Biochemistry, 7th Edition Study Aid - Berg

Biochemistry, 7th Edition Study Aid – Berg

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Biochemistry, 7th Edition Study Aid – Berg

What: TEST BANK
ISBN: 1429229365
Year Published: 2011
Authors: Berg
Edition: 7th

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Biochemistry, 7th Edition Study Aid – Berg

Biochemistry, 7th Edition Study Aid – Berg

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

AUTONUM

____________ 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

____________ 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.

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 elastase.

D)

chymotrypsin and trypsin.

B)

chymotrypsin and elastase.

E)

trypsin and 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 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

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.

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

PAGE  1

PAGE  2

Chapter 9   Catalytic Strategies

 

 

Biochemistry, 7th Edition Study Aid – Berg

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