Test Bank for Biochemistry: A Short Course, 2nd Edition, John L.

Tymoczko, ISBN-10: 14292836

Test Bank for Biochemistry: A Short Course, 2nd

Edition, John L. Tymoczko, ISBN-10: 1429283602,
ISBN-13: 9781429283601

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Chapter 7
1. Choose the correct answer from the list below. Not all of the answers will be used.
a) first-order reaction
b) second-order reaction
c) metabolism
d) ensemble
e) biomolecular
f) turnover number
g) Michaelis–Menten
h) equilibrium
i) bsequential
j) kinetics
k) initial velocity
l) allosteric
m) ping-pong
Reference: Ref 7-1

_______________: A complex array of enzyme reactions organized in multiple pathways.

Answer: c

2. Choose the correct answer from the list below. Not all of the answers will be used.
a) first-order reaction
b) second-order reaction
c) metabolism
d) ensemble
e) biomolecular
f) turnover number
g) Michaelis–Menten
h) equilibrium
i) bsequential
j) kinetics
k) initial velocity
l) allosteric
m) ping-pong
Reference: Ref 7-1

_______________: The study of rates of chemical reactions.

Answer: j

3. Choose the correct answer from the list below. Not all of the answers will be used.
a) first-order reaction
b) second-order reaction
c) metabolism
 d) ensemble
e) biomolecular
f) turnover number
g) Michaelis–Menten
h) equilibrium
i) bsequential
j) kinetics
k) initial velocity
l) allosteric
m) ping-pong
Reference: Ref 7-1

A reaction that is directly proportional to the concentration of reactant is a(n) ______________.

Answer: a

4. Choose the correct answer from the list below. Not all of the answers will be used.
a) first-order reaction
b) second-order reaction
c) metabolism
d) ensemble
e) biomolecular
f) turnover number
g) Michaelis–Menten
h) equilibrium
i) bsequential
j) kinetics
k) initial velocity
l) allosteric
m) ping-pong
Reference: Ref 7-1

A reaction with two substrates is considered a(n) _______________ reaction.

Answer: e

5. Choose the correct answer from the list below. Not all of the answers will be used.
a) first-order reaction
b) second-order reaction
c) metabolism
d) ensemble
e) biomolecular
f) turnover number
g) Michaelis–Menten
h) equilibrium
i) bsequential
 j) kinetics
k) initial velocity
l) allosteric
m) ping-pong
Reference: Ref 7-1

At _______________, there is no net change in the concentration of substrate or product.

Answer: h

6. Choose the correct answer from the list below. Not all of the answers will be used.
a) first-order reaction
b) second-order reaction
c) metabolism
d) ensemble
e) biomolecular
f) turnover number
g) Michaelis–Menten
h) equilibrium
i) bsequential
j) kinetics
k) initial velocity
l) allosteric
m) ping-pong
Reference: Ref 7-1

The value V0 is called the _______________.

Answer: k

7. Choose the correct answer from the list below. Not all of the answers will be used.
a) first-order reaction
b) second-order reaction
c) metabolism
d) ensemble
e) biomolecular
f) turnover number
g) Michaelis–Menten
h) equilibrium
i) bsequential
j) kinetics
k) initial velocity
l) allosteric
m) ping-pong
Reference: Ref 7-1
 The kcat is often referred to as the _______________.

Answer: f

8. Choose the correct answer from the list below. Not all of the answers will be used.
a) first-order reaction
b) second-order reaction
c) metabolism
d) ensemble
e) biomolecular
f) turnover number
g) Michaelis–Menten
h) equilibrium
i) bsequential
j) kinetics
k) initial velocity
l) allosteric
m) ping-pong
Reference: Ref 7-1

An enzyme's affinity for its substrate is measured by the _______________ constant.

Answer: g

9. Choose the correct answer from the list below. Not all of the answers will be used.
a) first-order reaction
b) second-order reaction
c) metabolism
d) ensemble
e) biomolecular
f) turnover number
g) Michaelis–Menten
h) equilibrium
i) bsequential
j) kinetics
k) initial velocity
l) allosteric
m) ping-pong
Reference: Ref 7-1

_______________: Enzymes that do not obey Michaelis–Menten kinetics.

Answer: l
10. Choose the correct answer from the list below. Not all of the answers will be used.
a) first-order reaction
b) second-order reaction
c) metabolism
d) ensemble
e) biomolecular
f) turnover number
g) Michaelis–Menten
h) equilibrium
i) bsequential
j) kinetics
k) initial velocity
l) allosteric
m) ping-pong
Reference: Ref 7-1

______________: Experiments that determine the kinetics of a population of enzyme molecules.

Answer: d

11. One way to measure the rate of an enzymatic reaction is to measure the loss of _______ over
time.

Answer: substrate

12. Reactions that have more two reactants or substrates are considered _______ reactions.

Answer: second-order

13. The _______ rule states that all subunits in an allosteric enzyme must be in either the T or the R
state; there can not be hybrids.

Answer: symmetry

14. The Michaelis–Menten model assumes that ______________ is the rate constant ignored because
producthas not accumulated.

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Answer: k–2

15. ______________ is directly dependent on enzyme concentration.

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Answer: Vmax

16. An enzyme will be most sensitive to changes in cellular concentration when the concentration is
______________.

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Answer: near the KM

17. The type of inhibition by a product of one enzyme on another enzyme in an earlier protein in a
metabolic pathway is considered a(an) _______ inhibitor.

Answer: feedback

18. Allosteric enzymes can be identified because the plot of initial velocity, V0, versus substrate
concentration, S, is not hyperbolic but _______ shaped.

Answer: sigmoidal

19. An allosteric _______ stabilizes the T state of the enzyme.

Answer: inhibitor

20. The y-intercept of a Lineweaver-Burk plot is ____________.

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Answer: 1/V0

21. A critical feature of the Michaelis–Menten model of enzyme catalysis is:

A. increasing the probability of product formation.
B. shifting the reaction equilibrium.
 C. the formation of an ES complex.
D. All of the above.
E. None of the above.

Answer: C

22. What value of [S], as a fraction of KM, is required to obtain 20% Vmax? [S] equals:

A. 0.2 KM
B. 0.25 KM
C. 0.5 KM
D. 0.75 KM
E. 0.8 KM

Answer: B

23. Allosteric proteins:

A. contain distinct regulatory sites and have multiple functional sites.
B. display cooperativity.
C. always consist of several identical subunits.
D. A and B.
E. A, B, and C.

Answer: D

24. Allosteric modifiers alter the equilibria between:

A. the ES state.
B. the R and T forms of a protein.
C. the forward and reverse reaction rate.
D. the formation of a product and its reverse reaction.
E. All of the above.

Answer: B

25.
The formula , describes the relationship between

A. the enzyme activity and the equilibrium constant.

B. the rate of a catalyzed reaction and the equilibrium constant.
C. enzyme activity as a function of substrate concentration.
D. All of the above.
E. None of the above.

Answer: C

26. The model describing allosteric regulation that requires all subunits to be in the same state is
called the:
 A. concerted model.
B. syncopated model.
C. cooperative model.
D. equilibrium model.
E. None of the above.

Answer: A

27. Loss of allosteric regulation in the production of purine nucleotides results in:
A. excess nucleotides for DNA.
B. loss of RNA due to ribose phosphate synthetase.
C. decreased urate degradation.
D. loss in urate concentration.
E. None of the above.

Answer: E

28. The KM is:

A. equal to the product concentration at initial reaction conditions.

B. equal to the substrate concentration when the reaction rate is half its maximal value.
C. proportional to the standard free energy.
D. All of the above.
E. None of the above.

Answer: B

29. Given are five KM values for the binding of substrates to a particular enzyme. Which has the
strongest affinity when k–1 is greater than k2?

A. 150 mM
B. 0.15 mM
C. 150 µM
D. 1.5 nM
E. 15,000 pM

Answer: D

30. When a substrate concentration is much greater than KM, the rate of catalysis is almost equal to:

A. KD
B. kcat.
C. Vmax.
D. All of the above.
E. None of the above.

Answer: C

31. Which of the following is true under these conditions: The enzyme concentration is 5 nM, the
 substrate concentration is 5 mM, and the KM is 5 µM.

A. The enzyme is saturated with substrate.

B. Most of the enzyme does not have substrate bound.
C. There is more enzyme than substrate.
D. All of the above.
E. None of the above.

Answer: A

32. Homotrophic effects of allosteric enzymes:

A. are due to the effects of substrates.
B. are due to the effects of allosteric activators.
C. shift the kinetics curve to the left.
D. shift the kinetics curve to the right.
E. None of the above.

Answer: A

33. Multiple substrate enzyme reactions are divided into two classes:
A. sequential displacement and double displacement.
B. double displacement and concerted displacement.
C. sequential displacement and concerted displacement.
D. A and C.
E. None of the above.

Answer: A

34. When [S] << KM, the enzymatic velocity depends on:

A. the values of kcat/KM, [S], and [E]t.

B. the Vmax of the reaction.
C. the affinity of the substrate for the catalytic site.
D. kcat.
E. the formation of the ES complex.

Answer: A

35. Allosteric effectors:

A. can cause large changes in enzymatic activity.
B. can lead to a decrease in the availability of a protein.
C. do not alter the sensitivity of a metabolic pathway.
D. decrease the sensitivity of the enzyme at nearly all concentrations of substrate.
E. alter enzyme activity by binding to the active site of an enzyme.

Answer: A

36. In many enzyme assays, the natural substrate and product are not used. Why?
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Answer: Many products are difficult to measure accurately. Some are simply difficult to measure, while
others are difficult to discern against the background of other molecules present in the reaction.
Instead, substrates are chosen that the enzyme can still process but that result in products that can be
easily measured. For example, substrates are chosen that result in products that are colored and can
be detected spectrophotometrically.

37. A protease hydrolyzes the peptide backbone. What is/are the substrate(s) and product for this
reaction? Assuming that the concentration of water is so high (~55M) that it does not appreciably
change, to what kind of reaction order would one assign this reaction?

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Answer: The reaction would be Protein + H2O → Peptide 1 + peptide 2. As water doesn't significantly
change its concentration in an aqueous reaction, the concentration change is zero and can be ignored;
thus, the rate of the reaction is directly proportionate to the concentration of the protein and is a
first-order reaction.

38. The rate of a reaction is dependent on [ES]. Using an enzyme-catalyzed reaction scheme,
Equation (6) p. 107, describe the kinetic model for [ES].

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Answer: The concentration of an ES complex is described as the enzyme binding to substrate and can
be measured as one kinetic rate constant forming the ES complex. Loss of the ES can be described as
the separation of the two components without undergoing catalysis(k–1) or as reacting to completion
(ES → EP → E + P) (k2).

39. Figure 7.8 is a simplified version of a common set of converging metabolic pathways. Describe the
type of regulation necessary if each of the reactions were reversed and a product, A or G, were
preferred.

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Answer: A feed-forward inhibition where a product, G or H, inhibits E1, E2, E3, or E5. Another
possibility is that one or more of the products, A through F, inhibits E10 or E11.

40. Draw a Cleland notation for a sequential reaction and for a double-displacement reaction.

Answer: See Figure 7.6A and 7.6B.

41. What is the Michaelis–Menten equation? Define all parameters.

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Answer: V0 = Vmax(S/(S + KM))

Initial velocity
V0

Maximum velocity
Vmax

Substrate concentration
S

Michaelis constant
KM

42. What does Vmax indicate?

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Answer: The maximum velocity or rate of reaction as catalyzed by a specific amount of enzyme when
it is saturated with substrate.

43. What is the upper limit of kcat/KM?

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Answer: The diffusion-controlled interaction of the substrate and enzyme determines the upper limit of
the rate. The upper limit is 108 – 109 s–1M–1.

44. How do the intermediate steps in multisubstrate enzyme mechanisms differ?

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Answer: In a sequential displacement reaction, both substrates bind and a ternary complex of all three
is formed. In a double displacement (ping-pong), one or more products are released prior to binding of
all substrates. Thus, a substituted enzyme intermediate is formed.

45. Describe the difference between the concerted and the sequential model of allosteric regulation.

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Answer: The concerted model describes a situation where a multisubunit enzyme can only assume an
R or T conformation, whereas the sequential model assumes that the subunits can assume a
conformation different from the neighboring subunits. In the former, substrate influences the equilibria
between each subunit's R orT conformation and in the latter, substrate can have an intermediate
impact on affinity and conformation.

46. Would you expect the order of substrate binding to be critical for enzyme catalysis?

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Answer: Yes, in some cases. For example, in ping-pong reactions, the proper substrate would have to
bind to form the right substituted enzyme intermediate form. In sequential displacement, both
conditions are observed. Substrates may need to bind in a particular order (lactate dehydrogenase) or
the enzyme may bind substrates and release products in random order (creatine kinase).

47. What is the turnover number for an enzyme and what does this value tell us about the enzyme?

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Answer: The rate of reaction and dissociation of the ES complex to E + P is k2. That is the rate at
which an enzyme saturated with substrate converts substrate to product. This is basically the measure
of the reaction without an impact on substrate binding and is dependent on the concentration of
Test Bank for Biochemistry: A Short Course, 2nd Edition, John L. Tymoczko, ISBN-10: 14292836

enzymes and describes the relative speed of a reaction.

48. When designing a drug to inhibit the formation of a product which requires several enzymes in a
metabolic pathway, what should be the first piece of information a biochemist needs to develop
the drug?

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Answer: The biochemist should look for the rate-limiting step. In a metabolic pathway, there will be a
rate-limiting, committed enzyme step that is often the target of physiological regulation. This protein
would be the best target for a new drug.

49. How does the sequential model differ from the concerted model for allosteric enzymes?

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Answer: The concerted model does not allow for anything other than an “all or none” completely
tense-form or relaxed-form protein. In contrast, the sequential model allows for a mixed type of
protein, containing some tense and some relaxed subunits. The form of each subunit is determined
independently on binding of the ligand to a particular subunit.

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