Evening Core 2007
Exam 1; 10/31/07
Name (please print clearly)_________________________
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Notes to Students:
1.
Write your name on EACH PAGE. The pages will be separated for grading. If
your name is not on the page and we cannot identify your work you will not
receive points for that page. You don’t have to write your name on this page.
2.
Space for each question is provided on the FRONT of the exam pages. You
should not need to use the extra space on the back of the page. However, if you
make a mistake on the front, you may cross it out and write your answer on the
back.
3.
Answer completely, but CONCISELY and clearly. One or a few words may be
enough for some questions. Extraneous, unnecessary information will not gain
you points. If the extra information is wrong, then it may cause points to be taken
away. Diagrams, flow charts, and pictures are acceptable in addition to or in lieu
of text.
4.
The points on the exam add up to more than 100. The scores will be adjusted and
expressed as percent correct.
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Evening Core 2007
Exam 1; 10/31/07
Name (please print clearly)_________________________
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Part 1 (30 points):
1. Compare and contrast these molecules:
A
FAVILYW also depicted as PheAlaValIleLeuTyrTrp
C
B
E
D
Property:
Functional group,
building block, or
macromolecule?
Charged or
Uncharged
as shown?
Electrically
Polar or
Nonpolar?
Hydrophobic
or hydrophilic?
A
B
C
D
E
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Evening Core 2007
Exam 1; 10/31/07
Name (please print clearly)_________________________
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2. Indicate which of the circled atoms in these 4 pairs of molecules is oxidized (O) or
reduced (R) relative to the other (10 atoms total).
A
C
B
D
H
C
H
OH
C
H
OH
H
C
H
H
H
C
SH
H
3. The chemical properties of some, but not all, amino acids at the active site of an
enzyme are influenced by pH.
A. Which amino acids change with pH? Single or 3 letter code is OK.
B. Briefly explain the change.
C. How do these changes influence the activity of an enzyme? Restrict your answers to
this page.
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Evening Core 2007
Exam 1; 10/31/07
Name (please print clearly)_________________________
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Part 2 (10 points) :
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Evening Core 2007
Exam 1; 10/31/07
Name (please print clearly)_________________________
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Part 3 (30 points) :
1) (4 points)
After the removal of their amino nitrogen atoms (by transamination) the remaining carbon
atoms (which I call the “carbon skeleton”) of the amino acids glycine, serine, cysteine, alanine,
aspartate, and tryptophan can, subsequently, be found in the molecule, pyruvate. Now, in order
to undergo degradation and catabolism, this pyruvate must be converted into (the acetyl moiety
of) acetyl CoA.
a) What is the enzyme that catalyzes this formation of this acetyl CoA?
b) How is this enzyme regulated acutely?
2) (6 points)
The utilization of acetyl CoA for the production of chemical energy (ATP) takes place in two
phases, facilitated by two different metabolic pathways. One phase entails the oxidation of the
carbon atoms of the acetyl moiety. The other phase entails taking products from the oxidative
phase and using them in the second phase to generate ATP. What are the two metabolic
pathways involved here?
a) the metabolic pathway responsible for the oxidative phase is
b) the metabolic pathway responsible for the production of ATP-is
second
c) What is (or are) the product(s) generated by the first phase that are then utilized by the
phase?
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Evening Core 2007
Exam 1; 10/31/07
Name (please print clearly)_________________________
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3) (6 points)
Explain in your own words the concept that allows the mitochondrial electron transport
(MET) system to generate ATP. (Your explanation should include the words or the terms
oxidation/reduction cofactors, potential gradient, ΔG, and ATP synthase.)
4) (4 points)
a) What is transamination?
b) Identify the substrates of a transamination reaction.
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Evening Core 2007
Exam 1; 10/31/07
Name (please print clearly)_________________________
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5) (2 points)
What is the name of the enzyme that allows the amino nitrogen of any amino acid to become
the nitrogen of a molecule of ammonia?
6) (3 points)
Identify the (three) substrates involved in the rate-determining step of the urea cycle.
7) (5 points)
It is observed that the urea cycle takes place predominantly in the liver. Although most cells
contain DNA that encodes all of the proteins that are needed for growth, development,
maintenance, and even cell death, how is this tissue specificity achieved?
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Evening Core 2007
Exam 1; 10/31/07
Name (please print clearly)_________________________
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Part 4 (10 points):
(a) The left figure below is the structure of cytochrome B562. Estimate the number of
residues and calculate the length (in angstroms) of the helix marked by an arrow.
Cytochrome B562
variable domain of antibody light chain
(b) The figure on the right above is the structure of the variable domain of the light chain
of immunoglobulin. It consists of two β-sheets stacked together. The β-strand on the
back that is marked with two arrows has a disulfide bond to the strand above it (the one
before the last β-strand). Fill in amino acids that are likely to occupy the positions in the
sequence below for the strand marked with arrows in the figure, choosing from among
Alanine (Ala), Leucine (Leu), Lysine (Lys), Threonine (Thr), Serine (Ser), and Valine
(Val). The numbers are the residue positions in the polypeptide sequence. The position
of the cysteine residue is given. Hint: pay attention to the properties of β-sheets and
tertiary structures and the side chain properties of amino acids.
19
___
20
___
21
___
22
___
23
Cys
24
___
25
___
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Evening Core 2007
Exam 1; 10/31/07
Name (please print clearly)_________________________
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(c) List the force(s) that hold together (1) secondary and (2) tertiary structures of proteins.
Indicate whether each is covalent or non-covalent, and among main chain or side chain
groups.
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Evening Core 2007
Exam 1; 10/31/07
Name (please print clearly)_________________________
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Part 5 (10 points)
1.
Please answer the following questions that relate to the figure below, which
shows the posttranslational modifications on a sequence from a histone protein.
a.
Write out the name of the likely donor of the modifying group on residue 2.
(1 point)
b.
Write out the name of the likely donor of the modifying group on residue 10.
(1 point)
c.
What is the source of the oxygen atom in the box at residue 28, the protein or the
modifying group donor? (1 point)
d.
List the numbers of all unmodified residues that could be modified to carry the
same modification as residue 10. (2 points)
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Evening Core 2007
Exam 1; 10/31/07
Name (please print clearly)_________________________
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2.
Figure A below shows the structure of phospho-adenosine-phosphosulfate, the
cofactor for sulfotransferases. Figure B shows the reaction. Answer the following
questions using these figures.
a.
Draw a square around the atom that functions as the substrate electrophile in this
reaction. (1 point)
b.
Draw in the unshared pair of electrons on the substrate nucleophile in this
reaction. (1 point)
c.
The dark oval shape represents the transferase enzyme. Draw and name an amino
acid whose side chain could function as ‘B’. Show all the atoms and bonds and
any charges expected at physiological pH. (3 points)
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Evening Core 2007
Exam 1; 10/31/07
Name (please print clearly)_________________________
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Part 6 (10 points):
Exhaustion in graduate students is a troubling problem. In recent years, research in this
area has intensified, resulting in the discovery of the gene grd, which apparently causes
drowsiness. The gene grd codes for a 60-kDa protein, Grd. Grd is thought to cause rapid
lethargy by acting as a sponge, binding both the caffeine and aspartame supplied in diet
soft drinks.
a. The DNA sequence of the grd gene was cloned into a plasmid with a C-terminal tag,
known as MBP. The MBP tag binds to the simple carbohydrate maltose. Describe how
the recombinant Grd protein with a C-terminal MBP tag might be purified.
b. Grd protein was shown to comprise two domains, a 15-kDa N-terminal domain, and a
45-kDa C-terminal domain. Attempts to crystallize the full-length 60-kDa Grd protein
failed. Describe which technique or techniques could be used to solve the threedimensional structure of Grd domains.
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Evening Core 2007
Exam 1; 10/31/07
Name (please print clearly)_________________________
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Part 7 (10 points):
1. Define the terms “free energy change of a reaction”. Will the free energy change
for a spontaneous reaction increase, decrease or remain unchanged when the
reaction is catalyzed by an enzyme? Please give a brief and succinct reason for
your answer.
2. An enzyme can use two substrates S1 and S2. The Km values for S1 and S2 are
10-3 M and 10-4 M respectively. Which substrates would be catalyzed more
efficiently by the addition of this enzyme to a solution containing 10-4 M each of
substrates S1 and S2? Please explain your reasoning in brief with a graph if
required.
.
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Evening Core 2007
Exam 1; 10/31/07
Name (please print clearly)_________________________
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Part 8 (10 points):
The purification of a known neuronal intermediate filament protein, GFAP, has been
undertaken to identify its
post-translational
modification sites. A
partially purified tissue
fraction containing the GFAP
protein activity was subjected
to an additional purification
step using 2D gel
electrophoresis, shown on the
right, which was stained with
Coomassie blue.
A.
Please outline 2
different protein detection
and/or identification methods
to determine which of the
protein spots corresponds to
the known GFAP protein.
You need to provide a brief
outline (not just the name) of
the experimental procedures
for full credits.
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Evening Core 2007
Exam 1; 10/31/07
B.
Name (please print clearly)_________________________
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This GFAP protein was identified in over 50 2D gel spots by you using the
methods outlined in your answers to question (a), and was clustered into four
distinct groups (A, B, C and D) based on their relative sizes.
Which group is the most acidic form of GFAP?
Which group is the biggest in size?
C.
If the molecular weights (MW) of group A spots are equal to the theoretical
GFAP MW calculated from predicted protein sequence, what single posttranslational modification could lead to the production of group D? Provide a
brief rationale.
D.
If the 6 spots within group A are all identified as the GFAP protein, how can you
determine whether one or more of them is phosphorylated?
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