B1_MidtermExam1_2023_QUESTIONS_CompleteKey_updated101323
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BIOCHEMISTRY I (CHEM-UA 881)
Fall 2023
MIDTERM EXAM 1, Oct. 6, 2023
One point extra credit for completing the 3 lines below properly
NAME
:
___________________________
N-NUMBER
:
__________________________
TA & RECITATION TIME
:
__________________________
PLEASE WRITE LEGIBLY & BE CONCISE. Your answers must be your own! No
calculators, no use of electronic devices, no communication between students. Partial
credit will be given.
(There are a total of
9
pages in the exam, including this page)
USEFUL INFORMATION:
Group
Typical pKa
Terminal
a
-carboxyl group
3
Aspartic acid/Glutamic acid
4
Histidine
6
Terminal
a
-amino group
8
Cysteine
8
Tyrosine
10
Lysine
11
Arginine
12
USEFUL EQUATION:
pH = pKa + log([A
-
]/[HA])
QUESTION
PTS
YOUR SCORE
1
30
2
25
3
10
4
10
5
15
6
10
TOTAL
100
Page 2 of 10
1.
Multiple Choice. Circle the correct answer for each. (
3 points each; 30 total
)
i.
Which of the following statements is TRUE about Anfinsen’s famous folding
experiments on RNAse A?
a. Anfinsen concluded that the primary sequence of a protein alone is sufficient to
determine structure.
b. Formation of protein disulfide bonds alone was enough to restore the activity of
RNAse A.
c.
Addition of urea returned RNAse A to its native folded and active state.
d. Disulfide bonds in RNAse A could be formed with the addition of beta-
mercaptoethanol.
ii.
Cystic Fibrosis can be considered a protein folding disease associated with an amino
acid mutation. What best describes the effect of the altered protein folding?
a. Gain of function
b. Loss of function
c. Cooperative function
d. None of the above
iii.
What is the characteristic sequence of the alpha-helical keratin protein?
(Hyp= hydroxyproline)
a. Repeating (Gly-Pro-Pro)
b. Repeating (Gly-Hyp-Pro)
c. Repeating (Gly-Pro-Hyp)
d. Repeating (Gly-Gly-Hyp)
e. None of the above
iv.
Disulfide bonds represent important ____________ that influence protein tertiary
structure stability.
a. non-covalent interactions
b. van der Waals interactions
c. hydrogen bonds
d. salt bridges
e. covalent bonds
v.
On average, what percentage of lysine residues in a peptide are present in the
charged form at pH = 8?
a. 99% (actually 99.9%)
b. 90%
c. 50%
d. 10%
e. 1%
Page 3 of 10
vi.
Which of the following non-covalent interactions is driven primarily by changes in
entropy (
D
S)?
a. Hydrogen bonding
b. Hydrophobic effect
c. Cation-pi interactions
d. van der Waals interactions
e. Electrostatic interactions
vii.
In a protein structure, which amino acid is the most likely to exhibit variation in the
omega dihedral angle?
a. Tryptophan
b. Cysteine
c. Glycine
d. Proline
e. Arginine
viii.
Which of the following amino acid residues would most likely be found in the interior
of a water-soluble, globular protein?
a. Glu
b. Asp
c. Lys
d. Arg
e. Ile
ix.
Which of the following proteins does
not
represent a fibrous protein?
a. Silk fibroin
b. Keratin
c.
Myoglobin
d. Collagen
e. None of the above
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Page 4 of 10
x.
In recitation, we discussed dihedral angle determination using the following amino acid
depiction:
Which of the following is true about the dihedral angle represented by atoms 1-4?
(1 = N, 2 = C, 3= C, 4= N)
a. The angle is
f
(“phi”), and it equals 0
°
b. The angle is
f
(“phi”), and it equals 180
°
c. The angle is
y
(“psi”), and it equals 0
°
d. The angle is
y
(“psi”), and it equals 180
°
e. The angle is
w
(“omega”), and it equals 180
°
2
1
3
4
N
N
C
C
O
Page 5 of 10
Part II: Short answer
. Please provide a brief response to each question (5 pts each).
2A.
List three of the techniques that we discussed in lecture that are used to determine
the three-dimensional structure of a protein at atomic resolution.
X-ray crystallography
NMR spectroscopy
Cryoelectron microscopy
2B.
A titration curve for the individual amino acid Alanine is shown below.
Draw the structure of Alanine at point A, showing stereochemistry and the proper charge
state. (Note this is for the free amino acid, not as part of a peptide.)
H
3
N
O
-
O
Page 6 of 10
2C.
In the space below, draw a cartoon representation of two parallel
b
-strands.
Do you think the strands be joined by a
b
-turn secondary structure? Explain briefly.
The N-termini are at the bottom of the arrow.
The C-termini are at the head of the arrow.
(this is implied by the depiction of the strands)
No, the N-terminus and C-terminus of beta-strands in a parallel beta-sheet are not in
proximity, so they cannot be joined by a short beta-turn. Beta-turns are typically 3 or 4
residues in length, not sufficient to make this kind of connection.
2D.
Both the Alzheimer’s beta-peptide and prion proteins can form amyloid deposits that
are characteristic of many neurodegenerative disorders. For both these proteins, a
conversion from a soluble form to an amyloid form is associated with a conformational
rearrangement. Describe the general feature of this conformational rearrangement. Why
does this allow formation of amyloid?
Both proteins undergo a rearrangement from alpha-helix to beta-strand (sheet) structure
as an early step in amyloid formation. This is because amyloid is formed by propagating
inter-molecular beta-sheet structures, which require the presence of beta-strands.
Hence, the important of the conformational rearrangement from alpha-helix to beta-
strand.
The phrase “conformational rearrangement” generally refers to a significant structural
alteration within the protein backbone. Typically, this occurs through an intramolecular
change in secondary structural features.
Many students correctly noted that in the formation of amyloid, individual beta-strands
or small beta-sheets can form intermolecular associations to create larger beta-sheets,
solenoids, fibrils, etc. Although this may not usually be described as a conformational
rearrangement, it is an alteration in (quaternary) structure features. These answers
received large partial credit.
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Page 7 of 10
2E.
Describe very briefly the function of the Hsp70 and GroEL/GroES protein systems.
Which of these molecular chaperones/chaperonins rely on ATP hydrolysis for their
function?
Both protein systems help fold nascent proteins or refold improperly folded proteins.
Both rely on ATP hydrolysis.
Part III. Free response/Data Analysis.
Please respond to each question in the space
provided.
3.
You are studying a peptide with the following amino acid sequence (10 pts):
PRIME
a) In the space below, draw the chemical structure of your peptide at
pH = 9.0
,
including correct charges on side chains and the groups at the termini. Show
stereochemistry along the backbone.
6 points
b) What is the net charge on the peptide at
pH = 9.0
?
4 points
-1
4
.
You are purifying a protein that forms a homodimer quaternary structure stabilized by
a disulfide cystine crosslink. You are using size exclusion chromatography, and you
observe that the protein elutes (flows out of the bottom of the column) about 1 hour after
loading on the top of the column. You then repeat the purification in the presence of beta-
mercaptoethanol. Do you expect the protein to elute faster, or more slowly, or at the same
rate? Justify your answer using a description of the matrix (beads) that are used to
perform size exclusion chromatography. (10 pts)
The protein should elute more slowly. This is because the beta-mercaptoethanol has
destroyed the cystine crosslink of the dimers, creating protein monomers. This protein
will be smaller in size than the protein dimer. The smaller protein will be able to
penetrate the porous core of the size exclusion chromatography beads, which will cause
the proteins to take a longer time to pass through the column.
N
H
H
N
N
H
H
N
N
H
O
-
O
O
O
O
O
HN
H
2
N
NH
2
+
S
O
-
O
Page 8 of 10
5.
Assume that the following amino acid sequence forms an
a
-helix (15 pts):
AFHAYSEMASALD
a) Draw a helical wheel representation of the structure.
6 points
b) Is the structure amphiphilic? Explain your response very briefly.
3 points
Yes. Note that residues 3,6,7,10, and 13 form a polar face. While residues
1,2,4,5,8,9,11 and 12 form a hydrophobic face.
c)
Which two amino acids will form a favorable non-covalent interaction at pH = 5?
3 points
Histidine 3 and Glutamate 7. They are in proximity to form a salt bridge. Note
that the Aspartate is too far away to make a similar contact.
d) Estimate the distance (in Å) between the side chains from part C within the
a
-helix.
3 points
5.4 A. His 3 and Glu 7 are one helical turn away from each other. The
alpha helix is 5.4 Angstroms per turn.
Page 9 of 10
6.
Examine the structure of the two proteins labeled
(a)
and
(b)
below and the
Ramachandran plots for these proteins (10 pts).
a) Which one of the four common types of protein folds is seen in protein (a)? Which
one is seen in (b)?
3 points
a: alpha/beta (mixed alpha + beta is acceptable for full credit)
b: all alpha
b) Ramachandran plots show variations in the phi and psi dihedral angles but do not
bother to show the omega (amide) dihedral angle. Why?
4 points
Peptide bonds have a double bond character, and are typically trans in natural proteins,
such that omega is 180
°
(although some amino acids can form cis peptide bonds in
proteins, but this is less common). Because there is little variation, there is no reason to
include this angle in the plots.
c) Which of the two Ramachandran plots, labeled
c
and
d
above, is more likely to be
derived from protein
a
? Which plot is derived from protein
b
? Briefly explain your
answer.
3 points
The protein in
(a)
has primarily
b
-structure (represented by flat arrows) with a small
amount of
a
-helical structure (represented by coils). The protein in
(b)
has only
a
-helical
structure. In lecture,
we discussed that
b
-structures fall in the upper-left quadrant of the
Ramachandran plot. Plot
(c)
has many points in the upper-left quadrant, whereas part
(
d
) has few; so the plot that corresponds to
(a)
would be
(c)
. Right-handed
a
-helices
have dihedral angle values that put it into the lower-left quadrant of the Ramachandran
plot, so protein
(b)
must correspond to graph
(d)
.
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Page 10 of 10
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