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Biochemistry 423 Final Examination NAME: ________________________________________________________________ 1 Circle the single BEST answer (3 points each) 1. At equilibrium the free energy of a reaction ∆G A. B. C. D. 2. The presence of a catalyst, A. B. C. D. 3. lysine histidine glutamate arginine aspartate A tripeptide was treated with trypsin and produced a single amino acid and a dipeptide that had a UV absorbance. The same tripeptide, when exposed to chymotrypsin, produced a dipeptide and a single amino acid that had a UV absorbance. If hydrolysis of the tripeptide produced Ala, Lys, and Tyr, what was the sequence of the amino acids in the tripeptide? A. B. C. D. E. 5. decreases ∆G does not affect ∆G increases ∆G increases ∆G0’ Which amino acid has a side chain group with a pKa closest to physiological pH? A. B. C. D. E. 4. depends only on the temperature is positive is 0 is negative Ala-Lys-Tyr Ala-Tyr-Lys Tyr-Ala-Lys Tyr-Lys-Ala Lys-Ala-Tyr Which of the following statements is true? A. B. C. D. E. all fibrous proteins have quaternary structure all globular proteins have quaternary structure all proteins have quaternary structure the interactions between the eight helical regions is partially responsible for the quaternary structure of myoglobin only proteins with more than one subunit have quaternary structure 2 6. In a globular protein, a leucine residue would most likely be found A. B. C. D. E. 7. Which of the following peptides would most likely be found in the interior of the cell membrane? A. B. C. D. E. 8. C. D. E. each of the four oxygen molecules binds with equal facility the binding of the first oxygen molecule enhances the binding of the other three oxygen molecules the binding of the first oxygen molecule makes the binding of the other three oxygen molecules more difficult the binding of the first oxygen molecule has no effect on the binding of the remaining three oxygen molecules. each successive oxygen bound makes the remaining sites less likely to bind oxygen Under which of the following conditions will hemoglobin bind less oxygen? A. B. C. D. E. 10. Asp-Glu-Gln-Asp Lys-Arg-Val-Lys His-Glu-Ser-Asn Met-Val-Ile-Phe Ser-Met-Asp-Gln Which of the following statements describes the oxygen-binding curve of hemoglobin? A. B. 9. participating in hydrogen bonds involving R-groups on the outside surface on the interior both on the interior and outside surface leucine residues are rarely found in globular proteins the pH increases from 7.0 to 7.2 the oxygen pressure increases from 500 mm to 1000 mm the concentration of carbon dioxide increases the bis-phosphoglycerate is removed none of the above Which of the following techniques cannot give information about the size of a protein? A. B. C. D. E. amino acid composition SDS-electrophoresis ion-exchange chromatography gel-exclusion chromatography none of the above 3 11. Which of the following affects the rate of a reaction? A. B. C. D. E. 12. Which of the following is NOT true concerning competitive inhibition of an enzyme catalyzed reaction? A. B. C. D. E. 13. Km increases Km decreases Vmax increases Vmax decreases Vmax and Km decreases The Km is: A. B. C. D. E. 15. the inhibition cannot be overcome by increasing the concentration of the reactant the competitive inhibitor resembles the substrate the competitive inhibitor binds to the same site as does the substrate the competitive inhibitor does not allow the substrate to bind to the enzyme. The inhibition can be overcome by increasing the concentration of the reactant Which of the following statements is true about non-competitive inhibition? A. B. C. D. E. 14. the number of reactant collisions per unit time the energy of each collision the orientation of the particles in each collision the temperature all of the above the time for half of the substrate to be converted to product. The time for all of the substrate to be converted to product. The [S] that gives half of the maximum reaction rate The [S] that gives the maximum reaction rate The [P] that is produced when the enzyme is saturated with the substrate. Allosteric enzymes generally exhibit A. B. C. D. linear kinetics hyperbolic kinetics classical Michaelis-Menten kinetics sigmoidal kinetics 4 16. A zymogen is: A. B. C. D. E. 17. an inactive precursor an active precursor an inactive product an active product none of the above What coenzyme, or coenzyme pair, would you expect to be associated with the following conversion? OOC-CH2-CH2-COO A. B. C. D. E. 18. FAD / FADH2 NAD+ / NADH pyridoxal phosphate (B6) biotin B12 What coenzyme, or coenzyme pair, would you expect to be associated with the following conversion? O O C C O CH2 CH2 C O O A. B. C. D. E. 19. OOC-CH=CH-COO + O H3N CH C O CH3 O O C C O CH3 FAD / FADH2 NAD+ / NADH pyridoxal phosphate (B6) biotin B12 One-carbon transfers are mediated by A. B. C. D. E. THF deerivatives coenzyme A lipoic acid thiamine pyrophosphate pyridoxal phosphate 5 O H3N CH C O CH2 + CH2 C O O 20. Which of the following conversions is catalyzed by the enzyme 3-phosphoglycerate kinase? A. B. C. D. 21. Which of the following, as a starting material for glycolysis, will result in the highest net yield of ATP? A. B. C. D. 22. phosphofructokinase fructose bisphosphate phosphatase pyruvate kinase hexokinase glyceraldehyde 3-phosphate dehydrogenase Two carbons from a molecule of pyruvate enter the citric acid cycle by the actions of which two enzymes? A. B. C. D. 24. glucose fructose glycogen they would all produce equivalent net amounts of ATP Which of the following enzymes catalyzes reactions in both glycolysis and gluconeogenesis? A. B. C. D. E. 23. glycerate 2-phosphate to phosphoenolpyruvate glycerate 3-phosphate to glycerate 2-phosphate glycerate 1,3-bisphosphate to glycerate 3-phosphate glyceraldehyde 3-phosphate to dihydroxyacetone posphate pyruvate kinase and enolase pyruvate carboxylase and malate dehydrogenase pyruvate dehydrogenase and citrate synthetase pyruvate carboxylase and pyruvate dehydrogenase. All three carbons of pyruvate can enter the citric acid cycle by way of which of the following enzymes? A. B. C. D. E. pyruvate dehydrogenase pyruvate decarboxylase pyruvate carboxylase pyruvate kinase citrate synthetase 6 25. Which of the following is NOT a coenzyme for the pyruvate dehydrogenase complex? A. B. C. D. E. 26. Which oxidative phosphorylation complex is directly responsible for ATP production? A. B. C. D. E. 27. palmitoyl-CoA acetyl-CoA acetoacetyl-CoA malonyl-CoA linoleoyl-CoA The complete β-oxidation of palmitoyl-CoA to CO2 and water requires how many cycles through the pathway? A. B. C. D. E. 29. complex IV iron-sulfur complex F0 complex F1 complex F0/F1 complex Which of the following molecules is the direct product of an enzyme that uses biotin as a coenzyme? A. B. C. D. E. 28. CoASH thiamine pyrophosphate ATP FAD lipoic acid seven eight nine ten sixteen When in excess, amino acids may be degraded. The first step in degradation of most amino acids is: A. B. C. D. E. decarboxylation oxidation of the side chain elimination of functional groups such as hydroxyl and sulfhydryl groups transamination racemization 7 30. Ammonia is transported from skeletal muscle to the liver as: A. B. C. D. E. 31. The accumulation of an oxygen debt during strenuous physical exercise may be accompanied by: A. B. C. D. E. 32. production of NADPH production of ribose-5-phosphate remodeling of dietary carbon atoms into 2,3-bisphosphoglycerate synthesis of ATP reduction of H2O2 to two moles of H2O Under conditions of anaerobic glycolysis, the NAD+ required by glyceraldehyde 3phosphate dehydrogenase is supplied by a reaction catalyzed by A. B. C. D. E. 34. an increase in NAD+ in muscle an increase in lactate in blood a decrease in pyruvate in blood an increase in citrate in muscle an increase in ATP in muscle Which of the following represents the primary function of the pentose phosphate pathway in erythrocytes? A. B. C. D. E. 33. ammonium salts glutamine and alanine glutamate and aspartate urea uric acid pyruvate dehydrogenase α-ketoglutarate dehydrogenase glycerol 3-phosphate dehydrogenase malate dehydrogenase lactate dehydrogenase All of the following are essential amino acids except A. phenylalanine B. valine C. cysteine D. isoleucine E. leucine 8 35. The sequence of a DNA strand is 5'---pApGpCpG--3'. The sequence of a complementary segment of DNA is: A. 5'--pTpCpGpC--3' B. 5'--pCpGpCpU--3' C. 5'--pCpApTpA--3' D. 5'--pCpGpCpT--3' E. 5'--pUpCpGpC--3' 36. A codon is a three-nucleotide sequence of A. B. C. D. E. 37. Molecules involved in purine nucleotide synthesis include all of the following EXCEPT: A. B. C. D. E. 38. Phosphoribosyl pyrophosphate (PRPP) Aspartate S-adenosylmethionine (SAM) N10-formyl THF CO2 One-carbon carriers in biosynthetic processes include all of the following EXCEPT: A. B. C. D. 39. tRNA DNA, read in the 5' to 3' direction mRNA, read in the 5' to 3' direction rRNA mRNA, read in the 3' to 5' direction SAM Thymine THF Biotin All of the following are glucogenic amino acids EXCEPT: A. B. C. D. E. Glycine Leucine Alanine Aspartate Serine 9 40. Which of the following provides the energy to move the ribosome along the mRNA? A. B. C. D. E. 41. ATP dATP GTP UTP dUTP Which of the following statements is false? A. B. C. D. E. There is at least one tRNA for each of the amino acids. The attachment site for the amino acid is at the 3' end of the tRNA molecule. Each tRNA accepts a specific amino acid. A, C, G and U are the only bases in tRNA. There is a specific tRNA for initiation of protein synthesis. Select ALL Correct Responses (3 points each) 42. Fatty acid synthesis requires which of the following cofactors? (CIRCLE ALL CORRECT ANSWERS) A. B. C. D. E. carnitine NADPH FAD biotin thiamine pyrophosphate 10 Fill in the Blank 43. Indicate where in the eukaryotic cell the following processes take place: (2 pts each) A. Glycolysis ____________________________________________________ B. Urea Cycle ___________________________________________________ C. DNA replication _______________________________________________ D. RNA synthesis _________________________________________________ E. Fatty acid synthesis _____________________________________________ F. Protein synthesis _______________________________________________ G. Fatty acid oxidation _____________________________________________ 44. Mark each of the following statements T (true) or F (false) (2 pts each) _____ E. coli DNA polymerases contain both polymerase and nuclease activities on the same polypeptide chain. _____ DNA polymerase I does not require a template. _____ Only DNA polymerase III is capable of “editing” (i.e., has 3' to 5'-nuclease activity). _____ The link between nucleotides in RNA and DNA is a phosphodiester bond. _____ A highly processive enzyme stays bound to its substrate as it catalyzes a sequence of reactions. _____ Thymine (rather than uracil) is found in DNA in order to ensure that chemical damage to DNA is repaired. _____ Prokaryotic and eukaryotic ribosomes contain the same number of rRNA molecules. _____ Transfer RNA (tRNA) is the largest type of RNA. _____ RNA polymerase binds to DNA at promoter regions. _____ In protein synthesis, four high energy bonds are hydrolyzed for each peptide bond formed. 11 45. Mark each of the following statements T (true) or F (false) (2 pts each) _____ Acyl carrier protein is the principal regulated protein of fatty acid synthesis. _____ Membranes are phospholipid monolayers containing imbedded proteins. _____ A membrane channel accomplishes transport of a molecule or ion against a concentration gradient. _____ Carbon atoms in the purine base ring structure come from CO2, N5,N10formylTHF and alanine. _____ Ribonucleotides are reduced to deoxyribonucleotides at the di- phosphorylation level. _____ The principal positive allosteric effectors of pyrimidine synthesis are purine nucleotides. _____ Phospholipids contain glycerol, two fatty acids, phosphate and an aromatic amino acid. _____ Triacylglycerols (TAGs) are the principal component of storage fat. _____ DNA polymerase II of E. coli is primarily responsible for DNA repair. _____ DNA replication is semi-conservative. _____ DNA with high GC content has a lower melting point than DNA with high AT content. _____ Eukaryotic DNA is linear. _____ Okazaki fragments are involved in the synthesis of the lagging strand of DNA during replication. _____ RNA polymerases require a primer. _____ The direction of the strands in the DNA double helix is parallel. _____ In eukaryotes, all proteins are synthesized in the compartment in which they will function. 12 46. Fill in the blanks. (2 pts each). 1. In prokaryotes, a system of genes under coordinated regulation is called ________________________. 2. An inducer binds to a _________________ protein that is the product of a regulator gene. 3. If the concentration of glucose in E. coli is low, the bacteria make ________________________. 4. Proteins whose synthesis can not be induced or repressed are called ________________________. 5. Eukaryotic DNA and histone proteins are condensed into structures called ________________________. 47. On the last page is a genetic code table. Determine the sequence of the protein segment that would be synthesized by transcription and translation of the following DNA sequence: (4 points) 5' -pApTpCpCpCpGpGpApCpCpApT- 3' 3' - TpApGpGpGpCpCpTpGpGpTpAp- 5' 13 THE GENETIC CODE First Position 5’ end U C A G U Phe Phe Leu Leu Leu Leu Leu Leu Ile Ile Ile Met Val Val Val Val Second Position C A Ser Tyr Ser Tyr Ser STOP Ser STOP Pro His Pro His Pro Gln Pro Gln Thr Asn Thr Asn Thr Lys Thr Lys Ala Asp Ala Asp Ala Glu Ala Glu 14 G Cys Cys STOP Trp Arg Arg Arg Arg Ser Ser Arg Arg Gly Gly Gly Gly Third Position 3’ end U C A G U C A G U C A G U C A G