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BIOCHEMISTRY (CHEM 360)
EXAM 3
November 27, 2013
There are six pages, TEN questions, and a total of 116 points in this exam.
Please read each question carefully and possibly more than once. Good luck…
(18)
1.
The standard reduction potentials (Eo’ ) for the following half reactions are given.
FAD + 2H+ + 2efumarate + 2H+ + 2e-
FADH2
E0' = -0.219V
succinate
E0' = 0.031V
1.1.
Write the spontaneous overall reaction which would take place, if you mixed succinate,
fumarate, FAD and FADH2 together, all at 1.0 M concentration and in the presence of
an appropriate enzyme.
1.2.
Calculate E and G0’ for the overall reaction (in the direction you predicted). Show
your work.
(The Faraday constant, F, is 96.5 kJ/V.mol)
1.3.
Does the spontaneous reaction you have written above contradict the step involving
succinate and fumarate in the Citric acid cycle? Explain.
Yes, the step in the citric acid cycle: succinate
1.4.
fumarate
Explain what component(s) is/are different in the actual citric acid cycle step involving
succinate and fumarate, and why that makes a difference.
In the citric acid cycle the succinate is oxidized by a coenzyme, whose reduction
potential needs to be a “higher positive number” than 0.031 V
(10)
2.


The only reaction where a C-C bond is formed in the citric acid cycle is given below:
In a mutant organism the cycle is fueled by acetoacetyl CoA instead of acetyl CoA. Assuming that
the mutant organism possesses the necessary enzyme to catalyze the reaction, identify the structure
of the metabolite formed instead of citrate.
Outline brief details of the C-C bond formation mechanism.
2.1.
The metabolite formed instead of citrate undergoes decarboxylation right away. Give the
structure of the decarboxylation product.
(9)
3.
The following reaction in the presence of malate dehydrogenase yields a deuterated NADH.
Identify the origin (and the precise location) of the deuterium atom and the structures of the
missing reagent and the product.
3
Submitted by Jinn (“help!”)
(7)
4.
Merritt’s dog Jinn has been starved for more than 12 hours, after which an increased level of
alanine uptake is detected. Suggest a process and explain how and why alanine is metabolized.
Identify the C-4 intermediate formed during the process.
After 12 hours of starving the body needs to generate glucose by gluconeogenesis. However, since
there is not much pyruvate available, alanine undergoes transamination to form pyruvate.
The C-4 intermediate formed is oxaloacetate, which is the carboxylation product of pyruvate in
gluconeogenesis.
Page 2
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5.
Assuming that 13C labeled glucose at C-6 is fed to various living organisms, identify where (on
which carbon) the labeled carbon would end up.
Show your work (no points for blind-guessing).
5.1.
in pyruvate at the end of glycolysis?
5.2.
in -ketogluterate in the first turn of the citric acid cycle?
5.3.
at the end of the glyoxylate pathway?
(9)
6.
A representation of the thioester intermediate formed (following oxidation) in the active site of
glyceraldehyde-3-phosphate dehydrogenase is shown below.
6.1.
Give the next step of the reaction by showing the additional species and the structure of
the product formed. Use curly arrows to outline the mechanism.
(use the space above)
6.2.
Why do you think the cysteine side chain is involved here instead of the serine side chain
(as in protease enzymes) to form an acyl intermediate?
The cysteine side chain forms a thio-ester, instead of a normal ester with serine.
Thio-esters are more reactive and thus more susceptible to nucleophilic attack especially
since the hydrogen phosphate is a weak nucleophile.
Page 3
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7.
Circle the best correct answer for the multiple choice questions given below:
7.1.
Glucose can enter red blood cells through passive transport either through a carrier
protein or through channels and pores. How would the kinetics of two transport types
differ on a graph where rate of glucose transport is plotted v.s. extracellular glucose
concentration?
(a)
(b)
(c)
(d)
in transport through a carrier protein there would be a limit on the rate of
transport which would indicate protein saturation.
there would not be any difference in the kinetics of either type of transport.
transport rate through channels and pores would increase linearly v.s glucose
concentration.
transport rate through a carrier protein would be slower in the beginning, but
would get faster as the glucose concentration increases, maximizing at diffusion
rate.
(1) b only
(2) d only
(3) a, c, and d
(4) a and c
7.2.
Compounds with higher (more positive) standard reduction potentials are generally:
(1) reductants. (2) oxidants.
(3) both reductants and oxidants.
(4) it depends whether it is a one-electron or two-electron transfer.
7.3.
Hamsters love to run on exercise wheels. Prolonged running at high speed requires ATP.
Could a hamster with a defective gene for the enzyme lactate dehydrogenase meet the
extra ATP demand for prolonged fast wheel running by maintaining a high rate of
glycolysis? Why or why not?
(1) No, not enough NAD+ can be generated for glycolysis to continue at a high rate.
(2) No, the defective gene will cause a rapid decline in pH in the muscles used for
running.
(3) Yes, the defective gene and the reduced enzyme concentration will have no effect on
the glycolytic pathway.
(4) Yes, the enzyme alcohol dehydrogenase will supply the needed NAD +.
7.4.
Which of the following does not involve ATP or ADP
(1) phosphorylation of glucose
(2) phosphorylation of fructose-6-phosphate
(3) phosphorylation of glycerate-3-phosphate
(4) dephosphorylation of phosphoenol pyruvate
7.5.
The centers labeled (a) and (b) in the structure below are:
(a)
OH
CO 2H
HO 2C
(b)
(1) a-prochiral, b-prochiral
(3) a-prochiral, b-chiral
(2) a-chiral, b-chiral
(4) a-chiral, b-prochiral
Page 4
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8.
Complete the following reaction by showing the full structure of the missing product.
8.1.
Glycogen phosphorylase is an enzyme which can be covalently modified. Assuming that
another enzyme, protein phosphatase, converts glycogen phosphorylase into its inactive
form, illustrate the active form of glycogen phosphorylase.
8.2.
Glycogen synthase can also be covalently modified by protein phosphatase. Illustrate the
active form of glycogen synthase.
8.3.
Insulin is known to activate protein phosphatase. What is the effect of insulin on
glycogen phosphorylase?
Deactivates glycogen phosphorylase
8.4.
What is the overall effect of insulin on glycogen?
Slows down the formation of glucose from glycogen
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9.
Although “Aldolase” type enzymes are commonly known to catalyze C-C bond cleavage in the
glycolysis pathway, they also catalyze amino acid transformations (also undergoing C-C bond
cleavage). Complete the reaction below and outline the mechanism of the reaction with curly
arrows in the presence of a representative (generic) enzyme illustrating acid or base catalysis.
Page 5
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10.
A researcher is hoping to be able to predict whether reaction 1 or reaction 2 proceeds
spontaneously.
2
OPO3
CO 2
+
CO 2
CO 2
NH 2
H3N
N
H
H3N
NH 2
NH 2
N
H
N
H
2
PO3
O
+
CO 2
Reaction 1
Phosphoenolpyruvate
2
CO 2
H3N
NH 2
N
H
N
H
2
PO3
OPO3
OH
+
CO 2
CO 2
CO 2
+
H3N
NH 2
N
H
Reaction 2
Phosphocreatine
10.1.
Which one(s) of the species above can be classified as “energy rich” (circle the correct
answer)
(1)
(2)
(3)
(4)
10.2.
only phosphoenolpyruvate
only phosphocreatine
both phosphoenolpyruvate and phosphocreatine
all four species above are “energy rich”
Suggest a well-known simple molecule which can be phosphorylated by one and/or two
of the molecules above.
water
10.3.
What type of specific thermodynamic parameter obtained from the experiment in 10.2
help the researcher with his/her dilemma?
G of hydrolysis
Page 6
NH 2