Fundamentals of Biochemistry 4th

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 Chapter 11: Enzyme Catalysis

Matching

A) high
B) deprotonated
C) protonated
D) catalytic mechanism
E) covalent
F) rate-determining step
G) leaving group
H) formation of ES
I) amino acid
J) low
K) coenzymes
L) concerted acid-base
M) orientation
N) oxidation

1. For efficient nucleophilic catalysis, a group such as the sulfhydryl on a cysteine residue must
be able to form a good ______, in addition to being a good nucleophile.

Ans: G
Level of Difficulty: Easy
Section: 11.3.B
Learning objective: Catalytic Mechanisms

2. If an enzyme-catalyzed reaction has a low rate at low pH and high rate at higher pH, this
implies that a group on either the enzyme or the substrate must be ______ for an efficient
reaction.

Ans: B
Level of Difficulty: Easy
Section: 11.3.A
Learning objective: Catalytic Mechanisms
3. On a transition state diagram for a multistep reaction, the step with the greatest G is the
______.

Ans: F
Level of Difficulty: Easy
Section: 11.2
Learning objective: Activation Energy and the Reaction Coordinate

4. On a transition state diagram for a one-step very spontaneous reaction a large peak (high 
G‡)would imply a ______ rate for the reaction.

Ans: J
Level of Difficulty: Easy
Section: 11.2
Learning objective: Activation Energy and the Reaction Coordinate

5. Metal ion cofactors can coordinate to the substrate or stabilize electrostatic effects by
enabling proper ______in the active site.

Ans: M
Level of Difficulty: Easy
Section: 11.3.C
Learning objective: Catalytic Mechanisms

6. Large rate enhancement in enzyme catalysis may occur when binding the substrate via
_________ attachment.

Ans: E
Level of Difficulty: Easy
Section: 11.2
Learning objective: Activation Energy and the Reaction Coordinate

7. Metal ion cofactors offer various ______ states that allow enzymes to accomplished oxidation
reduction reactions.

Ans: N
Level of Difficulty: Easy
Section: 11.3.C
Learning objective: Catalytic Mechanisms
8. Since proteins are limited in their abilities to catalyze oxidation-reduction reactions, enzymes
often employ ______ to assist with catalysis.

Ans: K
Level of Difficulty: Easy
Section: 11.1.C
Learning objective: General Properties of Enzymes

9. Some serine proteases are believed to have developed by convergent evolution, because the
______ sequences of some serine proteases show no resemblance to those of others.

Ans: I
Level of Difficulty: Easy
Section: 11.5.B
Learning objective: Serine Proteases

10. Clustering several amino acid residues with appropriate pK values at an active site can
promote a(n) _________ catalytic mechanism.

Ans: L
Level of Difficulty: Easy
Section: 11.3.A
Learning objective: Catalytic Mechanisms

Multiple Choice

11. An uncatalyzed reaction has a rate of 4.2 × 10–7 sec–1. When an enzyme is added the rate is
3.2 × 104 sec–1. Calculate the rate enhancement caused by the enzyme.

A) 3.2 × 104
B) 7.4 × 10–3
C) 1.3 × 10–2
D) 7.6 × 1010
E) The data are not appropriate for the calculation requested.

Ans: D
Level of Difficulty: Moderate
Section: 11.2
Learning objective: Activation Energy and the Reaction Coordinate
12. Which of these amino acid groups would not make a good nucleophilic catalyst?

A) amino
B) sulfhydryl
C) imidazole
D) methyl
E) hydroxyl

Ans: D
Level of Difficulty: Easy
Section: 11.3.B
Learning objective: Catalytic Mechanisms

13. The imidazole side chain of histidine can function as either a general acid catalyst or a
general base catalyst because

I. the imidazole group has a pKa in the physiological pH range.

II. in the physiological pH range, the nitrogen in the ring can be easily protonated/deprotonated.
III. one guanidino group is protonated, and the other is deprotonated at physiological pH.
IV. the imidazole group is a strong reducing agent at physiological pH.

A) I, II
B) I
C) II, IV
D) II, III
E) IV

Ans: A
Level of Difficulty: Moderate
Section: 11.3.A
Learning objective: Catalytic Mechanisms

14. A new serine protease was discovered that preferentially cleaves a peptide bond adjoining a
negatively charged side chain. Which of the following is true?

A) The specificity pocket would mimic that of chymotrypsin.

B) The specificity pocket would mimic that of trypsin.
C) The specificity pocket is likely lined with amino acids such as Arg and Lys.
D) It likely reacts much slower than chymotrypsin.
E) It likely reaction much faster than chymotrypsin.

Ans: C
Level of Difficulty: Moderate
Section: 11.5.C
Learning objective: Serine Proteases
15. If you add enzyme to a solution containing only the product(s) of a reaction, would you
expect any substrate to form?

A) It depends on the time interval and temperature of reaction.

B) It depends on the concentration of products added.
C) It depends on the energy difference between E + P and the transition state.
D) All of the above may determine if product forms.
E) None of the above determines if product forms.

Ans: C
Level of Difficulty: Difficult
Section: 11.3.E
Learning objective: Catalytic Mechanisms

16. Which one of the following is correct?

I. All enzymes are highly specific for the reactions they catalyze.
II. Prosthetic groups are loosely associated with the polypeptide chain of an enzyme.
III. If an enzyme-catalyzed reaction requires a group with a low pK to be deprotonated
and a group with a higher pK to be protonated, the pH vs. rate curve will have a peak
in the middle of the two pK values.
IV. When comparing types of catalysis, the proximity effect provides the largest rate
enhancement.

A) I, II, III, IV
B) I, III
C) I
D) III
E) IV

Ans: D
Level of Difficulty: Difficult
Section: 11.3
Learning objective: Catalytic Mechanisms
17. Which of the following amino acid residues would not provide a side chain for acid-base
catalysis at physiological pH? (Assume pK values of each amino acid are equal to the pK value
for the free amino acid in solution.)

I. leucine
II. lysine
III. aspartic acid
IV. histidine

A) I, II, III
B) I, II
C) I
D) II
E) I, III

Ans: A
Level of Difficulty: Difficult
Section: 11.3.A
Learning objective: Catalytic Mechanisms

18. Which of the following amino acid residues would provide a side chain capable of
increasing the hydrophobicity of a binding site?

A) histidine
B) lysine
C) isoleucine
D) arginine
E) serine

Ans: C
Level of Difficulty: Moderate
Section: 11.3
Learning objective: Catalytic Mechanisms
19. Which of the following is TRUE about enzymes?

I. Enzymes typically catalyze reactions at much higher rates than chemical catalyst.
II. Enzymes are often very specific for their substrates.
III. Enzyme activities can often be regulated.
IV. Enzymes typically act under milder conditions of temperature and pH than chemical
catalysts.

A) I, II, III
B) I, II, III, IV
C) II, II
D) III, IV
E) II, III, IV

Ans: B
Level of Difficulty: Moderate
Section: 11.3.E
Learning objective: Catalytic Mechanisms

20. In affinity labeling, a technique used to study enzyme mechanisms,

A) A compound designed to bind at the active site reacts with and therefore permits the
identification of a nearby group.
B) A fluorescent group is attached to the substrate to identify the position of the active site.
C) Highly purified enzyme is obtained by affinity chromatography for mechanistic studies.
D) A radioactive isotope is incorporated into the substrate to identify the position of the active
site.
E) Genetic modification of amino acid residues is used to alter the binding affinity of the active
site.

Ans: A
Level of Difficulty: Moderate
Section: 11.5.A
Learning objective: Serine Proteases

21. Which of the following is TRUE regarding cofactors?

A) Coenzymes are often separate from the enzyme and do not need recharged.
B) Metal ions must be covalently attached to function as a cofactor.
C) Cofactor is a broad term used for all enzyme "helpers".
D) Prosthetic groups can dissociate readily and be regenerated for use in another enzyme.
E) An apoenzyme implies that a cofactor is present.
Ans: C
Level of Difficulty: Easy
Section: 11.1.C
Learning objective: General Properties of Enzymes

22. A peptide with the sequence "Glu-Ser-Val-Asp-Lys" will likely be cut next to "Val" rapidly
by _______ and very slowly by ____.

I. chymotrypsin
II. trypsin
III. trypsinogen
IV. elastase

A) I,IV
B) I, II
C) II, III
D) IV, II
E) IV, I

Ans: E
Level of Difficulty: Easy
Section: 11.5.B
Learning objective: Serine Proteases

23. Alcohol dehydrogenase catalyzes the conversion of methanol to _________ and is,
therefore, classified as a(an)________.

A) acetic acid; transferase

B) formaldehyde; oxidoreductase
C) acetic acid; oxidoreductase
D) ethanol; lyase
E) formaldehyde; transferase

Ans: B
Level of Difficulty: Easy
Section: 11.1.A
Learning objective: General Properties of Enzymes

24. Carbohydrate metabolic enzymes bind D-glucose specifically. D-glucose has an estimated
caloric value of 1 kcal per 4 grams of carbohydrate. Based on the methods used to convert the
energy of D-glucose into a useable form, what would you estimate the caloric value of L-glucose
to be using the same method?
A) 1 kcal per 4 grams
B) 1 kcal per 2 grams
C) 1 kcal per 8 grams
D) 0 kcal per 4 grams
E) 2 kcal per 8 grams

Ans: D
Level of Difficulty: Difficult
Section: 11.1.B
Learning objective: General Properties of Enzymes

25. Glu 35 of lysozyme is found in a nonpolar environment. Which of the following is true?

A) Its pK is lower than the usual value in this environment.

B) Its pK is higher than the usual value in this environment.
C) Its pK would not change in this environment.
D) Its pK would depend on the sample buffer.
E) None of the above is correct.

Ans: B
Level of Difficulty: Easy
Section: 11.4B
Learning objective: Activation Energy and the Reaction Coordinate

26. ______ metals are the most common metallic enzyme cofactors.

A) Actinide
B) Alkali
C) Heavy
D) Rare earth
E) Transition

Ans: E
Level of Difficulty: Easy
Section: 11.3.C
Learning objective: Catalytic Mechanisms
27. Curved arrows are conventionally used to illustrate the movement of

A) electron pairs.
B) single electrons.
C) protons.
D) anions.
E) All of the above use this convention.

Ans: A
Level of Difficulty: Easy
Section: 11.3
Learning objective: Catalytic Mechanisms

28. Proton transfer from an acid, lowering the free energy of a reaction’s transition state, is
characteristic of

A) electrostatic catalysis.
B) nucleophilic catalysis.
C) general base catalysis.
D) general acid catalysis.
E) concerted acid-base catalysis.

Ans: D
Level of Difficulty: Easy
Section: 11.3.A
Learning objective: Catalytic Mechanisms

29. Simultaneous stimulation of a reaction by general acid and general base catalysis is defined
as

A) covalent catalysis.
B) electrostatic catalysis.
C) proximity catalysis.
D) concerted acid-base catalysis.
E) transition state catalysis.

Ans: D
Level of Difficulty: Easy
Section: 11.3.A
Learning objective: Catalytic Mechanisms
30. A pH versus rate curve with an inflection point at pH~4 suggests the involvement of a(n)
________ in the catalytic step.

A) proton abstraction that requires a metal ion in close proximity

B) proton transfer with a pK close to 4
C) proton donation that is mediated by a coenzyme
D) free proton surrounded by a hydrophobic environment
E) redox cofactor

Ans: B
Level of Difficulty: Moderate
Section: 11.3.A
Learning objective: Catalytic Mechanisms

31. The catalytic mechanism of bovine pancreatic RNase A relies upon acid-base catalysis
involving the amino acid __________.

A) imidazole
B) lysine
C) histidine
D) aspartic acid
E) glutamic acid

Ans: C
Level of Difficulty: Easy
Section: 11.3.A
Learning objective: Catalytic Mechanisms

32. Consider the Schiff base formation reaction discussed in the catalytic mechanisms section of
the chapter. What would probably happen if the carboxylate group was stabilized by a nearby
positive charge?

A) The Schiff base would donate a lone pair of electrons to the substrate.
B) The Schiff base would form prior to decarboxylation.
C) The reaction would proceed with nucleophilic attack on the enzyme by the electrophilic
substrate.
D) All of the above would be possible given the discussed mechanism with a stabilized carboxyl
group.
E) None of the above is plausible considering the discussed mechanism with a stabilized
carboxylate group.

Ans: E
Level of Difficulty: Difficult
Section: 11.3.B
Learning objective: Catalytic Mechanisms
33. During the course of a catalytic reaction the following occurs: 1) Substrate is covalently
bound and oriented with proximity to the active site residues. 2) Negative charge builds up on
the substrate and is stabilized. 3) Oxidation of the enzyme followed by reduction to complete
the catalytic cycle. What type of chemical species can facilitate these reactions?

A) nucleophilic amino acids

B) electrophilic groups
C) prosthetic phosphate groups
D) transition metal anions
E) transition metal cations

Ans: E
Level of Difficulty: Moderate
Section: 11.3.C
Learning objective: Catalytic Mechanisms

34. Which of the following processes would yield and increase in rate?

A) the proximity of the reacting groups

B) the rotational motions of the substrates and catalytic groups
C) the orientations of the substrates and catalytic groups
D) all of the above
E) none of the above

Ans: D
Level of Difficulty: Easy
Section: 11.3.D
Learning objective: Catalytic Mechanisms

35. Enzymes that bind reaction transition states with greater affinity than substrates or products
A) have a lower free energy ES complex than E + S.
B) increase reaction rates by decreasing the concentration of the transition state .
C) progress slowly due to the stability of the transition state complex.
D) compensate for small differences in the energy of the free substrate and free product.
E) All of the above are correct.

Ans: A
Level of Difficulty: Difficult
Section: 11.3.E
Learning objective: Catalytic Mechanisms
36. Lysozyme requires _____ for effective catalysis.

I. an Asp in a nonpolar environment

II. a negatively charged Asp
III. a Glu that functions as an acid catalyst
IV. a Glu that is deprotonated

A) I, II, III, IV
B) I, III
C) II, III
D) II, IV
E) I, IV

Ans: C
Level of Difficulty: Moderate
Section: 11.4
Learning objective: Lysozyme

37. Zymogens are not enzymatically active because

A) the active site amino acids have been mutated.

B) they have not yet bound the proper cofactor.
C) their environment has the wrong pH.
D) they are not yet shaped such that essential proximity and orientation catalysis can occur.
E) None of the above is correct.

Ans: D
Level of Difficulty: Moderate
Section: 11.5.D
Learning objective: Serine Proteases

38. Serine proteases use _________ to catalyze the cleavage of a peptide bond.

I. covalent catalysis
II. proximity and orientation effects
III. general base catalysis
IV. electrostatic catalysis

A) I, II
B) II
C) III
D) I, II, III
E) I, II, III, IV
Ans: E
Level of Difficulty: Easy
Section: 11.5.C
Learning objective: Serine Proteases

39. Which of the following would result in the greatest decrease in function of the catalytic triad
found in serine proteases?

A) Mutation to Ser, Cys, Asp

B) Mutation to Ser, His, Asp
C) Mutation to Cys, His, Asp
D) Mutation to Ser, His, Glu
E) Mutation to Cys, His, Glu

Ans: C
Level of Difficulty: Difficult
Section: 11.5.B
Learning objective: Serine Proteases

40. In the lysozome reaction the D ring in NAM is in the ________ conformation providing a
contribution of catalytic energy via the ____ distortion.

A) half-chair; electrostatic
B) chair; strain
C) boat; strain
D) boat; electrostatic
E) half-chair; strain

Ans: E
Level of Difficulty: Easy
Section: 11.4.B
Learning objective: Lysozyme
41. Enzyme X catalyzes the addition of a hydroxyl group to substrate Y. In the process a metal
cofactor is reduced and then reoxidized. What class of enzyme is X?

A) oxidoreductase
B) ligase
C) hydrolase
D) isomerase
E) lyase

Ans: A
Level of Difficulty: Easy
Section: 11.1.A and B
Learning objective: General Properties of Enzymes

42. The transition state of an enzyme and substrate reaction

A) must always bind the enzyme active site with lower energy than the products.
B) is stabilized by enhancing the reverse reaction of E + S→ES.
C) is composed of true covalent bonds which decrease its energy.
D) is stabilized due to the specificity of the active site for the substrate.
E) is stabilized by decreasing the effective concentration.

Ans: D
Level of Difficulty: Moderate
Section: 11.2
Learning objective: Activation Energy and the Reaction Coordinate

43. Proximity effects

A) result from active site specificity.

B) result from substrate channeling.
C) result in increased effective concentration of substrate.
D) lower the energy of activation.
E) All of the above of the above are correct.

Ans: D
Level of Difficulty: Difficult
Section: 11.3.D
Learning objective: Catalytic Mechanisms
44. In the serine protease trypsin, the specificity for one substrate over another describes what
type of catalysis?

A) proximity
B) acid-base
C) covalent
D) strain
E) none of the above

Ans: A
Level of Difficulty: Moderate
Section: 11.5.A, B, C
Learning objective: Serine Proteases

45. Which type of catalysis may be carried out using redistribution of electron density to
facilitate the transfer of a proton?

I. proximity
II. acid-base
III. covalent
IV. strain

A) I
B) II
C) III
D) II, III
E) II, IV

Ans: D
Level of Difficulty: Difficult
Section: 11.3.B
Learning objective: Catalytic Mechanisms

46. In trypsin the specificity for one substrate over another comes from

A) the negatively charged pocket.

B) the positively charge pocket.
C) the hydrophobic pocket.
D) the amino acid serine.
E) the amino acid histidine.

Ans: A
Level of Difficulty: Easy
Section: 11.5.A, B, C
47. Which of the following is TRUE regarding transition state?

A) The free energy between the transition state and the reactants must be negative.
B) The transition state can be stabilized by covalent catalysis.
C) The transition state represents the ES complex.
D) Transition state analogs bind the substrate not the enzyme
E) All of the above are true.

Ans: B
Level of Difficulty: Moderate
Section: 11.2
Learning objective: Activation Energy and the Reaction Coordinate

48. Research scientists are trying to clone a gene. In order to accomplish this task they join two
pieces of DNA. Which class of the enzymes below might accomplish this task?

A) oxidoreductase
B) ligase
C) hydrolase
D) isomerase
E) lyase

Ans: B
Level of Difficulty: Moderate
Section: 11.1.A
Learning objective: General Properties of Enzymes
49. The enzyme pictured below is shown in two configurations, A (open) and B (closed). Upon
binding substrate in the active site, the enzyme converts the structure shown in B. Which of the
following is true based on the given information?

A) The enzyme requires a high concentration of substrate to function

B) This example exemplifies the “lock-and-key” model.
C) This enzyme must require ATP.
D) This example exemplifies the of “induced fit” model.
E) None of these are true.

Ans: D
Level of Difficulty: Moderate
Section: 11.1.B
Learning objective: General Properties of Enzymes

50. Why can histidine NOT act as a base in the lysosome (an organelle where the pH is close to
4.5)?

A) Histidine has a positive charge at pH 4.5.

B) Histidine has a side chain pK close to 6.
C) Histidine would be protonated at pH 4.5.
D) All of the above are correct.
E) None of the above is correct.

Ans: D
Level of Difficulty: Moderate
Section: 11.3.A
Learning objective: Catalytic Mechanisms
51. A recent discovery has suggested that a gene mutation results in several amino acid
substitutions within an active site. The following substitutions have been identified and are each
expected to form the active site:

Normal protein amino acids Substitutions

Valine Lysine
Leucine Arginine
Valine Arginine
Serine Deleted and replaced with a coenzyme capable of covalent
binding
Histidine Histidine (note no mutation)
Aspartate Glutamate

It was also noticed that a coenzyme molecule containing a hydroxyl (—OH) group binds to the
mutated protein in approximately the same location as the original serine but does not alter the
structure of the protein in anyway. Based on your knowledge of amino acids, enzymes, and
catalysis, which of the following is a REASONABLE conclusion?

A) The mutant protein cleaves on the carboxy side of phenylalanine.

B) The mutant protein cleaves peptide bonds on the carboxy side of glutamate or aspartate.
C) The mutant protein cleaves peptide bonds on the carboxy side of lysine or arginine.
D) The mutant protein functions identical to chymotrypsin.
E) The mutant protein has no function.

Ans: B
Level of Difficulty: Difficult
Section: 11.5.A, B, C
Learning objective: Serine Proteases
52. The following diagram shows a portion of a reaction sequence of an enzyme. What type(s)
of catalysis is (are) occurring in this first step?

A) proximity catalysis
B) acid-base catalysis
C) covalent catalysis
D) All of the above are occurring.
E) None of the above is occurring.

Ans: B
Level of Difficulty: Moderate
Section: 11.5.A, B, C
Learning objective: Serine Proteases

53. Acid-base catalysis may be accomplished by:

A) active site specificity

B) charge delocalization
C) buffer effects
D) induced strain
E) conformational change

Ans: B
Level of Difficulty: Difficult
Section: 11.3.A
Learning objective: Catalytic Mechanisms