C483 Fall 2015
Exam 1
Name ______________________________________________
This exam contains 110 points. The highest score you may earn on this exam is 100 points.
Section 1: Reading guides (50 points)
1. 20 pts. Fill in the blanks (2 points each.)
A. A process with a ___________________(negative/positive) enthalpy and a
_______________________(negative/positive entropy) will always be a spontaneous process.
B. An aqueous solution with hydroxide concentration of 1 x 10 -3 has a pH of ________.
C. The exclusion of nonpolar molecules from aqueous solution is known as the
________________________________.
D. At pH 5, the major species of phosphate ion has a charge of _____________.
E. A _________________________ is a DNA cutting enzyme that recognizes particular sequences, often palindromes.
F. The amino acids __________________ and ________________ are not likely to be found in a

-helix because they disrupt the regular conformation of this secondary structure.
G. Proteins may be made up of one or more ___________________, which are tertiary structural units with their own stable fold.
H. An allosteric protein in its __________________ state is ____________ likely to bind a small molecule than when it is in its relaxed state.
I. At room temperature, a transition state must be lowered approximately _______ kJ in order to increase the rate by 1000 fold.
J. Hemoglobin’s oxygen binding affinity can be altered by binding to _____________________.
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2. 10 pts. True or false (1 points each)
A. ____________ The melting point of DNA is the temperature at which the double helix is fully denatured.
B. ____________ The chemical nature of the peptide bond makes the carbonyl-C  bond rigid.
C. ____________ The largest force governing protein structure is the hydrophobic effect.
D. ____________ The interior of a protein is more likely to have regular secondary structure, and the exterior is more likely to have irregular structure.
E. ____________ SDS-PAGE (sodium dodecylsulfate polyacrylamide gel electrophoresis) separates proteins based on net charge.
F. ____________ Myoglobin has a lower P
50
(oxygen pressure at half saturation) than hemoglobin.
G. ____________ Nucleotide triphosphate binding and hydrolysis are essential in microtubule polymerization and depolymerization, but not in fibrous proteins such as collagen and keratin.
H. ____________ Charged amino acids are most likely to be found in the protein core.
I. _____________ In the active sight, a serine residue is more likely to participate in covalent catalysis than a isoleucine residue.
J. _____________ If the lock and key model of enzyme binding were correct, then the specificity of an enzyme catalyzed reaction would be lower than predicted.
3. 20 pts. Short answer (5 points each)
A. Draw the nucleobases of the AT base pair and indicate the hydrogen bonds.
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B. Ammonium has a pKa of 9.25. Draw the titration curve of ammonium with pH as a function of % acid dissociation. Label the midpoint of the curve.
C. Draw a structure for the peptide bond in the cis conformation that explains why it has limited rotation.
D. Below is the template strand for a (very) small gene. Draw the coding strand sequence and the mRNA produced. What tripeptide is coded?
3’-TCCGTAACC-5’
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Section 2: Problems (10 points each)
4. The catalytic triad of chymotrypsin involves an aspartate residue hydrogen bonded to a histidine residue, hydrogen bonded to a serine residue in the active site.
A. Draw these residues hydrogen bonded to each other in their most prevalent ionization state at pH 7. Indicate formal charges on each atom as appropriate.
B. In the course of the reaction, serine must be made into a strong nucleophile so that it can participate in covalent catalysis. What are the functions of the aspartate and histidine residues?
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5. Metabolic acidosis is a general term that describes a number of metabolic disorders in the body that result in a lowering of the blood pH from 7.4 to 7.35 or below. The kidney plays a vital role in regulating blood pH. The kidney can either excrete or reabsorb various ions such as
H
2
PO
4
-
, NH
4
+
, and HCO
3
-
. Which ions will be excreted and which will be reabsorbed in metabolic acidosis? Explain using relevant chemical equations.
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6. A 24-residue peptide called Pandinin 2 was isolated from scorpion venom and was found to have both antimicrobial and hemolytic properties. The sequence of the first 18 residues of this peptide is shown below:
FWGALAKGALKLIPSLFS
A. Use the helical wheel to plot the sequence of this peptide.
B. Draw the full structure of following portion of this peptide at pH 7.
…WGALAK…
C. Propose a hypothesis that explains why the peptide has the ability to lyse bacteria and red blood cells.
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7. Below is a schematic of the urea cycle. In the table below, match the following enzyme names with the appropriate reaction of the urea cycle: Arginase, argininosuccinate lyase, argininosuccinate synthetase, ornithine transcarbamolylase. In the second column, provide the enzyme class to which each of the enzymes belong.
Reaction Enzyme Name
1
2
Enzyme class
3
4
In the space below, list the other two enzyme classes not represented in the figure above:
______________________________ and _________________________________
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8. An experiment requires 1 L of a 0.1M ACES buffer at pH 7.4.
A. What is the effective buffering range for ACES? _______________
B. What is the concentration of ACES in its conjugate base form in this buffer?
C. If 1.00 mL of a 10.0 M HCl solution were added to this buffer, what would the pH of the solution be?
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Section 3: Case study (10pts) From Box 5-B in Pratt and Cornely
The affinity of hemoglobin for carbon monoxide is about 250 times higher than its affinity for oxygen. However, the concentration of CO in the atmosphere is only about 0.1 ppm compared to
O
2
concentrations of 200,000 ppm. Normally, only about 1% of hemoglocin molecules in an individual are in the carboxyhemoglobin (Hb .
CO) form, probably due to CO naturally produced in the body.
Danger arises when environmental CO levels rise. Smokers can reach up to 15% carboxyhemoglobin, although CO poisoning symptoms are generally not present. Levels of 25% carboxyhemoglobin can cause dizziness and confusion, and levels above 50% can trigger coma and death.
There are two problems caused by CO binding in hemoglobin. The first is more obvious; when
CO is bound to a hemoglobin subunit, the lower affinity O
2
is not able to displace it and be carried to the tissue. But the second problem is equally severe—when even one subunit of hemoglobin is in the carboxyhemoglobin form, it causes the tetramer to shift equilibrium to a form with high affinity for oxygen.
A. Draw the oxygen-binding curves of hemoglobin and carboxyhemoglobin on the same graph, given that the pressure of oxygen at which hemoglobin is half-satureated ( p 50) is 26 torr.
B. Refer to the graph above to explain why binding of CO in one subunit of hemoglobin has detrimental physiological effects even though the other three subunits can bind oxygen.
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Data Tables
Amino acid pKa values
C-terminal
N-terminal
3.1
8.0
Aspartate, glutamate 4.1
Histidine 6.1
Cysteine
Tyrosine
Lysine
Arginine
8.3
10.9
10.8
12.5
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