Biochemistry

For the reaction of glucose with oxygen to produce carbon dioxide and water, Glucose $+6 \mathrm{O}_{2} \rightarrow 6 \mathrm{CO}_{2}+6 \mathrm{H}_{2} \mathrm{O}$ the $\Delta G^{\circ}$ is $-2880 \mathrm{kJ} \mathrm{mol}^{-1}$, a strongly exergonic reaction. However, a sample of glucose can be maintained indefinitely in an oxygencontaining atmosphere. Reconcile these two statements.

Sam Limsuwannarot

Numerade Educator

00:28

Problem 6

Would nature rely on the same enzyme to catalyze a reaction either way (forward or backward) if the $\Delta G^{\circ}$ were -0.8 kcal mol $^{-1}$ ? If it were -5.3 kcal mol $^{-1}$ ?

Sam Limsuwannarot

Numerade Educator

Problem 7

Suggest a reason why heating a solution containing an enzyme markedly decreases its activity. Why is the decrease of activity frequently much less when the solution contains high concentrations of the substrate?

Sam Limsuwannarot

Numerade Educator

Problem 8

A model is proposed to explain the reaction catalyzed by an enzyme. Experimentally obtained rate data fit the model to within experimental error. Do these findings prove the model?

Sam Limsuwannarot

Numerade Educator

Problem 9

Does the presence of a catalyst alter the standard free energy change of a chemical reaction?

Sam Limsuwannarot

Numerade Educator

00:08

Problem 10

What effect does a catalyst have on the activation energy of a reaction?

Sam Limsuwannarot

Numerade Educator

Problem 11

An enzyme catalyzes the formation of ATP from ADP and phosphate ion. What is its effect on the rate of hydrolysis of ATP to ADP and phosphate ion?

Sam Limsuwannarot

Numerade Educator

Problem 12

Can the presence of a catalyst increase the amount of product obtained in a reaction?

Sam Limsuwannarot

Numerade Educator

00:16

Problem 13

For the hypothetical reaction $3 A+2 B \rightarrow 2 C+3 D$ the rate was experimentally determined to be Rate $=k[\mathrm{A}]^{1}[\mathrm{B}]^{1}$ What is the order of the reaction with respect to A? With respect to B? What is the overall order of the reaction? Suggest how many molecules each of $\mathrm{A}$ and $\mathrm{B}$ are likely to be involved in the detailed mechanism of the reaction.

Sam Limsuwannarot

Numerade Educator

00:19

Problem 14

The enzyme lactate dehydrogenase catalyzes the reaction Pyruvate $+\mathrm{NADH}+\mathrm{H}^{+} \rightarrow$ lactate $+\mathrm{NAD}^{+}$ NADH absorbs light at $340 \mathrm{nm}$ in the near-ultraviolet region of the electromagnetic spectrum, but $\mathrm{NAD}^{+}$ does not. Suggest an experimental method for following the rate of this reaction, assuming that you have available a spectrophotometer capable of measuring light at this wavelength.

Sam Limsuwannarot

Numerade Educator

Problem 15

Would you use a pH meter to monitor the progress of the reaction described in Question 14 ? Why or why not?

Sam Limsuwannarot

Numerade Educator

Problem 16

Suggest a reason for carrying out enzymatic reactions in buffer solutions.

Sam Limsuwannarot

Numerade Educator

00:19

Problem 17

Distinguish between the lock-and-key and induced-fit models for binding of a substrate to an enzyme.

Sam Limsuwannarot

Numerade Educator

02:23

Problem 18

Using an energy diagram, show why the lock-and-key model could lead to an inefficient enzyme mechanism. Hint: Remember that the distance to the transition state must be minimized for an enzyme to be an effective catalyst.

Yokshitha Reddy Bathula

Numerade Educator

Problem 19

Other things being equal, what is a potential disadvantage of an enzyme having a very high affinity for its substrate?

Sam Limsuwannarot

Numerade Educator

00:07

Problem 20

Amino acids that are far apart in the amino acid sequence of an enzyme can be essential for its catalytic activity What does this suggest about its active site?

Sam Limsuwannarot

Numerade Educator

Problem 21

If only a few of the amino acid residues of an enzyme are involved in its catalytic activity, why does the enzyme need such a large number of amino acids?

Sam Limsuwannarot

Numerade Educator

00:21

Problem 22

Show graphically how the reaction velocity depends on the enzyme concentration. Can a reaction be saturated with enzyme?

Sam Limsuwannarot

Numerade Educator

00:24

Problem 23

Define steady state, and comment on the relevance of this concept to theories of enzyme reactivity.

Sam Limsuwannarot

Numerade Educator

00:11

Problem 24

How is the turnover number of an enzyme related to $V_{\max }$ ?

Sam Limsuwannarot

Numerade Educator

00:27

Problem 25

For an enzyme that displays Michaelis-Menten kinetics, what is the reaction velocity, $\left.V \text { (as a percentage of } V_{\max }\right)$, observed at the following values?
(a) $[\mathrm{S}]=K_{\mathrm{M}}$
(b) $[\mathrm{S}]=0.5 K_{\mathrm{M}}$
(c) $[\mathrm{S}]=0.1 K_{\mathrm{M}}$
(d) $[\mathrm{S}]=2 K_{\mathrm{M}}$
$(\mathrm{e})[\mathrm{S}]=10 K_{\mathrm{Y}}$

Sam Limsuwannarot

Numerade Educator

00:23

Problem 26

Determine the values of $K_{\mathrm{M}}$ and $V_{\max }$ for the decarboxylation of a $\beta$ -keto acid given the following data.
$$\begin{array}{cc}\text { Substrate Concentration }\left(\mathrm{mol} \mathrm{L}^{-1}\right) & \text {Velocity }\left(\mathrm{m} M \mathrm{min}^{-1}\right) \\2.500 & 0.588 \\1.000 & 0.500 \\0.714 & 0.417 \\0.526 & 0.370 \\0.250 & 0.256 \\\hline\end{array}$$

Sam Limsuwannarot

Numerade Educator

Problem 27

The kinetic data in the following table were obtained for the reaction of carbon dioxide and water to produce bicarbonate and hydrogen ion catalyzed by carbonic anhydrase: $\mathrm{CO}_{2}+\mathrm{H}_{2} \mathrm{O} \rightarrow \mathrm{HCO}_{3}^{-}+\mathrm{H}^{+}$
$$\begin{array}{cc}\text { Carbon Dioxide Concentration } & \text { 1/Velocity } \\\left(\mathrm{mmol} \mathrm{L}^{-1}\right) &\left(M^{-1} \mathrm{sec}\right) \\1.25 & 36 \times 10^{3} \\2.5 & 20 \times 10^{3} \\5.0 & 12 \times 10^{3} \\20.0 & 6 \times 10^{9} \\
\hline\end{array}$$

Sam Limsuwannarot

Numerade Educator

00:07

Problem 28

The enzyme $\beta$ -methylaspartase catalyzes the deamination of $\beta$ -methylaspartate
[V. Williams and J. Selbin, J. Biol. Chem. 239, 1636(1964) ]. The rate of the reaction was determined by monitoring the absorbance of the product at $240 \mathrm{nm}\left(\mathrm{A}_{240}\right) .$ From the data in the following table, determine $K_{\mathrm{M}}$ for the reaction. How does the method of calculation differ from that in Questions 26 and 27 ?
$$\begin{array}{cc}\text { Substrate Concentration }\left(\mathrm{mmol} \mathrm{L}^{-1}\right) & \text {Velocity }\left(\Delta\mathrm{A}_{240} \mathrm{min}^{-1}\right) \\ 0.002 & 0.045 \\0.005 & 0.115 \\0.020 & 0.285 \\0.040 & 0.380 \\0.060 & 0.460 \\0.080 & 0.475 \\0.100 & 0.505 \\ \hline\end{array}$$

Sam Limsuwannarot

Numerade Educator

00:20

Problem 29

The hydrolysis of a phenylalanine-containing peptide is catalyzed by $\alpha$ -chymotrypsin with the following results. Calculate $K_{\mathrm{M}}$ and $V_{\max }$ for the reaction.
$$\begin{array}{cc}\text { Peptide Concentration }(M) & \text { Velocity }\left(M \min ^{-1}\right) \\2.5 \times 10^{-4} & 2.2 \times 10^{-6}\\5.0 \times 10^{-4} & 5.8 \times 10^{-6} \\10.0 \times 10^{-4} & 5.9 \times 10^{-6} \\15.0 \times 10^{-4} & 7.1 \times 10^{-6} \\\hline\end{array}$$

Sam Limsuwannarot

Numerade Educator

00:15

Problem 30

For the $V_{\max }$ obtained in Question $26,$ calculate the turnover number (catalytic rate constant) assuming that $1 \times$ $10^{-4}$ mol of enzyme were used.

Sam Limsuwannarot

Numerade Educator

Problem 31

You do an enzyme kinetic experiment and calculate a $V_{\max }$ of 100 \mumol of product per minute. If each assay used $0.1 \mathrm{mL}$ of an enzyme solution that had a concentration of $0.2 \mathrm{mg} /$ $\mathrm{mL},$ what would be the turnover number if the enzyme had a molecular weight of $128,000 \mathrm{g} / \mathrm{mol}$ ?

Sam Limsuwannarot

Numerade Educator

00:19

Problem 32

The enzyme D-amino acid oxidase has a very high turnover number because the $\mathrm{p}$ -amino acids are potentially toxic. The $K_{\mathrm{M}}$ for the enzyme is in the range of 1 to $2 \mathrm{m} M$ for the aromatic amino acids and in the range of 15 to $20 \mathrm{m} M$ for such amino acids as serine, alanine, and the acidic amino acids. Which of these amino acids are the preferred substrates for the enzyme?

Sam Limsuwannarot

Numerade Educator

Problem 33

Why is it useful to plot rate data for enzymatic reactions as a straight line rather than as a curve?

Sam Limsuwannarot

Numerade Educator

Problem 34

Under what conditions can we assume that $K_{\mathrm{M}}$ indicates the binding affinity between substrate and enzyme?

Sam Limsuwannarot

Numerade Educator

Problem 35

Why does acetazolamide make beer taste flat?

Sam Limsuwannarot

Numerade Educator

Problem 36

How did scientists determine that carbonic anhydrase is a chemical sensor for $\mathrm{CO}_{2}$ ?

Sam Limsuwannarot

Numerade Educator

Problem 37

How do the $K_{\mathrm{M}}$ values for glucokinase and hexokinase reflect their roles in sugar metabolism?

Sam Limsuwannarot

Numerade Educator

00:20

Problem 38

When does the $k_{\mathrm{ral}} / K_{\mathrm{M}}$ value approximate the catalytic efficiency of an enzyme?

Sam Limsuwannarot

Numerade Educator

Problem 39

What are the three most common mechanisms for enzymecatalyzed reactions that have two substrates?

Sam Limsuwannarot

Numerade Educator

00:16

Problem 40

What is the biggest difference between a ping-pong mechanism and either an ordered mechanism or random mechanism?

Sam Limsuwannarot

Numerade Educator

00:15

Problem 41

How do scientists determine the $K_{\mathrm{M}}$ of a substrate that is part of an ordered reaction with two substrates?

Sam Limsuwannarot

Numerade Educator

Problem 42

If you graph the velocity of an enzyme-catalyzed reaction vs. a $[\mathrm{S}]$ for each of two substrates that are part of a random mechanism, would you expect to see the same shape curve? Why or why not?

Sam Limsuwannarot

Numerade Educator

00:16

Problem 43

Show graphically the dependence of reaction velocity on substrate concentration for an enzyme that follows MichaelisMenten kinetics and for an allosteric enzyme.

Sam Limsuwannarot

Numerade Educator

00:09

Problem 44

Do all enzymes display kinetics that obey the MichaelisMenten equation? Which ones do not?

Sam Limsuwannarot

Numerade Educator

Problem 45

How can you recognize an enzyme that does not display Michaelis-Menten kinetics?

Sam Limsuwannarot

Numerade Educator

Problem 46

If we describe an enzyme like aspartate transcarbamoylase and say that it exhibits cooperativity, what do we mean?

Sam Limsuwannarot

Numerade Educator

Problem 47

How can competitive and pure noncompetitive inhibition be distinguished in terms of $K_{\mathrm{M}}$ ?

Sam Limsuwannarot

Numerade Educator

00:09

Problem 48

Why does a competitive inhibitor not change $V_{\max } ?$

Sam Limsuwannarot

Numerade Educator

Problem 49

Why does a pure noncompetitive inhibitor not change the observed $K_{\mathrm{M}}$

Sam Limsuwannarot

Numerade Educator

00:29

Problem 50

Distinguish between the molecular mechanisms of competitive and noncompetitive inhibition.

Sam Limsuwannarot

Numerade Educator

00:06

Problem 51

Can enzyme inhibition be reversed in all cases?

Sam Limsuwannarot

Numerade Educator

Problem 52

Why is a Lineweaver-Burk plot useful in analyzing kinetic data from enzymatic reactions?

Sam Limsuwannarot

Numerade Educator

Problem 53

Where do lines intersect on a Lineweaver-Burk plot showing competitive inhibition? On a Lineweaver-Burk plot showing noncompetitive inhibition?

Sam Limsuwannarot

Numerade Educator

00:11

Problem 54

What is the difference between pure and mixed noncompetitive inhibition?

Sam Limsuwannarot

Numerade Educator

Problem 55

Why can we say that having a pure noncompetitive inhibitor present is similar to just having less enzyme present?

Sam Limsuwannarot

Numerade Educator

00:23

Problem 56

When we compare the binding of I and of S to the enzyme in a mixed noncompetitive inhibitor, we assumed that the binding of I decreased the affinity of the enzyme for S. What would happen if the opposite were true?

Sam Limsuwannarot

Numerade Educator

Problem 57

Why does the apparent $K_{\mathrm{M}}$ decrease in the presence of an uncompetitive inhibitor?

Sam Limsuwannarot

Numerade Educator

Problem 58

What is a suicide substrate? Why are they important?

Sam Limsuwannarot

Numerade Educator

Problem 59

If we made a Lineweaver-Burk plot of an irreversible inhibitor, which type of reversible inhibition would it be most likely to resemble?

Sam Limsuwannarot

Numerade Educator

00:21

Problem 60

Draw Lineweaver-Burk plots for the behavior of an enzyme for which the following experimental data are available.
$$\begin{array}{ccc}{[\mathrm{S}]} & V, \text { No Inhibitor } & V, \text { Inhibitor Present } \\(\mathrm{mM}) & \left(\mathrm{mmol} \mathrm{min}^{-1}\right) & \left(\mathrm{mmol} \mathrm{min}^{-1}\right) \\3.0 & 4.58 & 3.66 \\5.0 & 6.40 & 5.12 \\7.0 & 7.72 & 6.18 \\
9.0 & 8.72 & 6.98 \\11.0 & 9.50 & 7.60 \\\hline\end{array}$$
What are the $K_{\mathrm{M}}$ and $V_{\max }$ values for the inhibited and uninhibited reactions? Is the inhibitor competitive or noncompetitive?

Sam Limsuwannarot

Numerade Educator

Problem 61

For the following aspartase reaction (see Question 28 ) in the presence of the inhibitor hydroxymethylaspartate, determine $K_{\mathrm{M}}$ and whether the inhibition is competitive or noncompetitive.
$$\begin{array}{ccc}{[\mathrm{S}]} & V, \text { No Inhibitor } & V, \text { Inhibitor Present } \\(\text { molarity }) & (\text { arbitrary units })& (\text { same arbitrary units }) \\1 \times 10^{-4} & 0.026 & 0.010 \\5 \times 10^{-4} & 0.092 & 0.040 \\1.5 \times 10^{-3} & 0.136 & 0.086\\2.5 \times 10^{-3} & 0.150 & 0.120 \\5 \times 10^{-3} & 0.165 & 0.142 \\\hline\end{array}$$

Sam Limsuwannarot

Numerade Educator

00:11

Problem 62

Is it good (or bad) that enzymes can be reversibly inhibited? Why?

Sam Limsuwannarot

Numerade Educator

Problem 63

Noncompetitive inhibition is a limiting case in which the effect of binding inhibitor has no effect on the affinity for the substrate and vice versa. Suggest what a Lineweaver-Burk plot would look like for an inhibitor that had a reaction scheme similar to that on page 151 (noncompetitive inhibition reaction), but where binding inhibitor lowered the affinity of EI for the substrate.

Sam Limsuwannarot

Numerade Educator

Problem 64

You have been hired by a pharmaceutical company to work on development of drugs to treat AIDS. What information from this chapter will be useful to you?

Sam Limsuwannarot

Numerade Educator