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TEST BANK FOR BIOCHEMISTRY 7TH

EDITION BY JEREMY

Sample

Chapter 9 Catalytic Strategies Matching Questions Use the following to answer questions 1-10: Choose the best answer from the list below. Not all of the answers will be used. a) hydrolysis b) stopped-flow c) site-directed mutagenesis d) chymotrypsin e) zinc f) P-loop g) magnesium h) two-fold rotational i) methylation j) peptide bond cleavage k) papain l) hydrogenation m) sodium

n) PCR o) two-fold mirror

AUTONUM ____________ An enzyme that temporarily

undergoes covalent catalysis as part of its mechanism.

Ans: d

Section: Introduction and 9.1

AUTONUM ____________ The type of reaction catalyzed

by proteases.

Ans: a

Section: 9.1

AUTONUM ____________ The metal ion required by

carbonic anhydrase for activity.

Ans: E

Section: 9.2

AUTONUM ____________ The process by which

chymotrypsinogen is converted into active

chymotrypsin.

Ans: j

Section: 9.1

AUTONUM ____________ A technique that requires only

milliseconds to perform an enzyme-catalyzed

reaction.

Ans: b

Section: 9.1

AUTONUM ____________ The process by which host

DNA is protected from cleavage by the host

restriction endonucleases.

Ans: I

Section: 9.3

AUTONU

M ____________ A technique that allows an

investigator to test the role of individual amino

acids in the determination of

structure/function

relationships in enzymes.

Ans: c

Section: 9.1

AUTONUM

____________ The metal ion frequently found

at active sites containing phosphate groups.

Ans: g

Section: 9.3

AUTONUM

____________

____________ A

Inverted

repeats technique that

in double- can be used to

stranded DNA determine

create this type mechanisms

of symmetry. when chiral

molecules are involved in reactions.

Ans: H f

Section: 9.3 Section: 9.3

AUTONUM ____________ Structures in proteins named for

the fact that they interact with phosphoryl groups.

Ans: F

Section: 9.4

Fill-in-the-Blank Questions

AUTONUM Effective protease inhibitors are

often _________________ for one enzyme.

Ans: specific Section: 9.1

AUTONUM The catalytic mechanism of adenylate

kinase, in which the substrates are simply oriented to stabilize the

transition state, is called ___________________.

Ans: catalysis by

approximation Section: Introduction

AUTONUM A-T base pairs are easily interrupted, as they

contain only _____ hydrogen bonds versus _______ hydrogen bonds found in G-C base

pairs.

Ans: two, three Section: 9.3

AUTONUM The mechanism of chymotrypsin involves the

formation of an unstable

__________________ -shaped intermediate

that is stabilized by the oxyanion hole.

Ans: tetrahetral Section: 9.1

AUTONUM In trypsin, the specificity pocket contains a/an

______________ residue that binds to the positive charge of the K or R residue of the

substrate.

Ans: aspartyl, aspartic, or

D Section: 9.1

AUTONUM The reaction center of most carbonic

anhydrases is a zinc ion bound to water and _______________ residues of the enzyme.

Ans: histidine Section: 9.2

AUTONUM In chymotrypsin, the tetrahedral intermediate

transition state is stabilized by a structural feature referred to as the

“___________________” hole.

Ans: oxyanion Section: 9.2

AUTONUM In proteases such as papain, a

___________________ residue is activated by hydrogen-bonding to a histidine residue.

Ans: cysteine Section: 9.1

AUTONUM Myosins hydrolyze _____________ in a

controlled manner and use the free energy of

hydrolysis to promote conformational changes within myosin itself.

Ans: ATP Section: 9.4

AUTONUM Kinetic studies on myosins, in the presence

and absence of divalent cations, show that

________________ is the true substrate for this enzyme.

Ans: ATP-

Mg2+

Section: 9.4

Multiple-Choice Questions

AUTONUM Which amino acids in chymotrypsin are found

in the active site and are participants in

substrate

cleavage?

A) His, Ser, Asp B) His, Ser C) Asp, Lys D) Lys, Arg E) His, Ser, Arg

Ans: A Section: 9.1

AUTONUM How is specificity determined by

chymotrypsin?

A) interaction of the active site amino acids with

the substrate

B) binding of the N-terminus amino acid at the

active site

C) covalent binding of a his residue to the

substrate

D) large conformational change of a P-loop upon

binding of substrate

E) binding of the proper amino acid into a deep

pocket on the enzyme

Ans: E Section: 9.1

AUTONUM Where does cleavage of the scissile bond by

chymotrypsin occur?

A) between a his and ser amino acid

B) on the N-terminal side of a Phe or Trp residue

C) on the C-terminal side of a Phe or Trp residue

D) at the N-terminal amino acid

E) on the C-terminal side of an Arg or Lys amino

acid

Ans: C Section: 9.1

AUTONUM Which of the following is NOT a way in which

enzymes stabilize a transition state?

A) causing the temperature of the environment to

increase

B) covalent catalysis

C) using binding energy

D) general acid-base catalysis

E) catalysis by approximation

Ans: A Section: Introduction

AUTONUM What do trypsin, subtilisin, and elastase have in

common?

A) All contain Asp in the active site.

B) All bind hydrophobic amino acids.

C) All are synthesized in the pancreas.

D) All contain a catalytic triad at the active site.

E) All contain a hydrophilic substrate-binding

pocket.

Ans: D Section: 9.1

AUTONUM Convergent evolution is attributed to

similarities found between

A) trypsin and D) chymotrypsin

elastase. and trypsin.

B) chymotrypsin E) trypsin and and elastase. kinase.

C) chymotrypsin

and subtilisin.

Ans: C Section: 9.1

AUTONUM If you carried out site-directed mutagenesis of

subtilisin, changing serine 221 to isoleucine, what would you expect?

A) a large change D) a and c in KM

B) a small change E) b and c in KM

a large change

C)

in kcat

Ans: E Section: 9.1

AUTONUM The metal most commonly found at the active

site of metalloproteases is

A) zinc. B) calcium. C) selenium. D) magnesium. E) sodium.

Ans: A Section: 9.1

AUTONU

M Carbonic anhydrases are necessary because

A) spontaneous hydration and dehydration of

carbon dioxide occur very slowly.

B) spontaneous hydration and dehydration of

carbon dioxide are rapid, but not at speeds

necessary for biochemical processes.

C) hydration and dehydration of carbon dioxide

are sometimes coupled to other biochemical

processes.

D) a and c.

E) b and c.

Ans: E Section: 9.2

AUTONUM Binding of a water molecule to the zinc ion

induces

A) a hydronium ion to form.

B) a large conformation change in the binding site.

C) ionization of a His residue, which functions as a

strong nucleophile.

D) a lowered pKa for water, which leads to

formation of a zinc bound hydroxide ion.

E) an altered KM value.

Ans: D Section: 9.2

AUTONUM Restriction endonucleases cut DNA at specific

sites. How many different patterns can be formed by a four-base sequence combination of

any four bases?

A) 64 B) 256 C) 16 D) 1024 E) 4096

Ans: B

Section: 9.3

AUTONUM Type II restriction enzymes cut

A) double-stranded DNA, forming a 5′ phosphoryl

group and a 3′ hydroxyl group on each strand.

B) single-stranded DNA, forming a 5′ phosphoryl

group and a 3′ hydroxyl group on the strand.

C) double-stranded DNA, forming a 5′ phosphoryl

group and a 3′ hydroxyl group on one strand.

D) double-stranded DNA, forming a 3′ phosphoryl

group and a 5′ hydroxyl group on each strand.

E) single-stranded DNA, forming two hydroxyl

groups and loss of a phosphate group.

Ans: A

Section: 9.3

AUTONUM EcoRV cleaves cognate DNA with a specificity

approximately _____ times that of non-cognate

DNA.

A) 10 B) 1000 C) 10,000 D)

1,000,000 E) 100,000,000,000

Ans: D Section: 9.3

AUTONUM Myosins function to

A) transfer the phosphate from NTP to NDP.

B) couple ATP hydrolysis to large conformational

changes.

C) couple ATP hydrolysis to glycogen oxidation.

D) phosphorylate NADH.

E) couple ATP hydrolysis to protein synthesis in

muscle.

Ans: B Section: 9.4

AUTONUM Metal ion catalysis is facilitated by any of

several mechanisms, including

A) stabilizing negative charges on an intermediate.

B) promoting formation of nucleophiles

C) metals binding directly to substrates

D) a and c.

E) All of the above.

Ans: E Section: Introduction

Short-Answer Questions

AUTONUM Complete the structure of the catalytic triad of chymotrypsin by drawing the proper structure

of the missing residue side chain in the box provided. Show the proper hydrogen bonding

involved in this triad.

Ans:

Section: 9.1

AUTONUM What is the challenge for a protease to facilitate

hydrolysis of a peptide bond?

Ans:

The peptide bond contains a carbonyl that is

not

very reactive; therefore, the catalytic

mechanism must employ a feature that

promotes nucleophilic attack of this carbonyl group by a strong nucleophile so the peptide

bond can be cleaved.

Section: 9.1

AUTONUM How can covalent modification be used to

determine the mechanism of action of an

enzyme?

Ans: If a particular amino acid side chain is

suspected of participating in a catalytic mechanism, covalent modification of the residue may alter it sufficiently that the enzyme

activity is altered or inhibited. However, this method is usually confirmed by other

techniques, such as site-directed mutagenesis,

to rule out other possible reasons for the loss of activity, such as global conformational change

as a result of the modification.

Section: 9.1

AUTONUM Why are substrate analogs often used to

monitor enzyme activity?

Ans: Enzyme assays must be designed so that

formation of a product is rapidly and easily

monitored. Substrates that form a colored

product are easy to observe in a quantitative

manner using spectrophotometers.

Section: 9.1

AUTONUM

What caused a “burst” of activity followed

by a

steady state reaction when chymotrypsin

was

studied by stop-flow techniques?

Ans: Chymotrypsin cleaves peptide bonds in a two-

step reaction, in which the first step,

formation

of the acyl enzyme intermediate, is faster than

the second step, hydrolysis.

Section: 9.1

AUTONUM What supports the theory that a catalytic triad

strategy is a result of convergent evolution?

Ans: A number of different enzymes, including the

peptidase family, some esterases, and others,

have similar mechanisms of actions. While the strategy is similar, the actual participating amino acids differ, suggesting a mechanism commonly employed as a result of convergent evolution.

Section: 9.1

AUTONUM What is common strategy for cysteine, metallo-

, and aspartyl proteases?

Ans: All employ a mechanism whereby a

nucleophile is generated that attacks the

carbonyl of the peptide bond.

Section: 9.1

AUTONUM What is the common nucleophile found in

cysteine, metallo, and aspartyl proteases?

Ans: The common nucleophile is water.

Section: 9.1

AUTONUM Designing drugs to inhibit enzymes is a large

part of pharmaceutical research. What are

some

of the enzymatic features that would be

important?

Ans: The enzyme could be inhibited by interaction of

a potential drug at the active site or at a site that

alters conformation or regulation of the

enzyme. The structure of natural substrates

and

activators, and their binding sites, would be useful features to study a new drug design. The binding affinity and specificity would be important, and standard enzyme assays would be used to determine the effect of the inhibitors on Kcat, KM, and Vmax.

Section: 9.1

AUTONUM How is the bicarbonate formed when carbonic

anhydrase is present?

Ans: The zinc promotes formation of a hydroxide

ion, which attacks the carbon dioxide.

Section: 9.2

AUTONUM What features of carbonic anhydrase allow the

rapid hydration of carbon dioxide?

Ans: Bringing the two reactants (carbon dioxide and

water) into proximity facilitates the rapid reaction rate, and the presence of a buffer

system aids in proton transfer and release.

Section: 9.2

AUTONUM What mechanism is responsible for restriction

endonuclease cleavage of DNA?

Ans: An activated water molecule directly attacks

the phosphorous atom in a single displacement reaction.

Section: 9.3

AUTONUM The sequence 6 bp restriction cleavage site for

EcoRV is GATXXX. What is the complete

sequence of the double-stranded restriction site?

Ans: GATATC

CTATAG

Section: 9.3

AUTONUM What is significant about the slow rate for

myosin’s hydrolysis of ATP?

Ans: The persitance of a conformation of myosin

with ATP hydrolyzed but still bound is

critical

for coupling conformational changes that

take

place in the course of the reaction to other

processes.

Section: 9.4

AUTONUM

Describe the secondary and tertiary

structures

in domains that form P-loops and bind

phosphoryl groups.

Ans: This domain structure consists of a central β

sheet, surrounded on both sides by α helices. Characteristically, there is a loop between the first β strand and the first helix that contains several glycine residues.

Section: 9.4