Exam 1_F13

CH 369 Exam 1 September 24 2013Name: __________________________________________ eID ________________

Helpful Equations:

degrees K = 273 + °C

Section I (32 points): 1 point each

1. In humans, approximately _____ % of the genome encodes proteins. A) 78 B) 45 C) 33 D) 11 E) 1.5

2. The similarity of one organism to another (for example a bacteria versus a human) is most easily done by comparing which biopolymer?

A) nucleic acids D) lipids B) polysaccharides E) all of the above C) proteins

3. During the initial synthesis of collagen molecules, _____ and _____ are most often incorporated into the growing protein.

A) Ser; Gly B) Pro; Ala C) Gly; Pro D) Ala; Gly E) Ser; Pro

4. A base found exclusively in DNA is _____ while _____ is found only in RNA. A) adenine; cytosine D) cytosine; guanine B) guanine; thymine E) thymine; uracil C) uracil; adenine

5. The purines found in nucleic acids are _____ and _____. A) adenine; cytosine D) adenine; guanine B) guanine; thymine E) thymine; uracil C) uracil; adenine

6. What is the N-terminal residue of the peptide AYSDG? A) glutamic acid D) alanine B) glycine E) none of these choices C) aspartic acid

7. When a non-polar substance is added to water, how do the molecules of water behave? A) the regular hydrogen bond pattern is disrupted resulting in a decrease of entropy B) the regular hydrogen bond pattern is disrupted resulting in an increase of entropy C) the regular hydrogen bond pattern is disrupted resulting in a decrease of enthalpy D) the regular hydrogen bond pattern is disrupted resulting in an increase of enthalpy E) none of the above

Scrambled version A

8. What type of bond is made between nucleotides? A) ester D) glycosidic B) phosphate ester E) none of the above C) phosphodiester

9. A technique for determining protein structure that requires crystals of the protein is ___. A) NMR spectroscopy D) mass spectrometry B) X-ray crystallography E) none of these choices C) electron crystallography

10. Each kinesin head contains a binding site for _____ and a binding site for _____. A) tubulin; GTP D) actin; ATP B) another kinesin molecule; GTP E) tubulin; ATP C) myosin; ATP

11. What is the most prevalent secondary structure observed in the proteins of intermediate filaments? A) α-helices D) β-sheets B) β-helices E) both α-helices and β-helices are observed C) α-sheets

12. The formation of a dipeptide from two amino acids requires ___. A) reduction of the α-carboxyl group D) loss of water B) protonation of the α-amine group E) none of these choices C) interaction of the two side-chains

13. The 5ʹ′ end of a polynucleotide contains _____ while the 3ʹ′ end contains _____. A) a hydroxyl group; a phosphate group D) a hydroxyl group; a hydroxyl group B) a phosphate group; a hydroxyl group E) none of the above C) a phosphate group; a phosphate group

14. Fatty acid anions most commonly assemble into _____ in aqueous solution. A) lipid bilayers D) liposomes B) solvent-filled vesicles E) none of the above C) micelles

15. Disulfide bonds form between two residues of which amino acid? A) Met B) Ser C) Asn D) Thr E) Cys

16. Which of the following is a physical property of water that results from hydrogen bonding? A) high boiling point relative to molecular weight B) a solid state that is less dense than the liquid state C) high surface tension D) ability to solubilize polar molecules E) all of the above

Scrambled version A

17. What level of protein structure is characterized by the amino acid sequence? A) primary D) quaternary B) secondary E) none of these choices C) tertiary

18. What is the prominent type of secondary structure observed in myoglobin? A) β-helices D) antiparallel β-sheets B) α-bends E) α-helices C) parallel β-sheets

19. Which amino acid is critical for crosslinking of collagen trimers? A) Ser B) Lys C) His D) Cys E) Gln

20. Entropy is used to measure _____. A) free energy D) randomness B) heat content E) all of the above C) temperature

21. The predominant non-covalent interaction seen in α-helices and β-sheets is ___. A) electrostatic interactions D) hydrophobic interactions B) hydrogen bonds E) all of these choices C) dipole-dipole interactions

22. Due to the formation of hydrogen bonds, _____ is highly soluble in water. A) carbon dioxide D) octane B) sodium chloride E) cholesterol C) methanol

23. Which of the following molecules would be prevented from readily crossing a lipid bilayer? A) glucose D) water B) sodium ions E) all of the above C) potassium ions

24. The most common base pairs in DNA are _____ and _____. A) A-T; A-G B) G-C; C-A C) T-A; A-U D) C-G; T-A E) G-U; A-T

25. The individual hemoglobin subunits and myoglobin share similar _____ structure but have rather different _____ structure.

A) primary; secondary D) secondary and tertiary; primary B) secondary; tertiary E) primary and secondary; tertiary C) primary; tertiary

26. The central ion of the heme group of hemoglobin is _____. A) Cu+ D) Fe3+

B) Cu2+ E) none of the above C) Fe2+

Scrambled version A

27. An A-T base pair consists of _____ H-bond(s); a C-G base pair consists of _____ H-bond(s). A) 1; 2 B) 2; 1 C) 2; 2 D) 3; 2 E) 2; 3

28. Which of the following is an example of a conservative amino acid substitution? A) Ile → Leu B) Ser → Glu C) Phe → Tyr D) Asp → Gln E) Arg → Cys

29. Molecular chaperones assist proteins in the formation of ___. A) aggregates D) primary structure B) tertiary structure E) none of these choices C) peptide bonds

30. The strongest non-covalent interactions are _____. A) van der Waals interactions D) dipole-dipole interactions B) London dispersion forces E) ionic interactions C) hydrogen bonds

31. Based upon its side chain, how is the amino acid Ser classified? A) non-polar D) negatively charged B) polar E) none of these choices C) positively charged

32. What functional groups are present in the following molecule?

A) amine and carboxylic acid D) alcohol, amine, amide and carboxylic acid B) amine, ketone and carboxylic acid E) none of the above are correct C) amine, amide and carboxylic acid

Section II (50 points): 2 points each

33. If the following mixture of proteins was applied to a size-exclusion chromatography column, what would be the order of elution? (A Da or Dalton is in units of g/mol.)

Proteins with molecular weights: myoglobin (17.7 kDa) , hemoglobin (64.5 kDa) , lysozyme (14.3 kDa) and triose phosphate isomerase (57.4 kDa)

A) lysozyme, myoglobin, triose phosphate isomerase, hemoglobin B) triose phosphate isomerase, hemoglobin, lysozyme, myoglobin C) hemoglobin, myoglobin, lysozyme, triose phosphate isomerase D) hemoglobin, triose phosphate isomerase, myoglobin, lysozyme, E) cannot be determined

Scrambled version A

34. The helical structure of collagen contains _____. A) three right-handed helices wound around each other in a right-handed triple helix B) three right-handed helices wound around each other in a left-handed triple helix C) three left-handed helices wound around each other in a left-handed triple helix D) three left-handed helices wound around each other in a right-handed triple helix E) none of the above

35. If a protein underwent a mutation such that a Glu residue was changed to another amino acid, which of the following amino acids would least likely result in a change in the overall structure of the protein?

A) Ser B) Asp C) Gln D) Lys E) Ala

36. If a reaction at 37°C has a ΔH of 23 kJ/mol and a ΔS of 337 J/K•mol, what is the ΔG for the reaction? A) 65 kJ/mol D) -19 kJ/mol B) -42 kJ/mol E) none of the above C) 18 kJ/mol

37. Which of the following structures shows the prevalent form of histidine at pH 5?

A) a D) d B) b E) none of these choices C) c

38. The following is an example of ___.

A) parallel α-helix D) antiparallel β-sheet B) parallel β-sheet E) none of these choices C) antiparallel α-helix

Scrambled version A

39. What is the pH of a solution that contains three parts of acetic acid and one part sodium acetate? The pK for acetic acid is 4.76.

A) 5.24 B) 5.06 C) 4.46 D) 4.28 E) cannot be determined from the given information

40. When oxygen is bound to the heme group of myoglobin, it is coordinated between _____ and _____. A) F8 His; Fe3+ of heme D) E7 His; Fe2+ of heme B) E7 His; Fe3+ of heme E) none of the above C) F8 His; Fe2+ of heme

41. The side chain of serine could interact with the side chain of ___ using a(n) ___. A) Val; hydrophobic interaction D) Asn; electrostatic interaction B) His; hydrogen bond E) none of these choices C) Gln; hydrophobic interaction

42. An open reading frame is defined by _____. A) a start and stop codon D) presence of transposable elements B) homology with other species E) absence of highly repetitive sequences C) placement on a genome map

43. Which of the following is a characteristic of Chargaff's rules? A) A + T = C + G B) A + G = C + T C) A + G = C + U D) all organisms have identical amounts of all four nucleotides E) none of the above

44. Which of the following explains the conversion of hemoglobin subunits from deoxy to oxy state? A) all four subunits switch simultaneously B) each subunit switches only upon oxygen binding to the particular subunit C) both α subunits simultaneously switch first followed by both β subunits D) both β subunits simultaneously switch first followed by both α subunits E) none of the above

45. Which of the following biopolymers is correctly paired with the bond that forms between the monomers? A) protein: ester bond D) RNA: phosphate bond B) polysaccharide: glycosidic bond E) all of the above C) DNA: phosphate bond

46. Which of the following non-covalent interactions is the most important in maintaining the structure of the double helix?

A) phosphodiester bonds D) van der Waals interactions B) hydrogen bonds E) ionic interactions C) London dispersion forces

Scrambled version A

47. Which of the following functional groups has two hydrogen bond donors and one hydrogen bond acceptor? A) alcohol D) amine B) ester E) amide (N atom only) C) thiol

48. Considering the energetics of transferring nonpolar molecules from water to a nonpolar solvent, the factor TΔS is generally _____, causing ΔG to be _____.

A) positive; negative C) positive; positive B) negative; negative D) negligible; either positive or negative

49. In the following figure, which bond would be unable to rotate?


50. Which of the following occurs in hemoglobin upon oxygen binding? A) the heme Fe2+ is pulled out of the plane of the heme group B) the His coordinated to the heme Fe2+ is pushed away from the heme group C) the central cavity between the four subunits is decreased in size D) hemoglobin changes from the R state to the T state E) all of the above occur

51. How does CO2 affect hemoglobin-oxygen binding? A) CO2 binds directly to the oxygen binding site, displacing oxygen and thus promoting the deoxy state B) CO2 displaces BPG, thus promoting the oxy state

C) CO2 is converted to bicarbonate and H+ which promotes the oxy state

D) CO2 is converted to bicarbonate and H+ which promotes the deoxy state E) none of the above

52. At a pH above its pKa, the ε-amino group of lysine is ___. A) protonated and neutral D) deprotonated and negatively charged B) protonated and positively charged E) none of these choices C) deprotonated and neutral

Scrambled version A

53. Differences in structure between a DNA helix and an RNA helix can predominantly be attributed to the presence of _____ in RNA.

A) uracil D) smaller sizes of RNA molecules B) 2ʹ′ hydroxyl group E) none of the above C) 3ʹ′ hydroxyl group

54. If the pK values for phosphoric acid are 2.15, 6.82 and 12.38, at what pH would one observe equal amounts of H2PO4- and HPO42-?

A) 2.15 B) 4.49 C) 6.82 D) 9.60 E) 12.38

55. What would be the resulting pH if one ml of 1.0 M NaOH was added to one liter of pure water (assume pH 7.0)?

A) 1 B) 3 C) 7.3 D) 11 E) 13

56. In an aqueous solution, if the [OH-] is 3.0×10-5 M, what is the [H+]? A) 7.0×10-9 D) 3.3×10-10

B) 7.0×10-2 E) none of the above C) 3.3×10-3

57. Which of the following amino acids has a positively charged side chain at pH 7.4? A) Glu B) Ala C) Lys D) Leu E) His

Section III (18 points): 3 points each

58. You have a short piece of synthetic RNA that you want ot use as a probe to identify a gene in a sample of DNA. The RNA probe has a tendency to hybridize (form base pairs) with sequences that are only weakly complementary. Should you increase or decrease the temperature to improve your chances of tagging (binding) the correct sequence?

A) Increase temperature B) Decrease temperature

59. Considering a 0.1 M formic acid buffer, what is the concentration of formic acid present in a solution of pH 4.25 if the pK of formic acid is 3.75?

A) 0.024 M D) 0.076 M B) 0.033 M E) none of the above C) 0.067 M

60. Which one of the three structures below would not exist at ANY pH?

A) B) C)

61. 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) Will release more O2 B) Will release less O2

Scrambled version A

62. For the reaction in which reactant A is converted to product B, tell whether this process is favorable at (i) 4oC and (ii) 37oC.

A) The reaction is favorable at both temperatures. B) The reaction is favoarable at 4oC but not at 37oC. C) The reaction is favorable at 37oC but not at 4oC. D) The reaction is unfavorable at both temperatures.

63. You have a mixture of 3 proteins, listed in the table below with their relevant properties. You are interested in isolating aspartate transaminase using ion exchange chromatography with DEAE resin. Given the values in the table below: 1) what pH would you use in order to ensure that aspartate transaminase protein binds to the column and that the others do not? Assume that your efforts are successful -- 2) how will you elute aspartate transaminase from the column? Choose the correct conditions from the list below.

Protein pIAspartate transcarbamylase 9.8Myoglobin 7.0Aspartate transaminase 5.0

A) 1) Initial pH = 10.0; 2) lower pH to 6 D) 1) Initial pH = 6; 2) lower pH to 5 or less B) 1) Initial pH = 8; 2) raise pH to 10 E) 1) Initial pH = 8; 2) lower pH to 7 C) 1) Initial pH = 4; 2) raise pH to 5 or higher

Scrambled version A

Answer Key - Exam1_F13

1. E 2. A 3. C 4. E 5. D 6. D 7. A 8. C 9. B 10. E 11. A 12. D 13. B 14. C 15. E 16. E 17. A 18. E 19. B 20. D 21. B 22. C 23. E 24. D 25. D 26. C 27. E 28. A 29. B 30. E 31. B 32. C 33. D 34. D 35. B 36. E 37. C 38. D 39. D 40. D 41. B 42. A 43. B 44. A 45. B 46. D 47. D 48. A 49. B 50. C 51. D 52. C 53. B 54. C 55. D 56. D

Scrambled version A

57. C 58. A 59. A 60. B 61. A 62. C 63. D

Scrambled version A


Helpful Equations:












Scrambled version B Page 1












A) 2.15 B) 4.49 C) 6.82 D) 9.60 E) 12.38







A) 1 B) 3 C) 7.3 D) 11 E) 13



















A) B) C)





1. E 2. B 3. C 4. C 5. E 6. D 7. B 8. B 9. B 10. D 11. A 12. C 13. E 14. D 15. E 16. C 17. A 18. A 19. B 20. D 21. E 22. E 23. A 24. E 25. E 26. C 27. D 28. C 29. B 30. D 31. E 32. A 33. C 34. D 35. C 36. E 37. C 38. B 39. D 40. D 41. D 42. B 43. C 44. A 45. D 46. D 47. C 48. A 49. D 50. D 51. A 52. D 53. B 54. D 55. B 56. B


57. B 58. A 59. A 60. B 61. C 62. D 63. A



Helpful Equations:










Scrambled version C Page 1


A) 1 B) 3 C) 7.3 D) 11 E) 13

















A) 2.15 B) 4.49 C) 6.82 D) 9.60 E) 12.38















A) B) C)



1. A 2. C 3. C 4. E 5. B 6. D 7. E 8. B 9. E 10. A 11. B 12. E 13. E 14. B 15. B 16. A 17. C 18. E 19. C 20. E 21. B 22. C 23. E 24. E 25. D 26. A 27. A 28. D 29. D 30. C 31. D 32. D 33. D 34. D 35. A 36. D 37. D 38. C 39. D 40. D 41. B 42. C 43. B 44. E 45. D 46. D 47. C 48. B 49. C 50. B 51. B 52. A 53. D 54. B 55. C 56. D


57. A 58. D 59. A 60. A 61. C 62. A 63. B


Exam 1_F13

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