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Exam 1 with answers - LAST NAME FIRST NAME Exam#1 BIO 320...

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Unformatted text preview: LAST NAME:__________________ FIRST NAME:__________________ Exam #1 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. Which of the following is correct in terms of bond strength a. Hydrogen bonds > Hydrophobic interactions > Ionic bonds b. Ionic bonds > Hydrophobic interactions > Hydrogen bonds c. Hydrophobic interactions = Hydrogen bonds > Van der Waals forces d. Hydrophobic interactions > Van der Walls forces > Hydrogen bonds e. Ionic bonds > Hydrogen bonds > Hydrophobic interactions Which of the following is often found in a protein's quaternary structure? a. Methylation of Lysine residues b. Ubiquitination of Arginine residues c. Acetylation of Arginine residues d. Phosphorylation of threonine and tyrosine residues e. Disulfide bond formation between cysteine residues Which of the following amino acids can be phosphorylated? a. Glutamic acid b. Glycine c. Cysteine d. Serine e. Lysine In SDS-PAGE, which of the following is true? a. Proteins with a higher molecular weight will migrate faster than proteins with a lower molecular weight b. Proteins with a lower molecular weight will migrate faster than proteins with a higher molecular weight c. Integral membrane proteins will migrate faster than peripheral membrane proteins of the same molecular weight d. Membrane proteins will migrate more slowly than soluble proteins with the same molecular weight e. Proteins in a complex always migrate together at the same speed 2. 3. 4. 5. When compared to a conventional fluorescence microscope, a confocal fluorescence microscope: a. provides higher magnification b. allows signals that are less bright to be seen c. has higher signal-to-noise (caused by out-of-focus signal) ratio d. provides higher resolution e. none of the above 6. For membranes made up entirely of each of the following lipid molecules, which of the following is correct in terms of their thickness? a. Sphingomyelin > cholesterol > glycolipid b. Phosphoglyceride > sphingomyelin > cholesterol c. Cholesterol > phosphoglyceride > glycolipid d. Glycolipid > phosphoglyceride > cholesterol e. Saturated phospholipid > mono-unsaturated phospholipid with cis double bond > mono-unsaturated phospholipid with trans double bond 7. In normal mammalian cells, which lipid would NOT be found on the side of the plasma membrane facing the extracellular space? a. Phosphatidylcholine b. Sphingomyelin c. Phosphatidylethanolamine d. Sphingosine e. Phosphatidylserine 8. Many proteins are N-glycosylated in the ER lumen. Which amino acid are these sugars linked to? a. Lysine b. Methionine c. Glycine d. Asparagine e. Leucine 9. Which of the following is NOT a function of protein glycosylation? a. Restricts access to the surface of glycosylated proteins b. Assists in protein folding c. Helps in cell surface recognition by other molecules d. Helps anchor peripheral membrane proteins to the plasma membrane e. Makes some secreted proteins "slippery or slimy" 10. Which protein is responsible for pinching off of clathrin-coated vesicles? a. Sar1 b. Dynamin c. Sec13 d. Phosphatidylinositol e. ARF6 11. Which two proteins on transport vesicles are required for targeting to proper recipient compartment? 12. 13. 14. 15. 16. a. SAR1 and SNARES b. Rab and SNAPS c. NSF and SNARES d. SNAPS and SNARES e. Rab and SNARES Which two GTPases regulate vesicle budding? a. Sec13 and Sec31 b. Sec31 and Sar1 c. Sec13 and ARF6 d. Sar1 and ARF5 e. Sec24 and ARF1 Which COAT protein is responsible for retrograde movement from the Golgi to the ER? a. Synaptobrevin b. COPI c. COPII d. Clathrin e. Syntaxin Which protein(s) are required to recycle SNAREs? a. NSF b. Syntaxin c. Rab-GTP and Sar1 d. Dynamin e. PDI Electron microscopes have better resolving power than light microscopes because: a. Electrons scatter better than light. b. Electron microscopes have twice as many lenses c. Electrons have a shorter wavelength d. The resolving power increases if you double the electrons used e. Electrons are smaller and are able to pass through the sample better What is a major difference between HSP60 and HSP70? a. Multiple HSP60 proteins can bind to a given protein simultaneously b. HSP70 phosphorylates proteins while helping them fold whereas HSP60 does not c. HSP70 can hydrolyzes peptide bonds to help a protein fold more quickly d. HSP70 works better on shorter proteins while HSP60 is better for longer ones e. HSP60 has 2 folding chambers while HSP70 does not 17. Which of the following are found in particularly high concentrations in lipid rafts? a. Phosphatidylserine and cholesterol b. Phosphotidylenthanol and sphingosine c. Cholesterol and glycosphingolipids d. Phospholipids and integral membrane proteins e. Sphingosine and phosphotidylglycerol 18. Which of the following is not a characteristic of the SRP? a. It has a hydrophobic binding pocket lined with methionine residues b. It has a translational pause domain c. It contains a small RNA molecule d. It has a flexible hinge e. It recognizes a small amphipathic region on target proteins 19. Upon translocation through the ER membrane, the C-terminus of the triple-pass transmembrane protein X protrudes into the cytosol. After this protein reaches the plasma membrane, how is it oriented? a. The N-terminus is in the cytosol and the C-terminus is in the extracellular space b. Both the N-terminusand the C-terminus are in the extracellular space c. Both the N-terminus and the C-terminus are in the cytosol d. The C-terminus is in the cytosol and the N-terminus in the extracellular space e. None of the above 20. Vesicles leaving the ER for the Golgi are coated in which protein? a. t-SNAREs b. COPI c. COPII d. Sar1 e. Clathrin 21. Proteins that are not able to fold correctly in the ER are mostly targeted for degradation by: a. K63-linked polyubiquination b. the addition of a galactose chain to the N-terminus of the protein c. removal of a mannose sugar by mannosidase d. binding to HSP60 e. N-linked glycosylation 22. Retrieval of soluble ER proteins from the cis-Golgi: a. occurs in clathrin-coated vesicles b. is signaled by a KDEL sequence at the N-terminus of the protein c. is an example of anterograde transport 23. 24. 25. 26. 27. 28. d. does not occur because such proteins never leave the ER e. requires a slightly acidic environment in the cis-Golgi Which of the following statements is false: a. Polyubiquitination can occur through both K48- and K63-linkages b. HSP70 uses GTP to help fold proteins c. SNARE proteins require the use the energy of ATP hydrolysis to be recycled d. Botulinum toxin is a protease that cleaves t-SNAREs at neuromuscular junctions e. Cholesterol enhances membrane permeability to small water soluble molecules Which of the following factor(s) can affect the resolution of a microscope? a. The wavelength of light used b. the refractive index of the medium separating the specimen from the objective and condenser lenses c. the angular width of the cone of rays collected by the objective lens d. A and B e. All of the above In general, phospholipid molecules in a membrane are not readily free to: a. diffuse laterally b. flex their fatty acid tails c. rotate d. move from one monolayer to the other monolayer e. interact with neighboring phospholipid molecules Prion diseases are caused by defects in: a. protein glycosylation b. protein folding c. protein secretion d. protein synthesis e. phospholipid synthesis Resident ER membrane proteins that escape from the ER are retrieved because: a. they contain the KDEL sequence b. they are packaged into clathrin-coated vesicles at the cis-Golgi c. they are O-linked glycosylated in the cis-Golgi d. they contain the lysine-lysine-X-X (KKXX) sequence e. they have not undergone glucose trimming Molecular chaperones can tell that a protein is misfolded by: a. Detecting large amounts of hydrophobic amino acids exposed on the surface of a protein b. Detecting large amounts of hydrophilic amino acids in the core of a protein c. Detecting large amounts of lysine residues on the surface of a protein d. Detecting large amounts of hydrophilic amino acids exposed on the surface of a protein e. Detecting the absence of a mannose molecule on the surface of a protein 29. After one disrupts cells and their membranes by homogenization, one can easily separate smooth microsomes from rough microsomes by their differences in: a. glycosylation status b. phosphorylation status c. buoyant density d. size e. cholesterol content 30. Which of the following statements is CORRECT concerning a stop-transfer sequence and a start-transfer sequence? a. they are different in length b. they are different in sequence c. they are different in length and sequence d. they are similar in length and sequence e. they always function together (one cannot function without the other) Fill in the blank with one or a small number of appropriate words, 2 points each. 31. Different amino acids have different physical and chemical properties because they have different ____R groups___________________. 32. Detergent and lipid molecules are _________amphipathic/amphiphilic__________________. 33. The internal _____lysine_____________ residues of ubiquitin are critical for the formation of poly-ubiquitin chains. 34. In the laboratory, a peripheral membrane protein can be extracted from membrane by ___salt____________. 35. Disulfide bond formation cannot occur in the cytosol because the cytosol is a ____reducing___________ environment. 36. Clathrin drives vesicle budding at ___plasma membrane and trans-Golgi network________. 37. ___Phosphatidylinositol_____ is a phosphoglyceride that can be phosphorylated at multiple positions, resulting in products that can recruit different proteins. 38. KDEL sequence is the signal for __retrieval of soluble ER luminal protein from Golgi_______________________________________________. 39. The enzyme that activates a GTPase is called a ___GEF or guanine nucleotide exchange factor________. 40. A soluble protein that has entered into the ER lumen will end up ____secreted/outside cell_________ if it has no further targeting sequences. Assay questions. 1. Your friend is trying to create an in vitro system for generating a large amount of vesicles that are stably coated with COPII. He finds that to get efficient generation of COPII-coated vesicles from artificial membranes, he needs to add not only the necessary proteins known to be required for COPII vesicle budding, but also GMP-PNP (a functional analog of GTP that cannot be hydrolyzed). His experiment will not work if GTP is used instead. Explain why your friend needs to add GMP-PMP instead of GTP. (6 points) Sar1 GTPase can hydrolyze GTP to GDP. When this happens, Sar1 GDP can no longer bind adaptor proteins and COPII coat proteins. Hence, hydrolysis of GTP by Sar1 after vesicle budding leads to uncoating, resulting in loss of COPII coat from such vesicles. 2. Shown below is a protein that has stretches of hydrophobic residues (shaded). Residues of different charges flank one such stretch. The numbers represent the positions of these hydrophobic residues. If this protein ends up on the plasma membrane, draw the organization of this protein on this membrane. Be sure to label the cytoplasmic and extracellular face of your membrane and the N- terminus and C-terminus of your protein. If this protein is O-linked glycosylated, which segment(s) of this protein might be glycosylated? (8 points) 3. You expressed in cultured cells protein X, which has a known molecular weight of 30 kilodalton. To your disappointment, you found only a small amount of protein X of 30 kilodalton (as analyzed by SDS-PAGE) in these cultured cells. You suspected that the reason might be that protein X was degraded in these cells. Hence, you repeated the experiment by blocking all functions of the proteasome in these cells. Unfortunately, you did not see increased amount of protein X of 30 kilodalton. Explain why. (6 point) If protein X is degraded in the proteasome, it would have to be poly-ubiquitinated first. This poly- ubiquitination results in a form of protein X that is larger than 30 kilodaltons. Blocking proteasome functions will not block this poly-ubiquitination. Hence, protein X would continue to be ubiquited, resulting in no net increase in the amount of protein X of 30 kilodalton. ...
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