Question 1

What is the challenge for a protease to facilitate hydrolysis of a peptide bond?

Accepted Answer

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.

Question 2

The reaction center of most carbonic anhydrases is a zinc ion bound to water and _______________ residues of the enzyme.

Accepted Answer

histidine

Question 3

The mechanism of chymotrypsin involves the formation of an unstable __________________ -shaped intermediate that is stabilized by the oxyanion hole.

Accepted Answer

tetrahedral

Question 4

The catalytic mechanism ofcarbonic anhydrase,in which the substrates are simply oriented to stabilize the transition state,is called ___________________.

Accepted Answer

catalysis

Question 5

Designing drugs to inhibit enzymes is a large part of pharmaceutical research.What are some of the enzymatic features that would be important?

Accepted Answer

The enzyme could be inhibited by interac

Question 6

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

Accepted Answer

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 
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

Question 7

Myosins hydrolyze _____________ in a controlled manner and use the free energy of hydrolysis to promote conformational changes within myosin itself.

Accepted Answer

The answer of Myosins hydrolyze _____________ in a controlled manner...

Question 8

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

Accepted Answer

A)  stabilizing negative charges on an intermediate. 
B)  promoting formation of nucleophiles. 
C)  metals binding directly to substrates. 
D)  stabilizing negative charges on an intermediate and metals binding directly to substrates. 
E)  All of the answers are correct. 
A)  stabilizing negative charges on an intermediate. 
B)  promoting formation of nucleophiles. 
C)  metals binding directly to substrates. 
D)  stabilizing negative charges on an intermediate and metals binding directly to substrates. 
E)  All of the answers are correct.

Question 9

Type II restriction enzymes cut

Accepted Answer

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. 
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.

Question 10

The sequence 6 bp restriction cleavage site for EcoRV is GATXXX.What is the complete sequence of the double-stranded restriction site?

Accepted Answer

The answer of The sequence 6 bp restriction cleavage site...

Question 11

Kinetic studies on myosins,in the presence and absence of divalent cations,show that ________________ is the true substrate for this enzyme.

Accepted Answer

The answer of Kinetic studies on myosins,in the presence and...

Question 12

Where does cleavage of the scissile bond by chymotrypsin occur?

Accepted Answer

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 
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

Question 13

Why are substrate analogs often used to monitor enzyme activity?

Accepted Answer

Enzyme assays must be designed so that f

Question 14

How is the bicarbonate formed when carbonic anhydrase is present?

Accepted Answer

The zinc promotes fo

Question 15

How is specificity determined by chymotrypsin?

Accepted Answer

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 
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

Question 16

Restriction endonucleases cut DNA at specific sites.How many different patterns can be formed by a four-base sequence combination of any four bases?

Accepted Answer

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

Question 17

What type of symmetry is created by inverted repeats in double-stranded DNA?

Accepted Answer

A)  two-fold rotational 
B)  three-fold rotational 
C)  mirror plane 
D)  line 
E)  inversion center 
A)  two-fold rotational 
B)  three-fold rotational 
C)  mirror plane 
D)  line 
E)  inversion center

Question 18

What supports the theory that a catalytic triad strategy is a result of convergent evolution?

Accepted Answer

A number of different enzymes,including

Question 19

In trypsin,the specificity pocket contains a/an ______________ residue that binds to the positive charge of the K or R residue of the substrate.

Accepted Answer

aspartyl,a

Question 20

What process converts chymotrypsinogen to chymotrypsin?

Accepted Answer

A)  metal ion binding 
B)  peptide bond cleavage 
C)  coenzyme association 
D)  cysteine methylation 
E)  proline hydroxylation 
A)  metal ion binding 
B)  peptide bond cleavage 
C)  coenzyme association 
D)  cysteine methylation 
E)  proline hydroxylation

Exam 9: Catalytic Strategies

What is the challenge for a protease to facilitate hydrolysis of a peptide bond?

The reaction center of most carbonic anhydrases is a zinc ion bound to water and _______________ residues of the enzyme.

The mechanism of chymotrypsin involves the formation of an unstable __________________ -shaped intermediate that is stabilized by the oxyanion hole.

The catalytic mechanism ofcarbonic anhydrase,in which the substrates are simply oriented to stabilize the transition state,is called ___________________.

Designing drugs to inhibit enzymes is a large part of pharmaceutical research.What are some of the enzymatic features that would be important?

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

Myosins hydrolyze _____________ in a controlled manner and use the free energy of hydrolysis to promote conformational changes within myosin itself.

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

Type II restriction enzymes cut

The sequence 6 bp restriction cleavage site for EcoRV is GATXXX.What is the complete sequence of the double-stranded restriction site?

Kinetic studies on myosins,in the presence and absence of divalent cations,show that ________________ is the true substrate for this enzyme.

Where does cleavage of the scissile bond by chymotrypsin occur?

Why are substrate analogs often used to monitor enzyme activity?

How is the bicarbonate formed when carbonic anhydrase is present?

How is specificity determined by chymotrypsin?

Restriction endonucleases cut DNA at specific sites.How many different patterns can be formed by a four-base sequence combination of any four bases?

What type of symmetry is created by inverted repeats in double-stranded DNA?

What supports the theory that a catalytic triad strategy is a result of convergent evolution?

In trypsin,the specificity pocket contains a/an ______________ residue that binds to the positive charge of the K or R residue of the substrate.

What process converts chymotrypsinogen to chymotrypsin?

Biochemistry: An Evolving Science

Protein Composition and Structure

Exploring Proteins and Proteomes

DNA, RNA, and the Flow of Genetic Information

Exploring Genes and Genomes

Exploring Evolution and Bioinformatics

Hemoglobin: a Portrait of a Protein in Action

Enzymes: Basic Concepts and Kinetics

Regulatory Strategies

Carbohydrates

Lipids and Cell Membranes

Membrane Channels and Pumps

Signal-Transduction Pathways

Metabolism: Basic Concepts and Design

Glycolysis and Gluconeogenesis

The Citric Acid Cycle

Oxidative Phosphorylation

The Light Reactions of Photosynthesis

The Calvin Cycle and the Pentose Phosphate Pathway

Glycogen Metabolism

Fatty Acid Metabolism

Protein Turnover and Amino Acid Catabolism

The Biosynthesis of Amino Acids

Nucleotide Biosynthesis

Biosynthesis of Membrane Lipids and Steroids

The Integration of Metabolism

DNA Replication, repair, and Recombination

RNA Synthesis and Processing

Protein Synthesis

The Control of Gene Expression in Prokaryotes

The Control of Gene Expression in Eukaryotes

Sensory Systems

The Immune System

Molecular Motors

Drug Development

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