Fundamentals of Biochemistry: Life at the Molecular Level

Donald Voet, Judith G. Voet, Charlotte W. Pratt

Chapter 11

Enzymatic Catalysis - all with Video Answers

Educators

Chapter Questions

Problem 1

Choose the best description of an enzyme:
(a) It allows a chemical reaction to proceed extremely fast.
(b) It increases the rate at which a chemical reaction approaches equilibrium relative to its uncatalyzed rate.
(c) It makes a reaction thermodynamically favorable.

Temi Ajayi

Temi Ajayi

Numerade Educator

Problem 2

Which type of enzyme (Table $11-2$ ) catalyzes the following reactions?

Temi Ajayi

Numerade Educator

Problem 3

What is the relationship between the rate of an enzymecatalyzed reaction and the rate of the corresponding uncatalyzed reaction? Do enzymes enhance the rates of slow uncatalyzed reactions as much as they enhance the rates of fast uncatalyzed reactions?

Temi Ajayi

Numerade Educator

Problem 4

On the free energy diagram shown, label the intermediate(s) and transition state(s). Is the reaction thermodynamically favorable?

Temi Ajayi

Numerade Educator

Problem 5

Draw a transition state diagram of (a) a nonenzymatic reaction and the corresponding cnzyme-catalyzed reaction in which (b) S binds loosely to the enzyme and (c) S binds very tightly to the enzyme. Compare $\Delta G^{\prime}$ for each case. Why is tight binding of $\mathrm{S}$ not advantageous?

Temi Ajayi

Numerade Educator

Problem 6

Approximately how much does staphylococcal nuclease (Table $11-1$ ) decrease the activation free energy $\left(\Delta G^{*}\right)$ of its reaction (the hydrolysis of a phosphodiester bond) at $25^{\circ} \mathrm{C} ?$

Temi Ajayi

Numerade Educator

Problem 7

Studies at different $\mathrm{pH}$ 's show that an enzyme has two catalytically important residues whose $\mathrm{pK}$ 's are -4 and -10 . Chemical modification experiments indicate that a Glu and a Lys residue are essential for activity. Match the residues to their $\mathrm{pK}$ 's and explain whether they are likely to act as acid or base catalysts.

Temi Ajayi

Numerade Educator

Problem 8

The covalent catalytic mechanism of an enzyme depends on a single active site Cys whose $p K$ is $8 .$ A mutation in a nearby residue alters the microenvironment so that this $\mathrm{p} K$ increases to $10 .$ Would the mutation cause the reaction rate to increase or decrease? Explain.

Temi Ajayi

Numerade Educator

Problem 9

Explain why RNase A cannot catalyze the hydrolysis of DNA.

Temi Ajayi

Numerade Educator

Problem 10

Suggest a transition state analog for proline racemase that differs from those discussed in the text. Justify your suggestion.

Temi Ajayi

Numerade Educator

Problem 11

Wolfenden has stated that it is meaningless to distinguish between the "binding sites" and the "catalytic sites" of enzymes. Explain.

Temi Ajayi

Numerade Educator

Problem 12

Explain why lysozyme cleaves the artificial substrate (NAG)
-4000 times more slowly than it cleaves (NAG).

Temi Ajayi

Numerade Educator

Problem 13

Lysozyme residues Asp 101 and Arg 114 are required for efficient catalysis, although they are located at some distance from the active site Glu 35 and Asp $52 .$ Substituting Ala for either Asp 101 or Arg 114 does not significantly alter the enZyme's tertiary structure, but it significantly reduces its catalytic activity, Explain.

Jennifer Stoner

Jennifer Stoner

Numerade Educator

Problem 14

Design a chloromethylketone inhibitor of elastase.

John Nicolle

Numerade Educator

Problem 15

Under certain conditions, peptide bond formation rather than peptide bond hydrolysis is thermodynamically favorable. Would you expect chymotrypsin to catalyze peptide bond formation?

Mariana Roldan

Numerade Educator

Problem 16

Diagram the hydrogen-bonding interactions of the catalytic triad His-Lys Ser during catalysis in a hypothetical hydrolytic enzyme.

Temi Ajayi

Numerade Educator

Problem 17

The comparison of the active site geometries of chymotrypsin and subtilisin under the assumption that their similarities have catalytic significance has led to greater mechanistic understanding of both these enzymes. Discuss the validity of this strategy.

Hailey Tomashek

Hailey Tomashek

Numerade Educator

Problem 18

Predict the effect of mutating Asp 102 of trypsin to Asn (a) on substrate binding and (b) on catalysis.

Prashant Bana

Numerade Educator

Problem 19

A genetic defect in coagulation factor IX causes hemophilia b,
a disease characterized by a tendency to bleed profusely after very minor trauma. However, a genetic defect in coagulation factor XI has only mild clinical symptoms, Explain this discrepancy in terms of the mechanism for activation of coagulation proteases shown in Box $11-4$.

Jennifer Stoner

Jennifer Stoner

Numerade Educator

Problem 20

Why is the broad substrate specificity of chymotrypsin advantageous in vivo? Why would this be a disadvantage for some other proteases?

Sam Limsuwannarot

Sam Limsuwannarot

Numerade Educator

Problem 21

Tofu (bean curd), a high-protein soybean product, is prepared in such a way as to remove the trypsin inhibitor present in soybeans. Explain the reason(s) for this treatment.

Emily Himsel

Numerade Educator