Deck 9: Catalytic Strategies

Question 1

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

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

Answer 1

C

Question 2

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

Answer 2

catalysis by approximation

Question 3

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

Answer 3

tetrahedral

Question 4

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

Question 5

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

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

Question 6

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

Question 7

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

Question 8

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

Question 9

What process converts chymotrypsinogen to chymotrypsin?

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

Question 10

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

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

Question 11

What metal ion is required by carbonic anhydrase for activity?

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

Question 12

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?

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 13

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

Question 14

What type of reaction is catalyzed by proteases?

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

Question 15

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

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

Question 16

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

Question 17

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

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

Question 18

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

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

Question 19

Effective protease inhibitors are often _________________ for one enzyme.

Question 20

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

Question 21

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 pK_a for water, which leads to formation of a zinc bound hydroxide ion.
E) an altered K_M value.

Question 22

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

Question 23

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

Question 24

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

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

Question 25

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.

Question 26

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

A) a large change in K_M
B) a small change in K_M
C) a large change in k_cat
D) a large change in K_M and a large change in k_cat
E) a small change in K_M and a large change in k_cat

Question 27

Why are substrate analogs often used to monitor enzyme activity?

Question 28

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.

Question 29

How can covalent modification be used to determine the mechanism of action of an enzyme?

Question 30

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) 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 31

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.

Question 32

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

Question 33

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

Question 34

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

Question 35

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) stabilizing negative charges on an intermediate and metals binding directly to substrates.
E) All of the answers are correct.

Question 36

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

Question 37

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

Question 38

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

Question 39

Convergent evolution is attributed to similarities found between

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

Question 40

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.

Question 41

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

Question 42

How is the bicarbonate formed when carbonic anhydrase is present?

Question 43

What mechanism is responsible for restriction endonuclease cleavage of DNA?

Question 44

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

Question 45

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

Question 46

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

Question 47

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

Question 48

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

Question 49

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

Question 50

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