Question 1

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. E

Question 2

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 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 for 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 k_cat, K_M, and V_max.

Question 3

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

Accepted Answer

ATP-Mg²⁺

Question 4

Effective protease inhibitors are often _________________ for one enzyme.

Accepted Answer

The answer of Effective protease inhibitors are often _________________ for...

Question 5

Which of the following techniques allows investigators to test the role of individual amino acids in the determination of enzyme structure/function relationships even if the investigated amino acid is not present in the active site?

Accepted Answer

A)  stopped-flow assay 
B)  use of mechanism based inactivators 
C)  use of methylating agents 
D)  site-directed mutagenesis 
E)  None of the answers is correct. 
A)  stopped-flow assay 
B)  use of mechanism based inactivators 
C)  use of methylating agents 
D)  site-directed mutagenesis 
E)  None of the answers is correct.

Question 6

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 7

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

Accepted Answer

catalysis

Question 8

Why are substrate analogs often used to monitor enzyme activity?

Accepted Answer

Enzyme assays must be designed so that f

Question 9

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

Accepted Answer

The answer of The reaction center of most carbonic anhydrases...

Question 10

What structures found in proteins are named for the fact that they interact with phosphoryl groups?

Accepted Answer

A)  P-sheet 
B)  P-site 
C)  P-loop 
D)  P-helix 
E)  P-turn 
A)  P-sheet 
B)  P-site 
C)  P-loop 
D)  P-helix 
E)  P-turn

Question 11

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 12

What mechanism is responsible for restriction endonuclease cleavage of DNA?

Accepted Answer

An activated water molecule di

Question 13

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 14

What modification is made to DNA that protects the host DNA from cleavage by host restriction endonucleases?

Accepted Answer

A)  acetylation 
B)  methylation 
C)  phosphorylation 
D)  ubiquitination 
E)  adenylation 
A)  acetylation 
B)  methylation 
C)  phosphorylation 
D)  ubiquitination 
E)  adenylation

Question 15

How is the bicarbonate formed when carbonic anhydrase is present?

Accepted Answer

The zinc promotes fo

Question 16

Carbonic anhydrases are necessary because

Accepted Answer

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)  spontaneous hydration and dehydration of carbon dioxide occur very slowly, and hydration and dehydration of carbon dioxide are sometimes coupled to other biochemical processes 
E)  spontaneous hydration and dehydration of carbon dioxide are rapid, but not at speeds necessary for biochemical processes, and hydration and dehydration of carbon dioxide are sometimes coupled to other biochemical processes. 
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)  spontaneous hydration and dehydration of carbon dioxide occur very slowly, and hydration and dehydration of carbon dioxide are sometimes coupled to other biochemical processes 
E)  spontaneous hydration and dehydration of carbon dioxide are rapid, but not at speeds necessary for biochemical processes, and hydration and dehydration of carbon dioxide are sometimes coupled to other biochemical processes.

Question 17

Convergent evolution is attributed to similarities found between

Accepted Answer

A)  trypsin and elastase. 
B)  chymotrypsin and elastase. 
C)  chymotrypsin and subtilisin. 
D)  chymotrypsin and trypsin. 
E)  trypsin and kinase. 
A)  trypsin and elastase. 
B)  chymotrypsin and elastase. 
C)  chymotrypsin and subtilisin. 
D)  chymotrypsin and trypsin. 
E)  trypsin and kinase.

Question 18

Myosins function to

Accepted Answer

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. 
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.

Question 19

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

Accepted Answer

The peptide bond contains a carbonyl tha

Question 20

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

Exam 9: Catalytic Strategies

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

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

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

Effective protease inhibitors are often _________________ for one enzyme.

Which of the following techniques allows investigators to test the role of individual amino acids in the determination of enzyme structure/function relationships even if the investigated amino acid is not present in the active site?

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

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

Why are substrate analogs often used to monitor enzyme activity?

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

What structures found in proteins are named for the fact that they interact with phosphoryl groups?

Type II restriction enzymes cut

What mechanism is responsible for restriction endonuclease cleavage of DNA?

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

What modification is made to DNA that protects the host DNA from cleavage by host restriction endonucleases?

How is the bicarbonate formed when carbonic anhydrase is present?

Carbonic anhydrases are necessary because

Convergent evolution is attributed to similarities found between

Myosins function to

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

Where does cleavage of the scissile bond by chymotrypsin occur?

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

Oxidative Phosphorylation

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

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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