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Home assignment 1
Student Name:
Fall 2014
cell membrane.
nucleolus.
nuclear tire.
nucleoplasm.
nucleosome.
nuclear envelope.
3. The bacterium E. coli requires simple organic molecules for growth and energyit is therefore a:
A)
B)
C)
D)
chemoautotroph.
lithotroph.
lithograph.
chemoheterotroph.
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 12C 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)
B)
C)
D)
E)
hydrogen bonds
hydrophobic interactions
ionic interactions
van der Waals interactions
carbon-carbon bonds
7. Stereoisomers that are nonsuperimposable mirror images of each other are known as:
A)
B)
C)
D)
E)
anomers.
cis-trans isomers.
diastereoisomers.
geometric isomers.
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)
C)
D)
E)
biological activity.
stereospecificity.
chiral activity.
racemization.
stereoisomerization.
9. If someone wishes you on your birthday Happy highest entropy to you, this usually means that
he/she wishes you to:
A)
B)
C)
D)
E)
F)
10. If the free energy change G for a reaction is -46.11 kJ/mol, the reaction is:
A)
B)
C)
D)
E)
at equilibrium.
endergonic.
endothermic.
exergonic.
exothermic.
UPS
adenosine monophosphate.
adenosine triphosphate.
FedEx
cytosine tetraphosphate.
uridine diphosphate.
12. The atmosphere of early earth probably contained the following molecules:
A)
B)
C)
D)
E)
15. Phosphoric acid is tribasic, with pKas of 2.14, 6.86, and 12.4. The ionic form that predominates at
pH 3.2 is:
A)
B)
C)
D)
E)
H3PO4.
HPO42.
PO43.
H2PO4.
None of the above.
allows the graphic determination of the molecular weight of a weak acid from its pH alone.
does not explain the behavior of di- or tri-basic weak acids
employs the same value for pKa for all weak acids.
relates the pH of a solution to the pKa and the concentrations of acid and conjugate base.
is equally useful with solutions of acetic acid and of hydrochloric acid.
18. Consider an acetate buffer, initially at the same pH as its pKa (4.76). When sodium hydroxide
(NaOH) is mixed with this buffer, the:
A)
B)
C)
D)
E)
pH remains constant.
pH rises more than if an equal amount of NaOH is added to an acetate buffer initially at pH 6.76.
pH rises more than if an equal amount of NaOH is added to unbuffered water at pH 4.76.
sodium acetate formed precipitates because it is less soluble than acetic acid.
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)
B)
C)
D)
E)
20. Of the 20 standard amino acids, only ___________ is not optically active. The reason is that its
side chain ___________.
A)
B)
C)
D)
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)
B)
C)
D)
E)
25. At pH 7.0, converting a proline to hydroxyproline will have what effect on the overall charge of the
protein containing it?
A)
B)
C)
D)
E)
26. At pH 7.0, converting a glutamic acid to -carboxyglutamate will have what effect on the overall
charge of the protein containing it?
A)
B)
C)
D)
E)
27. Which of the following tripeptides would be expected to be the most hydrophobic:
A)
B)
C)
D)
E)
KYG
KYA
GYA
DYA
DYG
28. At pH 7, arginine (pKs are alpha-carboxylate 1.82, alpha-amino 8.99, guanidino 12.48) would be
charged as follows:
A)
B)
C)
D)
E)
29. At pH 7, aspartic acid (pKs are alpha-carboxylate 1.99, alpha-amino 9.9, beta-carboxylate 3.9 )
would be charged as follows:
A)
B)
C)
D)
E)
30. At pH 11, glutamic acid (pKs are alpha-carboxylate 2.1, alpha-amino 9.47, gamma-carboxylate
4.07. would be charged as follows:
A)
B)
C)
D)
E)
31. At pH 4, histidine (pKs are alpha-carboxylate 1.8, alpha-amino 9.33, 6.04 imidazole) would be
charged as follows:
A)
B)
C)
D)
33. At pH 1, lysine (pKs are alpha-carboxylate 2.16, alpha-amino 9.06, epsilon-amino 10.54 ) would be
charged as follows:
A)
B)
C)
D)
E)
35. The formation of a peptide bond between two amino acids is an example of a(n) ______________
reaction.
A)
B)
C)
D)
E)
cleavage
condensation
group transfer
isomerization
oxidation reduction
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.
B) The number 110 reflects the higher proportion of small amino acids in proteins, as well as the
39. In a mixture of the five proteins listed below, which should elute second in size-exclusion (gelfiltration) chromatography?
E)
A)
B)
C)
D)
serum albumin
cytochrome c
immunoglobulin G
ribonuclease A
RNA polymerase
Mr = 68,500
Mr = 13,000
Mr = 145,000
Mr = 13,700
Mr = 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)
(b) Edman reagent (phenylisothiocyanate)
(c) FDNB
(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 (SS) 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)
B)
C)
D)
E)
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:
A) proteins with similar isoelectric points become further separated according to their molecular
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) removing cystines from protein sequences by proteolytic cleavage.
E) sequencing proteins that do not contain cysteinyl residues.
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
of the native peptide with trypsin gave a pentapeptide, a tripeptide, and free Lys. 2,4Dinitrophenyl-histidine was recovered from the pentapeptide, and 2,4-dinitrophenylphenylalanine
was recovered from the tripeptide. Digestion with the enzyme pepsin produced a dipeptide, a
tripeptide, and a tetrapeptide. The tetrapeptide was composed of (Lys) 2, Phe, and Gly. The native
sequence was determined to be:
A)
B)
C)
D)
E)
GlyPheLysLysGlyLeuMetPheHis.
HisLeuGlyLysLysPhePheGlyMet.
HisLeuPheGlyLysLysPheMetGly.
HisPheLeuGlyLysLysPheMetGly.
MetLeuPheLysPheGlyGlyLysHis.
46. In the diagram below, the plane drawn behind the peptide bond indicates the:
A)
B)
C)
D)
E)
absence of rotation around the CN bond because of its partial double-bond character.
plane of rotation around the CN bond.
region of steric hindrance determined by the large C=O group.
region of the peptide bond that contributes to a Ramachandran plot.
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 chainsas in hair wavingwhat subsequent steps are required?
A)
B)
C)
D)
E)
A)
B)
C)
D)
E)
50. Experiments on denaturation and renaturation after the reduction and reoxidation of the SS
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 SS 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.
53. (a)Briefly define isotonic, hypotonic, and hypertonic solutions. (b) Describe what happens
when a cell is placed in each of these types of solutions.
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 pKa for the weak acid, and
indicate the region in which the buffering capacity of the system is greatest.
55. Leucine has two dissociable protons, one with a pKa of 2.3, the other with a pKa of 9.7. Sketch a
properly labeled titration curve for leucine titrated with NaOH; indicate where the pH = pK and the
region(s) in which buffering occurs.
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
(b) size-exclusion (gel filtration) chromatography
(c) affinity 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:
pI
(isoelectric
Size
Bind to
point)
Mr
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
59. How can isoelectric focusing be used in conjunction with SDS gel electrophoresis?
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 aminoterminal residues, in roughly equal amounts.
(b) Your protein has an apparent Mr of 80,000, as determined by SDS-polyacrylamide gel
electrophoresis. After treatment of the protein with performic acid, the same technique
reveals two proteins of Mr 35,000 and 45,000.
(c) Size-exclusion chromatography (gel filtration) experiments indicate the native protein has
an apparent Mr of 160,000.
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)
(b)
(c)
(d)
urea
high temperature
detergent
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.
67. Problem: The attached ppt represents the MS/MS spectrum of a synthetic peptide. Determine the
sequence of this peptide using de novo sequencing, described in the attached pdf material. The
theoretical m/z of the precursor is [MH]+ = 1570.67 (monoisotopic) and [MH]2= 785.84.
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.