Biochemistry 423 Final Examination NAME:

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1 Biochemistry 423 Final Examination NAME: 1

2 Circle the single BEST answer (3 points each) 1. At equilibrium the free energy of a reaction G A. depends only on the temperature B. is positive C. is 0 D. is negative 2. The presence of a catalyst, A. decreases G B. does not affect G C. increases G D. increases G 0 3. Which amino acid has a side chain group with a pka closest to physiological ph? A. lysine B. histidine C. glutamate D. arginine E. aspartate 4. 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. Ala-Lys-Tyr B. Ala-Tyr-Lys C. Tyr-Ala-Lys D. Tyr-Lys-Ala E. Lys-Ala-Tyr 5. Which of the following statements is true? A. all fibrous proteins have quaternary structure B. all globular proteins have quaternary structure C. all proteins have quaternary structure D. the interactions between the eight helical regions is partially responsible for the quaternary structure of myoglobin E. only proteins with more than one subunit have quaternary structure 2

3 6. In a globular protein, a leucine residue would most likely be found A. participating in hydrogen bonds involving R-groups B. on the outside surface C. on the interior D. both on the interior and outside surface E. leucine residues are rarely found in globular proteins 7. Which of the following peptides would most likely be found in the interior of the cell membrane? A. Asp-Glu-Gln-Asp B. Lys-Arg-Val-Lys C. His-Glu-Ser-Asn D. Met-Val-Ile-Phe E. Ser-Met-Asp-Gln 8. Which of the following statements describes the oxygen-binding curve of hemoglobin? A. each of the four oxygen molecules binds with equal facility B. the binding of the first oxygen molecule enhances the binding of the other three oxygen molecules C. the binding of the first oxygen molecule makes the binding of the other three oxygen molecules more difficult D. the binding of the first oxygen molecule has no effect on the binding of the remaining three oxygen molecules. E. each successive oxygen bound makes the remaining sites less likely to bind oxygen 9. Under which of the following conditions will hemoglobin bind less oxygen? A. the ph increases from 7.0 to 7.2 B. the oxygen pressure increases from 500 mm to 1000 mm C. the concentration of carbon dioxide increases D. the bis-phosphoglycerate is removed E. none of the above 10. Which of the following techniques cannot give information about the size of a protein? A. amino acid composition B. SDS-electrophoresis C. ion-exchange chromatography D. gel-exclusion chromatography E. none of the above 3

4 11. Which of the following affects the rate of a reaction? A. the number of reactant collisions per unit time B. the energy of each collision C. the orientation of the particles in each collision D. the temperature E. all of the above 12. Which of the following is NT true concerning competitive inhibition of an enzyme catalyzed reaction? A. the inhibition cannot be overcome by increasing the concentration of the reactant B. the competitive inhibitor resembles the substrate C. the competitive inhibitor binds to the same site as does the substrate D. the competitive inhibitor does not allow the substrate to bind to the enzyme. E. The inhibition can be overcome by increasing the concentration of the reactant 13. Which of the following statements is true about non-competitive inhibition? A. Km increases B. Km decreases C. Vmax increases D. Vmax decreases E. Vmax and Km decreases 14. The Km is: A. the time for half of the substrate to be converted to product. B. The time for all of the substrate to be converted to product. C. The [S] that gives half of the maximum reaction rate D. The [S] that gives the maximum reaction rate E. The [P] that is produced when the enzyme is saturated with the substrate. 15. Allosteric enzymes generally exhibit A. linear kinetics B. hyperbolic kinetics C. classical Michaelis-Menten kinetics D. sigmoidal kinetics 4

5 16. A zymogen is: A. an inactive precursor B. an active precursor C. an inactive product D. an active product E. none of the above 17. What coenzyme, or coenzyme pair, would you expect to be associated with the following conversion? C-CH 2 -CH 2 -C C-CH=CH-C A. FAD / FADH 2 B. NAD + / NADH C. pyridoxal phosphate (B 6 ) D. biotin E. B What coenzyme, or coenzyme pair, would you expect to be associated with the following conversion? C C CH 2 CH 2 C + H 3 N CH C C C + CH 3 CH 3 H 3 N CH C CH 2 CH 2 C A. FAD / FADH 2 B. NAD + / NADH C. pyridoxal phosphate (B 6 ) D. biotin E. B ne-carbon transfers are mediated by A. THF deerivatives B. coenzyme A C. lipoic acid D. thiamine pyrophosphate E. pyridoxal phosphate 5

6 20. Which of the following conversions is catalyzed by the enzyme 3-phosphoglycerate kinase? A. glycerate 2-phosphate to phosphoenolpyruvate B. glycerate 3-phosphate to glycerate 2-phosphate C. glycerate 1,3-bisphosphate to glycerate 3-phosphate D. glyceraldehyde 3-phosphate to dihydroxyacetone posphate 21. Which of the following, as a starting material for glycolysis, will result in the highest net yield of ATP? A. glucose B. fructose C. glycogen D. they would all produce equivalent net amounts of ATP 22. Which of the following enzymes catalyzes reactions in both glycolysis and gluconeogenesis? A. phosphofructokinase B. fructose bisphosphate phosphatase C. pyruvate kinase D. hexokinase E. glyceraldehyde 3-phosphate dehydrogenase 23. Two carbons from a molecule of pyruvate enter the citric acid cycle by the actions of which two enzymes? A. pyruvate kinase and enolase B. pyruvate carboxylase and malate dehydrogenase C. pyruvate dehydrogenase and citrate synthetase D. pyruvate carboxylase and pyruvate dehydrogenase. 24. All three carbons of pyruvate can enter the citric acid cycle by way of which of the following enzymes? A. pyruvate dehydrogenase B. pyruvate decarboxylase C. pyruvate carboxylase D. pyruvate kinase E. citrate synthetase 6

7 25. Which of the following is NT a coenzyme for the pyruvate dehydrogenase complex? A. CoASH B. thiamine pyrophosphate C. ATP D. FAD E. lipoic acid 26. Which oxidative phosphorylation complex is directly responsible for ATP production? A. complex IV B. iron-sulfur complex C. F 0 complex D. F 1 complex E. F 0 /F 1 complex 27. Which of the following molecules is the direct product of an enzyme that uses biotin as a coenzyme? A. palmitoyl-coa B. acetyl-coa C. acetoacetyl-coa D. malonyl-coa E. linoleoyl-coa 28. The complete β-oxidation of palmitoyl-coa to C 2 and water requires how many cycles through the pathway? A. seven B. eight C. nine D. ten E. sixteen 29. When in excess, amino acids may be degraded. The first step in degradation of most amino acids is: A. decarboxylation B. oxidation of the side chain C. elimination of functional groups such as hydroxyl and sulfhydryl groups D. transamination E. racemization 7

8 30. Ammonia is transported from skeletal muscle to the liver as: A. ammonium salts B. glutamine and alanine C. glutamate and aspartate D. urea E. uric acid 31. The accumulation of an oxygen debt during strenuous physical exercise may be accompanied by: A. an increase in NAD + in muscle B. an increase in lactate in blood C. a decrease in pyruvate in blood D. an increase in citrate in muscle E. an increase in ATP in muscle 32. Which of the following represents the primary function of the pentose phosphate pathway in erythrocytes? A. production of NADPH B. production of ribose-5-phosphate C. remodeling of dietary carbon atoms into 2,3-bisphosphoglycerate D. synthesis of ATP E. reduction of H 2 2 to two moles of H Under conditions of anaerobic glycolysis, the NAD + required by glyceraldehyde 3- phosphate dehydrogenase is supplied by a reaction catalyzed by A. pyruvate dehydrogenase B. α-ketoglutarate dehydrogenase C. glycerol 3-phosphate dehydrogenase D. malate dehydrogenase E. lactate dehydrogenase 34. All of the following are essential amino acids except A. phenylalanine B. valine C. cysteine D. isoleucine E. leucine 8

9 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. trna B. DNA, read in the 5' to 3' direction C. mrna, read in the 5' to 3' direction D. rrna E. mrna, read in the 3' to 5' direction 37. Molecules involved in purine nucleotide synthesis include all of the following EXCEPT: A. Phosphoribosyl pyrophosphate (PRPP) B. Aspartate C. S-adenosylmethionine (SAM) D. N 10 -formyl THF E. C ne-carbon carriers in biosynthetic processes include all of the following EXCEPT: A. SAM B. Thymine C. THF D. Biotin 39. All of the following are glucogenic amino acids EXCEPT: A. Glycine B. Leucine C. Alanine D. Aspartate E. Serine 9

10 40. Which of the following provides the energy to move the ribosome along the mrna? A. ATP B. datp C. GTP D. UTP E. dutp 41. Which of the following statements is false? A. There is at least one trna for each of the amino acids. B. The attachment site for the amino acid is at the 3' end of the trna molecule. C. Each trna accepts a specific amino acid. D. A, C, G and U are the only bases in trna. E. 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 CRRECT ANSWERS) A. carnitine B. NADPH C. FAD D. biotin E. thiamine pyrophosphate 10

11 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. nly 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

12 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 C 2, N 5,N 10 - formylthf 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. kazaki 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

13 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. n 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

14 THE GENETIC CDE First Position Second Position Third Position 5 end U C A G 3 end U Phe Ser Tyr Cys U Phe Ser Tyr Cys C Leu Ser STP STP A Leu Ser STP Trp G C Leu Pro His Arg U Leu Pro His Arg C Leu Pro Gln Arg A Leu Pro Gln Arg G A Ile Thr Asn Ser U Ile Thr Asn Ser C Ile Thr Lys Arg A Met Thr Lys Arg G G Val Ala Asp Gly U Val Ala Asp Gly C Val Ala Glu Gly A Val Ala Glu Gly G 14