CH 369 Exam 1 February 7, 2012Name: __________________________ eID _____________ Grade_______________

Helpful Equations:

[ ][ ]abase

pH = pK logacid

+

2

2

O + OpY

K p= G H T S = degrees K = 273 + C

Section I (32 points): 1 point each

1. Consider the structure of the coenzyme NADP

Which arrow points at an amide bond?A) A B) B C) C D) D E) E

2. Which of the molecules alanine, glucose, palmitate, and cholesterol would be insoluble in water?A) Palmitate and cholesterol C) Alanine and palmitateB) Alanine and glucose D) Glucose and cholesterol

3. A spontaneous processA) occurs without the addition of free energy. D) all of the aboveB) has a G

5. The strongest non-covalent interactions are:A) van der Waal forces D) dipole-dipole interactionB) London dispersion forces E) ionic interactionsC) hydrogen bonds

6. In water solvent, globules of up to several thousand amphiphilic molecules arranged with the hydrophilic groups on the surface and the hydrophobic groups buried in the center are called:A) micelles B) liposomes C) vacuoles D) bilayer membranes E) none of the above

7. In a hydrogen bond between a water molecule and another biomolecule:A) a hydrogen ion on the water molecule forms an ionic bond with a hydride ion on the other molecule.B) the partial charge on a hydrogen of the water interacts with the partial charge on a hydrogen of the other

molecule.C) the hydrogen bond will typically form between a hydrogen atom and either a nitrogen, sulfur, or oxygen

atom.D) a hydrogen on the water molecule forms a covalent bond to a hydrogen atom on the other molecule.E) the hydrogen atom is located between an oxygen atom of the water and a carbon atom of the other molecule.

8. Which of the following amino acids has a charged polar side chain at pH 7?A) Trp B) Ala C) Glu D) Leu E) Met

9. The disulfide bond between two cysteine molecules:A) is a weak ion-induced dipole attraction.B) is a peptide bond.C) is an ionic bond that is stable at physiological pH.D) is a covalent bond formed by oxidation.E) is a hydrogen bond between the two sulfhydryl groups.

10. In the molecule below, are there more hydrogen bond donor or hydrogen bond acceptor groups?

A) More donor groups B) More acceptor groups C) Equal number of donor and acceptor groups

11. Amino acid side-chain residues have:A) a positive charge in every situationB) pKs that assure the solubility of every proteinC) different pKs in peptides as compared to the free amino acidsD) constant pKs no matter what aqueous environment they are found inE) polar functional groups

12. All the standard amino acids except ____ are optically active.A) Arg B) Pro C) Gly D) Phe E) Trp

13. _________ is a triple-helical fibrous protein.A) -Keratin B) -Keratin C) Collagen D) RNase A E) None of the above

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14. In the ______ form of hemoglobin, the iron ion is out of the plane of the porphyrin ring.A) R B) C) T D)

15. How many of the following processes represent a positive change in entropy?a) Dry ice sublimates b) Sodium chloride dissolves in water c) Water freezes d) Lipid molecules associate to form a membrane e) Water evaporatesA) 0 B) 1 C) 2 D) 3 E) 4 F) 5

16. Which of the following energy diagrams represents a spontaneous reaction?

A) A B) BC

17. According to the table below, which of the elements listed would most likely be the strongest H-bond acceptor?

A) C B) F C) H D) N E) O

18. Which of the following amino acids has a sulfur atom in its side chain?A) Ser B) Asn C) Phe D) Met E) Tyr

19. At pH 4, histidine (pKs are -carboxylate 1.8, -amino 9.33, 6.04 imidazole) would be charged as follows:A) 0 -carboxylate, + -amino, +1 imidazole, +2 net chargeB) -1 -carboxylate, +1 -amino, 0 imidazole, 0 net chargeC) -1 -carboxylate, +1 -amino, +1 imidazole, +1 net chargeD) +1 -carboxylate, 0 -amino, -1 imidazole, 0 net chargeE) +1 -carboxylate, +1 -amino, -1 imidazole, +1 net charge

20. At a pH below its pK, the -amino group of lysine isA) protonated. B) deprotonated. C) zero.

21. Which of the following proteins assembles into filaments as dimers?A) collagen B) tubulin C) actin D) keratin

22. The movement of myosin can be described as where as that of kinesin can be described as .A) walking, grabbing B) twirling, grabbing C) grabbing, walking D) grabbing, twirling

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23. A protein found in hair, horn, nails, and feathers isA) collagen. B) keratin. C) actin. D) tubulin. E) kinesin.

24. Protein folding in vivo is assisted by aA) molecular chaperone. D) rotation of the peptide bond.B) keratin. E) tertiary structure.C) collagen.

25. The polarity of the OH bond is caused by the ______ of oxygen.A) negative entropy C) tetrahedral structure arrangementB) higher electronegativity D) positive entropy

26. During the T to R conformational shift, Fe(II) drags the F-helix via a bond to the side chain of ________.A) Leu FG3 B) Leu F7 C) Leu F4 D) His F8 E) Val FG5

Match the structure of the amino acid with its correct name.

27.A) Trp B) His C) Pro D) Ala E) Ile F) Arg G) Gln H) Asp

28.A) Trp B) His C) Pro D) Ala E) Ile F) Arg G) Gln H) Asp

29.A) Leu B) His C) Val D) Ala E) Ile F) Arg G) Gln H) Asp

30.A) Trp B) His C) Pro D) Ala E) Ile F) Arg G) Thr H) Asp

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31.A) Asn B) His C) Gln D) Ala E) Ile F) Arg G) Thr H) Asp

32.A) Asn B) Val C) Gln D) Ala E) Ile F) Arg G) Thr H) Asp

Section II (50 points): 2 points each

33. For a given reaction, the value of H is 15 kJ mol-1 and the value of S is 51 J K-1 mol-1. Above what temperature will this reaction be spontaneous? Recall that 273 K = 0C.A) 294C B) 21C C) 3.4C D) 0C

34. Which of the proteins listed below contain ATP binding sites?A) myosin and kinesin D) myosin, kinesin, actin, and tubulinB) myosin, kinesin, and tubulin E) myosin, kinesin, and collagenC) myosin, kinesin, and actin

35. Highly active muscle generates lactic acid by respiration so fast that the blood passing through the muscle actually experiences a drop in pH from about 7.4 to about 7.2. Under these conditions, would hemoglobin release more or less O2 than it does at pH 7.4?A) Release more O2 B) Release less O2 C) No change

36. The more fully reduced a compound, the greater the free energy yield when it is completely oxidized. Which of the two compounds below could therefore produce the greatest yield in free energy?

A) Stearate B) -Linolenate

37. A phosphate (pK1 = 2.15; pK2 = 6.82; pK3 = 12.38) buffer solution at a pH = pK1 = 2.15 would have equal amounts of phosphate in the ______ form and the H2PO4 form.A) HPO4 2 B) H2PO4 C) H3PO4

38. The pH of a 0.1M solution of sodium acetate would be:A) basic, because of the acetate ion reacts with water to form acetic acid and OH.B) acidic, because the acetate ion is acidic.C) acidic, because the acetate ion forms acetic acid.D) neutral, because salts are neither acidic nor basic.E) basic, because the Na+ ionizes and combines with OH.

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39. _____ is exceptionally soluble in water due to the formation of hydrogen bonds.A) oxygen B) benzene C) NaCl D) ethanol E) sodium palmitate

40. A rigid, planar structure consisting of about 40% double bond character is characteristic of aA) beta sheet B) alpha helix C) tertiary structure. D) peptide link. E) alpha loop

41. The arrangement of the regular structural elements and the three-dimensional positions of atoms in the protein are considered part ofA) primary structure C) tertiary structure.B) regular secondary structure D) quaternary structure.

42. To which of the four classes of biomolecules do the following compounds belong? Which of these is capable of forming a polymeric molecule?

a) b) A) a) Amino acid; b) Carbohydrate; Both can form polymersB) a) Amino acid; b) Lipid; Only (a) can form polymersC) a) Carbohydrate; b) Lipid; Only (a) can form polymersD) a) Carbohydrate; b) Lipid; Neither can form polymersE) a) Nucleotide; b) Lipid; Only (b) can form polymers

43. Which of the following amino acids is most likely to be found on the exterior, membrane-contacting, surface of an integral membrane protein?A) Gly B) Gln C) Glu D) Ala E) Asp

44. Which of the following is the best explanation for the hydrophobic effect?A) It is caused by an affinity of hydrophobic groups for each other.B) It is an entropic effect, caused by the desire of water molecules to increase their entropy by forming highly

ordered structures (called clathrates) around the hydrophobic groups.C) It is an entropic effect caused by the desire of hydrophobic groups to increase their entropy by associating

with other hydrophobic groups.D) It is an entropic effect, caused by the desire of water molecules to increase their entropy by excluding

hydrophobic groups, which they must otherwise surround with highly ordered structures (called clathrates).E) It is caused by the affinity of water for hydrophobic groups.

45. Which of the following is not a ligand to the porphyrin ring Fe2+ ion in oxymyoglobin?A) all are ligandsB) His E7 (the His residue above the porphyrin ring)C) OxygenD) His F8 (the His residue below the porphyrin ring)E) Nitrogen atoms in the porphyrin ring

46. The absence of 2,3-BPG causes hemoglobin's affinity for oxygen toA) Remain the same B) decrease. C) increase.

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47. Which one of these characteristics is not true for the helix?A) It is right-handed.B) A hydrogen bond forms between the carbonyl oxygen of the nth amino acid residue and the -NH group of the

(n + 4)th amino acid residue.C) Proline is typically not found in the helix.D) There are 3.6 amino acids per turn.E) There is a requirement for glycine every third amino acid residue.

48. In two homologous proteins, which residue is most likely to replace a Glu residue as a conservative substitution?A) Trp B) Ile C) Met D) Asp E) Lys

49. What would be the net charge on the following peptide at physiological pH? Table of pK values on exam cover.Arg-Lys-Asp-Val-TyrA) +3 B) +2 C) +1 D) 0 E) -1 F) -2

50. What is the sequence of the peptide below?

A) Phe-Ala-Ala-Phe-Leu D) Trp-Gly-Gly-Phe-ArgB) Tyr-Gly-Gly-Phe-Met E) Tyr-Ala-Ala-Phe-MetC) Tyr-Ala-Ala-Phe-Cys

51. A sample of the amino acid tyrosine is barely soluble in water. Would a polypeptide containing only Tyr residues, poly(Tyr), be more or less soluble, assuming the total number of Tyr residues is the same in both cases?A) The polypeptide would be more soluble. B) The polypeptide would be less soluble.

52. Which of the following molecules would have the highest boiling point?

A) B) C) D)A) A B) B C) C D) D

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53. Which of the following substances might be able to cross a bilayer?

a) CO2 b) Ca2+ c) d) A) All can cross E) (a) and (d)B) Only (a) F) (b) and (c)C) (a) and (c) G) (c) and (d)D) (a) and (b) H) (a), (c) and (d)

The G value at 37C of the arginine kinase reaction was recently determined. The H for the reaction is -8.19 kJ mol-1 and the value of S is 2.20 J K-1 mol-1. Based on this information, answer the following two questions.

54. What is the value of G for the reaction? Is the reaction spontaneous?A) -8.27 kJ mol-1, spontaneous C) -8.87 kJ mol-1, spontaneousB) 8870 kJ mol-1, nonspontaneous D) 9.47 kJ mol-1, nonspontaneous

55. Is the reaction exothermic or endothermic? What value allowed you to determine this?A) Exothermic, S D) Endothermic, SB) Exothermic, G E) Endothermic, HC) Exothermic, H F) Endothermic, G

Consider the following two peptides in answering the next two questions:

a) Ile-Gln-Glu-Val-Glu-Arg-Asp b) Trp-Gln-Glu-Tyr-Gly-Arg-Asp

56. In which protein would these sequences most likely be found?A) Collagen B) Keratin C) Actin D) Tubulin E) Myosin

57. Of the two peptides, which would be more likely to appear in the protein specified in the previous question?A) Peptide (a) B) Peptide (b)

Section III (18 points): 3 points each

58. At a CO2 partial pressure (pCO2) of 5 torr, the p50 value for hemoglobin is 15 torr. When the CO2 partial pressure is 80 torr the p50 value for hemoglobin is 40 torr. As the concentration of CO2 increases, how does this affect the affinity of hemoglobin (Hb) for oxygen?A) As pCO2 increases, the affinity of Hb for O2 decreasesB) As pCO2 increases, the affinity of Hb for O2 increasesC) As pCO2 increases, there is no change in the affinity of Hb for O2

59. What is the volume (in mL) of a stock solution of 6.0 M HCl that must be added to the 0.1 M HEPES to achieve the desired pH of 8.0?A) 5.9 B) 0.0044 C) 0.0059 D) 4.4

60. What is the pH of 1.0 L of water to which 1.5 mL of 3.0 M NaOH has been added?A) 13.6 B) 2.3 C) 11.6 D) 8.2

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61. In your laboratory, you plan to use ion exchange chromatography to separate the peptide shown below (using three-letter codes) from a mixture of different peptides at pH 7.0. Should you choose a matrix containing DEAE (+ charge) or CM (- charge) groups?

Peptide: GlyLeuGluLysSerLeuValArgLeuGlyAspValGlnProSerLeuGlyLysGluSerArgAlaLysLysPheGlnArgGlnA) DEAE B) CM

62. To make an acetate buffer at pH 4.76 (pK = 4.76) starting with 500 mL of 0.1 M sodium acetate (pK = 4.76), you could add:A) 0.1 moles of HCl.B) 0.025 moles of HCl.C) You can't make a buffer by adding HCl or NaOH.D) 0.1 moles of NaOH.E) 0.2 moles of HCl.

63. Proteins can be unfolded, or denatured, by agents that alter the balance of weak noncovalent forces that maintain the native conformation. How would the following agents cause a protein to denature?a) Amphiphilic detergents b) Reducing agents A) a) disrupt ionic interactions; b) disrupt disulfide bondsB) a) disrupt hydrogen bonding of secondary structure: b) disrupt ionic interactionsC) a) disrupt hydrogen bonding with water; b) disrupt hydrophobic interactions on surfaceD) a) disrupt internal hydrophobic interactions of tertiary structure; b) disrupt disulfide bondsE) a) disrupt ionic interactions; disrupt peptide bonds

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Answer Key

1. B2. A3. D4. B5. E6. A7. C8. C9. D

10. A11. C12. C13. C14. C15. D16. B17. B18. D19. C20. A21. B22. C23. B24. A25. B26. D27. C28. F29. E30. G31. C32. B33. B34. C35. A36. A37. C38. A39. D40. D41. C42. C43. D44. D45. B46. C47. E48. D49. C50. B51. B52. C53. E

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54. C55. C56. B57. A58. A59. D60. C61. B62. B63. D

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