Deck 3: Energy, Catalysis, and Biosynthesis

Question 1

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.

Answer 1

B

Question 2

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

Answer 2

C

Question 3

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

Answer 3

D

Question 4

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

Question 5

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.

Question 6

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.

Question 7

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.

Question 8

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

Question 9

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

Question 10

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.

Question 11

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.

Question 12

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 + P_i → 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

Question 13

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.

Question 14

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

Question 15

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

Question 16

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.

Question 17

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.

Question 18

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°.

Question 19

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.

Question 20

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.

Question 21

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/V_max and 1/K_m
B)1/V and 1/[S]
C)V_max and K_m
D)V and [S]

Question 22

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? Figure 3-34

A)½V_max
B)K_m
C)V_max
D)V_max − K_m

Question 23

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)k_on/k_off = K
B)K = [A][B]/[AB]
C)K = [AB]/[A][B]
D)(A) and (C)

Question 24

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

Question 25

The maximum velocity (V_max) 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

Question 26

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 ?G° 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?
                              X-X-X ...+ H₂O ? X + X-X ...?G° = ?4.5 kcal/mole
                              X + ATP ? X-P + ADP ?G° = ?2.8 kcal/mole
                              ATP + H₂O ? ADP + P ?G° = ?7.3 kcal/mole
Table 3-27

A)1:10⁶
B)1:10⁴
C)1:1
D)10⁴:1

Question 27

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

Question 28

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

Question 29

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.

Question 30

The graph in Figure 3-34 illustrates the relationship between reaction rates and substrate concentration for an enzyme-catalyzed reaction.What does the K_m value indicate with respect to enzyme-substrate interactions? Figure 3-34

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

Question 31

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

Question 32

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.

Question 33

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

Question 34

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 K_eq for ES = 10
E + I → EI K_eq for EI = 2
Given the equilibrium constant values, which one of the following statements is TRUE?

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.

Question 35

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.

Question 36

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

Question 37

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

Question 38

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]

Question 39

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

Question 40

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)V_max
B)V
C)V_max and K_m
D)K_m

Question 42

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.
Figure 3-64

Question 43

If you weigh yourself on a scale one morning, then eat four pounds of food during the day, will you weigh four pounds more the next morning? Why or why not? (Hint: What happens to the atoms from the food you ingested?)

Question 44

Hydrolysis reactions are commonly used inside the cell to split high-energy covalent bonds.For each of the three reactions below, use the ΔG° for each reaction to determine the equilibrium constants (K).Assume that each reaction occurs independently of the other two.
ΔG° (kcal/mole)
Reaction 1: acetyl-P → acetate + P −10.3
Reaction 2: ATP → ADP + P −7.3
Reaction 3: glucose 6-P → glucose + P −3.3

Question 45

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

Question 46

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)

Question 48

For each of the pairs A-D in Figure 3-54, pick the more reduced member of the pair.
Figure 3-54

Question 50

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. $\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\text {hydrolysis}$
$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\underline{\text {reaction}}$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$ $\Delta G^{\circ}$
$\text { creatine + ATP } \quad\quad\quad\quad \stackrel{\text { enzyme A }}{\longrightarrow} \text { creatine phosphate + ADP +3 kcal/mole }$

$\text { ATP }+\mathrm{H}_{2} \mathrm{O} \quad\quad\quad\quad\quad \stackrel{\text { enzyme B }}{\longrightarrow} \mathrm{ADP}+\text { phosphate } \quad \quad\quad\quad-7.3 \mathrm{kcal} / \text { mole }$

$\text { pyrophosphate }+\mathrm{H}_{2} \mathrm{O} \quad \stackrel{\text { enzyme } \mathrm{C}}{\longrightarrow} 2 \text { phosphate } \quad\quad\quad\quad \quad\quad\quad\quad-7 \mathrm{kcal} / \text { mole }$

glucose 6-phosphate $+\mathrm{H}_{2} \mathrm{O} \quad\stackrel{\text { enzyme D }}{\longrightarrow}$ qlucose + phosphate $\quad\quad\quad\quad\quad\quad\quad-3.3 \mathrm{kcal} / \mathrm{mole}$
Table 3-43
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

Question 51

Consider a description of an enzymatic reaction pathway that begins with the binding of substrate S to enzyme E, and ends with the release of product P from the enzyme.
E + S → ES → EP → E + P
In many circumstances,
K_m = [E][S]/[ES]
A.What proportion of enzyme molecules is bound to substrate when [S] = K_m?
B.Recall that when [S] = K_m, the reaction rate is ½V_max.Does your answer to part A make sense in the light of this rate information?

Question 52

The synthesis of glutamine from glutamic acid requires the production of an activated intermediate followed by a condensation step that completes the process.Both amino acids are shown in Figure 3-46. Figure 3-46
Which molecule is added to glutamic acid in the activation step?

A)phosphate
B)NH₃
C)ATP
D)ADP

Question 53

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

Question 54

The synthesis of glutamine from glutamic acid requires the production of an activated intermediate followed by a condensation step that completes the process.Both amino acids are shown in Figure 3-47. Figure 3-47
In the condensation step, __________ is displaced by __________.

A)OH; NH₃.
B)ADP; NH₂.
C)ATP; NH₃.
D)phosphate; NH₃.

Question 55

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.

Question 58

The anhydride formed between a carboxylic acid and a phosphate (Figure 3-45A) is a high-energy intermediate for some reactions in which ATP is the energy source.Arsenate can also be incorporated into a similar high-energy intermediate in place of the phosphate (Figure 3-45B).Figure 3-45C shows the reaction profiles for the hydrolysis of these two high-energy intermediates.What is the effect of substituting arsenate for phosphate in this reaction? (A)


(B)




Figure 3-45

A)It forms a high-energy intermediate of lower energy.
B)It forms a high-energy intermediate of the same energy.
C)It decreases the stability of the high-energy intermediate.
D)It increases the stability of the high-energy intermediate.

Question 61

In general, there is a positive change in free energy associated with reduction reactions, and most of them are coupled with oxidation reactions.The last step in the biosynthesis of cholesterol involves the reduction of a carbon-carbon double bond.What activated carrier molecule is used in this reaction (and generally for the reduction of lipids) and how would this reaction be influenced by the levels of available ATP?

Question 62

Coenzyme A can be converted to acetyl CoA, which is an important activated carrier molecule that has a central role in metabolism and can be used to add two carbons in each successive cycle of fatty acid synthesis.
A.Identify the location and type of high-energy bond in the acetyl CoA molecule shown in Figure 3-77.
B.How does the bond energy help promote the synthesis of fatty acids?
C.What function does the rest of the coenzyme A molecule serve in these reaction pathways?
Figure 3-77

Question 63

Although the biochemical study of reaction rates and free energies is important for understanding each biological reaction individually, these studies do not provide an accurate picture of what is happening to reactants and products inside the cell.Why not?

Question 64

Consider an analogy between reaction-coupling and money.In a simple economy, barter provides a means of direct exchange of material goods.For example, the owner of a cow may have excess milk and need eggs, whereas a chicken owner has excess eggs and needs milk.Provided that these two people are in close proximity and can communicate, they may exchange or barter eggs for milk.But in a more complex economy, money serves as a mediator for the exchanges of goods or services.For instance, the cow owner with excess milk may not need other goods until three months from now, or may want goods from someone who does not need milk.In this case, the "energy" from providing milk to the economy can be temporarily "stored" as money, which is a form of "energy" used for many transactions in the economy.Using barter and money as analogies, describe two mechanisms that can serve to drive an unfavorable chemical reaction in the cell.

Question 65

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.

Question 66

Enzymes A and B catalyze different reactions, but use the same reactant molecule as a substrate.The graph in Figure 3-74 presents the reaction rates observed when enzyme A and enzyme B are mixed together in a single test tube containing molecule X.What are the V_max and the apparent K_m values for each enzyme under these conditions? How might these values change for enzyme B if it were analyzed in the absence of enzyme A? Explain your answer.
Figure 3-74

Question 67

The addition of a new deoxynucleotide to a growing DNA chain requires more energy than can be obtained by the hydrolysis of ATP to ADP + P_i.What alternative series of reactions is used, and how does this help overcome the energy barrier for DNA synthesis?

Question 68

Two college roommates do not agree on the best way to handle the clutter piled up in your dorm room.Roommate 1 explains that chaos is inevitable, so why fight it? Roommate 2 counters that maintaining an organized environment makes life easier in many ways, and that chaos is not inevitable.What law of thermodynamics drives the thinking of Roommate 1? What thermodynamic argument can be used to support Roommate 2?

Question 69

Activated carriers store energy in different types of high energy bonds.Match the groups used in high-energy linkages (right column) for each of the of the activated carriers (left column).Each group number may be used more than once.
_____ ATP 1.glucose
_____ NADH 2.electrons and hydrogens
_____ acetyl CoA 3.carboxyl group
_____ carboxylated biotin 4.phosphate
_____ NADPH 5.methyl group
_____ S-adenosylmethionine 6.acetyl group
_____ FADH₂
_____ uridine diphosphate

Question 70

Figure 3-72 illustrates the amount of energy per molecule for a population in a contained, controlled environment.Most molecules will have the average energy of the population, shown in region 1.The number of molecules in the population with enough energy to be converted to product is shown in region 2.The number of molecules with enough energy to react in the presence of enzyme is shown in region 3.Use this information to explain how enzymes catalyze reactions.
Figure 3-72

Question 71

Chemical reactions are reversible; they can proceed in both the forward and reverse directions.If the ΔG° for the reaction Y→X is energetically favorable, how can you explain the fact that not all of the Y molecules will be converted to X molecules?

Question 72

Assume that the average human adult requires 2000 kilocalories per day to sustain all normal processes and maintain a constant weight.If manufactured solar panels could somehow provide power directly to the human body, what size solar panel would be required (in cm²)? Assume there are 10 hours of sunlight per day, and that the usable energy output for a typical solar panel is 850 kJ/ft² per hour.
Note: 1 kcal = 4.184 kJ
1 ft² = 929.03 cm²

Question 73

In the cytoplasm, materials are organized, separated, and sorted by membranes.Cells exploit the selective permeability of these membranes to partition populations of molecules and generate chemical energy for the cell.Use the principles of the first and second laws of thermodynamics to explain how membranes can be used to produce chemical energy.