Deck 6: Mechanisms of Enzymes

Question 1

On the energy diagram below, which arrows) represent the activation energy for the forward and reverse reactions?

A) Arrow 1 is the activation energy for both the forward and reverse reactions.
B) Arrow 1 is the activation energy for the forward reaction and arrow 2 is the activation energy for the reverse reaction.
C) Arrow 1 is the activation energy for the forward reaction and arrow 3 is the activation energy for the reverse reaction.
D) Arrow 3 is the activation energy for the forward reaction and arrow 2 is the activation energy for the reverse reaction.

Answer 1

Arrow 1 is the activation energy for the forward reaction and arrow 2 is the activation energy for the reverse reaction.

Question 2

In this reaction, the carbon is .

A) oxidized
B) reduced
C) neutralized
D) hydrolyzed

Answer 2

reduced

Question 3

Which represents a hydride ion?

A) H₂^-
B) H^-
C) H⁺
D) H₃O⁺

Answer 3

H^-

Question 4

Which modes) of catalysis is/are classified as chemical effects? 1. Transition state stabilization
2. Acid-base catalysis
3. Covalent catalysis
4. Proximity effect

A) 3 only
B) 1,2 and 3
C) 2 and 3
D) all of them

Question 5

A chemical group that has a negative charge or an unshared electron pair is called aan)

A) transition state
B) neutrophile
C) electrophile
D) nucleophile

Question 6

Replacement of the amino acid at or near an active site of an enzyme is more likely to change enzyme activity than the replacement of at or near the active site.

A) histidine; leucine
B) leucine; histidine
C) leucine; isoleucine
D) histidine; aspartate

Question 7

Which amino acid is least likely to participate in acid-base catalysis?

A) lysine
B) tyrosine
C) aspartate
D) histidine

Question 8

Which statement does not apply to transition states?

A) Many have been detected experimentally.
B) Chemical bonds are in the process of being formed and broken.
C) have lifetimes on the order of 10^-14 to 10^-13 seconds
D) differ in energy from the ground state by the activation energy

Question 9

In the following chemical reaction which species is the reducing agent? CH₄ + 2 O₂ → CO₂ + 2 H₂O

A) CH₄
B) O₂
C) CO₂
D) H₂O
E) none of the above, this is not an oxidation-reduction reaction

Question 10

The following pH dependence was found for the activity of a certain enzyme-catalyzed reaction. If it is known that the only two ionizable residues in the active site are both glutamates, which conclusion can be drawn?

A) The glutamates have different microenvironments which cause their pK_aʹs to differ.
B) One of the glutamates must be amidated.
C) Both glutamates have a pK_a equal to 5.0.
D) Both glutamates are deprotonated during the reaction.

Question 11

A histidine was determined to be the critical residue involved in an enzyme-catalyzed reaction. If the pK_a of the histidine is known to be 6.5 in the active site and the pH of maximum catalytic activity is 7.2, what is likely the primary role of histidine in the catalytic reaction?

A) acts as a proton donor
B) forms a covalent bond with the substrate
C) stabilizes a charged intermediate
D) reduces the entropy of the substrate

Question 12

On the energy diagram below, which point represents a transition state?

A) Point 1
B) Point 2
C) Point 3
D) Point 4

Question 13

An enzyme stabilizes the transition state that is bound in the active site. What effect will this have on the energy diagram below? The diagram shown below is for the uncatalyzed reaction.

A) Energy of point 1 is raised.
B) Energy of point 2 is raised.
C) Energy of point 2 is lowered.
D) Energy of point 3 is lowered.
E) Energy of point 4 is raised.

Question 14

In the reaction below Y^- is . Y^- + CH₂X → CH₂Y + X^-

A) the leaving group
B) the attacking electrophile
C) the reaction intermediate
D) a nucleophile

Question 15

How many intermediates are indicated by the energy diagram below?

A) one
B) two
C) three
D) four

Question 16

On the energy diagram below, which point represents an intermediate?

A) Point 1
B) Point 2
C) Point 3
D) Point 4

Question 17

The movement of is key to understanding chemical and enzymatic reactions.

A) protons
B) electrons
C) nucleophiles
D) electrophiles

Question 18

Cleavage of a C-C bond produces a carbanion that both electrons and a carbocation that both electrons.

A) loses; loses
B) loses; keeps
C) keeps; loses
D) keeps; keeps

Question 19

Site directed mutagenesis is used to study enzymes by

A) changing the location of the active site.
B) producing enzymes with different amino acid residues.
C) producing enzymes with modified R groups.
D) changing the pH of the environment.

Question 20

A detailed description of a chemical reaction in terms of the molecular, atomic or subatomic events is called the reaction .

A) mechanism
B) pathway
C) primary sequence
D) motif

Question 21

A key role of the hydroxyl group at position 6 in the purine ring in the formation of a transition state by the enzyme adenosine deaminase is obtained by comparing a and a .

A) competitive inhibitor; noncompetitive inhibitor
B) transition state analog; normal substrate
C) noncompetitive inhibitor; transition state analog
D) competitive inhibitor; transition state analog
E) All of the above

Question 22

A reaction that occurs with every collision between reactant molecules is called a/an .

A) saturation point
B) diffusion-controlled reaction
C) rate-determining step
D) first order reaction

Question 23

The graphs below all represent the same chemical reaction, but each employing a different catalyst. Which enzyme uses the most efficient mechanism of catalysis?

A) see graph I
B) see graph II
C) see graph III
D) see graph IV

Question 24

The proximity effect of speeding an enzyme-catalyzed reaction is explained by .

A) a large loss of entropy when reactive groups are brought close to each other
B) a large gain in entropy due to binding of the substrate
C) a conversion of a reaction from endergonic to exergonic
D) increasing the flexibility of the substrate by increasing its degrees of freedom of rotation

Question 25

In the nonpolar environment of most enzyme active sites, which statement applies to charge-charge interactions between the enzyme and the substrate?

A) They are rare due to the non-polar environment.
B) They are frequent, but not very strong in the nonpolar environment.
C) They are stronger in the nonpolar environment.
D) The polarity of the active site has no effect on the strength of the charge-charge interactions.

Question 26

An enzymeʹs active site contains an arginine residue and a glutamate residue with pK_aʹs of 2.9 and 9.1, respectively. Both residues are actively involved in the catalytic mechanism and they are the only two ionizable residues in the active site. What would you expect for the optimum pH of the enzyme?

A) 6.0
B) 7.0
C) 7.4
D) No pH can be determined since the information is irrelevant to the optimum pH.

Question 27

The enzyme has an active site which

A) fits the substrate exactly.
B) fits the transition state.
C) may contain hydrogen bonds which are covalent-like.
D) A and C
E) B and C

Question 28

Acid-base catalysis is estimated to accelerate a typical enzymatic reaction by what factor?

A) 1 to 2 fold increase
B) 10 to 100 fold increase
C) 10⁶ fold increase
D) 10²³ fold increase

Question 29

Some antibody molecules are enzymatic if they are formed against

A) enzymes.
B) enzymes bound to other proteins.
C) transition state analogs bound to other proteins.
D) transition state analogs.
E) All of the above

Question 30

The reaction catalyzed by a certain phosphatase enzyme is found to follow ping-pong kinetics and involves the transfer of a phosphate group from substrate A to substrate B. Which mode of catalysis is likely for this reaction?

A) sequential catalysis
B) acid-base catalysis
C) transfer catalysis
D) covalent catalysis

Question 31

A thermodynamic pit occurs when

A) ES is not very stable.
B) ES forms faster than it dissociates.
C) ES is highly stable.
D) S is not bound tightly to an enzyme.
E) S is positioned incorrectly to the enzyme.

Question 32

An update of Fischerʹs lock-and-key theory of enzyme specificity view the as the lock and as the key.

A) enzyme; substrate
B) substrate; enzyme
C) enzyme; transition state
D) transition state; enzyme
E) substrate; transition state

Question 33

Superoxide dismutase enzyme catalysis is faster than the rate of diffusion because it

A) is an acid-base catalyst.
B) is a two-step reaction.
C) has an electric field around the active site.
D) occurs in very high quantities in cells.

Question 34

The active site of a certain enzyme contains a serine residue. When the enzyme is incubated for a short time with its substrate, a form of the enzyme in which the active site serine is acetylated can be isolated and purified. In the native protein the serine is never found to be acetylated. This information supports .

A) a covalent catalysis mode
B) intermediate state stabilization effects
C) the acid-base catalysis mode
D) a polar group catalytic mechanism

Question 35

What shape would a graph of reaction velocity versus pH have for an enzyme that uses both a proton donor and a proton acceptor during catalysis both acid and base catalysis)?

A) sigmoidal
B) hyperbolic
C) exponential
D) bell-shaped
E) linear

Question 36

Most K_m values of enzymes for their substrates are on the order of M.

A) 10^-2
B) 10^-3
C) 10^-4
D) 10^-5
E) 10^-6

Question 37

When the concentration of a substrate inside a cell falls below the substrate concentration at half maximal velocity .

A) ES is formed more easily
B) ES dissociates to E + S
C) ES is closer to the ground state than to the transition state
D) E + S is in equilibrium with ES
E) the reaction will not proceed

Question 38

Which graph might you expect for the pH profile of an enzymeʹs activity if the only ionizable residue in the active site is aspartate?

A) I
B) II
C) III
D) IV

Question 39

Transition state analogs should

A) stabilize transition states.
B) have a dissociation constant of 10^-13 M or less.
C) bind very tightly to the enzyme.
D) A and C
E) B and C

Question 40

Aspartate and lysine are in the active site of an enzyme. They are both known to participate directly in catalysis. The pK_aʹs of the residues are found to be 3.2 and 9.6, respectively for aspartate and lysine. The optimum pH for the enzyme is 6.4. Which forms of these two residues will predominate when the enzyme is most active?

A) aspartate is protonated; lysine is deprotonated
B) both residues are protonated
C) aspartate is deprotonated; lysine is protonated
D) both residues are deprotonated

Question 41

The roles of amino acid residues at the active site of enzymes can be determined by removing certain residues using the technique of

A) specific hydrolysis.
B) covalent binding.
C) acylation of specific residues.
D) site mutagenesis.
E) All of the above

Question 42

Induced fit studies by Koshland using the enzyme hexokinase showed that there are enzyme forms

A) which react with the hydroxyl group of water.
B) which react only with ATP and glucose present together.
C) which are hydrophobic, excluding the competing hydroxyl group from water.
D) with and without glucose bound to each.
E) that hydrolyze ATP.

Question 43

Nucleophiles are often anions or have unshared electrons.

Question 44

X-ray crystallographic examination of the active site of arginine kinase was possible because

A) it could be crystallized in the different structural forms.
B) nitrate could be substituted for phosphate in the reaction.
C) it was readily purified unlike most other enzymes).
D) MgADP was involved in the reaction.
E) All of the above

Question 45

A nucleophile is an electron poor species.

Question 46

Intermediates are more stable and have longer lifetimes than transition states.

Question 47

Glycoside hydrolases such as bacterial cellulase have been shown to differ in mechanisms from that of lysozyme. They

A) are alkaline catalysts.
B) form a boat form of the sugar.
C) form a covalent sugar-enzyme intermediate.
D) do not distort the substrate.
E) have no active site side chain interactions.

Question 48

The mechanism of action of lysozyme includes

A) distortion of the substrate.
B) acid catalysis.
C) proximity effects.
D) formation of a half-chair sugar form.
E) All of the above

Question 49

The catalytic triad of chymotrypsin and other serine proteases consists of

A) three subunits of the enzyme.
B) three amino acid residues adjacent in the primary structure which act to make serine a strong nucleophile.
C) three amino acid residues close enough in space to make serine a strong nucleophile.
D) three enzymes with very similar structural features.
E) None of the above.

Question 50

The role of serine at the active site of serine proteases is to act as an) catalyst, while the histidine residue serves as an) catalyst.

A) strong; weak
B) weak; strong
C) acid-base; covalent
D) covalent; acid-base
E) anionic; ionic

Question 51

Induced fit of enzyme activation is a result of

A) contact binding) of substrate.
B) constant small and rapid motions of protein atoms.
C) change to an active form.
D) A and B
E) A, B, and C

Question 52

The role of ser-195 in chymotrypsin cleavage of a peptide bond is that of an)

A) acid catalyst.
B) proximity effector.
C) strong nucleophile.
D) weak nucleophile.

Question 53

Active trypsin formation by the action of enteropeptidase can be viewed as the master activation step because

A) enteropeptidase can activate its own zymogen.
B) it is allosterically controlled.
C) trypsin activates other pancreatic zymogens.
D) All of the above

Question 54

The relative orientation of colliding molecules only affects reactions rates when the energy during impact is low. If the energy of impact is high enough, orientation is unimportant.

Question 55

The substrate specificity of serine proteases is primarily due to

A) a specificity pocket in the protein.
B) the positions of specific side chains of serine, histidine, and aspartate.
C) distinct backbone conformations of the individual proteins.
D) A and B
E) A, B and C

Question 56

Experiments on the bacterial serine protease subtilisin show that even when all three residues of the catalytic triad are mutated, the catalytic rate of the enzyme is still 3000 times the uncatalyzed reaction rate. Which mode of catalysis is likely responsible for this remaining catalytic activity?

A) acid-base catalysis
B) covalent catalysis
C) transition-state stabilization
D) hydrophobic effects

Question 57

Reaction intermediates are impossible to isolate experimentally.

Question 58

Zymogens are inactive enzyme precursors which are made active by

A) a change in structure.
B) selective proteolysis.
C) secretion to new types of cells.
D) A and B
E) A, B and C

Question 59

What is the biological function of lysozyme?

A) converts trypsinogen to trypsin
B) is a ligase that accelerates the polymerization of glycogen
C) it regulates vascular constriction in chickens
D) hydrolyzes polysaccharides of bacterial cell walls

Question 60

Radicals are stable, unreactive species that have an unpaired electron.

Question 61

Transition state analogs are usually more potent inhibitors of enzyme activity than substrate analogs.

Question 62

Superoxide dismutase and triosphosphate isomerase are two enzymes that catalyze diffusion-controlled reactions.

Question 63

Unlike lysozyme, other glycoside hydrolases such as bacterial cellulase, form covalent glycosyl-enzyme intermediates.

Question 64

In the Ser-His-Asp catalytic triad in serine proteases, the serine residue serves as an acid-base catalyst, while the histidine residue serves as a covalent catalyst.

Question 65

If a plot of enzyme activity versus pH is sigmoidal then acid-base catalysis can be ruled out as a mode of catalysis.

Question 66

Zymogens are often active only in the environment in which they are functional.

Question 67

Chemical modes of catalysis are more important than binding modes of catalysis in accounting for the accelerated rates of enzymatic reactions.

Question 68

Antibodies raised against transition state analogs are always enzymatic.

Question 69

Enzyme-catalyzed reactions that are diffusion-controlled reactions can never proceed any faster than the rate determined by random collision rates.

Question 70

Weak substrate binding is an important feature to help describe enzyme catalysis.

Question 71

Transitions states bind to their enzymes more tightly than their substrates do.

Question 72

In the modified ʺlock-and-keyʺ theory of enzyme specificity, the key is still the enzyme while the lock is still the substrate.

Question 73

Enzymes which have induced fit to the substrate are generally more effective than those in an active form initially.

Question 74

Both trypsin and its zymogen trypsinogen have a hydrophobic substrate-binding pocket.

Question 75

Trypsin as well as chymotrypsin can activate chymotrypsinogen to chymotrypsin.