SC/BIOL Biochemistry

Transcription

1 SC/BIOL Biochemistry Midterm #1 Name: Student ID: Feb 7 th, 2013 Time: 1 hr and 15 min This test has multiple choice: 24 Marks. Fill in the blanks: 10 Marks Peptide structure: 6 Marks There are a total of 10 pages of this exam. You are allowed to use a non-programmable calculator. For multiple choice: Choose the BEST answer and indicate your choice on the scantron. Please use a pencil. 1

2 1. Which of the following weak interactions is NOT due to differences in electrical charge distribution? a) hydrophobic interactions. b) hydrogen bonds. c) dipole-diople interactions. d) ionic interactions. e) London dispersion forces. 2. Which of the following amino acids could form a hydrogen-bonding interaction between their R groups? a) Glutamine and Alanine b) Glutamine and Valine c) Glutamine and Phenylalanine d) Glutamine and Isoleucine e) Glutamine and Tryptophan 3. There are several amino acid side chains that are always charged at physiological ph. These are: a) Gln, Asn, Lys, and Arg. b) Glu, Asp, Lys, and Arg. c) Lys, His, and Arg. d) Glu, Asp, Lys, Arg, and His. 4. After synthesis, a globular protein spontaneously folds because: a) water interacts with polar residues on the protein surface. b) nonpolar residues coalesce through the hydrophobic effect. c) disulphide bridges form. d) thermal energy randomly achieves the most stable conformation. e) polar residues form hydrogen bonds within the protein. 5. If an aqueous solution has a hydrogen ion concentration of 10-5 M what is the concentration of the hydroxyl ion? a) 10-5 M b) 10-7 M c) 10-9 M d) M 2

3 e) M 6. An acid, HA, has a concentration of M and its conjugate base, A -,has a concentration of 0.025M at ph 6. What is the pka of HA? a) 5.52 b) 6.48 c) 6.00 d) 7.60 e) A BIO 2020 student does a Western blot, shown below. Unfortunately the Western blot reveals 5 different bands, due to the poor specificity of the antibody. Which band is most likely the right one given the protein of interest is 200 amino acids in length? A molecular weight ladder is given to the left. 72 kd 55 kd kd kd 26 kd 17 kd A B C D E 8. An alpha helix is a secondary structure that is characterized by: a) Every C=O in the polypeptide backbone has a hydrogen bond to an N-H group 4 residues along the helix. b) The C=O in the polypeptide backbone hydrogen bonds with N-H groups in an adjacent helix backbone. c) Proline is modified to hydroxyl-proline which allows hydrogen bonding within the helix. d) Mostly random coil regions, characterized by proline residues. e) Hydrogen bonding of R-groups on the outside of the helix with water. 9. The initial O 2 molecule to bind to the hemoglobin protein results in: 3

4 a) the dissociation of other O 2 molecules that were previously bound. b) a decrease in hemoglobin's affinity to bind a second O 2. c) dissociation of the hemoglobin subunits. d) the diffusion of oxygen into muscle tissue. e) an increased affinity for O 2 in the remaining subunits. 10. Noncovalent forces that stabilize protein structure include all of the following except? a) the hydrophobic effect b) salt bridges c) electrostatic interactions with metal ions d) hydrogen bonding e) disulfide bridges 11. If Histidine 143 in hemoglobin was mutated, so that 2,3- Bisphophateglycerate was no longer able to bind, what would be the effect? a) Heme would no longer be able respond to oxygen binding, and therefore allosteric regulation of hemoglobin would be lost. b) This would lead to hemoglobin aggregation and thus sickle cell anaemia. c) Hemoglobin would have a higher affinity for oxygen, favouring the R state. d) Hemoglobin would have a lower affinity for oxygen, favouring the T state. e) Carbon dioxide would no longer have an effect on hemoglobin, favouring R-state. 12. Where do anti-parallel β sheets fall on the Ramachandran plot? a) A b) B c) C d) D e) E 13. Find the initial velocity for an enzymatic reaction when V max = mol sec 1, [S] = M, K M = M and the enzyme concentration at 4

5 time zero is µm. a) mol sec 1 b) mol sec 1 c) mol sec 1 d) mol sec I propose to design a new drug which will act as an inhibitor for an enzyme. If I have used all current information about the mechanism of this enzyme to design this inhibitor and I carefully engineer it with similar chemical properties to the transition state, what type of inhibitor am I attempting to engineer and how will I know if I have succeeded? a) A competitive inhibitor, collect kinetic data both in the presence and absence of inhibitor and watch for a change in V max. b) A competitive inhibitor, collect kinetic data both in the presence and absence of inhibitor and watch for a change in K M. c) A uncompetitive inhibitor, collect kinetic data both in the presence and absence of inhibitor and watch for a change in K M. d) A uncompetitive inhibitor, collect kinetic data both in the presence and absence of inhibitor and watch for a change in V max. e) An irreversible inhibitor collect kinetic data both in the presence and absence of inhibitor and watch for a change in V max. 15. This is a reaction coordinate diagram for uncatalyzed and enzyme-catalyzed conversion of a substrate S to its product P (S P): Activation energy for the catalyzed conversion of P S is represented by which arrow? a) A b) B c) C d) D e) E 5

6 16. Poly(L-proline) is an effective competitive inhibitor of prolyl hydroxylase and is used in the treatment of cancer. What are the potential side effects of using this inhibitor? a) Anemia, due to the development of sickle cells. b) Loss of teeth due to the loss of collagen structural integrity. c) Insoluble protein aggregation in the brain, leading to Alzhiemers. d) Inflammation in the extremities due to accumulation of urate cyrstals. e) Rapid aging due to the mis-regulation of the nuclear lamina. 17. The ingestion of methanol is very dangerous because alcohol dehydrogenase (ADH) converts it into formaldehyde which can lead to blindness. ADH has a K M for methanol of 1.3 x 10-1 M and K M for ethanol of 2.1 x 10-3 M. Given what you know, is it possible that a treatment with ethanol could prevent methanol poisoning? a) Yes, ethanol has a much higher affinity for ADH and it occupies the enzyme until methanol can be excreted harmlessly in the urine. b) No, the high K M of methanol will prevent any treatments, because it highly specific for ADH, and is rapidly converted to formaldehyde. c) Yes, ethanol is an allosteric inhibitor of ADH, and lowers the affinity of the enzyme for methanol. d) No, this will only work in individuals that lack a functional mitochondrial aldehyde dehydrogenase (low K M ), since formaldehyde will not form. 18. Which protein is NOT an integral membrane protein? a) 7-trans membrane receptors b) Prostagladin H 2 Synthase c) ABC Transporters d) Na + -K + ATPase e) Porins 19. Examining this standard Michaelis-Menten plot, what type of inhibitor is being observed? a) Competitive b) Noncompetitive c) Uncompetitive d) Irreversible e) Allosteric 6

7 20. Choose the molecule or ion with the lowest permeability through a plasma membrane. a) Water b) Tryptophan c) Sodium ion d) Glucose e) Chloride Ion 21. Bacteria often become penicillin-resistant. One possible reason for this is: a) A mutation of histidine in the active site of chymotrypsin. b) A mutation in serine in the active site of acetylcholinesterase. c) The fusion of BCR and c-abl proteins. d) A mutation in a serine of the active site of Glycopeptide transpeptidase. e) The loss of the bacterial cell wall. 22. Which of the following fatty acids has the lowest melting temperature? a) cis, cis 9, 12 Octadecadienoate (18:2) b) cis 9 Octadecadienoate (18:1) c) n- Octadecadienoate 18:0) d) n-hexadecenoate (16:0) e) cis,cis,cis,cis-δ 5 Δ 8,Δ 11,Δ 14 Octadecadienoate (18:4) 23. Farnesyl transferase inhibitors are currently being used to treat the rare genetic disease Hutchinson Gilford Progeria Syndrome. What would be the likely outcome expected by clinicians? a) Cardiac complications would be improved through the stimulation of Na + - K + ATPase. b) Would allow the proper maturation of lamin A, preventing nuclear abnormalities and premature aging. c) Would prevent prostaglandin H2 from associating with the membrane, and reduce arthritis by preventing inflammation. d) Would prevent the Gα protein from associating with the membrane, and prevent stress induced aging. e) Corrects the imbalance of phospholipids in the nuclear membrane and thus prevents the misshapen nuclei from causing genomic instability. 7

8 24. A BIO 2020 student thinks it would be a good idea to treat cholera with purified caffeine. Predict the outcome. a) This would reduce the symptoms of cholera by promoting water retention through activation of the Glucose-Na + transporter. b) This would make the cholera worse since the camp levels would be even higher, given that phosphodiesterase is blocked. c) This would have no effect, since only the heart rate would be affected. d) Would promote urination and would allow the cholera bacteria to be excreted from the body. e) Would increase blood pressure allowing fluids to be replenished to all the tissues. Part 2: Fill in the blank questions: Total Marks: 10 Please note that acronyms for chemicals are fine, i.e. ATP instead of Adenosine Triphosphate or DNA instead of deoxynucleic acid. 1) Please provide the chemical reaction catalyzed by the enzyme carbonic anhydrase found in red blood cells (2 marks). + 2) Please provide the names of all the all the components of this enzyme structure, reaction and regulation (2 marks). 8

9 A D No activity B C A) B) C) D) 3) Please answer the True/False questions about this cellular signaling pathway. Circle either True (T) or False (F). (6 marks) C D 1 D 2 E a) A could be adenylate cyclase T F 9

10 b) A could have 7 trans-membrane helices T F c) B is a receptor protein T F d) B could be a hormone T F e) C is an adaptor or docking protein T F f) C has a lipid anchor T F g) D1 is a kinase T F h) D1 produces camp T F i) D2 could be a target of Cholera toxin T F j) D2 hydrolyzes GTP T F k) E is the substrate of a kinase T F l) E could translocate to the nucleus T F PART 3: Peptide structure. Please draw and label the chemical structure of the tri-peptide Glycine-Arginine- Isoleucine in the zwitter-ionic form. Use the space provided (6 Marks). 10