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Test Bank for Biochemistry 7th Edition by Berg Tymoczko and Stryer 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

Ans:

____________ A technique that requires only milliseconds to perform an enzyme-catalyzed reaction.

b

Section: 9.1 AUTONU M

____________ The process by which host DNA is protected from cleavage by the host restriction endonucleases.

Ans:

I Section: 9.3

AUTONU ____________ A technique that allows an M investigator to test the role of individual amino acids in the determination of structure/function relationships in enzymes.

Ans :

c Section: 9.1

AUTONU

____________ The metal ion frequently found


M

atctivitescotaiingphosphat egroups.

Ans:

g 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

Answer: two, three

A-T base pairs are easily interrupted, as they contain only _____ hydrogen bonds versus _______ hydrogen bonds found in G-C base pairs


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

AUTONUM

Section: 9.1

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

AUTONUM

Section: 9.1

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: ATP2+ Mg

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 C) Asp,Lys D) Lys, Arg

B) His, Ser 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

A)

Which of the following is NOT a way in which enzymes stabilize a transition state? 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 elastase.

D)

chymotrypsin and trypsin.

B)

chymotrypsin and elastase.

E)

trypsin and kinase.

C)

chymotrypsin and subtilisin.

Ans: C Section: 9.1 AUTONU


M

If you carried out site-directed mutagenesis of subtilisin, changing serine 221 to isoleucine, what would you expect?

A)

a large change in KM

D)

a and c

B)

a small change in KM

E)

b and c

C)

a large change in kcat

Ans: E Section: 9.1 AUTONU M

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

B) 256 Ans: Section :

C) 16 D) 1024 E) 4096

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 AUTONUM

Section :

9.3

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) D) E)

couple ATP hydrolysis to glycogen oxidation. phosphorylate NADH.

couple ATP hydrolysis to protein synthesis in muscle. Ans: B Section: 9.4

AUTONUM

A)

B)

C)

Metal ion catalysis is facilitated by any of several mechanisms, including

stabilizing negative charges on an intermediate.

promoting formation of nucleophiles

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 reactive; therefore, the catalytic chanism must employ a feature that motes nucleophilic attack of this bonyl group by a strong nucleophile so peptide bond can be cleaved.

Section: 9.1 How can covalent modification be used to determine the mechanism of action of an enzyme? AUTONUM

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 What caused a “burst� of activity followed AUTONUM by a steady state reaction when chymotrypsin was studied by stop-flow techniques?

Ans:

Chymotrypsin cleaves peptide bonds in a twostep reaction, in which the first step, formation is faster than

of the acyl enzyme intermediate, 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, the

have similar mechanisms of actions.

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


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.

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. Ans:

Section: 9.4

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Test Bank for Biochemistry 7th Edition by Berg Tymoczko and Stryer  

link full download :https://bit.ly/2FJ5Wtu Product Details ISBN-10: 1429229365 ISBN-13: 978-1429229364 People Also Search: biochemistry 7th...

Test Bank for Biochemistry 7th Edition by Berg Tymoczko and Stryer  

link full download :https://bit.ly/2FJ5Wtu Product Details ISBN-10: 1429229365 ISBN-13: 978-1429229364 People Also Search: biochemistry 7th...

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