Student Name: Grade: _____/100 points
Assignment date: 09/04/14
Grading:
a)  One point for each correct answer for multiple choice questions. There are 50 multiple
choice questions, so you may earn up to maximum of 50 points.
b)  
Two points for each correct answer for short answer questions. Do not exceed the space
provided. Be succinct. There are 15 short answer questions, so you may earn up to
maximum of 30 points.
Five points for the correct answers to the problem #66.
d)  Seven points for identifying the correct sequence of the peptides from the problem #67.
e)  
Four points for a correct answer for the problem #68.
f)  
Four points for a correct answer for the problem #69.
Multiple Choice Questions
1.   In eukaryotes, the nucleus is enclosed by a double membrane called the:
A)  cell membrane. B)  nucleolus. C)  nuclear tire. D)  nucleoplasm.
E)  nucleosome. F)  nuclear envelope.
2.  The biological classification system categorizes organisms into the domains:
A) bacteria, eukarya, and vertebrate. B) archaea and eukarya. C) bacteria, eukarya, and archaea. D) eukarya and bacteria. E) none of the above
3.   The bacterium E. coli requires simple organic molecules for growth and energy — it is therefore a:
A)  chemoautotroph. B)
E)   photoautotroph. F)   phototraph.
4.   The term molecular weight  is a term used by biochemists that refers to
A) the density of a particle. B) a dimensionless quantity that is defined as the ratio of the mass of the particle to 1/12 the mass of
a 12
C atom. C) Daltons divided by the mass of a hydrogen atom. D) all of the above E) none of the above
5.   Which of the following is not true of eukaryotes:
A) They contain organelles like mitochondria, chloroplasts, ribosomes, and a nucleus B) They are usually 10 to 100 microns in diameter
C) They can be both uni or multicellular D) They are also called archaea E) All of the above are true of eukaryotes
6.  
The three-dimensional structure of macromolecules is formed and maintained primarily through
noncovalent interactions. Which one of the following is not  considered a noncovalent interaction?
A)  hydrogen bonds
E)  van der Waals interactions F)  carbon-carbon bonds
7.   Stereoisomers that are nonsuperimposable mirror images of each other are known as:
A)  
D)  geometric isomers. E)  enantiomers.
8.  The enzyme fumarase catalyzes the reversible hydration of fumaric acid to l-malate, but it will not
catalyze the hydration of maleic acid, the cis isomer of fumaric acid. This is an example of:
A)  
B)  stereospecificity. C)  chiral activity. D)  racemization. E)  stereoisomerization.
 
 
A)  have a dynamic steady state. B)  have a great activation energy for their enzymes
C)  have a lower metabolism D)  be disintegrated E)  have more free energy F)  none of the above
10.   If the free energy change G for a reaction is -46.11 kJ/mol, the reaction is:
A)  at equilibrium. B)
The major carrier of chemical energy in all cells is:
A)  UPS
B)  adenosine monophosphate. C)  adenosine triphosphate. D)  FedEx D) cytosine tetraphosphate. E) uridine diphosphate.
12.  The atmosphere of early earth probably contained the following molecules:
A) H2O, CO2, N2 , CH4, and NH3.
B) H2O, CO2, CH4, C6H6O6, and NH3. C) H2O, CO2, CH4, C6H6O6, and COOHCH2 NH3.
D) H2O, CO2, CH4, COOHCH2 NH3, and NH3. E) none of the above
13.  Which of the following statements about water is incorrect?
A) Water is an excellent solvent for polar molecules B) Pure water has a concentration of approximately 55.5 M C) Cations are solvated by shells of water molecules oriented with their hydrogen atoms pointed
toward the ions D) Non-polar molecules do not dissolve in water, but form a separate phase E) Amphiphilic detergents often form micelles with the polar groups on the outside exposed to the
water (solvent) and the non-polar groups sequestered in the interior
14.  The pH of a sample of blood is 7.4, while gastric juice is pH 1.4. The blood sample has:
A)  5.29 times lower [H + ] than the gastric juice.
B)  6 times lower [H + ] than the gastric juice.
 
 
15.  Phosphoric acid is tribasic, with p K a’s of 2.14, 6.86, and 12.4. The ionic form that predominates at
 pH 3.2 is:
16. Which of the following statements about buffers is true?
 
 
When pH = p K a, the weak acid and salt concentrations in a buffer are equal.
E)  The pH of a buffered solution remains constant no matter how much acid or base is added to the solution.
17.  The Henderson-Hasselbalch equation:
A)  allows the graphic determination of the molecular weight of a weak acid from its pH alone. B)  does not explain the behavior of di- or tri-basic weak acids C)  employs the same value for p K a for all weak acids.
 
is equally useful with solutions of acetic acid and of hydrochloric acid.
18.  Consider an acetate buffer, initially at the same pH as its p K a (4.76). When sodium hydroxide (NaOH) is mixed with this buffer, the:
A)   pH remains constant. B)
 
 pH rises more than if an equal amount of NaOH is added to an acetate buffer initially at pH 6.76. C)   pH rises more than if an equal amount of NaOH is added to unbuffered water at pH 4.76. D)  sodium acetate formed precipitates because it is less soluble than acetic acid.
E)  ratio of acetic acid to sodium acetate in the buffer falls.
19.  The chirality of an amino acid results from the fact that its  carbon:
A)  
has no net charge.
B)  is bonded to four different chemical groups. C)  is a carboxylic acid.
D)  is in the L absolute configuration in naturally occurring proteins. E)  is symmetric.
20.  
Of the 20 standard amino acids, only ___________ is not optically active. The reason is that its side chain ___________.
 
 
 
E)   proline; forms a covalent bond with the amino group
21.  Which of the following statements about aromatic amino acids is correct?
A)  All are strongly hydrophilic. B)  Histidine’s ring structure results in its being categorized as aromatic or basic, depending on pH. C)  The major contribution to the characteristic absorption of light at 280 nm by proteins is the
 phenylalanine R group. D)  On a molar basis, tryptophan absorbs more ultraviolet light than tyrosine. E)  The presence of a ring structure in its R group determines whether or not an amino acid is
aromatic.
22.  Which of the following statements about cystine is correct?
A)  
 
Cystine is formed by the oxidation of the carboxylic acid group on cysteine.
C)  Cystine forms when the — CH2 — SH R group is oxidized to form a — CH2 — S — S — CH2 —   disulfide bridge between two cysteines.
D)  Cystine is formed through a peptide linkage between two cysteines.
E)  Two cystines are released when a — CH2 — S — S — CH2 —  disulfide bridge is reduced to — CH2 —  SH.
23. The uncommon amino acid selenocysteine has an R group with the structure  — CH2 — SeH (p K a   5). In an aqueous solution, pH = 7.0, selenocysteine would:
A)   be found in proteins as D-selenocysteine. B)  never be found in a protein. C)   be nonionic. D)   be a fully ionized zwitterion with no net charge.
E)  not be optically active.
24.  For amino acids with neutral R groups, at any pH below the pI of the amino acid, the population of amino acids in solution will have:
A)  a net negative charge. B)  a net positive charge.
C)  no charged groups. D)
 
 positive and negative charges in equal concentration.
25.  At pH 7.0, converting a proline to hydroxyproline will have what effect on the overall charge of the
 protein containing it?
 
It will become more positive. C)  There is not enough information to answer the question.
D)  It will stay the same. E)  the answer depends on the salt concentration.
 
 
A)  It will become more negative
B)  It will become more positive. C)  It will stay the same. D)  There is not enough information to answer the question. E)  The answer depends on the salt concentration.
27.  Which of the following tripeptides would be expected to be the most hydrophobic:
A) KYG B) KYA C) GYA
D) DYA E) DYG
28.  
At pH 7, arginine (p K s are alpha-carboxylate 1.82, alpha-amino 8.99, guanidino 12.48) would be
charged as follows:
A) 0 alpha-carboxylate, 0 alpha-amino, +1 guanidino, +1 net charge
B) +1 alpha-carboxylate, 0 alpha-amino, -1 guanidino, 0 net charge C) +1 alpha-carboxylate, -1 alpha-amino, -1 guanidino, -1 net charge
D) -1 alpha-carboxylate, +1 alpha-amino, +1 guanidino, +1 net charge E) -1 alpha-carboxylate, 0 alpha-amino, +1 guanidino, 0 net charge
29.  
At pH 7, aspartic acid (p K s are alpha-carboxylate 1.99, alpha-amino 9.9, beta-carboxylate 3.9 )
would be charged as follows:
A) 0 alpha-carboxylate, +1 alpha-amino, 0 beta-carboxylate, +1 net charge
B) -1 alpha-carboxylate, +1 alpha-amino, -1 beta-carboxylate, -1 net charge C) 0 alpha-carboxylate, -1 alpha-amino, 0 beta-carboxylate, -1 net charge D) +1 alpha-carboxylate, -1 alpha-amino, +1 beta-carboxylate, +1 net charge E) +1 alpha-carboxylate, +1 alpha-amino, +1 beta-carboxylate, +3 net charge
30.  At pH 11, glutamic acid (p K s are alpha-carboxylate 2.1, alpha-amino 9.47, gamma-carboxylate 4.07. would be charged as follows:
A) +1 alpha-carboxylate, 0 alpha-amino, +1 gamma-carboxylate, +2 net charge
B) -1 alpha-carboxylate, +1 alpha-amino, -1 gamma-carboxylate, -1 net charge C) 0 alpha-carboxylate, 0 alpha-amino, 0 gamma-carboxylate, 0 net charge D) +1 alpha-carboxylate, -1 alpha-amino, +1 gamma-carboxylate, +1 net charge
E) -1 alpha-carboxylate, 0 alpha-amino, -1 gamma-carboxylate, -2 net charge
31. At pH 4, histidine (p K s are alpha-carboxylate 1.8, alpha-amino 9.33, 6.04 imidazole) would be charged as follows:
 
 
E) 0 alpha-carboxylate, + alpha-amino, +1 imidazole, +2 net charge
32.  At pH 5, cysteine (p K s are alpha-carboxylate 1.92, alpha-amino 10.7, sulfhydryl 8.37 ) would be charged as follows:
A) 0 alpha-carboxylate, 0 alpha-amino, 0 sulfhydryl, 0 net charge B) +1 alpha-carboxylate, -1 alpha-amino, -1 sulfhydryl, -1 net charge
C) -1 alpha-carboxylate, +1 alpha-amino, +1 sulfhydryl, +1 net charge D) -1 alpha-carboxylate, +1 alpha-amino, 0 sulfhydryl, 0 net charge E) +1 alpha-carboxylate, -1 alpha-amino, 0 sulfhydryl, 0 net charge
33.  At pH 1, lysine (p K s are alpha-carboxylate 2.16, alpha-amino 9.06, epsilon-amino 10.54 ) would be
charged as follows:
A) 0 alpha-carboxylate, -1 alpha-amino, -1 epsilon-amino, -2 net charge B) -1 alpha-carboxylate, +1 alpha-amino, +1 epsilon-amino, +1 net charge
C) +1 alpha-carboxylate, +2 alpha-amino, +2 epsilon-amino, +5 net charge D) 0 alpha-carboxylate, +1 alpha-amino, +1 epsilon-amino, +2 net charge E) +2 alpha-carboxylate, +1 alpha-amino, +1 epsilon-amino, +4 net charge
34.  
Amino acid side-chain residues have:
A) a positive charge in every situation B) pKs that assure the solubility of every protein
C) constant pKs no matter what aqueous environment they are found in D) different pKs in peptides as compared to the free amino acids
E) polar functional groups
35.  The formation of a peptide bond between two amino acids is an example of a(n) ______________
reaction.
A)  
D)  isomerization E)  oxidation reduction
36. At the isoelectric pH of a tetrapeptide:
 
the total net charge is zero.
D)  there are four ionic charges. E)  two internal amino acids of the tetrapeptide cannot have ionizable R groups.
37.  The average molecular weight of the 20 standard amino acids is 138, but biochemists use 110 when
estimating the number of amino acids in a protein of known molecular weight. Why?
A)  The number 110 is based on the fact that the average molecular weight of a protein is 110,000 with an average of 1,000 amino acids.
 
 
loss of water when the peptide bond forms. C)  The number 110 reflects the number of amino acids found in the typical small protein, and only
small proteins have their molecular weight estimated this way. D)  The number 110 takes into account the relatively small size of nonstandard amino acids. E)  The number 138 represents the molecular weight of conjugated amino acids.
38.  For the study of a protein in detail, an effort is usually made to first:
A)  conjugate the protein to a known molecule. B)  determine its amino acid composition. C)  determine its amino acid sequence. D)  determine its molecular weight.
E)   purify the protein.
39.  
In a mixture of the five proteins listed below, which should elute second in size-exclusion (gel- filtration) chromatography?
E) serum albumin  M r  = 68,500 A) cytochrome c   M r  = 13,000
B)  immunoglobulin G  M r  = 145,000 C) ribonuclease A  M r  = 13,700
D) RNA polymerase  M r  = 450,000
40.  The following reagents are often used in protein chemistry. Match the reagent with the purpose for
which it is best suited. Some answers may be used more than once or not at all; more than one reagent may be suitable for a given purpose.
(a) CNBr (cyanogen bromide) (e) performic acid (b) Edman reagent (phenylisothiocyanate) (f) chymotrypsin
(c) FDNB (g) trypsin (d) dithiothreitol
 ___ hydrolysis of peptide bonds on the carboxyl side of Lys and Arg  ___ cleavage of peptide bonds on the carboxyl side of Met
 ___ breakage of disulfide ( — S — S — ) bonds  ___ determination of the amino acid sequence of a peptide  ___ determining the amino-terminal amino acid in a polypeptide
41. By adding SDS (sodium dodecyl sulfate) during the electrophoresis of proteins, it is possible to:
A)  determine a protein’s isoelectric point. B)
  determine an enzyme’s specific activity. C)  determine the amino acid composition of the protein. D)   preserve a protein’s native structure and biological activity. E)  separate proteins exclusively on the basis of molecular weight.
42.  The first step in two-dimensional gel electrophoresis generates a series of protein bands by isoelectric focusing. In a second step, a strip of this gel is turned 90 degrees, placed on another gel containing SDS, and electric current is again applied. In this second step:
 
 
weights. B)  the individual bands become stained so that the isoelectric focus pattern can be visualized.
C)  the individual bands become visualized by interacting with protein-specific antibodies in the second gel.
D)  the individual bands undergo a second, more intense isoelectric focusing. E)  the proteins in the bands separate more completely because the second electric current is in the
opposite polarity to the first current.
43.  One method used to prevent disulfide bond interference with protein sequencing procedures is:
A)  cleaving proteins with proteases that specifically recognize disulfide bonds. B)   protecting the disulfide bridge against spontaneous reduction to cysteinyl sulfhydryl groups.
C)  reducing disulfide bridges and preventing their re-formation by further modifying the — SH groups.
D)  
 
44.  Which one of the tripeptides below:
A B C D E  __________________________________________________________________
Tyr-Lys-Met Gly-Pro-Arg Asp-Trp-Tyr Asp-His-Glu Leu-Val-Phe
 ____(a) is most negatively charged at pH 7?
 ____(b) will yield DNP-tyrosine when reacted with l-fluoro-2,4-dinitrobenzene and hydrolyzed in acid?
 ____(c) contains the largest number of nonpolar R groups?  ____(d) contains sulfur?  ____(e) will have the greatest light absorbance at 280 nm?
45.  A nonapeptide was determined to have the following amino acid composition: (Lys) 2, (Gly) 2, (Phe) 
2, His, Leu, Met. The native peptide was incubated with 1-fluoro-2,4-dinitrobenzene (FDNB) and then hydrolyzed; 2,4-dinitrophenylhistidine was identified by HPLC. When the native peptide was exposed to cyanogen bromide (CNBr), an octapeptide and free glycine were recovered. Incubation
 
His – Leu – Gly – Lys – Lys – Phe – Phe – Gly – Met.
C)  His – Leu – Phe – Gly – Lys – Lys – Phe – Met – Gly. D)  His – Phe – Leu – Gly – Lys – Lys – Phe – Met – Gly. E)  Met – Leu – Phe – Lys – Phe – Gly – Gly – Lys – His.
 
 
A)  absence of rotation around the C —  N bond because of its partial double-bond character.
B)   plane of rotation around the C —  N bond. C) region of steric hindrance determined by the large C=O group.
D) region of the peptide bond that contributes to a Ramachandran plot.
E) theoretical space between – 180 and +180 degrees that can be occupied by the  and  angles in the peptide bond.
47.  
The -keratin chains indicated by the diagram below have undergone one chemical step. To alter
the shape of the -keratin chains — as in hair waving — what subsequent steps are required?
A)  Chemical oxidation and then shape remodeling
B)  Chemical reduction and then chemical oxidation C)
 
Chemical reduction and then shape remodeling
D)  Shape remodeling and then chemical oxidation E)  Shape remodeling and then chemical reduction
48.  Which of the following statements about oligomeric proteins is  false?
A)  
A subunit may be similar to other proteins. B)  All subunits must be identical. C)  Many have regulatory roles.
D)  Some oligomeric proteins can further associate into large fibers. E)  Some subunits may have nonprotein prosthetic groups.
49. An average protein will not  be denatured by:
 
 
A)  a detergent such as sodium dodecyl sulfate. B)  heating to 90°C.
C)  iodoacetic acid. D)   pH 10. E)  urea.
50.  Experiments on denaturation and renaturation after the reduction and reoxidation of the  — S — S —  
 bonds in the enzyme ribonuclease (RNase) have shown that:
A)  folding of denatured RNase into the native, active conformation requires the input of energy in the form of heat.
B)  native ribonuclease does not have a unique secondary and tertiary structure.
C)  the completely unfolded enzyme, with all  — S — S —  bonds broken, is still enzymatically active. D)  the enzyme, dissolved in water, is thermodynamically stable relative to the mixture of amino
acids whose residues are contained in RNase. E)
 
the primary sequence of RNase is sufficient to determine its specific secondary and tertiary
structure.
Short Answer Questions
51.  Why is an asymmetric carbon atom called a chiral center?
52.  Differentiate between configuration and conformation.
53.  
 
 
54.  Give the general Henderson-Hasselbalch equation and sketch the plot it describes (pH against amount of NaOH added to a weak acid). On your curve label the p K a for the weak acid, and indicate the region in which the buffering capacity of the system is greatest.
 
 
56.  Draw the structure of a) Arginine, b) Glutamate, 3) Tyrosine and 4) +H3N-Arg-Glu-Tyr-COO- in zwiterionic form and their ionized forms at low pH, neutral pH and high pH
57.  For each of these methods of separating proteins, describe the principle of the method, and tell what  property of proteins allows their separation by this technique.
(a) ion-exchange chromatography
 
 
58. A biochemist is attempting to separate a DNA-binding protein (protein X) from other proteins in a solution. Only three other proteins (A, B, and C) are present. The proteins have the following
 properties:
 point)  M r   DNA?  ––––––––––––––––––––––––––––––––––––––––––  
 protein A 7.4 82,000 yes  protein B 3.8 21,500 yes  protein C 7.9 23,000 no
 protein X 7.8 22,000 yes  ––––––––––––––––––––––––––––––––––––––––––  
What type of protein separation techniques might she use to separate (a) protein X from protein A?
 
 
60.  In one or two sentences, describe the usefulness of each of the following reagents or reactions in the analysis of protein structure:
(a) Edman reagent (phenylisothiocyanate) (b) Sanger reagent (1-fluoro-2,4-dinitrobenzene, FDNB) (c)  trypsin
61.  A biochemist wishes to determine the sequence of a protein that contains 123 amino acid residues.
After breaking all of the disulfide bonds, the protein is treated with cyanogen bromide (CNBr), and it is determined that that this treatment breaks up the protein into seven conveniently sized peptides,
which are separated from each other. It is your turn to take over. Outline the steps you would take to determine, unambiguously, the sequence of amino acid residues in the original protein.
62.  
You are trying to determine the sequence of a protein that you know is pure. Give the most likely
explanation for each of the following experimental observations. You may use a simple diagram for your answer.
(a) The Sanger reagent (FDNB, fluorodinitrobenzene) identifies Ala and Leu as amino- terminal residues, in roughly equal amounts.
 
 
63. Describe two major differences between chemical synthesis of polypeptides and synthesis of  polypeptides in the living cell.
64.  
Explain how circular dichroism spectroscopy could be used to measure the denaturation of a
 protein.
65.  
Each of the following reagents or conditions will denature a protein. For each, describe in one or
two sentences what the reagent/condition does to destroy native protein structure.
(a) urea (b) high temperature
(c) detergent (d) low pH
 
 
66.  Problem: 
In one of the attached ppt there are two ESI-MS spectra of two proteins. Determine charge state of two adjacent peaks from each spectrum and use them to identify the mass of each protein.
 
 
Slide 1 shows the full MS/MS spectrum of the precursor, observed as m/z of [MH]2+ as 785.85. Peaks 1384.61 and 1441.63 have low intensity, but are shown because they are important for
determining the peptide sequence. Slides 2 and 3 show the enhanced MSMS spectrum already shown in slide 1. Slide 4 shows the precursor ion.
After you determined the sequence of the peptide, look at slide 5 and try to explain the pairs of peaks that appear at 942.58 and 924.55, 1056.60 and 1039.56, 1171.61 and 1154.68, and 1285.65 and
1268.69, just by looking at the sequence of the peptide and at the intrinsic properties of particular amino acids. Do the same for the pair of peaks from slide 6.
68.  
Problem: Describe a purification procedure for a mitochondrial (membrane or soluble) protein from
either plant or animal source.