Download 1. Given the following metabolic pathway (as it occurs in the cell): a

Chem 153A
Week 9 Practice Problems
1. Given the following metabolic pathway (as it occurs in the cell):
a. Would you expect enzyme 1 to be regulated? Briefly explain why or why not.
b. If you answered ‘yes’ to part a, which molecules would you expect to act as positive
effectors? Negative effectors?
c. Would you expect enzyme 2 to be regulated? Briefly explain why or why not.
d. If you answered ‘yes’ to part c, which molecules would you expect to act as positive
effectors? Negative effectors?
e. For the remaining enzymes (3-9), which would you expect to be regulated? List their
numbers.
2. Which of the following features of a reaction suggest that it would be used by opposing pathways in a
cell? List all that apply.
a. The enzyme catalyzing the reaction is found in multiple cellular locations.
b. The standard free energy change of the reaction is small in magnitude.
c. The standard free energy change of the reaction is large in magnitude.
d. The cellular concentrations of products and reactants are nearly equal.
e. The reaction in the cell is close to equilibrium.
f. The reactants and products of the reaction are at steady state.
g. The enzyme catalyzing the reaction is regulated by allosteric effectors.
h. The enzyme catalyzing the reaction is subject to simple feedback inhibition.
3. The reaction catalyzed by phosphoglycerate kinase (PGK) is readily reversible in the cell, although its
∆G°' = ‒18.8 kJ/mol. Explain why this reaction is not highly spontaneous in the cell. Be specific.
(30 words or fewer.)
4. Other than coupling to ATP hydrolysis or phosphoryl transfer (or hydrolysis/phosphoryl transfer
involving another nucleotide triphosphate), describe a specific way to make a highly unfavorable
reaction spontaneous in the cell (20 words or fewer).
5. Given the following reactions:
Explain why the conversion of B→C would be spontaneous in the cell (30 words or fewer).
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Chem 153A
Week 9 Practice Problems
6. An aspiring chef, you decide to try making sauerkraut (sour cabbage) at home. The recipe tells you to
tightly pack the shredded & salted cabbage into a container that will not let in air. The container is
then left to sit, during which time the cabbage acquires its sour taste.
a. Name the process that causes the cabbage to sour, and the compound produced by this
process.
b. Why is it important that air not be let into the container? (20 words or fewer.)
7. Which of the following statements about pyruvate dehydrogenase complex (and its mechanism) are
true?
a.
b.
c.
d.
e.
The decarboxylase activity of enzyme 1 is due to the nucleophilicity of TPP.
Enzyme 2 is identical to that of α-ketoglutarate dehydrogenase complex.
The activity of the complex is important to aerobic and anaerobic metabolism.
FAD is reduced in the formation of a disulfide bond.
Lipoic acid is attached to enzyme 2 through a thioester bond.
8. You perform a carbon-labeling experiment to examine
metabolism in a newly discovered single-celled
eukaryote. You begin by synthesizing glucose with 14C
at position 1 and feeding it to the organism. Based on
what you know about metabolism in other organisms,
where would you expect this carbon to end up in the
compounds shown at the right? Circle each carbon that
could be labeled.
9. In the reaction catalyzed by malate dehydrogenase, which
compound is the oxidant?
10. You perform a carbon-labeling experiment to see how quickly a cell metabolizes glucose. Rather
than labeling only one carbon of glucose, you label all carbons. Assuming all intermediates are used
in catabolic processes, what fraction of the labeled carbons will be expelled as CO2 by the end of the
first, second, and third rounds of the citric acid cycle? Show your reasoning.
11. Pyruvate carboxylase is virtually inactive in the absence of acetyl-CoA. Why is this feature of its
regulation important to the cell? Explain in 30 words or fewer.
12. True or False?
a. Reactions used in both catabolic and anabolic pathways are called ‘anaplerotic.’
b. Succinyl-CoA is hydrolyzed to succinate and CoA in the reaction catalyzed by succinyl-CoA
synthetase.
c. The reaction catalyzed by fumarase always produces the same isomer of malate because
fumarate is prochiral.
13. Briefly define ‘antiporter.’ Would you expect to find antiporters in the outer mitochondrial
membrane? Briefly explain why or why not.
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Chem 153A
Week 9 Practice Problems
14. You are studying a new organism, and based on the sequence, you find what you think is the gene for
pyruvate dehydrogenase complex enzyme 2 (E2). To test your hypothesis, you change the gene so
that all lysine residues that were in the enzyme will be arginine instead. You then check the growth
of the organism under anaerobic and aerobic conditions, using glucose as the food source.
a. How would lysine → arginine mutations affect the function of pyruvate dehydrogenase
complex E2? Explain in 25 words or fewer.
b. If your hypothesis is correct, how will the organism’s growth differ from normal under
anaerobic conditions? Explain why in 15 words or fewer.
c. If your hypothesis is correct, how will the organism’s growth differ from normal under
aerobic conditions? Explain why in 15 words or fewer.
The differences in growth match what you expect based on your hypothesis. But when you extract
the cell contents from the mutated organism and check for the enzyme’s activity, you find that
pyruvate can be converted into acetyl-CoA at normal rates. Further, you find a build-up of one of the
intermediates of the citric acid cycle.
d. Why does the organism’s growth differ as expected, but pyruvate is converted normally?
Explain in 15 words or fewer.
e. Which citric acid cycle intermediate do you find in excess?
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