final.pdf

Name: ___________________________________________
Bi/Ch 110 Final Exam
The FIRST EXAM QUESTION is to write the name, the one letter code, the three letter
code, and the structure of the twenty amino acids. This portion of the test is CLOSED
BOOK.
Only the Stryer “Biochemistry” textbook, your lecture notes, this year’s (Fall 2012)
homework sets solutions, and materials on this year’s Bi110 course website (or that were
emailed to the class) can be used for the remaining open book section of the test. NO
INTERNET.
You may use calculators, graphing programs such as Excel, and the standard wordprocessing
software if you are going to type your answers. You may not use computers
for any other resources.
The time limit on the exam is 6 hours not counting the time writing the twenty amino
acids. You may take the exam in two sittings as long as you don’t go over 6 hours for
the whole exam. You are NOT allowed to study during your break.
Write your name on every page submitted and number each page as well. Do not put
answers to different questions on the same piece of paper or you will lose points.
You may e-mail the TAs for clarifications on the questions, but you may not ask about
the validity of your answers. Your e-mails must be sent at least 12 hours prior to the
deadline. Please address the emails to all of the TAs for the final exam.
If you cannot read a figure on your printed exam, please refer to the electronic version of
the exam.
The strict due date is 4:30pm Friday, Dec. 14 th at Margot Hoyt’s office, 148 Braun.
Late exams will not be accepted. Extensions will not be granted.

Name: ___________________________________________
Open the exam to begin the CLOSED BOOK portion.

Problem 1: Amino Acids (20 points)
(CLOSED BOOK, NOTES, AND COURSE WEBSITE)
Name: ___________________________________________
Draw the 20 amino acids by hand. Do not worry about stereochemistry.

Problem 2: Enzyme Kinetics
Name: ___________________________________________
Glyphosate is the herbicide also known as Roundup. It is a broad-spectrum herbicide that
inhibits the enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), which catalyzes
the reaction of shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP) to form 5enolpyruvyl-shikimate-3-phosphate
(ESP):
PEP + S3P ESP + phosphate
ESP is dephosphorylated to chorismate, a precursor for the aromatic amino acids
phenylalanine, tyrosine, and tryptophan, which plants must synthesize in order to survive
(animals get these amino acids from their diet).
a. (10 points) The following two plots show the effect of glyphosate on EPSPS activity
when measuring PEP. What type of inhibitor is glyphosate, based on this experiment?

Problem 2, page 2
Name: ___________________________________________
b. (10 points) The following plot shows the effect of glyphosate on EPSPS activity when
measuring S3P. What type of inhibitor is glyphosate, based on this experiment?
c. (10 points) Based on your above two answers, propose the mechanism or mechanisms
by which glyphosate inhibits EPSPS. Answer in no more than four sentences or by
drawing a simple picture with labels. You do not need to know the intricacies of the
molecular pathways; just describe how you think glyphosate, EPSPS, PEP, and S3P
interact with each other.

Problem 3: TCA Cycle
Name: ___________________________________________
Fluoroacetate is a popular and potent rat poison that is found in the leaves of certain
poisonous plants. Sodium fluoroacetate is metabolized into fluoroacetyl-CoA by the enzyme
acetate thiokinase and then is incorporated into fluorocitrate as shown.
A scientist studying the effect of sodium fluoroacetate on mammalian muscle cells found a
decrease in the rate of glycolysis and in the amount of citric acid cycle (TCA) intermediates.
However, citrate levels increased several fold.
a. (10 points) What step in the TCA cycle appears to be blocked? Why do citrate levels
increase dramatically, while the levels of the other TCA intermediates decrease?

Problem 3, page 2
Name: ___________________________________________
b. (10 points) Aconitase catalyzes a reaction with fluorocitrate that yields the following
molecule:
* Represents a 14 C label originating in the fluoroacetate, as shown above. (Hint: Recall the
prochirality of citrate in the TCA cycle).
Draw the aconitase-catalyzed reaction that would generate this product in the presence of
fluorocitrate.
c. (10 points) How does this product cause the effects on the TCA cycle described above
(molecular mechanism, stating the specific molecules involved)?

Problem 4: ATCase and Cooperativity
Name: ___________________________________________
Aspartate transcarbamoylase (ATCase) is an enzyme at the beginning of the pyrimidine
biosynthesis pathway, which catalyzes the formation of carbamoyl aspartate from
carbamoylphosphate and aspartate.
a. (5 points) Does the ATCase (control curve shown below) follow typical Michaelis-Menten
behavior? If not, what type of enzyme might this be?

Problem 4, page 2
Name: ___________________________________________
b. (5 points) Low millimolar concentrations of CTP and ATP affect the relative reaction rate
of ATCase. Which curve (either A or B) would you expect to see in the presence of
CTP? How about ATP? Explain briefly (3 sentence maximum).
c. (15 points) Maleate binds to the same site in ATCase as the substrate aspartate
preventing the concomitant binding of aspartate. The KI of maleate is significantly
smaller than the Km of aspartate. Upon heating and renaturation, the enzyme has
activity that is inhibited by maleate as shown in the figure below. However, the native
enzyme is activated at low concentrations of maleate and inhibited at high
concentrations of maleate. Explain this result.

Problem 4, page 3
Name: ___________________________________________
The data shown below were gathered at a constant aspartate concentration of 10-3 M
and constant carbamyl phosphate concentration of 3.6 x 10-3 M:
d. (10 points) Compare the effect of maleate on ATCase with the effect of carbon monoxide
on oxygen delivery by hemoglobin.
e. (5 points) Demonstrate why the Hill coefficient, n, can be equal to or less than, but never
more than, the number of substrate binding subunits in an allosteric cooperative protein.
E.g. for hemoglobin, n ≤ 4.

Problem 5: ATP Synthase
Name: ___________________________________________
In 1961 Peter Mitchell proposed that a proton gradient across the mitochondrial membrane is
used to create ATP. The inside of mitochondria has a pH 1.4 units higher than the outside, and
the voltage difference is 0.14 V with the outside being positive.
a. (15 points) Using this information and the equation on page 385 of your book, calculate
the free energy associated with pumping 1 mole of protons from the mitochondrial matrix
to the cytosol.
b. (10 points) Considering the free energy associated with synthesis of ATP from ADP and
phosphate is 30.5 kJ/mol, what would you expect to be the minimum number of protons
transferred across the membrane per ATP molecule produced?
c. (10 points) How many protons are actually required for each ATP molecule? What
percentage efficiency does this correspond to?

Problem 6: Mechanism (20 points)
Name: ___________________________________________
Propose a mechanism for the conversion of Δ 3 – friedelin (1) to Δ 13(18) – oleanene (2).

Problem 7: pH Optimum of an Enzyme (20 points)
Name: ___________________________________________
The active site of lysozyme contains two amino acid residues essential for catalysis: Glu 35 and
Asp 52 . The pKa values of the carboxyl side chains of these residues are 5.9 and 4.5,
respectively. What is the ionization state (protonated or deprotonated) of each residue at pH
5.2, the pH optimum of lysozyme? How can the ionization states of these residues explain the
pH-activity profile of lysozyme shown below?

Problem 8: Protein Folding and Structure
Name: ___________________________________________
a. (10 points) Explain why β-sheets are less likely to form than α-helices during the earliest
stages of protein folding.
b. (25 points) Indicate the probable effects of the following mutational changes on the
structure of a protein. Explain your reasoning.
i. Changing a Leu to a Phe
ii. Changing a Lys to a Gly
iii. Changing a Val to a Thr
iv. Changing a Gly to an Ala

Problem 8, page 2
v. Changing a Met to a Pro
Name: ___________________________________________
c. (10 points) Explain why Trp rings are usually completely immobile in proteins that have
rapidly flipping Phe and Tyr rings.
d. The unfolding of the α helix of a polypeptide to a randomly coiled is accompanied by a
large decrease in a property called specific rotation, a measure of a solution’s capacity
to rotate circularly polarized light. Polyglutamate, a polypeptide made up of only L-Glu
residues, has the α-helical conformation at pH 3. When the pH is raised to 7, there is a
large decrease in the specific rotation of the solution. Similarly polylysine (L-Lys
residues) is an α helix at pH 10, but when the pH is lowered to 7 the specific rotation
also decreases, as shown by the following graph:

Problem 8, page 3
Name: ___________________________________________
i. (10 points) What is the explanation for the effect of the pH changes on the
conformations of poy(Glu) and poly(Lys)?
ii. (10 points) Why does the transition occur over such a narrow range of pH?

Problem 9: Alcohol Dehydrogenase
Name: ___________________________________________
a. (10 points) Write down the reaction catalyzed by alcohol dehydrogenase when ethanol is
the substrate. Be sure to label where the hydrogen in NADH goes.
b. (10 points) What’s the function of Zn 2+ in alcohol dehydrogenase?
c. It is found that if monodeuterated alcohol (CH3CDHOH) is used as the substrate, there
can be two different outcomes of this reaction. In one outcome, NADD and CH3CHO are
generated and in the other outcome, NADH and CH3CDO are generated. If these two
outcomes don’t appear randomly,
i. (5 points) What can be the causes of the difference between these two
outcomes?

Problem 9, page 2
Name: ___________________________________________
ii. (5 points) In what condition can only one outcome happen (using the same
enzyme)?
d. (15 points) The consumption of ethanol, especially after periods of strenuous activity or
after not eating for several hours, results in a deficiency of glucose in the blood, a
condition known as hypoglycemia. The first step in the metabolism of ethanol by the
liver is oxidation to acetaldehyde, catalyzed by liver alcohol dehydrogenase:
CH3CH2OH + NAD + CH3CHO + NADH + H +
Explain how this reaction inhibits the transformation of lactate to pyruvate. Why does
this lead to hypoglycemia?

Problem 10: GroEL/ES (25 points)
Name: ___________________________________________
The GroEL/ES cycle diagrammed below only circulates in the clockwise direction. Explain the
basis for this irreversibility in terms of the sequence of structural and binding changes in the
GroEL/ES system. Write on the back of the page or a different page if you need more room.

Problem 11: The Pasteur Effect
Name: ___________________________________________
When oxygen is added to an anaerobic suspension of cells consuming glucose at a high rate,
the rate of glucose consumption declines greatly as the oxygen is used up, and accumulation of
lactate ceases. This effect, first observed by Louis Pasteur in the 1860s, is characteristic of
most cells capable of both aerobic and anaerobic glucose catabolism.
a. (10 points) Why does the accumulation of lactate cease after oxygen is added?
b. (10 points) Why does the presence of oxygen decrease the rate of glucose
consumption?
c. (10 points) How does the onset of oxygen consumption slow down the rate of
glucose consumption? Explain in terms of specific enzymes.