________________________28. List the different types of protein lipidation AND indicate whether they are typically found onintracellular or extracellular molecules. (5 points)9. List the amino acids that can be modified by phosphorylation? (4 points)10. List factors, as defined in lecture, than can influence proteolytic mechanisms. (3 points):11. Provide examples of TWO protein-protein interaction domains AND define the motif thatthey interact with. (3 points)12. List the four basic principles of signal transduction, as defined in lecture. (4 points)13. Describe the role(s) of the basic components/modules of a GPCR signal transduction system. (6 points)14. Draw/Depict in cartoon fashion the general structural features of ABC proteins (usedescriptive labels). (3 points)BCMB 8020 Exam III Name: _____________________________315. Label each blank to indicate whether the term is typically indicative of a Channel (C), ActiveTransporter (T), or Both(B)? (4 points)____ Continuous pore____ Easily saturable____ Energetically uphill transport____ Energetically downhill transport____ ATP requiring____ Fast, relative to passive diffusion____ Cargo specific____ Facilitated16. Briefly compare AND contrast the properties of aquaporin and OmpF porin channels interms of A) secondary structure, B) quaternary structure, C) pore location, and D) poreselectivity. (8 points)17. Briefly describe the biophysical properties that make fluorochromes a good FRET pair? (6 points)18. What is the basis for the differential effects of TPCK and TLCK on Chymotrypsin andTrypsin? (4 points)19. The farnesyltransferase (FTase) and geranylgeranyltransfersase I (GGTaseI) share acommon α subunit and have distinct β subunits. The FTase β subunit can bind both farnesylbisphosphate (Fpp) and geranygeranyl bisphosphate (GGpp), but only Fpp is efficiently utilizedas a substrate. Briefly describe why this is the case. (3 points)BCMB 8020 Exam III Name: _____________________________420. Vibrio cholerae is responsible for cholera, a diarrheal type of disease. The causative agent isa toxin that is produced by this organism. The toxin exerts its effect on intestinal epithelial cells.Briefly describe (10 points total):A) the mechanism used by cholera toxin for secretion from Vibrio cholerae. (3 points)B) the mechanism used for uptake and dispersion of the toxin in the cytoplasm of epithelial cells. (4 points)C) the target(s) of the toxin and the immediate cellular effect(s). (3 points)21. You have isolated a new compound that is an inhibitor of the HIV aspartyl protease. Youhave obtained kinetic data on the inhibitory nature of your compound that is represented in theLineweaver-Burke plot shown. Set A data was obtained by measuring the velocity (rate) ofproteolytic activity in the presence of varying substrate concentrations. Set B data was obtainedas in A but included the antiviral compound in the reactions. (5 points total)A. What type of inhibition is occurring? (1 point)B. Your compound is likely a mimic of what? (2 points)C. Your compound has a single hydroxyl group. Whenyour compound is synthesized as an ester-derivative, it ismore effective on infected intact cells. Why is this likelyto be the case? (2 points)0.00.20.40.60.81.01/Velocity-0.4 -0.2 0 0.2 0.4 0.61/[S]Set ASet BBCMB 8020 Exam III Name: _____________________________522. You have a sample preparation containing both P- and V-type ATPases. The combinedactivity of both ATPases contributes to the measured activity of the total sample as determinedby a colorimetric assay that can detect Pi release. How could you use the same type of assay tosimply determine the relative contribution of each enzymatic activity? (4 points)23. You obtained the following data from a protease protection experiment that was designed todetermine the topology of a peroxisomal membrane protein that you are studying (calledunknown in the diagram). Draw the simplest topology that is supported by the data. (2 points)24. List the key events required for vesicular fusion as described in the lecture notes (5 points).25. List AND briefly describe TWO biochemical methods that could be used to evaluatewhether a protein is part of an enzymatic complex. (2 points)N-termSite of reporter:C-termTX-100:Prot. K:+---+-+++---+-++peroxisomalmatrix proteinUnknownBCMB 8020 Exam III Name: _____________________________6Extra Point Questions (5 points total) – Note that the maximum exam score is 1001. What is the byproduct of the condensation reaction carried out by the fatty acid synthase (1 point)2. Relate one piece of experimental evidence that supports either the pore or proximity modelfor vesicular fusion. (2 points)3. Describe the role of regulated intramembrane proteolysis in the maturation of a transcriptionfactor. (2