Question 1

Which of the following best describes the role of the catalytic triad in chymotrypsin's mechanism of peptide bond hydrolysis?

Accepted Answer

It generates a highly reactive alkoxide ion from serine, which attacks the peptide carbonyl, with histidine acting as a base and aspartate orienting histidine.

Question 2

Which catalytic strategy is primarily used by carbonic anhydrase to accelerate the hydration of carbon dioxide?

Accepted Answer

Metal ion catalysis

Question 3

A mutation replaces serine 195 with alanine in chymotrypsin. What is the most likely effect on enzyme activity?

Accepted Answer

The enzyme will lose most of its activity because alanine cannot form the necessary covalent intermediate.

Question 4

Which of the following equations represents the hydrolysis of a peptide bond by a protease?

Accepted Answer

$$R_1CONH R_2$ + H_2O \rightarrow R_1COOH + R_2NH_2$$

Question 5

Why is the peptide bond resistant to hydrolysis under physiological conditions?

Accepted Answer

Because the peptide bond is stabilized by resonance, making the carbonyl carbon less electrophilic.

Question 6

Which experimental approach was used to identify the role of histidine 57 in chymotrypsin catalysis?

Accepted Answer

Affinity labeling with TPCK

Question 7

What is the function of the oxyanion hole in serine proteases such as chymotrypsin?

Accepted Answer

It stabilizes the negative charge on the tetrahedral intermediate during catalysis.

Question 8

Which of the following statements about the specificity pocket of chymotrypsin is correct?

Accepted Answer

It is deep and lined with hydrophobic residues, favoring binding of large hydrophobic side chains such as phenylalanine.

Question 9

Which of the following is a correct description of the catalytic mechanism of carbonic anhydrase?

Accepted Answer

A zinc ion activates a water molecule, lowering its $$pK_a to $$generate a nucleophilic hydroxide ion that attacks carbon dioxide.

Question 10

Which of the following best explains why buffers increase the rate of carbon dioxide hydration by carbonic anhydrase?

Accepted Answer

Buffers accept protons from the active site histidine, facilitating rapid regeneration of the nucleophilic hydroxide ion.

Question 11

Restriction enzymes such as EcoRV require which cofactor for catalytic activity?

Accepted Answer

Magnesium ions

Question 12

How do bacteria protect their own DNA from cleavage by their restriction enzymes?

Accepted Answer

By methylating specific bases within the recognition sequence, preventing enzyme binding and distortion.

Question 13

Which of the following is a real-world application of protease inhibitors?

Accepted Answer

Treatment of AIDS by inhibiting HIV aspartyl protease with drugs such as indinavir.

Question 14

Which of the following best describes the mechanism by which myosin couples ATP hydrolysis to mechanical work?

Accepted Answer

ATP hydrolysis causes a large conformational change in myosin, which is amplified from small changes at the active site to large movements at the carboxyl terminus.

Question 15

Which of the following is NOT a general catalytic strategy used by enzymes?

Accepted Answer

Substrate methylation

Question 16

Which of the following protease classes uses a histidine-activated cysteine to attack the peptide carbonyl group?

Accepted Answer

Cysteine proteases

Question 17

A chromogenic substrate is used to study chymotrypsin activity. What is the advantage of using such a substrate?

Accepted Answer

It generates a colored product upon cleavage, enabling kinetic measurements of enzyme activity.

Question 18

Which of the following statements about the evolution of the catalytic triad in proteases is correct?

Accepted Answer

The catalytic triad has independently evolved multiple times in different protease families.

Question 19

Which of the following best explains the importance of the P-loop structure in myosin and related enzymes?

Accepted Answer

It is a structural motif that binds nucleotides such as ATP, facilitating their hydrolysis.

Biochemistry Chapter 9: Catalytic Strategies – Study Notes

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