Question 1

Which of the following best describes the difference between convergent and divergent evolution in protein structure and function?

Accepted Answer

Convergent evolution results in proteins with similar functions and structures from different ancestral origins, while divergent evolution results in proteins with different functions from a common ancestor.

Question 2

Lysozymes are important antibacterial enzymes. Which of the following best describes their biological role?

Accepted Answer

They hydrolyze peptidoglycan by cleaving the glycosidic bond between N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) in bacterial cell walls.

Question 3

The active site of Hen Egg White Lysozyme (HEWL) binds six residues of its polymer substrate. What is the significance of the NAM lactyl group in substrate binding?

Accepted Answer

The NAM lactyl group causes steric hindrance, preventing it from fitting into certain binding sites (C & E) of the enzyme.

Question 4

Which two amino acid residues are critical for the catalytic activity of HEWL?

Accepted Answer

Glu35 and Asp52

Question 5

Phillips originally proposed an $$S_N1$$ mechanism for HEWL catalysis. What is the key feature of an $$S_N1$$ mechanism in this context?

Accepted Answer

Formation of a glycosyl/oxonium ion intermediate after departure of the leaving group, followed by nucleophilic attack.

Question 6

Withers proposed an $$S_N2$$ mechanism for HEWL. Which experimental evidence supports this mechanism?

Accepted Answer

The E35Q mutant and fluorinated substrate slow the reaction and allow trapping of a covalent intermediate.

Question 7

What is a major caveat in interpreting experiments that trap covalent intermediates in enzyme mechanisms?

Accepted Answer

Mutations or substrate modifications used to trap intermediates may perturb the natural mechanism of the enzyme.

Question 8

Why is closing the active site cleft, as seen in hexokinase, advantageous for catalysis?

Accepted Answer

It excludes bulk water, removes competing nucleophiles, and enhances polar interactions such as hydrogen bonds and salt bridges.

Question 9

Which of the following statements best describes the induced fit model of enzyme-substrate interaction?

Accepted Answer

The enzyme undergoes a conformational change upon substrate binding, optimizing the active site for catalysis.

Question 10

A mutation in HEWL replaces Glu35 with Gln (E35Q). What is the most likely effect on the enzyme's catalytic mechanism?

Accepted Answer

The mutation slows the reaction and allows trapping of a covalent intermediate, supporting an $$S_N2$$ mechanism.

Question 11

Which of the following is NOT a benefit of the enzyme active site closing around the substrate?

Accepted Answer

Increasing the dielectric constant to make the environment more like water.

Question 12

In the context of enzyme mechanisms, what does the term 'covalent catalysis' refer to?

Accepted Answer

The enzyme forms a transient covalent bond with the substrate during the reaction.

Question 13

Which of the following best explains why the NAG3 polymer is considered a poor substrate but a good inhibitor for HEWL?

Accepted Answer

It binds very tightly in the active site but is too short to be efficiently hydrolyzed.

Question 14

Which of the following statements about the lock-and-key and induced fit models is correct?

Accepted Answer

The lock-and-key model assumes a rigid active site, while the induced fit model involves conformational changes in the enzyme upon substrate binding.

Question 15

Which of the following is a key observation that supports the $$S_N2$$ mechanism for HEWL?

Accepted Answer

Trapping of a covalent intermediate using the E35Q mutant and a fluorinated substrate.

Question 16

A patient is found to have a mutation in a lysozyme gene that prevents the enzyme from closing its active site cleft. Which of the following is the most likely consequence?

Accepted Answer

The enzyme will be less efficient due to increased access of water and competing nucleophiles, leading to more side reactions.

Question 17

Which of the following best describes the role of Glu35 in the HEWL catalytic mechanism?

Accepted Answer

Acts as a general acid/base catalyst, donating and accepting protons during the reaction.

Question 18

In the context of protein evolution, which scenario best exemplifies convergent evolution?

Accepted Answer

Lysozymes from T4 phage and humans have similar functions but evolved independently from different ancestors.

Question 19

Which of the following is a fundamental difference between $$S_N1$$ and $$S_N2$$ mechanisms in enzyme catalysis?

Accepted Answer

$$S_N1$$ involves a two-step process with a carbocation intermediate, while $$S_N2 is a $$concerted one-step process with simultaneous bond making and breaking.

Enzyme Mechanisms: Lysozyme, Mechanistic Models, and Protein-Ligand Interactions

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