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Exam 2 with answers

Exam 2 with answers - LAST NAME FIRST NAME Exam#2 BIO 320...

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Unformatted text preview: LAST NAME: __________________ FIRST NAME: __________________ Exam #2 BIO 320 There are 30 multiple-choice questions worth 2 points each. Use a #2 pencil to answer the multiple-choice questions. WRITE AND MARK OFF THE BUBBLES FOR YOUR LAST NAME AND UT EID ON THE SCANTRON FORM There are 10 fill-in-the-blank questions, 2 points each. There are 3 essay questions worth a total of 20 points. Use a pen if you want a regrade for these questions Write legibly and please do not ramble Multiple choice questions, 2 points each 1. In nuclear import/export, Ran-GTP performs which of the following functions? a. Allows export cargo to bind exportin in the nucleus b. Allows export cargo to bind exportin in the cytosol c. Allows import cargo to bind importin in the cytosol d. Allows import cargo to bind importin in the nucleus e. None of the above 2. Which of the following statement concerning nuclear trafficking is INCORRECT? a. NLS targets a protein into the nucleus b. Importin recognizes NLS c. All proteins that reside in the nucleus have NLS d. Exportin recognizes NES e. A protein may contain both NLS and NES 3. In the nuclear pore complex, the cross-linking between the nucleoporins that contain FG- repeats most likely involves which kind of interaction? a. Ionic b. Covalent c. Van der Waals d. Hydrophobic e. Hydrophilic 4. At the trans-Golgi network, a soluble protein in the lumen that has no additional sorting signals will end up: a. in the regulated secretory granule b. outside the cell c. in the endosome d. in the lysosome e. in the autophagosome 5. Which of the following is INCORRECT concerning the mannose-6-phosphate receptor? a. It shuttles between the trans-Golgi network and endosome b. Its binding to mannose-6-phosphate is affected by pH c. It helps to retrieve proteins that contain mannose-6-phosphate to the trans-Golgi network d. It is packaged into COPII-coated vesicles e. It binds only to proteins that has undergone N-linked glycosylation in the ER lumen 6. Which of the following processes is NOT part of autophagy? getting rid of damaged mitochondria getting rid of misfolded protein aggregates generating amino acids under starvation conditions getting rid of plasma membrane receptors that have been endocytosed generation of membrane vesicles that have 2 membranes 7. In epithelial cells, GPI-anchored proteins: a. become anchored to membranes through the attachment of prenyl groups b. are sorted to the basolateral membrane at the trans-Golgi network c. are transcytosed from the basolateral to the apical membrane d. are concentrated in lipid rafts on the plasma membrane e. become concentrated in lipid rafts on the trans-Golgi membrane 8. When cells are bathed in a solution of the fluorescent dye Lucifer yellow, vesicles that contain Lucifer yellow are soon observed inside the cells. None of these vesicles will appear if which of the following proteins is inactivated in such cells: a. caveolin b. clathrin c. dynamin d. ubiquitin e. lysosomal hydrolases 9. At nerve terminals, synaptic vesicles fuse with the plasma membrane within milliseconds of excitation. This rapid response is possible because: a. these synaptic vesicles have extraordinary high abundance of v-SNARE b. the plasma membrane at this site has extraordinary high abundance of t-SNARE c. these synaptic vesicles have extraordinary high abundance of Rab d. the plasma membrane at this site has extraordinary high abundance of Rab effector e. the v-SNARE and t-SNARE are already partially paired before excitation 10. At nerve terminals, most synaptic vesicles are derived from: a. the trans-Golgi membrane. b. the cis-Golgi membrane. c. the ER membrane d. the nerve terminal plasma membrane e. late endosomal membrane 11. When isolated mitochondria are incubated with the precursor form of the mitochondrial matrix protein cytochrome c oxidase, this protein becomes imported into the mitochondrial matrix. What will happen to this precursor protein if the isolated mitochondria are pretreated with the uncoupler dinitrophenol, which dissipates the proton-motive force? a. Protein will not bind mitochondria a. b. c. d. e. 12. 13. 14. 15. Protein will bind mitochondria but will be found entirely outside mitochondria Protein will pass through outer but not inner mitochondrial membrane Protein will be stuck spanning outer and inner mitochondrial membranes Protein will be imported into mitochondrial matrix but will not be cleaved In the import of a protein into the mitochondrial matrix, ATP is required as an energy source: a. to generate proton-motive force b. to keep the protein unfolded before import c. to pull the protein into the matrix d. a and b e. b and c Which of the following is INCORRECT about the LDL receptor? a. Defects in LDL receptor can lead to atherosclerosis b. It is endocytosed only when bound to LDL c. It is packaged into clathrin-coated vesicles d. It is needed for the change in localization of SREBP in response to extracellular LDL e. It is not degraded in the lysosome When levels of LDL are high, SREBP is found predominately in which cellular organelle? a. Endoplamic reticulum b. Golgi apparatus c. Nucleus d. Late Endosome e. Lysosome When SCAP is not made in a cell, what would happen to the expression of the HMG-CoA reductase gene? a. Unusually low expression under all conditions b. Unusually high expression under all conditions c. Unusually low expression only when cholesterol level is low d. Unusually high expression only when cholesterol level is high e. Normal expression b. c. d. e. 16. Which of the following is NOT a characteristic of BOTH microtubules and microfilaments? a. Nucleation is rate-limiting b. Use of a nucleotide for both assembly and disassembly c. Exhibit dynamic instability d. Filaments have polarity e. Subunit addition occurs faster at the plus end 17. In the process of microtubule assembly/disassembly, reducing the concentration of free tubulin DOES NOT have the effect of: a. reducing the rate of assembly b. increasing the rate of disassembly c. increasing the likelihood of catastrophe d. decreasing the likelihood of rescue e. decreasing the total amount of microtubules that can be assembled 18. The GTP on -tubulin is: a. hydrolyzed upon assembly b. exchangeable with cellular GTP when tubulin dimer is not assembled into microtubule c. trapped at the interface between neighboring tubulin dimers in a microtubule d. trapped at the interface between the two subunits of a tubulin dimer e. a and b 19. -TuRC serves: a. to organize the centrioles b. as the MTOC and cap the plus end of the microtubule c. as a template to nucleate microtubule assembly and caps the plus end of the microtubule d. as a template to nucleate microtubule assembly and caps the minus end of the microtubule e. to increase dynamic behavior of microtubules 20. Each centriole: a. is made up of 13 regular microtubules b. is made up of 10 regular microtubules c. is normally found parallel to its neighboring centriole d. directly nucleates microtubule assembly e. is made up of triplet microtubules 21. Which of the following functions with tubulin dimers? a. Stathmin b. EB1 c. Kinesin-13 d. Tau e. Katanin 22. In bacterial cells: a. there are no proteins that have properties of actin or tubulin b. there are proteins that have properties of actin c. there are proteins that have properties of tubulin 23. 24. 25. 26. 27. 28. d. there are proteins that have properties of actin and other proteins that have properties of tubulin e. there are proteins that have properties of both actin and tubulin Which of the following statements about microtubule motors is INCORRECT a. Kinesins and dyneins have very different structures b. Two motors can act against each other c. All dyneins are minus end-directed d. All kinesins are plus end-directed e. Different motors have different processivity A motor domain of kinesin-1 is most tightly bound to microtubules when it is: a. not bound to nucleotides b. GTP-bound c. ATP-bound d. right after hydrolysis of bound nucleotide triphosphate e. right after release of bound inorganic phosphate (after triphosphate hydrolysis) Which of the following pairs of proteins act in opposition to each other? a. ARP2 and ARP3 b. ARP and formin c. Cofilin and gelsolin d. Fimbrin and filamin e. Profilin and thymosin Which of the following is an activating factor for actin nucleation? a. Profilin b. Cdc42 GTPase c. Thymoxin d. CapZ e. Gelsolin Formin dimers: a. associate with ADP-bound F-actin b. nucleate assembly of a microfilament at the minus end c. nucleate assembly of a microfilament at the plus end and caps it there d. are activated by WASP e. nucleate assembly of a microfilament at the plus end, which does not become capped Which of the following proteins bind preferentially to ADP-actin: a. formin b. fimbrin c. cofilin d. WASP e. -actinin 29. Which of the following processes is NOT driven by actin assembly or disassembly? a. Intracellular pathogen movement b. Organelle movement c. Sperm acrosome reaction d. Membrane protrusions e. All are driven by actin polymerization or depolymerization 30. Cleavage of the SREBP transcription factor occurs: a. in the nucleus b. at the ER c. at the Golgi d. when level of cellular cholesterol is high e. when cholesterol synthesis is no longer needed Fill in the blank with one or a small number of appropriate words, 2 points each. 1. GDP-tubulin differs from GTP-tubulin in that GDP-tubulin has a conformation (shape) that is more ____bent/curved___________________. 2. In a typical mammalian cell, the microtubule ends found near the plasma membrane are mostly ____plus_________ends. 3. Association of importin with _____Ran-GTP____ causes cargo dissociation from importin. 4. In actin polymerization, the situation where the rate of growth = the rate of shrinkage is reached when the concentration of G-actin is at _____critical concentration____. 5. ___ARP complex___________________ is responsible for the branched network of microfilaments found near the plasma membrane. 6. Statins are drugs that _____inhibit HMG-CoA reductase/inhibit cholesterol synthesis_______. 7. An important characteristic of the signal sequence for mitochondrial protein import is that it is folded into __an amphiphilic -helix with positive charge on one side_________________________. 8. The plasma membrane is preferentially permeabilized by the detergent digitonin because ___plasma membrane has high cholesterol content_________________. 9. For a kinesin motor protein to be processive, each motor head has to spend _______>50%_________ of its ATP hydrolysis cycle (time) attached to a microtubule. 10. Stress fibers in a cell are often nucleated by __formin dimers____ at the plasma membrane. Assay questions. 1. The Cox4 protein is a mitochondrial matrix protein that is encoded by a nuclear gene. In cell fractionation and SDS-PAGE studies (shown on the right), Cox4 from wild- type cells is found exclusively in the mitochondrial fraction (M) and not the cytoplasmic fraction (C). Strains 1, 2 and 3 are defective in the SAM complex, the TOM complex, or the matrix signal peptidase (and you don't know yet which strain is defective in which protein). Results from studies of Cox4 from these three strains are also shown on the right. From these results, explain which protein is defective in each strain. (8 points) Strain 1 is defective in the peptidase since Cox4 is found associated with (actually in) the mitochondria but is not cleaved (leading to a protein that is larger in size due to the presence of the mitochondrial signal sequence). Strain 2 is defective in the TOM complex since it is found in the cytosol. TOM complex is required for all imported proteins to pass through the outer membrane. Without entering the matrix, Cox4 is also not cleaved. Strain 3 is defective in the SAM complex, which is NOT required for the import of proteins into the matrix. 2. MT1 is a protein that binds only to GTP-bound tubulin. You have expressed in human cells a MT1-GFP fusion protein that retains MT1 function. These same cells also express a -tubulin-RFP fusion protein that is fully functional. (6 points) a. You examine both fusion proteins in human cells. Do you think that you will see MT1-GFP associating with all microtubules? Explain. In human cells, some microtubule ends are in the assembly phase with GTP-capped ends. Other ends are in the disassembly phase with GDP-capped ends. Hence, MT1-GFP will only be seen at the ends of the microtubules that are in the assembly phase (i.e., not all ends). b. If you were to visualize over time only MT1-GFP (and not -tubulin-RFP), what would you expect to see? Describe what you think would happen to MT1-GFP over time with respect to its localization inside this cell. MT1-GFP will be seen as (comet-shaped) streaks that stream towards the cell periphery. Such streaks will disappear abruptly as the GTP-capped ends to which MT1-GFP binds become GDP- capped and disassemble. This will be similar to the pattern one sees with EB1-GFP. 3. With the help of a graph, show how the amount of F-actin varies as a function of time when one carries out an actin assembly assay in vitro, starting with G-actin. Label each portion of the graph. Briefly explain what is happening at each of these stages. (6 points) ...
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