Chapter 7 Biochemistry

slope of the line

On a plot of [product] versus time for an enzyme-catalyzed reaction, the v0 is equal to the a. slope of the line / [S]. b. [P] at the lowest time point. c. slope of the line. d. y-intercept.

dehydration

The conversion of 2-phosphoglycerate to phosphoenolpyruvate is an example of which type of reaction? a. hydrolysis b. dehydration c. isomerization d. condensation

prosthetic group

The dihydrolipoyl transacetylase enzyme contains a lipoyl group. The lipoyl group is a(n) a. ion. b. apoenzyme. c. prosthetic group. d. holo group.

irreversible inhibitor

Acetylcholinesterase is an important enzyme in the nervous system. Acetylcholinesterase activity is blocked by the nerve agent sarin gas, which forms a covalent bond with a Ser in the active site of the enzyme. Sarin gas is a(n) a. allosteric effector. b. competitive inhibitor. c. reversible inhibitor. d. irreversible inhibitor.

stabilizes the transition state; orients the substrate appropriately for the reaction to occur

A reaction coordinate diagram comparing an uncatalyzed reaction with an enzyme-catalyzed reaction can directly illustrate that the enzyme __________, but will not directly illustrate that the enzyme __________. a. orients the substrates appropriately for the reaction to occur; provides an alternative path for product formation b. provides an alternative path for product formation; stabilizes the transition state c. stabilizes the transition state; orients the substrates appropriately for the reaction to occur d. stabilizes the transition state; provides an alternative path for product formation

ANS: CTP is an allosteric inhibitor of aspartate transcarbamoylase. Its presence would shift the curve to the right.

A plot of v0 versus substrate concentration for aspartate transcarbamoylase displays a sigmoidal curve. Explain how the plot would change in the presence of CTP.

right; T state; CTP

A plot of vo versus [S] for aspartyl transcarbamoylase displays three sigmoidal lines. If the line in the middle represents the enzyme activity in the absence of any allosteric effectors, then the line to the __________ represents the enzyme in the __________ when bound to __________. a. right; R state; CTP b. right; T state; CTP c. left; R state; GTP d. left; T state; GTP

is uncomptitive

A Lineweaver-Burk plot displays parallel lines for an enzyme in the absence and presence of increasing amounts of an inhibitor. The inhibitor in this experiment a. binds both the free enzyme and the ES complex. b. is competitive. c. alters the Km but not the vmax. d. is uncompetitive.

covalent modification

A kinase adds a phosphate group to a target enzyme, altering the catalytic efficiency of the enzyme. This is an example of a. covalent modification. b. proteolytic processing. c. binding of regulatory molecules. d. feedback inhibition.

the inhibitor is a reversible inhibitor

A mixture of enzyme and inhibitor is run through a size-exclusion chromatography column. The activity of the enzyme is assessed before and after the chromatography. The enzyme has more activity after the chromatography step. Which of the following is true? a. The enzyme was not eluted fully from the column. b. The enzyme was denatured during chromatography. c. The inhibitor is a reversible inhibitor. d. The inhibitor is an irreversible inhibitor.

enzyme can no longer hold the intermediate in the correct orientation for catalysis.

A mutation of Lys229 in aldolase leads to a loss of enzyme activity. This is most likely because the a. active site can no longer exclude water. b. active site can no longer include water. c. enzyme can no longer hold the intermediate in the correct orientation for catalysis. d. product will remain bound to the enzyme active site.

preferentially hydrolyze substrates containing phenylalanine

A mutation results in the change of Ser to Asp in the substrate binding pocket of chymotrypsin. Most likely, the mutant enzyme will a. no longer catalyze the hydrolysis of a peptide bond because Asp cannot facilitate the nucleophilic attack. b. no longer catalyze the hydrolysis of a peptide bond because Asp is unable to be deprotonated by His57. c. preferentially hydrolyze substrates containing phenylalanine. d. preferentially hydrolyze substrates containing lysine.

ANS: Beriberi disease is caused by reduced pyruvate dehydrogenase complex activity. Pyruvate dehydrogenase complex activity can be reduced if the cofactor thiamine pyrophosphate is lacking, leading to an apoenzyme.

A patient presents with symptoms associated with the disease beriberi. An analysis of pyruvate dehydrogenase complex activity shows significantly reduced levels from normal. Predict how a deficiency in a coenzyme may be the culprit. Specify the coenzyme involved

Lineweaver-Burk; Km/vmax

A plot of 1 / v0 versus 1/[S] is called a __________ plot. Data in this plot have a slope equal a. Lineweaver-Burk; Km/vmax b. Lineweaver-Burk; −1/Km c. Michaelis-Menten; Km/vmax d. Michaelis-Menten; vmax

van der Waals

All of the following are common catalytic reaction mechanisms in enzyme active sites EXCEPT __________ catalysis. a. acid-base b. covalent c. metal ion d. van der Waals

lowering; transition state

An enzyme can increase the rate of a reaction inside a cell by __________ the energy of the __________. a. lowering; transition state b. increasing; product c. lowering; substrate d. increasing; transition state

ANS: The enzyme follows the induced-fit model of enzyme catalysis. Adding the substrate caused the enzyme to change conformation, which caused the crystal to shatter.

An enzyme is crystallized in preparation for X-ray crystallography. The crystal is then soaked in a solution of substrate and the crystal shatters. Propose a reason for this result.

oxidoreductases

An enzyme that requires the coenzyme nicotinamide adenine dinucleotide belongs to which enzyme class? a. transferases b. isomerases c. ligases d. oxidoreductases

Tyr → Phe

An enzyme undergoes a mutation that causes it to lose the ability to be regulated via phosphorylation. Which of the following mutations may lead to this loss of regulation? Assume that the overall structure is not altered by the mutation. a. Ser→Thr b. Thr→Ser c. Tyr → Phe d. Ser→Tyr

A chemical group within the enzyme that has a pKa of around 7 is likely involved in the catalytic mechanism.

An experiment is performed in which the kinetics of an enzyme-catalyzed reaction at different pHs is monitored. It is found that the Km does not change but that the kcat increases as the pH goes above 7. Which of the following is true? a. A chemical group within the enzyme that has a pKa of around 7 is likely involved in the catalytic mechanism. b. A chemical group with a pKa of around 7 must be deprotonated in order for substrate to bind. c. A chemical group with a pKa of around 7 must be positively charged in order for the substrate to bind. d. Protons are acting as positive heterotropic allosteric effectors of this enzyme.

uncompetitive

An inhibitor that binds only to the ES complex and not free enzyme is known as a(n) __________ inhibitor. a. irreversible b. competitive c. uncompetitive d. mixed

Induced-fit

Binding of glucose to hexokinase causes a conformational change in the enzyme. This is an example of the __________ model of enzyme catalysis. a. substrate-induced b. lock and key c. induced-fit d. glove and hand

undergo a nucleophilic attack

Both the substrate and the tetrahedral intermediate, when associated with chymotrypsin, a. contain an oxyanion. b. interact with the oxyanion hole. c. undergo a nucleophilic attack. d. hydrogen bond to Asp102.

ANS: forming hydrogen bonds with the oxyanion.

Complete the following statement: The NH groups of Ser195 and Gly193 in chymotrypsin are able to stabilize the intermediate of the reaction by

ANS: By considering the reaction at an early time, when the velocity is the initial velocity (v0), no appreciable product has been generated. Therefore the back reaction, where ES forms from EP with a rate constant k−2, is negligible.

Connect the use of v0 to the ability to treat k−2 as negligible in Michaelis-Menten kinetics.

ANS: Zymogen is the inactive precursor of an enzyme, or proenzyme, that must be cleaved by a protease to generate the active enzyme

Define the term zymogen.

ANS: The catalytic subunits are brought closer together. The catalytic subunits rotate.

Describe two conformational changes that occur when aspartate transcarbamoylase shifts from the R state to the T state.

are a pocket or cleft

Enzyme active sites a. are nonspecific. b. are a pocket or cleft. c. always exclude water. d. can only bind a single substrate at a time.

high; high

Enzymes usually bind substrates with __________ affinity and __________ specificity. a. high; high. b. high; low c. low; low d. low; high

ANS: Catalytic efficiency can be controlled by the binding of regulatory molecules or by covalent modification.

Explain the two ways that catalytic efficiency of enzymes can be controlled within a cell.

is a second-order rate constant

For a reaction of Q + R → P, the rate constant a. is equal to [Q][R] / [P]. b. has units of s−1 . c. is a second-order rate constant. d. is equal to [P] / [Q][R].

k

For a reaction of S → P, the rate constant of the reaction is equal to a. k. b. −k. c. 1/v. d. [S]/v.

deadenylated.

Glutamine synthetase is in the R state when Tyr397 is a. deadenylated. b. uridylated. c. phosphorylated. d. dephosphorylated.

ANS: The enzyme activity would be lower at the higher pH. The cytoplasm has a near neutral pH and hexokinase likely has optimal activity at that pH.

Hexokinase catalyzes the first step of glycolysis, which occurs in the cell cytoplasm. The protocol for an in vitro enzyme activity assay of hexokinase suggests that the assay is carried out at a pH of 7.4. Predict what may occur if the assay is carried out at a pH of 8.8 instead. Explain your reasoning.

transferase

Hexokinase catalyzes the phosphorylation of glucose to glucose 6-phosphate. Hexokinase belongs to which enzyme class? a. transferase b. ligase c. oxidoreductase d. hydrolase

histidine

If an enzyme carries out acid-base catalysis, which of the following amino acids could act as general acid? a. phenylalanine b. glycine c. histidine d. alanine

R plus Q to a product

If the rate constant for a reaction is determined to be equal to v / [Q][R], the reaction is the conversion of a. QtoR. b. RtoQ. c. R plus Q to a product. d. It is impossible to determine the reaction given the information provided.

The

In a reversible covalent modification reaction involving the phosphorylation of a target protein, which of the following amino acids is LEAST likely to be modified with a phosphate group? a. Ser b. Phe c. Tyr d. Thr

mixed

In the formation of an ESI complex, __________ inhibition can result. a. mixed b. competitive c. covalent d. anticompetitive

[ES]

In the steady-state condition assumed in Michaelis-Menten kinetics, __________ is relatively constant. a. [ES] b. [S] c. v0 d. [ES] / [S]

ANS: Arginine decarboxylase activity is regulated by proteolytic processing. When the proteases responsible for activating arginine decarboxylase are inhibited, the activity of arginine decarboxylase is reduced.

In vivo arginine decarboxylase activity is monitored over several days in the absence and presence of protease inhibitors. The activity is greatly reduced when protease inhibitors are present. Arginine decarboxylase is not a protease. Interpret these findings.

ANS: An enzyme that catalyzes a hydrolysis reaction uses water as a substrate within the microenvironment of the active site. Excess water that is not specifically acting as a substrate in the reaction mechanism is still excluded.

Justify how an enzyme that catalyzes a hydrolysis reaction does not contradict the concept that enzyme active sites are microenvironments that exclude excess water.

(k−1+k2)/k1

KM is equal to a. k1/(k−1+k2). b. (k−1+k2)/k1. c. 1⁄2 vmax. d. vmax[S] / v0.

stable

Many medicinal drugs are transition state analogs. They are good drugs because they can interact with the target enzyme active site and are a. higher in energy than the transition state. b. identical in structure to the transition state. c. stable. d. polar.

cofactor; holoenzyme

Nitrite reductase contains two histidine amino acids that coordinate a Cu2+ ion. When the ion is present in the enzyme, the ion is a __________ and the enzyme is a __________. a. cofactor; apoenzyme b. cofactor; holoenzyme c. coenzyme; apoenzyme d. coenzyme; holoenzyme

Ser14; R state

Phosphorylation of __________ in glycogen phosphorylase shifts the enzyme to the __________. a. Tyr397; T state b. Tyr397; R state c. Ser14; T state d. Ser14; R state

C, D, B, A

Place the following HMG-CoA reductase steps in the correct order: A. Reduction of aldehyde B. Breakdown of hemithioacetal C. Reduction of thioester D. Cofactor exchange a. A,D,C,B b. C,D,B,A c. A,B,D,C d. C,B,D,A

a zymogen

Procathepsin B is a lysosomal protease that is first translated as a proenzyme. On autocleavage it is fully activated. Procathepsin B is a. a zymogen. b. in the T state after autocleavage. c. an allosteric enzyme. d. inactive at low pH.

ANS: To determine the presence of a predicted hydrophobic channel, determine the structure of the enzyme in the presence of polyethylene glycol using X-ray crystallography. If a channel is there, the hydrophobic polyethylene glycol should bind into the channel.

Propose an experiment to determine the presence of a predicted hydrophobic channel in a newly discovered enzyme. At your disposal you have the purified enzyme, the ability to analyze the enzyme by X-ray crystallography, a spectrophotometer, the enzyme substrate, and polyethylene glycol. Be sure to explain how the results will determine if the protein contains a hydrophobic channel.

below the E + S

Reaction coordinate diagrams clearly show that the energy of an enzyme bound to a transition state is higher than the energies of the E + S, E + P, and ES that occur along the same reaction coordinate. The energy of an enzyme bound to a transition state analog would lie __________ in the diagram. a. above the E + S but below the transition state b. below the E+S c. above the transition state d. above E+S but below ES

ANS: The higher temperature destabilizes the protein structure to the point where the enzyme is no longer folded properly. The enzyme cannot act as a catalyst when unfolded.

The activity of an enzyme is monitored as a function of temperature. At low temperature very little activity is seen; the activity peaks as the temperature increases and then dramatically decreases to zero as higher temperatures are attained. Explain why the activity drops off completely at higher temperatures.

Asp102

The catalytic triad of chymotrypsin is composed of His57, Ser195, and a. Gly193. b. Glu103. c. Asp120. d. Asp102.

a conformational change triggers the exchange of NADP+ for NADPH.

The glutamate side chain in the active site of HMG-CoA reductase acts as a general base only after a. the mevalonate binds to the active site. b. the hydride from the second NADPH attacks the carbonyl center of the aldehyde. c. a conformational change triggers the exchange of NADP+ for NADPH. d. CoA is reduced to CoA-SH.

Lys267

The hemithioacetal intermediate formed during the action of HMG-CoA reductase is stabilized by a. Lys267. b. Asp283. c. His381. d. Glu83.

the maximum velocity

The initial velocity of an enzyme-catalyzed reaction is followed at various substrate concentrations. At very high substrate concentrations it is observed that the initial velocity no longer increases as more substrate is added. The velocity under these conditions is known as a. the ultimate velocity. b. the maximum velocity. c. v[S]. d. optimal velocity.

Two NADPH

The mechanism of HMG-CoA reductase involves a. two NADPH. b. one NADPH. c. two NADH. d. one NADH.

reversible covalent modifications

The regulation of a biomolecule through the addition or removal of a molecular tag involves __________ reactions. a. coenzyme-dependent redox b. reversible covalent modification c. metabolite transformation d. isomerization

act as a general acid on the intermediate

The role of Glu211 in the mechanism of enolase is to a. facilitate the orientation of the phosphate group of the substrate. b. act as a general base on the substrate. c. act as a general acid on the intermediate. d. make the proton at the C-2 position more acidic.

a aromatic group

The side chains of the amino acids that make up the catalytic triad of chymotrypsin contain all EXCEPT a. a hydroxyl group. b. a carboxylic acid. c. an aromatic group. d. an imidazole.

kcat / Km

The specificity constant is equal to a. [Et][S] / v0. b. Km/v0. c. kcat / Km. d. kcat / [Et].

trypsin; Asp

The substrate binding pocket of __________ contains a(n) __________, which facilitates substrate specificity. a. trypsin; Ser b. chymotrypsin; Asp c. trypsin; Asp d. elastase; Gly

elastase

The substrate binding pocket of __________ is best at accommodating substrates with small side chains. a. elastase b. chymotrypsin c. enolase d. trypsin

hydrophobic collapse reactions

The three general categories of enzyme-mediated reactions, which are determined on the basis of the work they accomplish, include all EXCEPT a. coenzyme-dependent redox reactions. b. reversible covalent modification. c. hydrophobic collapse reactions. d. metabolite transformation reactions.

higher in free energy than the product

The transition state of a reaction is a. higher in free energy than the product. b. lower in free energy than the ground state of the substrate. c. easily isolated. d. equal to the ∆G‡ of the uncatalyzed reaction minus the ∆G‡ of the catalyzed reaction.

1/vo.

The y-axis of a Lineweaver-Burk plot is a. v0. b. 1/vo. c. Km/vmax. d. 1/[S].

ANS: Initial velocity (v0) for an enzyme-catalyzed reaction is the reaction rate at the beginning of the reaction before the substrate concentration has changed significantly.

Using words, define initial velocity (v0) for an enzyme-catalyzed reaction

ANS: Henry Eyring's transition state theory states that the conversion of substrate to product involves a high-energy transition state in which a molecule can either become a product or remain a substrate.

What is Henry Eyring's transition state theory?

A, C, B

What is the appropriate order of the following steps? A. Glutamine binding to uridylyltransferase B. Adenylation of glutamine synthetase C. Deuridylation of glutamine synthetase adenylyltransferase a. C,B,A b. A,C,B c. A,B,C d. C,A,B

200

What is the rate enhancement as a result of the presence of an enzyme if the uncatalyzed rate of the reaction is 1.2 × 102 mmol/sec and the catalyzed rate is 2.4 × 104 mmol/sec? a. 0.005 b. 200 c. 2.88 × 106 d. 2

ANS: Serine, threonine, tyrosine

What three amino acids are targeted for phosphorylation by kinases?

insulin; protein phosphatase 1

When __________ is increased, __________ is activated, which acts on glycogen phosphorylase, leading to a decrease in the activity of the enzyme. a. glucagon; phosphorylase kinase b. epinephrine; phosphorylase kinase c. insulin; protein phosphatase 1 d. glucagon; protein phosphatase 1

covalent

When a nucleophile present in the enzyme attacks an electrophilic substrate to form an enzyme-substrate intermediate, this is an example of __________ catalysis. a. covalent b. acid-base c. metal ion d. hydrophobic

has greater separation of the catalytic subunits

When compared with the T state of aspartate transcarbamoylase, the R state a. has dissociated into two C3R3 complexes. b. has greater separation of the catalytic subunits. c. is bound to CTP . d. has substrate bound in the ATP binding site.

His57

Which amino acid acts as a general acid and a general base in the mechanism of chymotrypsin? a. Ser195 b. His57 c. Gly193 d. Asp102

ATP; allosteric activator

Which answer correctly classifies the compound with its relationship to asparate transcarbamoylase? a. A TP; allosteric inhibitor b. A TP; allosteric activator c. CTP; allosteric activator d. CTP; substrate

isomerase; intramolecular rearrangements

Which answer correctly pairs the enzyme class with the type of reaction catalyzed? a. lyase; formation of two products by hydrolyzing a substrate b. transferase; transfer of H or O atoms c. isomerase; intramolecular rearrangements d. oxidoreductase; transfer of groups within molecules

Lys345

Which of the following functions as a general base in the mechanism of enolase? a. Lys345 b. His57 c. Mg2+ d. Glu211

electrophilic attack on the scissile bond

Which of the following is NOT a function of the Mg2+ ions in the mechanism of enolase? a. orientation of substrate in the active site b. stabilizing the intermediate c. making the proton at the C-2 position more acidic d. electrophilic attack on the scissile bond

cofactor degradation

Which of the following is NOT a primary mechanism that affects catalytic efficiency? a. binding of regulatory molecules b. covalent modification c. proteolytic processing d. cofactor degradation

pyruvate kinase with a bound K+

Which of the following is a holoenzyme? a. pyruvate kinase with a bound K+ b. alcohol dehydrogenase c. nitrite reductase d. hexokinase

heme

Which of the following is a prosthetic group? a. Mg2+ b. NADH c. Zn2+ d. heme

orienting substrates appropriately for the reaction to occur

Which of the following is a way that an enzyme can increase the rate of a reaction inside a cell? a. increasing the temperature of the cell b. increasing the pressure inside the cell c. increasing the substrate concentration inside the cell d. orienting substrates appropriately for the reaction to occur

The conversion of EP→ E + P is rapid.

Which of the following is an assumption made when using Michaelis-Menten kinetics? a. The conversion of E + P → ES does not occur. b. k1>k2 c. v0=vmaxatlow[S] d. The conversion of EP → E + P is rapid.

it is loosely associated with the enzyme

Which of the following is true of a coenzyme but NOT true of a prosthetic group? a. It contains an organic component. b. It is loosely associated with the enzyme. c. It is necessary for enzyme function. d. It is present in a holoenzyme but not an apoenzyme.

It involves a conformation change of the enzyme

Which of the following is true of the induced-fit model of enzyme catalysis but NOT of the lock and key model of enzyme catalysis. a. It was proposed by Emil Fisher. b. it involves weak interactions of a substrate with an enzyme c. it involves a conformational change of the enzyme d. it involves non covalent interactions of the substrate with the enzyme.

it contains an oxyanion

Which of the following is true of the tetrahedral intermediate in the chymotrypsin mechanism? a. It is lower in free energy than the substrate. b. It is partially positively charged. c. All bonds are the same length. d. It contains an oxyanion.

hydrogen bonding; reversible

Which of the following pairs correctly matches the type of interaction observed between an inhibitor and an enzyme with the type of inhibition? a. ionic; irreversible b. covalent; irreversible c. hydrogen bonding; reversible d. hydrophobic; irreversible

ATCase is regulated by feedback inhibition

Which of the following statements are true? a. A TCase is regulated by feedback inhibition. b. CTP is an allosteric activator of ATCase. c. A TP is an allosteric inhibitor of A TCase. d. GTP is an allosteric inhibitor of ATCase.

NAD+/NADH; redox at C-O bonds

Which pair correctly matches the coenzymes most often used to mediate the described redox reactions? a. NAD+/NADH; redox at C-O bonds b. NADP+/NADPH; redox at C-C bonds c. FAD/FADH2; redox at C-O bonds d. FMN/FMNH2 ; redox at C-O bonds

covalent bond

Which type of interaction is more likely to be found between an enzyme and an irreversible inhibitor? a. covalent bond b. hydrogen bond c. ionic interaction d. van der Waals interaction

isomerization

Which type of reaction does not change the molecular formula of the product compared with that of the substrate? a. condensation b. reduction c. hydrolysis d. isomerization