C483 Summer 2015
Exam 1
Name ______________________________________________
Section 1: Reading guides (50 points)
1. 20 pts. Fill in the blanks (2 points each.)
A. The major structural difference between DNA and RNA is ________________________,
which makes RNA _______________(more/less) stable toward hydrolysis.
B. According to the central dogma, ___________________ is the process by which information
is conveyed from DNA to mRNA.
C. _________________ and ______________ are amino acids that are positively charge at
almost all physiological pHs.
D. -Helices form H-bonds between the __________ group of the n amino acid and the
_______________ group of the n+4 amino acid.
E. ___________________ agents can be used to cause a protein to unfold in vitro.
F. A protein composed of three identical subunits is called a __________________. A protein of
2 different subunits is called a ______________________________.
G. When a hemoglobin subunit is in its tense state, it binds oxygen __________ (tighter, less
tightly) than when it is in its ____________ state.
H. The Bohr effect is seen in active muscle tissue, where high CO2 concentration leads to a(n)
_____________________ (increase/decrease) of H+, which causes hemoglobin to more readily
_____________________ (bind/release) oxygen.
I. Using the rule of thumb from class, a transition state can be lowered by _________kJ/mol to
produce a 1000x increase in rate.
J. Three types of chemical catalysis are _______________, _________________, and metal ion
catalysis.
2. 10 pts. True or false (1 points each)
A. ____________ A process which is endothermic with a positive change in entropy is
sometimes spontaneous.
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B. _____________ GC rich DNA strands are harder to separate because GC base pairs form
more H-bonds.
C. _____________ Parallel -sheets are stabilized by formation of many H-bonds, while
antiparallel -sheets are stabilized by the hydrophobic effect.
D. _____________ Proline and glycine are two amino acids commonly found in irregular
secondary structures such as loops.
E. _____________ Charged amino acids most commonly exist in the core of protein tertiary
structure.
F. _____________ 2,3-bisphosphoglycerate (BPG) binds to hemoglobin, destabilizing the tense
state.
G. _____________ Actin and tubulin are both globular proteins that bind ATP to facilitate
polymerization to form microfilaments that serve both structural purposes and cellular
movement.
H. _____________ Kinesin is a highly processive motor protein that transforms chemical energy
into mechanical energy.
I. _____________ Induced fit of glucose in hexokinase prevents water from binding in the active
site to hydrolyze ATP.
J. _____________ The catalytic triad of chymotrypsin work together to deprotonate a water
molecule as the nucleophile used to hydrolyze a peptide (amide) bond.)
3. 20 pts. Short answer (5 points each)
A. A 50 mM solution of imidazole (conjugate acid pKa = 7.0) is adjusted to pH 6.0. What percentage of
the imidazole is in its conjugate acid form? Show all work.
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B. In the Sanger method of DNA sequencing, what is the role of a DNA polymerase? What is the
role of a ddNTP?
C. Draw the chemical structure of the DNA strand pdApdTpdC. Label the 5’ and 3’ ends. Label
the phosphodiester bond(s).
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D. Use the figure below to explain, in four short statement, how ATP chemical energy is
transformed by myosin into mechanical energy in muscle tissue.
Section 2: Problems (10 points each)
4. Use data from table 4.1 to estimate the pI of an Asp-Val dipeptide. Draw a titration curve for
this dipeptide.
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5. Draw the oligopeptide WACPR. What is its net charge at pH 7?
6. Propose a primary sequence of a 20 residue amphipathic peptide that has a high %N
composition.
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7. The amino acid tryptophan is converted into the hormone melatonin as shown below. In the
first column of the table, fill in one of the following enzyme names as appropriate:
methyltransferase, hydroxylase, acetyltransferase, decarboxylase. In the second column, indicate
the EC class name for each enzyme.
Enzyme
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2
3
4
Name
EC class
Many enzymes catalyze the formation of new bonds, but ligases are distinguished from other
enzymes in what way?
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8. An open reading frame (ORF) is a portion of the genome that potentially codes for a protein.
A given nucleotide sequence of mRNA potentially has three different reading frames, only one
of which is correct. A portion of the coding strand of the gene for type 2 human collagen is
shown below.
5’...AGGTCTTCAGGGAATGCCTGGCGAGAG...3’
A. Draw the mRNA that this gene codes, and label its 5’ and 3’ end.
B. Refer to the table to predict the primary sequence of this portion of the collagen molecule.
Choose the ORF that makes sense for collagen.
C. This mutation is likely to cause a serious defect in collagen. Why?
5’...AGGTCTTCAGGGAATGCCTGACGAGAG...3’
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Section 3: Case study (10pts) While most humans are able to hold their breath for only a minute
of two, crocodiles can stay submerged under water for an hour or longer. This adaptation allows
the crocodiles to kill their prey by drowning. In 1995, Nagai and colleagues suggested that
bicarbonate (HCO3-) binds to crocodile hemoglobin in a manner analogous to BPG binding in
humans.
A. Consider the hypothesis that bicarbonate serves as an allosteric modulator of oxygen binding
in hemoglobin. What is the source of bicarbonate in crocodiles, and how does its concentration
change during submersion?
B. Draw oxygen binding curves for crocodile hemoglobin in the presence and absence of
bicarbonate. Which conditions increase the p50 value for crocodile Hb? What does this mean for
the oxygen binding affinity of Hb under those conditions?
C. The investigators found that the bicarbonate binding site was located at the 12 subunit
interface. Why is a subunit interface a good location for an allosteric site?
D. The binding site for bicarbonate is thought to be between the Tyr residue (in its conjugate
base form) and a Lys residue (in its typical physiological ionization state.) Draw these sidechains
and a bicarbonate ion, and explain why bicarbonate binds well in this location.
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