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

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Chapter 8
1. Choose the correct answer from the list below. Not all of the answers will be used.
a) hydrolysis
b) affinity label
c) tyrosinase
d) chymotrypsin
e) pepsin
f) noncompetitive
g) uncompetitive
h) heterotropic
i) approximation and orientation
j) acid–base
h) competitive
Reference: Ref 8-1

____________: An enzyme that temporarily undergoes covalent catalysis as part of its mechanism.

Answer: d

2. Choose the correct answer from the list below. Not all of the answers will be used.
a) hydrolysis
b) affinity label
c) tyrosinase
d) chymotrypsin
e) pepsin
f) noncompetitive
g) uncompetitive
h) heterotropic
i) approximation and orientation
j) acid–base
h) competitive
Reference: Ref 8-1

____________: The type of reaction catalyzed by proteases.

Answer: a

3. Choose the correct answer from the list below. Not all of the answers will be used.
a) hydrolysis
b) affinity label
c) tyrosinase
d) chymotrypsin
e) pepsin
f) noncompetitive
g) uncompetitive
 h) heterotropic
i) approximation and orientation
j) acid–base
h) competitive
Reference: Ref 8-1

____________: A protease enzyme with a low pH optimum.

Answer: e

4. Choose the correct answer from the list below. Not all of the answers will be used.
a) hydrolysis
b) affinity label
c) tyrosinase
d) chymotrypsin
e) pepsin
f) noncompetitive
g) uncompetitive
h) heterotropic
i) approximation and orientation
j) acid–base
h) competitive
Reference: Ref 8-1

____________: The type of catalysis in which two substrates are brought into close proximity.

Answer: j

5. Choose the correct answer from the list below. Not all of the answers will be used.
a) hydrolysis
b) affinity label
c) tyrosinase
d) chymotrypsin
e) pepsin
f) noncompetitive
g) uncompetitive
h) heterotropic
i) approximation and orientation
j) acid–base
h) competitive
Reference: Ref 8-1

____________: A molecule that is also known as a substrate analog.

Answer: b

6. Choose the correct answer from the list below. Not all of the answers will be used.
a) hydrolysis
b) affinity label
c) tyrosinase
d) chymotrypsin
e) pepsin
f) noncompetitive
g) uncompetitive
h) heterotropic
i) approximation and orientation
j) acid–base
h) competitive
Reference: Ref 8-1

____________: The inhibitor which binds only to the ES complex and lowers the Vmax and KM.

Answer: g

7. Choose the correct answer from the list below. Not all of the answers will be used.
a) hydrolysis
b) affinity label
c) tyrosinase
d) chymotrypsin
e) pepsin
f) noncompetitive
g) uncompetitive
h) heterotropic
i) approximation and orientation
j) acid–base
h) competitive
Reference: Ref 8-1

____________: The enzyme inhibition that can be overcome by increasing the concentration of
substrate.

Answer: k

8. Choose the correct answer from the list below. Not all of the answers will be used.
a) hydrolysis
b) affinity label
c) tyrosinase
d) chymotrypsin
e) pepsin
f) noncompetitive
g) uncompetitive
 h) heterotropic
i) approximation and orientation
j) acid–base
h) competitive
Reference: Ref 8-1

____________: A type of catalysis where the proton donor is not water.

Answer: i

9. Choose the correct answer from the list below. Not all of the answers will be used.
a) hydrolysis
b) affinity label
c) tyrosinase
d) chymotrypsin
e) pepsin
f) noncompetitive
g) uncompetitive
h) heterotropic
i) approximation and orientation
j) acid–base
h) competitive
Reference: Ref 8-1

____________: A type of enzyme inhibitor where KM is unaltered.

Answer: h

10. Choose the correct answer from the list below. Not all of the answers will be used.
a) hydrolysis
b) affinity label
c) tyrosinase
d) chymotrypsin
e) pepsin
f) noncompetitive
g) uncompetitive
h) heterotropic
i) approximation and orientation
j) acid–base
h) competitive
Reference: Ref 8-1

____________: An enzyme that is part of a pigment formation pathway and has a low optimum
temperature.
Answer: c

11. An enzyme catalyst mechanism that uses a metal cation to stabilize a negative charge in the
active site is _______ .

Answer: metal ion catalysis

12. A _______ catalytic mechanism that forces two substrates into an appropriate three-dimensional
arrangement for the reaction to occur.

Answer: catalysis by approximation and orientation

13. The antibiotic penicillin is an example of a(n) _______ inhibitor.

Answer: irreversible

14. In conducting an experiment with a new drug, you find that regardless of the concentration of
substrate, the drug is able to inhibit the enzyme activity. You are likely to not have a(n) _______
type of inhibitor.

Answer: competitive

15. An uncompetitive inhibitor will have two _______ lines on a double-reciprocal plot.

Answer: parallel

16. A _______ inhibitor binds irreversibly to the active site of an enzyme.

Answer: suicide

17. The _______ stabilizes the tetrahedral intermediate of the hydrolysis of a peptide bond by
chymotrypsin.

Answer: oxyanion hole

18. A(n) _______ inhibitor has a structure similar to the substrate and reversibly binds to the active
site of the enzyme.

Answer: competitive

19. The straight-line kinetic plot of 1/V0 versus 1/S is called a _______ .
Answer: Lineweaver-Burk plot, or double-reciprocal plot

20. The mechanism of chymotrypsin involves the formation of an unstable _______ -shaped
intermediate that is stabilized by the oxyanion hole.

Answer: tetrahedral

21. What conclusion can be drawn concerning an inhibitor if the KM is the same in the presence and
absence of the inhibitor?
A. The inhibitor binds to the substrate.
B. The inhibitor has a structure that is not very similar to the substrate.
C. The inhibitor forms a reversible covalent bond with the enzyme.
D. The inhibitor binds to the same active site as the substrate.
E. The Vmax is larger in the presence of the inhibitor.

Answer: B

22. Which type(s) of inhibition can be reversed?

A. competitive
B. noncompetitive
C. uncompetitive
D. All of the above.
E. None of the above.

Answer: D

23. In this type of inhibition, the inhibitor can only bind to the ES complex to form an ESI complex.
A. competitive
B. noncompetitive
C. irreversible
D. uncompetitive
E. None of the above.

Answer: D

24. Which amino acids in chymotrypsin are found in the active site and are participants in substrate
cleavage?
A. his, ser, asp
B. his, ser
C. asp, lys
D. lys, arg
E. his, ser, arg

Answer: A

25. How is specificity determined by chymotrypsin?

 A. by an interaction of the active site amino acids with the substrate
B. by a binding of the N-terminus amino acid at the active site
C. by a covalent binding of a his residue to the substrate
D. by a conformational change upon the binding of substrate
E. by a binding of the proper amino acid into a deep pocket on the enzyme

Answer: E

26. Where does cleavage of the scissile bond by chymotrypsin occur?

A. between a his and a ser amino acid
B. on the N-terminal side of a phe or trp residue
C. on the C-terminal side of a phe or trp residue
D. at the N-terminal amino acid
E. on the C-terminal side of an arg or lys amino acid

Answer: C

27. A protein that is optimally active at neutral pH is likely to have which in the active site?
A. the side chains of aspartate and glutamine
B. two histidine amino acid side chains
C. a glycine amino acid
D. one or more carboxyl groups
E. two amino groups

Answer: A

28. The metal most commonly found at the active site of metalloproteases is:
A. zinc.
B. calcium.
C. selenium.
D. magnesium.
E. sodium.

Answer: A

29. Binding of a water molecule to the zinc ion induces:

A. a hydronium ion to form.
B. a large conformation change in the binding site.
C. ionization of a his residue, which functions as a strong nucleophile.
D. a lowered pKa for water, which leads to the formation of a zinc-bound hydroxide ion.
E. an altered KM value.

Answer: D

30. How are the types of inhibition kinetically distinguishable?

 HTML Editor

Answer: Competitive inhibition can be overcome by the presence of large amounts of substrate.
However, the apparent KM is increased. In noncompetitive inhibition, substrate can bind to the enzyme-
inhibitor complex; however, the Vmax is decreased. In mixed inhibition, both values may be altered.

31. Complete the structure of the catalytic triad of chymotrypsin by drawing the proper structure of
the missing residue side chain in the box provided. Show the proper hydrogen bonding involved in
this triad.

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Answer:

32. What is the challenge for a protease to facilitate hydrolysis of a peptide bond?

HTML Editor

Answer: The peptide bond contains a carbonyl that is not very reactive; therefore, the catalytic
mechanism must employ a feature that promotes nucleophilic attack of this carbonyl group so the
peptide bond can be cleaved.

33. How can covalent modification be used to determine the mechanism of action of an enzyme?
 HTML Editor

Answer: If a particular amino acid side chain is suspected of participating in a catalytic mechanism,
covalent modification of the residue may change it enough that the enzyme activity is altered or
inhibited. However, this method is usually confirmed by other techniques, such as site-directed
mutagenesis, to rule out other possible reasons for the loss of activity, such as conformational change.

34. What is an affinity label?

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Answer: This is a substrate analog that is structurally similar to the substrate, binds to the active site,
and chemically reacts with a residue in the active site. It is used to study enzyme structure and
mechanism.

35. Why are substrate analogs used to monitor enzyme activity?

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Answer: Enzyme assays must be designed so that the formation of a product is rapidly and easily
monitored. Substrates that form a colored product are easy to observe in a quantitative manner using
spectrophotometers.

36. What caused a “burst” of activity followed by a steady-state reaction when chymotrypsin was
studied by stop-flow techniques?

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Answer: Chymotrypsin cleaves peptide bonds in a two-step reaction, in which the first step, formation
of the acyl enzyme intermediate, is faster than the second step, hydrolysis.

37. Designing drugs to inhibit enzymes is a large part of pharmaceutical research. What are some of
the enzymatic features that would be important?
 HTML Editor

Answer: The enzyme could be inhibited by the interaction of a potential drug at the active site or at a
site that alters conformation or regulation of the enzyme. The structure of natural substrates and
activators, and their binding sites, would be useful features to study for a new drug design. The binding
affinity and specificity would be important, and standard enzyme assays would be used to determine
the effect of the inhibitors on Kcat, KM, and Vmax.

38. What factors should an enzymologist consider when designing an enzyme assay?

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Answer: Factors an enzymologist should consider when designing an enzyme assay include the pH for
optimal substrate binding and enzymatic activity, the temperature for proper catalytic function, and the
additional regulatory compounds needed to measure the enzyme's activity.

39. There is a key difference between an enzyme that uses a covalent catalysis mechanism and one
that uses other catalytic strategies. What is this key difference?

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Answer: For each of the other strategies of catalysis, a substrate and/or a cofactor are bound to the
site by noncovalent interactions with the amino acids of the enzyme. An enzyme that uses a covalent
catalyst strategy covalently binds the substrate to one or more of the amino acids in the active site.

40. Which of the following curves (no inhibitor, inhibitor 1, or inhibitor 2) represents the rate of
reaction versus substrate concentration for a competitive and an uncompetitive inhibitor? Draw
the double-reciprocal plot for each case.
Answer: Inhibitor 1 is a competitive inhibitor; inhibitor 2 is an uncompetitive inhibitor .

41. What is the difference between KM and KM app?

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Answer: The KM is the Michaelis–Menten constant, which measures the affinity of an enzyme for its
substrate. The KM app is the altered constant in the presence of an inhibitor.

42. Draw and describe the reaction pathway for a noncompetitive inhibitor.

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Answer: The figure should resemble the reaction pathway shown in Figure 8.9. Here, the pathway is
demonstrating that the substrate can bind irreversibly to the enzyme alone or to the enzyme already
bound to the inhibitor. The ESI complex can continue in this pathway to an ES + I state, but may not
continue to an EI + P product.

43. What are group-specific reagents?

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Answer: These are compounds which will form a defined chemical reaction with specific functional
groups of an amino acid. These are used to define the active-site amino acids of an enzyme, an
example of which is diisopropylphosphofluoridate (DIPF) which modifies a specific –OH group on a
serine in chymotrypsin.

44. Bacteria that become penicillin resistant express an enzyme called β-lactamase. This enzyme
hydrolyses the lactam ring on penicillin. Suggest a reason why this protein allows cells to grow in
the presence of penicillin.

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Answer: Penicillin is a suicide inhibitor of the transpeptidase enzyme that modifies the serine –OH in
the active site. β-lactamase reduces the concentration of the inhibitor, allowing the cell wall of the
bacteria to properly form.

45. The initial reaction kinetics of some enzymes results in a quick burst of product in a short period
of time, followed by a slower but sustained increase in product formation over time. What does
this type of kinetic response tell an enzymologist about the mechanism of the catalysis?

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Answer: These two-phase reactions (a rapid-burst phase and a steady-state phase) indicate that the
reaction takes place in two steps. The first step is very quick and will achieve equilibrium rapidly; the
second step of the reaction is slower.

46. A site-directed mutagenesis converting histidine-57 of chymotrypsin to a lysine results in an

inactive enzyme even though lysine has an amino group in its side chain. Describe why the
scientist may have thought this result surprising and why it wasn't.

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Answer: The side group of histidine has two nitrogens each of which can act as either a proton donor
or an acceptor. The scientist might have thought that lysine could substitute for histidine in the
catalytic triad. However, for the triad to function properly, the substitute would have to have the ability
to partially deproteinize the –OH group of the neighboring serine. Lysine does not have this capacity,
even with a nearby aspartate.

47. How is the enzyme chymotrypsin bind and hydrolyze its substrate? How does this differ from
other proteases?

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Answer: Chymotrypsin binds its substrate with a deep hydrophobic pocket, locking the substrate into
an appropriate conformation. If this binding site were altered or missing, the active site would remain
and the protein would bind many different substrates, as is the case for some of the other proteases.

48. Describe the mechanism for the proteolysis catalyzed by chymotrypsin.

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

HTML Editor

Answer: This is an acid–base, covalent catalysis that generates an unstable tetrahedral-intermediate.

The intermediate is stabilized by the interactions of the oxyanion hole. The reaction mechanism is
shown on Figure 8.25.

49. You measure the initial velocity of an enzyme in the absence and presence of two inhibitors. In
each case, the inhibitor is at 10 µM. Shown in the table below is the primary data for all three
cases. Construct a Lineweaver–Burk plot for each case. Calculate the KM and Vmax for each case,
both graphically and mathematically. Determine the mechanism for each inhibitor and where each
will interact on the enzyme.
Initial Velocity (µmol/ml min)
Enzyme Enzyme Enzyme
[S] mM Alone + Inhibitor 1 + Inhibitor 2
0.33 1.65 1.05 0.79
0.50 2.13 1.43 1.02
1.00 2.99 2.22 1.43
2.00 3.72 3.08 1.79
5.00 4.00 3.80 2.00

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Answer: Construct a double-reciprocal plot. From the intercept of the vertical axis, determine the
value for the intercept = 1/Vmax and the horizontal axis to determine the value for –1/KM.

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