Test bank for biochemistry 7th edition by jeremy

Section: Introduction and 9.1 AUTONUM ____________ The type of reaction catalyzed by proteases.. Section: 9.2 AUTONUM ____________ The process by which chymotrypsinogen is converted into

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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

Section: Introduction and 9.1

AUTONUM The type of reaction catalyzed

by proteases

Section: 9.1

AUTONUM The metal ion required by

carbonic anhydrase for activity

Section: 9.2

AUTONUM The process by which

chymotrypsinogen is converted into active chymotrypsin

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

Section: 9.3

AUTONUM A technique that allows an

investigator to test the role of individual amino acids in the determination of structure/function relationships in enzymes

Section: 9.1

AUTONUM The metal ion frequently found

at active sites containing phosphate groups

Section: 9.3

AUTONUM

Inverted repeats

in double-stranded DNA create this type

of symmetry

A technique that can be used to determine mechanisms when chiral

molecules are involved in reactions

Section: 9.3 Section: 9.3

AUTONUM Structures in proteins named for

the fact that they interact with phosphoryl groups

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

elastase

D) chymotrypsin

and trypsin

B) chymotrypsin

and elastase

E) trypsin and

kinase

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?

in KM

D) a and c

in KM

E) b and 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

AUTONUM 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

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

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

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 two-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?

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