Question 1

What type of reaction is catalyzed by proteases?

Accepted Answer

A)  oxidation-reduction 
B)  ligation 
C)  isomerization 
D)  hydrolysis 
E)  group transfer 
A)  oxidation-reduction 
B)  ligation 
C)  isomerization 
D)  hydrolysis 
E)  group transfer

Question 2

Which of the following is an enzyme that temporarily undergoes covalent catalysis as part of its mechanism?

Accepted Answer

A)  papain 
B)  chymotrypsin 
C)  caspase 
D)  elastase 
E)  All of the answers are correct. 
A)  papain 
B)  chymotrypsin 
C)  caspase 
D)  elastase 
E)  All of the answers are correct.

Question 3

What type of assay allows analysis of an enzyme catalyzed reaction in milliseconds?

Accepted Answer

A)  multiple wavelength absorbance spectroscopy 
B)  fluorescence lifetime 
C)  stopped-flow 
D)  NMR 
E)  None of the answers is correct. 
A)  multiple wavelength absorbance spectroscopy 
B)  fluorescence lifetime 
C)  stopped-flow 
D)  NMR 
E)  None of the answers is correct.

Question 4

Binding of a water molecule to the zinc ion induces

Accepted Answer

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. 
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.

Question 5

Describe the secondary and tertiary structures in domains that form P-loops and bind phosphoryl groups.

Accepted Answer

This domain structure consists of a cent

Question 6

The metal ion most commonly found at the active site of metalloproteases is

Accepted Answer

A)  zinc. 
B)  calcium. 
C)  selenium. 
D)  magnesium. 
E)  sodium. 
A)  zinc. 
B)  calcium. 
C)  selenium. 
D)  magnesium. 
E)  sodium.

Question 7

What is the common nucleophile found in cysteine, metallo-, and aspartyl proteases?

Accepted Answer

The common

Question 8

What do trypsin, subtilisin, and elastase have in common?

Accepted Answer

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. 
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.

Question 9

A-T base pairs, which contain _____ hydrogen bonds, are more easily interrupted than G-C base pairs with _______ hydrogen bonds.

Accepted Answer

The answer of A-T base pairs, which contain _____ hydrogen...

Question 10

What is significant about the slow rate for myosin's hydrolysis of ATP?

Accepted Answer

The persistence of a conformat

Question 11

EcoRV cleaves cognate DNA with a specificity approximately _____ times that of non-cognate DNA.

Accepted Answer

A)  10 
B)  1000 
C)  10,000 
D)  1,000,000 
E)  100,000,000,000 
A)  10 
B)  1000 
C)  10,000 
D)  1,000,000 
E)  100,000,000,000

Question 12

In chymotrypsin, the tetrahedral intermediate transition state is stabilized by a structural feature referred to as the "___________________" hole.

Accepted Answer

The answer of In chymotrypsin, the tetrahedral intermediate transition state...

Question 13

What metal ion is frequently found in enzyme active sites that act on phosphate-containing substrates?

Accepted Answer

A)  Zn2+ 
B)  Mg2+ 
C)  Cu2+ 
D)  Fe2+ 
E)  Ni2+ 
A)  Zn2+ 
B)  Mg2+ 
C)  Cu2+ 
D)  Fe2+ 
E)  Ni2+

Question 14

What features of carbonic anhydrase allow the rapid hydration of carbon dioxide?

Accepted Answer

Bringing the two reactants (ca

Question 15

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 16

In proteases such as papain, a ___________________ residue is activated by hydrogen-bonding to a histidine residue.

Accepted Answer

The answer of In proteases such as papain, a ___________________...

Question 17

What is the common strategy for cysteine, metallo-, and aspartyl proteases?

Accepted Answer

All employ a mechanism whereby

Question 18

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,

Question 19

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

Accepted Answer

A number of different enzymes, including

Question 20

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

Exam 9: Catalytic Strategies

What type of reaction is catalyzed by proteases?

Which of the following is an enzyme that temporarily undergoes covalent catalysis as part of its mechanism?

What type of assay allows analysis of an enzyme catalyzed reaction in milliseconds?

Binding of a water molecule to the zinc ion induces

Describe the secondary and tertiary structures in domains that form P-loops and bind phosphoryl groups.

The metal ion most commonly found at the active site of metalloproteases is

What is the common nucleophile found in cysteine, metallo-, and aspartyl proteases?

What do trypsin, subtilisin, and elastase have in common?

A-T base pairs, which contain _____ hydrogen bonds, are more easily interrupted than G-C base pairs with _______ hydrogen bonds.

What is significant about the slow rate for myosin's hydrolysis of ATP?

EcoRV cleaves cognate DNA with a specificity approximately _____ times that of non-cognate DNA.

In chymotrypsin, the tetrahedral intermediate transition state is stabilized by a structural feature referred to as the "___________________" hole.

What metal ion is frequently found in enzyme active sites that act on phosphate-containing substrates?

What features of carbonic anhydrase allow the rapid hydration of carbon dioxide?

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

In proteases such as papain, a ___________________ residue is activated by hydrogen-bonding to a histidine residue.

What is the common strategy for cysteine, metallo-, and aspartyl proteases?

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

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

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

Filters

A-T base pairs, which contain _ hydrogen bonds, are more easily interrupted than G-C base pairs with ___ hydrogen bonds.