6. Which one of the following are the four (4) most common elements of life in t
ID: 200349 • Letter: 6
Question
6. Which one of the following are the four (4) most common elements of life in the correct order of
abundance in humans (by number of atoms, not mass)?
A) hydrogen, oxygen, carbon, and nitrogen B) hydrogen, carbon, oxygen, and nitrogen
C) carbon, oxygen, hydrogen, and nitrogen D) carbon, hydrogen, oxygen, and nitrogen
7. Which one of the following is NOT one of the four key classes of biomolecules?
A) lipids B) carbohydrates C) organelles D) nucleic acids E) proteins
8. Which element is not found in nucleotides?
A) oxygen B) sulfur C) nitrogen D) phosphorus E) carbon
9. Which one of the following is found in the DNA but not the RNA of a living cell?
A) Thymine B) A double helix
C) An additional hydroxyl group D) Hydrogen bonds
10. A molecule of DNA contains all of the following EXCEPT:
A) deoxyribose sugar B) peptide bonds C) phosphodiester bonds D) nitrogenous bases
11. Which one of the following best describes the structural backbone of nucleic acids?
A) – base – sugar – base – sugar – B) – base – phosphate – base – phosphate –
C) – sugar – phosphate – sugar – phosphate – D) – base – sugar – sugar – base – sugar – sugar –
12. In DNA base pairing, A and T make __ hydrogen bonds whereas G and C make ___.
A) 2 and 2 B) 2 and 3 C) 3 and 1 D) 3 and 2 E) 3 and 3
Chapter 2 Water and pH
13. What is the type of bond found between the oxygen and the hydrogen within one water
molecule?
A) hydrogen B) van der Waals C) ionic D) covalent E) peptide
14. Molecules that are readily soluble in water are considered
A) hydrophobic B) amphipathic C) zwitterionic D) dielectric E) polar
15. Phosphoric acid is tribasic, with pKa’s of 2.14, 6.86, and 12.4. The ionic forms that are most
abundant at pH 6 are:
A) H3PO4 / PO4
?3 B) H2PO4
– / HPO4
?2 C) HPO4
?2 / PO4
?3 D) H3PO4 / HPO4
?2 E) H3PO4 / HPO4
?2
16. Which equation is the proper form for the Henderson-Hasselbach equation? Here “ln” means the
natural logarithm.
A) pH = pKa + log10 ( [HA]
[A
– ] ) B) pH = pKa + ln ( [ HA]
[ A
–] )
C) pH = pKa + log10 ( [A
– ]
[HA] ) D) pH = pKa + ln ( [ A
–]
[ HA] )
17. What is the [A?]/[HA] ratio when the weak acid is in a solution one pH unit above its pKa?
A) 2:1 B) 1:10 C) 10:1 D) 100:1 E) 1:100
18. When the pH is more than two (2) pH units below the pKa of an amino group, the base is:
A) protonated B) deprotonated C) denatured D) dissolved E) acidic
19. Tris has a pKa value of 8.06, at which one of the following pH values would Tris be within its
useful buffering range.
A) pH 3 B) pH 5 C) pH 7 D) pH 9 E) pH 11
20. Which one of the following is the key buffering component of blood?
A) oxygen B) carbon dioxide C) iron oxide D) phosphate ions E) water
21. Water CANNOT form a hydrogen bond with
A) carboxyl groups B) amine groups C) methyl groups D) hydroxyl groups E) carbonyl groups
Chapter 3 Amino acids
22. Which one of the following are the chiral type of amino acids found in proteins.
A) L-amino acids B) D-amino acids C) S-amino acids D) R-amino acids E) (+)-amino acids
23. What is the net charge of glycine at pH 12?
A) –2 B) –1 C) 0 D) +1 E) +2
24. Which one of the following amino acid backbone bonds corresponds to the phi (?) dihedral
angle?
A) C=O B) N—C? C) C?—C=O D) N—C=O E) C?—R
25. Interactions between side chains of and Aspartate and Arginine at neutral pH would be?
A) hydrophobic B) ionic C) hydrogen bonding D) steric E) covalent
26. Which one of the following is the naturally occurring amino acid?
A) B)
27. Which one of the following amino acids would most likely be soluble in a nonpolar solvent such
as benzene?
A) valine B) histidine C) glutamine D) glycine E) glutamate
28. Which one of the following amino acids has a chiral center in its side chain?
A) lysine B) leucine C) threonine D) glutamine E) valine
29. Disulfide bonds are formed by pairs of ____.
A) methionine B) cysteine C) both methionine and cysteine
30. The resonance structures that can be drawn for the peptide bond indicate that the peptide bond
A) still isn't completely understood by chemists. B) is weaker than an ordinary single bond.
C) has partial double bond character. D) actually extends to the ?-carbon.
Chapter 4 Proteins
31. How a protein folds is primarily determined by:
A) whether the environment is hydrophilic. B) the location in the cell in which the protein is located.
C) the pH of the cytoplasm. D) the order of the amino acids found in the sequence.
32. The overall 3D structure of a protein is referred to as:
A) primary structure B) secondary structure C) tertiary structure D) quaternary structure
33. A protein whose peptide backbone is mostly extended and hydrogen bonded to different strands
of the protein is composed mostly of the __ secondary structure.
A) ?-sheet B) ?-sheet C) ?-helix D) ?-helix E) ?-helix
34. A protein is considered to be ____ when it is converted into a randomly coiled structure without
its normal activity.
A) globular B) denatured C) insoluble D) infectious E) hydrophobic
35. In an ?-helix, the side chains on the amino acid residues:
A) alternate from the outside to the inside of the helix. B) are found on the outside of the helix spiral.
C) cause only left-handed helices to form. D) stack within the interior of the helix.
36. Which one of the following is NOT a tertiary interaction in proteins?
A) hydrophobic side chain interactions B) salt bridges via charged side chains
C) disulfide bonds of special side chains D) backbone hydrogen bonding in ?-helices
37. In a long ?-helix, amino acid number 7 would form a hydrogen bond with which two (2) other
amino acids?
A) 1 and 13 B) 2 and 12 C) 3 and 11 D) 4 and 10 E) 5 and 9
38. Due to the side group steric clash, almost all peptide bonds are ____ in their configuration.
A) cis B) trans C) parallel D) perpendicular E) circular
39. What is the approximate molecular weight (in Daltons) of a protein containing 300 amino acids?
A) 2,200 B) 11,000 C) 33,000 D) 110,000 E) 330,000
40. What are prions?
A) infectious proteins B) simple viral DNAs C) naked RNA strands D) primitive bacteria
Chapter 5 Purification
41. The ratio of enzyme activity relative to total protein is called:
A) percent yield B) purification level C) specific activity D) total enzymatic activity
42. In which one of the following techniques do the smallest proteins travel faster than the largest
proteins.
A) SDS-PAGE C) Gel-filtration chromatography
B) Size-exclusion chromatography D) Centrifugation
43. The next step in protein purification after complete cell breakage is usually
A) centrifugation B) mass spectrum C) sonication D) chromatography E) electrophoresis
44. Disulfide bonds in proteins can be reduced to free sulfhydryl groups using reagents such as
A) collagen peptides B) thiolase enzymes C) iron sulfide (Fe2S3) D) dithiothreitol (DTT)
45. Which one of the following does NOT affect the sedimentation of a particle.
A) particle mass B) particle shape C) solution density D) particle density E) ALL have an effect
46. This technique allows the detection of small amounts of target proteins as well as the ability to
determine the size of target proteins.
A) dialysis B) fluorescamine C) western blot D) sonication E) size exclusion
47. What is the difference between a agarose gel and acrylamide gel?
A) agarose gels involve a chemical polymerization and is therefore easily reversible
B) agarose gels involve a physical polymerization and is therefore easily reversible
C) agarose gels involve a chemical polymerization and is therefore NOT easily reversible
D) agarose gels involve a physical polymerization and is therefore NOT easily reversible
48. Which one of the following is NOT a correct difference between a hydrophobic interaction
column (HIC) and a reverse phase column (RPC)?
A) RPC uses organic solvents whereas HIC uses water with high salt.
B) RPC uses more hydrophobic ligands with strong binding than HIC.
C) RPC is often coupled with a HPLC.
D) RPC allows the protein to be in its native state whereas HIC causes denaturation.
49. What is the main advantage of adding SDS to gel electrophoresis?
A) SDS colors the proteins for visualization. B) SDS reduces disulfide bonds.
C) SDS allows proteins to separate by mass. D) SDS inhibits enzymatic activity.
Match the lettered description to the appropriate numbered chromatography column below. Letters
will be used more than once. All letters will be used. ½ point each this section.
A. Separation by size B. Separation by charge C. Separation by ligand D. Separation by solubility
__ 50. Reverse phase __ 51. Size exclusion
__ 52. Affinity __ 53. Gel filtration
__ 54. Hydrophobic interaction __ 55. Ion exchange
Chapter 6 Enzymes
56. This is a biochemically active combination of an enzyme with all its cofactors.
A) apoenzyme B) holoenzyme C) proenzyme D) coenzyme E) prosthetic enzyme
57. An enzyme will specifically bind its substrate because of:
A) tight lock-and-key binding mechanism. B) hydrophobic amino acids in the center of the protein.
C) weak interactions at the active site. D) several nonprotein cofactors.
58. The rate of a reaction, or how quickly a reaction will proceed, is best determined by the:
A) free energy B) enthalpy C) entropy D) temperature E) activation energy
59. A graph of product versus time for an enzyme is determined to be hyperbolic. Why does the
amount of product level off as time increases?
A) Forward and reverse reactions are occurring at a fixed rate. B) There is a product inhibition of the enzyme.
C) The enzyme has finished accelerating the reaction. D) The reaction runs out of reaction materials.
60. Which one of the following factors differ between the standard-state free energy, ?G°, and the
biochemical standard-state free energy is that ?G°?.
A) temperature B) pressure C) pH D) concentration E) volume
61. Which one of the following curves best describes enzyme activity as a function of temperature?
A) B) C) D)
62. Riboflavin is a water-soluble organic substance that is not synthesized by humans.
Metabolically, it is chemically converted into a substance called flavin adenine dinucleotide
(FAD), which is required by succinate dehydrogenase (SDH). Which of the following statements
is most correct?
A) Riboflavin is a coenzyme. B) Flavin adenine dinucleotide (FAD) is a vitamin.
C) Succiniate dehydrogenase (SDH) is a coenzyme. D) Flavin adenine dinucleotide (FAD) is a coenzyme.
63. In an enzymatic reaction in a test tube, the reaction will eventually reach equilibrium. Why does
this not happen in living organisms?
A) products are utilized in subsequent reactions. B) there are many different enzymes for same reaction.
C) separate enzymes for the reverse reaction exist. D) temperate and pH are highly variable within the cell.
64. If Keq < 1, what is the value of ?G°'?
A) zero B) negative C) positive D) infinite E) cannot determine
65. Does a reaction with an extremely large, negative free energy (?G ? –1000 kJ/mol) require an
enzyme?
A) Yes, because it would not have enough activation energy to happen.
B) Yes, because the free energy is negative and must be positive for the reaction to occur.
C) No, because the free energy is already negative and large
D) No, because no enzyme exists that could handle that much energy
Chapter 7 Kinetics
66. A simple reaction with two substrates is considered a(n) ___ reaction.
A) first-order reaction B) second-order reaction C) bi-sequential reaction D) ping-pong reaction
67. The Michaelis-Menten constant, KM has units of:
A) seconds (s) B) inverse moles (1/mol) C) moles per second (mol/s) D) Molarity (mol/L)
68. An enzyme will be most sensitive to changes in cellular concentration when the substrate
concentration is ___.
A) almost zero B) much smaller than the KM
C) near the KM D) much larger than the KM
69. The y-intercept of a Lineweaver-Burk plot is:
A) 1/V0 B) 1/Vmax C) –1/KM D) KM/Vmax E) Vmax/KM
Michaelis-Menten questions. The following questions are
about the table (on the right) of enzyme activity. The units
of substrate, [S], is nM; ignore the units for V0 and Vmax.
70. Using the table, what is the Vmax in the absence of inhibitor
(i.e., –inh)?
A) 25.0 B) 50.0
C) 100.0 D) 200.0
71. Using the table, what is the Vmax in the presence of
inhibitor (i.e., +inh)?
A) 25.0 B) 50.0
C) 100.0 D) 200.0
72. Using the table, what is the KM in the absence of inhibitor
(i.e., –inh)?
A) 0.0001 B) 0.0002 C) 0.0005 D) 0.001 E) 0.002
73. Using the table, what is the KM in the presence of inhibitor (i.e., +inh)?
A) 0.0001 B) 0.0002 C) 0.0005 D) 0.001 E) 0.002
74. Based on your findings above, what kind of inhibitor is this likely to be?
A) competitive B) uncompetitive C) noncompetitive D) incompetitive E) cooperative
Chapter 8 Mechanisms and Inhibitors
75. Which one of the following is NOT a catalytic mechanism used by the enzyme chymotrypsin?
A) Metal ion catalysis B) Covalent catalysis C) General acid-base catalysis
76. In conducting an experiment with a new drug, you find that regardless of the concentration of
substrate, the drug is able to inhibit the enzyme activity. You are likely to not have a(n) ___ type
of inhibitor.
A) competitive B) uncompetitive C) noncompetitive D) ultracompetitive E) irreversible
77. Which amino acids in chymotrypsin are found in the active site and are participants in substrate
cleavage?
A) his, ser, asp B) his, ser C) asp, lys D) lys, arg E) his, ser, arg
78. How is specificity determined by chymotrypsin?
A) by an interaction of the active site amino acids with the substrate
B) by a binding of the N-terminus amino acid at the active site
C) by a covalent binding of a his residue to the substrate
D) by a conformational change upon the binding of substrate
E) by a binding of the proper amino acid into a deep pocket on the enzyme
79. Given the following peptide sequence, Ala-Ser-Phe-Pro-Lys-Gly-Glu-Arg, at which peptide bond
location will chymotrypsin most likely cleave first?
A) Ser-Phe B) Phe-Pro C) Pro-Lys D) Lys-Gly E) Gly-Glu
[S]
0.0001 16.7 25.0
0.0002 28.6 33.3
0.0005 50.0 41.7
0.001 66.7 45.5
0.002 80.0 47.6
0.005 90.9 49.0
0.01 95.2 49.5
0.02 97.6 49.8
0.05 99.0 49.9
0.1 99.5 50.0
1 100.0 50.0
V0 (–inh) V0 (+ inh)
Chapter 9 Allosteric enzymes and hemoglobin
80. Which one of the following is necessary for an enzyme to exhibit cooperativity?
A) presence of an inhibitor B) multiple binding sites on the enzyme
C) high concentration of substrate D) negative feedback mechanism
81. Allosteric modifiers alter the equilibria between:
A) the ES and EP state. B) the R and T forms of a protein.
C) the forward and reverse reaction rate. D) the formation of a product and its reverse reaction.
82. The ___ model states that all subunits in an allosteric enzyme must be in either the T or the R
state; there can not be hybrids.
A) Michaelis-Menten B) sequential C) concerted D) induced fit E) lock and key
83. An allosteric inhibitor of an enzyme usually
A) denatures the enzyme. B) causes the enzyme to work faster
C) binds to the active site. D) participates in feedback regulation.
84. The shape of the myoglobin binding curve that shows that it is NOT regulated allosterically is:
A) hyperbolic B) parabolic C) sigmoidal D) linear E) bell shaped
85. Sickle-cell anemia is caused by:
A) a substitution of glutamic acid residue for histidine at the C terminal of the ? chain.
B) a decreased affinity for hemoglobin oxygen binding.
C) the loss of the heme group because the proximal His is oxidized.
D) a substitution of a valine residue for a glutamic acid residue at the ?6 position.
86. Which one of the following is a correct statement concerning adult hemoglobin (HbA) and fetal
hemoglobin (HbF)?
A) Both HbA and HbF are tetrameric proteins.
B) HbA exhibits a sigmoid-shaped O2 saturation curve, while HbF exhibits M-M hyperbolic curve.
C) HbA exhibits cooperative binding of O2, while HbF does not.
D) HbA exhibits a higher degree of O2 saturation at all relevant partial pressures of O2 than does HbF.
Select the best letter that matches for each of the following numbered statements about
hemoglobin. ½ point each this section.
A. Increases affinity for binding oxygen B. Decreases affinity for binding oxygen C. No change in affinity
__ 87. Presence of 2,3-BPG __ 88. Lower pH of 7.2
__ 89. Higher pH of 7.6 __ 90. Warmer temperature
__ 91. Cooler temperature __ 92. Increase of partial pressure of CO2
__ 93. R state __ 94. T state
__ 95. three heme already bound to oxygen __ 96. substitution of ? amino acid 6 to valine.
Short answer and sketching (#6# questions; #4# points each)
You MUST ELIMINATE THREE (3) questions to get full points. If you answer all questions, I will count all points, giving
you the WORST possible grade. Answer concisely yet thoroughly, you do not need to use complete sentences.
____ 1. Draw an approximate titration curve for the ionization of lactic acid, CH3CHOHCOOH with a pKa
value of 3.86 against amount of NaOH added. Be sure to label the axes of your figure.
____ 2. Fill in the appropriate boxes for the correct protonation state of histidine at pH values of 0, 4, 8
and 12. Put an “H” in the gray box if it is protonated and leave it blank if it is deprotonated. Use
the amino acid sheet at the back of the exam for help.
? ? ?
pH 0 ? pH 4 ? pH 8 ? pH 12
____ 3. Below is are two short polypeptides in a ?-sheet formation. Draw the missing hydrogen bonds for
the ?-sheet using dashed lines. Label this structure as a parallel or anti-parallel ?-sheet.
____ 4. Draw the four (4) amino acid peptide Ser-Ala-Pro-Leu at neutral pH.
____ 5. What are the differences between hemoglobin and myoglobin? Why is it advantageous for
hemoglobin to have allosteric properties?
____ 6. Answer the following questions for the five (5) proteins in the table on the right.
a. For each protein, draw their expected location on the 2D gel using the image shown.
b. You must label the axes (using numbers for pH and MW) on the 2D gel.
Protein pI MW (kD)
Cyto c 10.2 13.0
IgG 7.3 145.0
RNase A 9.3 13.7
GFP 6.2 28.0
Albumin 4.9 68.5
direction of
electrophoresis
direction of
isoelectric focusing
(+) (–)
Explanation / Answer
7) The answer is organelle.It is not a biomolecule.Biomolecules are large molecules formed by the union of monomers.As protein are made of amino acid,carbohydrates are made of saccharides,etc.
8) The answer is sulphur.It is not found in nuceotides.Nucleotides are made up of sugar,phoshpate group and a nitrogenous base.
9) Thymine is not present in RNA as it is replaced by Uracil.
10) The answer is peptide bond.As peptide bond is present in polypeptide not in DNA.
11) The answer is (c) as a phosphodiester bond is formed between 3' and 5' OH of the sugars.
12) The answer is b.There are two bydrogen bonds between A and T and three between G and C.
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