Chapter 3 Study Questions

The study of enzymes also includes an examination of how the activity is regulated. Molecules that can act as competitive inhibitors for a specific reaction are often similar in shape and size to the enzyme's substrate. Which variable or variables used to describe enzyme activity will remain the same in the presence and absence of a competitive inhibitor? a. Vmax b. V c. Vmax and Km d. Km

Vmax

Chemical reactions carried out by living systems depend on the ability of some organisms to capture and use atoms from nonliving sources in the environment. The specific subset of these reactions that break down nutrients in food can be described as a. metabolic. b. catabolic. c. anabolic. d. biosynthetic.

catabolic

Isomerization of glucose 1-phosphate to glucose 6-phosphate is energetically favorable. At 37°C, ΔG° = −1.42 log10K. What is the equilibrium constant for this reaction if ΔG° = −1.74 kcal/mole at 37°C? a. 16.98 b. 0.09 c. −0.09 d. 0.39

16.98

Indicate whether the following statements about enzymes are TRUE or FALSE. If a statement is false, explain why it is false. A. Enzymes alter the equilibrium point of a reaction. B. Vmax can be determined by measuring the amount of product accumulated late in the reaction. C. Competitive inhibitors bind irreversibly to the enzyme active site, lowering Vmax.

A. False. An enzyme catalyzes its reaction in both directions, lowering the energy of activation for both the forward and reverse reactions. Enzymes do not affect the free energy of the reactants and products, and thus they do not affect the reaction equilibrium. B False. Initial reaction velocities are measured to determine Vmax. C. False. Competitive inhibitors bind reversibly to an enzyme's active site.

Indicate whether the following statements are TRUE or FALSE. If a statement is false, explain why it is false. A. Reactions that are energetically favorable occur rapidly because there is no energy of activation. B. Enzymes accelerate reactions by transferring energy to reactant molecules. C. Spontaneous reactions are characterized by a negative change in free energy.

A. False. Reactions that are energetically favorable are spontaneous, but do not always occur rapidly. And, even though there is a net negative change in free energy for the reaction, there is still activation energy required for substrate molecules to react and yield products. B. False. Enzymes catalyze reactions by reducing the activation energy required for reactants to yield products. C. True

When there is an excess of nutrients available in the human body, insulin is released to stimulate the synthesis of glycogen from glucose. This is a specific example of a/an __________ process, a general process in which larger molecules are made from smaller molecules. a. metabolic b. catabolic c. anabolic d. biosynthetic

anabolic

The study of enzyme kinetics is usually performed with purified components and requires the characterization of several aspects of the reaction, including the rate of association with the substrate, the rate of catalysis, and: a. the enzyme's structure. b. the optimal pH of the reaction. c. the subcellular localization of the enzyme. d. the regulation of the enzyme activity.

d. the regulation of the enzyme activity.

Activated carriers store energy in different types of high energy bonds. Match the groups used in high-energy linkages (A-F) for each of the of the activated carriers (1-8). Group letters may be used more than once. A. glucose B. electrons and hydrogens C. carboxyl group D. phosphate E. methyl group F. acetyl group 1. _____ ATP 2. _____ NADH 3. _____ acetyl CoA 4. _____ carboxylated biotin 5. _____ NADPH 6. _____ S-adenosylmethionine 7. _____ FADH2 8. _____ uridine diphosphate glucose

1. D (phosphate) 2. B. (electrons and hydrogens) 3. F. (acetyl group) 4. C. (carboxyl group) 5. B. (electrons and hydrogens) 6. E. (methyl group) 7. B. (electrons and hydrogens) 8. A. (glucose)

In the first stage of photosynthesis, light energy can be converted into what other form, or forms, of energy? There may be more than one answer. a. electrical b. chemical c. potential d. kinetic

A, D

Arrange the following molecules in order with respect to their relative levels of oxidation (assign 5 to the most oxidized and 1 to the most reduced). _______ CH2O (formaldehyde) _______ CH4 (methane) _______ CHOOH (formic acid) _______ CH3OH (methanol) _______ CO2 (carbon dioxide)

__3__ CH2O (formaldehyde) __1__ CH4 (methane) __4__ CHOOH (formic acid) __2__ CH3OH (methanol) __5__ CO2 (carbon dioxide)

The net distance a molecule travels through the cytosol via diffusion is relatively short in comparison with the total distance it may need to travel. This is because movement governed by diffusion alone is a __________ process that is most effective for the dispersion of small molecules over short distances. a. slow b. random c. regulated d. complicated

a. slow

The equilibrium constant for complex formation between molecules A and B will depend on their relative concentrations, as well as the rates at which the molecules associate and dissociate. The association rate will be larger than the dissociation rate when complex formation is favorable. The energy that drives this process is referred to as __________ energy. a. dissociation b. association c. binding d. releasing

binding

ΔG° indicates the change in the standard free energy as a reactant is converted to product. Given what you know about these values, which reaction below is the most favorable? a. ADP + Pi → ATP (ΔG° = +7.3 kcal/mole) b. glucose 1-phosphate → glucose 6-phosphate (ΔG° = −1.7 kcal/mole) c. glucose + fructose → sucrose (ΔG° = +5.5 kcal/mole) d. glucose → CO2 + H2O (ΔG° = −686 kcal/mole)

d.

If proteins A and B have complementary surfaces, they may interact to form the dimeric complex AB. Which of the following is the correct way to calculate the equilibrium constant for the association between A and B? a. kon/koff = K b. K = [A][B]/[AB] c. K = [AB]/[A][B] d. (A) and (C)

d. (A) and (C)

NADH and NADPH are activated carrier molecules that function in completely different metabolic reactions. Both carry two additional __________ and one additional __________. This combination can also be referred to as a hydride ion. a. protons; electron. b. electrons; phosphate. c. hydrogens; electron. d. electrons; proton.

electrons; proton

Chemical reactions that lead to a release of free energy are referred to as "energetically favorable." Another way to describe these reactions is: a. uphill. b. uncatalyzed. c. spontaneous. d. activated.

spontaneous

For the reaction Y→X at standard conditions with [Y] = 1 M and [X] = 1 M, ΔG is initially a large negative number. As the reaction proceeds, [Y] decreases and [X] increases until the system reaches equilibrium. How do the values of ΔG and ΔG° change as the reaction equilibrates? a. ΔG becomes less negative and ΔG° stays the same. b. ΔG becomes positive and ΔG° becomes positive. c. ΔG stays the same and ΔG° becomes less negative. d.ΔG reaches zero and ΔG° becomes more negative

ΔG becomes less negative and ΔG° stays the same.

During respiration, energy is retrieved from the high-energy bonds found in certain organic molecules. Which of the following, in addition to energy, are the ultimate products of respiration? a. CO2; H2O b. CH3; H2O c. CH2OH; O2 d. CO2; O2

CO2; H2O

The energy used by the cell to generate specific biological molecules and highly ordered structures is stored in the form of a. Brownian motion. b. heat. c. light waves. d. chemical bonds.

chemical bonds

Energy cannot be created or destroyed, but it can be converted into other types of energy. Cells harvest some of the potential energy in the chemical bonds of foodstuffs to generate stored chemical energy in the form of activated carrier molecules, which are often employed to join two molecules together in __________ reactions. a. oxidation b. hydrolysis c. condensation d. dehydrogenation

condensation

You are studying a biochemical pathway that requires ATP as an energy source. To your dismay, the reactions soon stop, partly because the ATP is rapidly used up and partly because an excess of ADP builds up and inhibits the enzymes involved. You are about to give up when the following table from a biochemistry textbook catches your eye. Which of the following reagents is/are most likely to revitalize your reaction? a. a vast excess of ATP b. glucose 6-phosphate and enzyme D c. creatine phosphate and enzyme A d. pyrophosphate

creatine phosphate and enzyme A

Unlike what occurs when fuel is burned to make a fire, all living systems use the energy from heat-generating reactions to create and maintain a. movement. b. order. c. light. d. electricity

order

Even though cellular macromolecules contain a large number of carbon and hydrogen atoms, they are not all spontaneously converted into CO2 and H2O. This absence of spontaneous combustion is due to the fact that biological molecules are relatively __________ and an input of energy is required to reach lower energy states. a. large b. polar c. stable d. unstable

stable

In the case of a simple conversion reaction such as X→Y, which value of ΔG° is associated with a larger concentration of X than Y at equilibrium? (Hint: How is ΔG° related to K?) a. ΔG° = −5 b. ΔG° = −1 c. ΔG° = 0 d. ΔG° = 1

ΔG° = 1

A. activation B. chemical bond C. completely D. favorable E. free F. kinetic G. rapidly H. selectively I. slowly J. unfavorable 1. By definition, catalysis allows a reaction to occur more __________. 2. Chemical reactions occur only when there is a loss of __________ energy. 3. Enzymes act more __________ than other catalysts. 4. A catalyst decreases the __________ energy of a reaction.

1. G. rapidly 2. E. free 3. H. selectively 4. A. activation

What information regarding an enzyme-catalyzed reaction is obtained in a plot of the inverse of the initial velocities against the inverse of the corresponding substrate concentrations? a. 1/Vmax and 1/Km b. 1/V and 1/[S] c. Vmax and Km d. V and [S]

1/Vmax and 1/Km

Oxidation is a favorable process in an aerobic environment, which is the reason cells are able to derive energy from the oxidation of macromolecules. Once carbon has been oxidized to __________, its most stable form, it can only cycle back into the organic portion of the carbon cycle through __________. a. CO2; photosynthesis. b. CH3; combustion. c. CO2; respiration. d. CO; reduction.

CO2; photosynthesis

Protein E can bind to two different proteins, S and I. The binding reactions are described by the following equations and values: E + S → ES Keq for ES = 10 E + I → EI Keq for EI = 2 a. E binds I more tightly than S. b. When S is present in excess, no I molecules will bind to E. c. The binding energy of the ES interaction is greater than that of the EI interaction. d. Changing an amino acid on the binding surface of I from a basic amino acid to an acidic one will probably make the free energy of association with E more negative.

The binding energy of the ES interaction is greater than that of the EI interaction.

Which of the following statements is FALSE for a favorable binding reaction? a. The free-energy change is negative for the system. b. The concentration of the complex remains lower than the concentration of the unbound components. c. The complex dissociation rate is slower than the rate for component association. d. The binding energy for the association is large and negative.

The concentration of the complex remains lower than the concentration of the unbound components.

The small molecule cyclic AMP (cAMP) takes about 0.2 second to diffuse 10 μm, on average, in a cell. Suppose that cAMP is produced near the plasma membrane on one end of the cell; how long will it take for this cAMP to diffuse through the cytosol and reach the opposite end of a very large cell, on average? Assume that the cell is 200 μm in diameter. a. 4 seconds b. 16 seconds c. 80 seconds d. 200 seconds

a. 4 seconds

Figure 3-20 is an energy diagram for the reaction X→Y. Which equation below provides the correct calculation for the amount of free-energy change when X is converted to Y? a. a + b − c b. a − b c. a − c d. c − a

c − a

The graph in Figure 3-34 illustrates the relationship between reaction rates and substrate concentration for an enzyme-catalyzed reaction. What does the Km value indicate with respect to enzyme-substrate interactions? a. the maximum rate of catalysis b. the number of enzyme active sites c. the enzyme-substrate binding affinity d. the equilibrium rate of catalysis

c. the enzyme-substrate binding affinity

The equilibrium constant (K) for the reaction Y→X can be expressed with respect to the concentrations of the reactant and product molecules. Which of the expressions below shows the correct relationship between K, [Y], and [X]? a. K = [Y]/[X] b. K = [Y] * [X] c. K = [X]/[Y] d. K = [X] − [Y]

K = [X]/[Y]

The maximum velocity (Vmax) of an enzymatic reaction is an important piece of information regarding how the enzyme works. What series of measurements can be taken in order to infer the maximum velocity of an enzyme-catalyzed reaction? a. the rate of substrate consumption after the system reaches equilibrium, for several reactant concentrations b. the rate of product consumption shortly after mixing the enzyme and substrate c. the rate of substrate consumption at high levels of enzyme concentration d. the rate of substrate consumption shortly after mixing the enzyme and substrate, for several substrate concentrations

d. the rate of substrate consumption shortly after mixing the enzyme and substrate, for several substrate concentrations

The second law of thermodynamics states that the disorder in any system is always increasing. In simple terms, you can think about dropping NaCl crystals into a glass of water. The solvation and diffusion of ions is favored because there is an increase in: a. pH. b. entropy. c. ions. d. stored energy.

entropy

A chemical reaction is defined as spontaneous if there is a net loss of free energy during the reaction process. However, spontaneous reactions do not always occur rapidly. Favorable biological reactions require __________ to selectively speed up reactions and meet the demands of the cell. a. heat b. ATP c. ions d. enzymes

enzymes

At first glance, it may seem that living systems are able to defy the second law of thermodynamics. However, on closer examination, it becomes clear that although cells create organization from raw materials in the environment, they also contribute to disorder in the environment by releasing a. water. b. radiation. c. heat. d. proteins.

heat

ΔG measures the change of free energy in a system as it converts reactant (Y) into product (X). When [Y] = [X], ΔG is equal to a. ΔG° + RT. b. RT. c. ln [X]/[Y]. d. ΔG°.

ΔG°

Fill in the blanks, selecting from the choices below. CO, CO2, O2, H2, H2O, N2, NO Light + _________ + _________ → _________ + heat + sugars

H2O, CO2, O2

Oxidation is the process by which oxygen atoms are added to a target molecule. Generally, the atom that is oxidized will experience which of the following with respect to the electrons in its outer shell? a. a net gain b. a net loss c. no change d. an equal sharing

a net loss

The best way to know if an organic molecule has been reduced is to see if there was an increase in the number of __________ bonds. a. C-H b. C-O c. H-H d. C-N

C-H

The graph in Figure 3-34 illustrates the change in the rate of an enzyme-catalyzed reaction as the concentration of substrate is increased. Which of the values listed below is used to calculate the enzyme turnover number? a. ½Vmax b. Km c. Vmax d. Vmax − Km

c. Vmax

The reduction of a molecule can sometimes result in the acquisition of a proton, a reaction referred to as a. protonation. b. neutralization. c. hydrogenation. d. isomerization.

hydrogenation

The potential energy stored in high-energy bonds is commonly harnessed when the bonds are split by the addition of __________ in a process called __________. a. ATP; phosphorylation b. water; hydrolysis c. hydroxide; hydration d. acetate; acetylation

water; hydrolysis

All of the biological molecules listed below contain high-energy phosphate bonds. Which one is the key driver of most phosphorylation reactions and the transfer of metabolic energy? a. glucose-P b. creatine-P c. acetyl-P d. adenosine-P3

adenosine-P3

Enzymes facilitate reactions in living systems. Figure 3-21 presents an energy diagram for the reaction X→Y. The solid line in the energy diagram represents changes in energy as the reactant is converted to product under standard conditions. The dashed line shows changes observed when the same reaction takes place in the presence of a dedicated enzyme. Which equation below indicates how the presence of an enzyme affects the activation energy of the reaction (catalyzed versus uncatalyzed)? a. d − c versus b − c b. d − a versus b − a c. a + d versus a + b d. d − c versus b − a

d − a versus b − a

Catalysts are molecules that lower the activation energy for a given reaction. Cells produce their own catalysts, called a. proteins. b. enzymes. c. cofactors. d. complexes.

enzymes

Activated carriers are small molecules that can diffuse rapidly and be used to drive biosynthetic reactions in the cell. Their energy is stored in a readily transferable form such as high-energy electrons or chemical groups. Which of the molecules below donates a chemical group rather than electrons? a. FADH2 b. NADH c. NADPH d. ATP

ATP

Seed oils are often dehydrogenated and added back into processed foods. The new fatty acids have an increased number of carbon-carbon double bonds. The dehydrogenation reaction could also be described as a/an __________ reaction. a. isomerization. b. oxidation. c. reduction. d. protonation.

oxidation

Your body extracts energy from the food you ingest by catalyzing reactions that essentially "burn" the food molecules in a stepwise fashion. What is another way to describe this process? a. reduction b. oxidation c. dehydration d. solvation

oxidation

When elemental sodium is added to water, the sodium atoms ionize spontaneously. Uncharged Na becomes Na+. This means that the Na atoms have been a. protonated. b. oxidized. c. hydrogenated. d. reduced.

oxidized

The synthesis of glutamine from glutamic acid requires the production of an activated intermediate followed by a condensation step that completes the process. Which molecule is added to glutamic acid in the activation step? a. phosphate b. NH3 c. ATP d. ADP

phosphate

The synthesis of glutamine from glutamic acid requires the production of an activated intermediate followed by a condensation step that completes the process. In the condensation step, __________ is displaced by __________. a. OH; NH3. b. ADP; NH2. c. ATP; NH3. d. phosphate; NH3.

phosphate; NH3.

Indicate whether the following statements are TRUE or FALSE. If a statement is false, explain why it is false. A. Enzymes lower the free energy released by the reaction that they facilitate. B. Enzymes lower the activation energy for a specific reaction. C. Enzymes increase the probability that any given reactant molecule will be converted to product. D. Enzymes increase the average energy of reactant molecules.

A. False. Enzymes do not affect the initial energy of the reactants nor the final energy of the products after the reaction is complete, which are the values that determine the change in free energy of a reaction. B. True C. True D. False. By lowering the energy of activation, enzymes increase the number of molecules in a population that can overcome the activation barrier.

Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. When two macromolecules form a complex, the free energy of the system increases because there is a net increase of order within the cell. B. Sequential pathways can help drive unfavorable reactions by siphoning off the products into the next energetically favorable reaction in the series. C. The cytosol is densely packed with molecules, creating what is more an aqueous gel than a solution. D. The diffusion rates for smaller molecules in the cytosol are much lower than what is observed for the same molecules in water.

A. False. Even nonspecific interactions between macromolecules can be favorable if there is a large number of water molecules and ions displaced at the interaction interface. This would lead to an overall increase in disorder, even though the two larger molecules become associated and more ordered. B. True C. True D. False. Small molecules diffuse through the cytosol nearly as rapidly as they diffuse in water.

Indicate whether the following statements are TRUE or FALSE. If a statement is false, explain why it is false. A. Photosynthetic organisms release only O2 into the atmosphere, while non-photosynthetic organisms release only CO2. B. The cycling of carbon through the biosphere first requires the incorporation of inorganic CO2 into organic molecules. C. The oxidation of one molecule is always coupled to the reduction of a second molecule. D.During cellular respiration, carbon-containing molecules become successively more oxidized until they reach their most oxidized form, as CO2.

A. False. Plants, as well as photosynthetic algae and bacteria, perform both photosynthesis and respiration. This means that photosynthetic organisms release both O2 and CO2 into the atmosphere. B. True C. True. This forms the basis for redox pairs. D. True

1. Indicate whether the following statements are TRUE or FALSE. If a statement is false, explain why it is false. A. The second law of thermodynamics states that the total amount of energy in the universe remains constant. B. The source of all energy for living systems is chlorophyll. C. CO2 gas is fixed in a series of reactions that are light-dependent. D. H2 is the most stable and abundant form of hydrogen in the environment.

A. False. The second law of thermodynamics states that components of any system move toward greater disorder. It is the first law of thermodynamics that states that energy is neither created nor destroyed. B. False. The source of all energy for living organisms is sunlight C. False. The fixation of carbon from CO2 occurs independently of light D. False. The most stable form of hydrogen is H2O.

On the basis of the two reactions below, indicate whether the following statements are TRUE or FALSE. If a statement is false, explain why it is false. 1: ATP + Y → Y-P + ADP ΔG = −100 kcal/mole 2: Y-P + A → B ΔG = 50 kcal/mole A. Reaction 1 is favorable because of the large negative ΔG associated with the hydrolysis of ATP. B. Reaction 2 is an example of an unfavorable reaction. C. Reactions 1 and 2 are coupled reactions, and when they take place together, reaction 2 will proceed in the forward direction. D. Reaction 2 can be used to drive reaction 1 in the reverse direction.

A. True B. True C. True D. False. This is false for two reasons: (1) reaction 2 is unfavorable, as indicated by the positive free-energy change associated with the reaction; (2) the reverse reaction, although possibly more favorable, will yield the product for reaction 1, not reactants to help drive it forward.

A. You are measuring the effect of temperature on the rate of an enzyme-catalyzed reaction. If you plot reaction rate against temperature, which of the graphs in Figure 3-64 would you expect your plot to resemble? B. Explain why temperature has this effect.

An increase in temperature increases the number of collisions of sufficient energy to overcome the activation energy. A moderate increase in temperature could therefore increase the reaction rate. At higher temperatures enzymes will denature and no longer function as reaction catalysts.

When the polymer X-X-X . . . is broken down into monomers, it is "phosphorylyzed" rather than hydrolyzed, in the following repeated reaction: X-X-X . . . + P → X-P + X-X . . . (reaction 1) Given the ΔG° values of the reactions listed in Table 3-27, what is the expected ratio of X-phosphate (X-P) to free phosphate (P) at equilibrium for reaction 1? a. 1:106 b. 1:104 c. 1:1 d.104:1 X-X-X . . . + H2O → X + X-X . . . ΔG° = −4.5 kcal/mole X + ATP → X-P + ADP ΔG° = −2.8 kcal/mole ATP + H2O → ADP + P ΔG° = −7.3 kcal/mole

Because ΔG° values are additive, ΔG°total = 0, and if ΔG° = 0, Keq = 1, meaning that [products]/[reactants] = 1, and the ratio of X-P to P is 1:1.

For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Not all words or phrases will be used; each word or phrase should be used only once. activation free selectively chemical bond kinetic slowly completely rapidly unfavorable favorable By definition, catalysts allow a reaction to occur more __________. Chemical reactions occur only when there is a loss of __________ energy. Enzymes act more __________ than other catalysts. A catalyst decreases the __________ energy of a reaction.

By definition, catalysts allow a reaction to occur more rapidly. Chemical reactions occur only when there is a loss of free energy. Enzymes act more selectively than other catalysts. A catalyst decreases the activation energy of a reaction.