Chapter 11: Enzymatic Catalysis

Question 1

Enzymes differ from ordinary chemical catalysts in several important respects

Answer 1

Higher reaction rates

Milder reaction conditions

Greater reaction specificity

Capacity for regulation

Question 2

catalyzes the oxidation of alcohols by
removing hydrogen

Answer 2

alcohol dehydrogenase

Question 3

catalyzes the
hydrolysis of urea

Answer 3

urease

Question 4

Enzymes are commonly named by what?

Answer 4

appending the suffix-ase to the name of the enzyme’s substrate or to a phrase describing the enzyme’s catalytic action

Question 5

oxidation-reduction reactions

Answer 5

oxidoreductases

Question 6

transfer of functional groups

Answer 6

Transferases

Question 7

hydrolysis reactions

Answer 7

hydrolases

Question 8

group elimination to form double bonds

Answer 8

lyases

Question 9

isomerization

Answer 9

isomerases

Question 10

bond formation coupled with atp hydrolysis

Answer 10

ligases

Question 11

vary considerably in their degree of geometric specificity

Answer 11

Enzymes

Question 12

Although enzymes catalyze such reactions, they can do so only in
association with small

Answer 12

cofactors

Question 13

what are types of cofactors

Answer 13

metal

coenzymes

Question 14

organic molecules

Answer 14

coenzymes

Question 15

types of coenzymes

Answer 15

cosubstrates

prosthetic groups

Question 16

Permanently associated cofactors like
heme in cytochrome c.

Answer 16

prosthetic groups

Question 17

A catalytically active enzyme–cofactor complex is called

Answer 17

holoenzyme.

Question 18

The holoenzyme without the cofactor

Answer 18

apoenzyme

Question 19

If the activation energy of the 2nd step is greater than that of the
1st step, then the 2nd step is “bottleneck” or the

Answer 19

rate-determining step

Question 20

act by providing a reaction pathway with a transition state whose free energy is lower than that in the original reaction.

Answer 20

Catalysts

Question 21

The types of catalytic mechanisms that enzymes employ have been classified as

Answer 21

1. Acid–base catalysis
2. Covalent catalysis
3. Metal ion catalysis
4. Proximity and orientation effects
5. Preferential binding of the transition state complex

Question 22

a process in which proton transfer from an acid lowers the
free energy of a reaction’s transition state.

Answer 22

General acid catalysis

Question 23

the ability of enzymes to arrange several catalytic groups around their substrates makes concerted acid–base catalysis what

Answer 23

enzymatic mechanism

Question 24

the inflection points of the curve

Answer 24

observed pK

Question 25

often provide valuable clues to the
identities of the amino acid residues essential for enzymatic activity

Answer 25

observed pK’s

Question 26

pH effects on an enzymatic rate may reflect what

Answer 26

denaturation

Question 27

is a more reliable approach to
identifying residues that are required for substrate binding or catalysis.

Answer 27

The replacement of a particular residue by site-directed mutagenesis or comparisons of enzyme variants generated by evolution

Question 28

is a digestive enzyme that is secreted by the pancreas into the small intestine, where it hydrolyzes RNA to its component nucleotides.

Answer 28

Bovine pancreatic RNase A

Question 29

acting as a general base,
abstracts a proton from an RNA 2′
-OH group, thereby promoting its nucleophilic attack on the adjacent phosphorus atom

Answer 29

His 12

Question 30

acting as a general acid, promotes bond scission by protonating the leaving group.

Answer 30

His 119

Question 31

accelerates reaction rates through the transient formation of a catalyst–substrate covalent bond

Answer 31

Covalent catalysis

Question 32

Usually, this covalent bond is formed by the reaction of a nucleophilic group on the catalyst with an electrophilic group on the
substrate, and hence this form of catalysis is often also called

Answer 32

nucleophilic catalysis

Question 33

function in association with their apoenzymes as covalent catalysts

Answer 33

pyridoxal phosphate

Question 34

enzymes require metal ions for catalytic activity

Answer 34

metalloenzymes

Question 35

which often play a structural rather than a catalytic role in enzymes.

Answer 35

Na+
K+
Ca2+
Mg2+
Zn2+

Question 36

contain tightly bound metal ion cofactors, most commonly
transition metal ions such as

Fe2+
Fe3+
Cu2+
Mn2+
Co2+

Answer 36

metalloenzymes

Question 37

Metal ions participate in the catalytic process in 3 major ways

Answer 37

1. By binding to substrates to orient them properly for reaction.
2. By mediating redox reactions through reversible changes in the metal ion’s oxidation state.
3. By electrostatically stabilizing or shielding negative charges.

Question 38

By simply binding their substrates, enzymes facilitate their catalyzed reactions in 4 ways

Answer 38

1. Enzymes bring substrates into contact with their catalytic groups and, in reactions with more than
   one substrate, with each other to enhance reaction rates by a factor of ~5.
2. Enzymes bind their substrates in the proper orientations for reaction. It is estimated that properly
   orienting substrates can increase reaction rates by a factor of up to ~100.
3. Charged groups may help stabilize the transition state of the reaction, a phenomenon termed
   electrostatic
4. Enzymes freeze out the relative translational and rotational motions of their substrates and catalytic
   groups. This is an important aspect of catalysis because, in the transition state, the reacting groups
   have little relative motion. Indeed, experiments with model compounds suggest that this effect can
   promote rate enhancements of up to ~107

Question 39

Enzymes Catalyze Reactions by Preferentially what the Transition State

Answer 39

Binding

Question 40

An enzyme may bind the transition state of the reaction it catalyzes with what?

Answer 40

greater affinity than its substrates or products.

Question 41

stable molecules that geometrically and electronically resemble the transition state

Answer 41

analogs

Question 42

If an enzyme preferentially binds its transition state, then it can be expected that transition state what?

Answer 42

analogs

Question 43

is an enzyme that destroys bacterial cell walls.

Answer 43

Lysozyme

Question 44

include digestive enzymes from prokaryotes and eukaryotes, as well as more specialized proteins that participate in development, blood coagulation (clotting), inflammation, and numerous other processes.

Answer 44

Serine proteases

Question 45

The best studied serine proteases are

Answer 45

chymotrypsin, trypsin, and elastase

Question 46

what are serine proteases synthesized by

Answer 46

pancreas and secreted into the small intestine

Question 47

what do serine proteases catalyze

Answer 47

hydrolysis of peptide (amide) bonds but with different specificities

Question 48

is specific for a bulky hydrophobic residue (Phe, Trp, or T yr )

Answer 48

Chymotrypsin

Question 49

specific for a positively charged residue (Arg and Lys)

Answer 49

trypsin

Question 50

is specific for a small neutral residue (Ala, Gly , and Val).

Answer 50

elastase

Question 51

reacts only with Ser 195 of chymotrypsin, thereby demonstrating that this residue is the enzyme’s active site Ser.

Answer 51

Diisopropylphosphofluoridate (DIPF)

Question 52

are so toxic to
humans (death occurs through the inability to breathe) that it
has been used militarily as a nerve gas

Answer 52

Diisopropylphosphofluoridate (DIPF)

Question 53

DIPF inactivates what?

Answer 53

acetylcholinesterase

Question 54

is responsible for much of the catalytic efficiency of serine proteases

Answer 54

preferential binding of the transition state over the enzyme-substrate complex

Question 55

such an effective inhibitor of serine
proteases because its tetrahedral phosphate group makes this compound a transition state analog.

Answer 55

DIPF