Enzymes

Question 1

enzyme

Answer 1

powerful and specific catalysts

causes the substrate to reach its transition state

Question 2

major classes of enzymes

Answer 2

oxidoreductases 
transferases 
hydrolases 
lyases 
isomerases
ligases

Question 3

oxidoreductases

Answer 3

transfer electrons or hydrides

Question 4

transferases

Answer 4

a part of one substrate is transferred to a different substrate or enzyme

Question 5

hydrolases

Answer 5

a molecule is cleaved by the addition of water

Question 6

lyases

Answer 6

remove atoms from a compound to form a double bond, or catalyzes additions to double bonds

Question 7

isomerases

Answer 7

catalyzes rearrangements within molecules

Question 8

ligases

Answer 8

catalyzes the joining of molecules

typically powered by ATP hydrolysis

Question 9

cofactors

Answer 9

small molecules required by many enzymes for activity to take place
types: coenzymes, metals

Question 10

coenzymes

Answer 10

small organic molecules derived from vitamins

types: prosthetic groups, co-substrates

Question 11

prosthetic groups

Answer 11

tightly bound coenzyme (many times is inserted permanently into the enzyme as it is folded)
allow reactions that would otherwise be chemically difficult

Question 12

co-substrate

Answer 12

loosely bound coenzyme

Question 13

classes of multiple substrate reactions

Answer 13

sequential, double displacement

Question 14

sequential reaction mechanism

Answer 14

all substrates must bind to the enzyme before any product is released
types: ordered (when substrates bind to the enzyme in a specific order), random

Question 15

double displacement reaction mechanism

Answer 15

1+ products are released before all substrate bind to the enzyme

Question 16

Gibbs free energy

Answer 16

provides information about the spontaneity of a reaction, NOT the rate
a reaction is only spontaneous if it is negative; if it’s positive, there is no reaction; if it is 0, the reaction is at equilibrium

Question 17

active site

Answer 17

the region of an enzyme that binds the substrates
normally excludes water
most tightly binds to the transition state

Question 18

types of enzyme/substrate binding

Answer 18

induced fit

lock and key

Question 19

induced fit

Answer 19

binding of substrate leads to a conformational change in the active site that promotes association

Question 20

lock and key

Answer 20

complementary fit between the shapes of the enzyme’s active site and substrate

Question 21

catalytic strategies

Answer 21

covalent catalysis
general acid/base catalysis
metal ion catalysis
catalysis by approximation and orientation

Question 22

covalent catalysis

Answer 22

the active site of an an enzyme has a reactive group that forms a covalent intermediate during the reaction

Question 23

general acid/base catalysis

Answer 23

a molecule in the active site besides water functions as a proton donor or acceptor during the reaction

Question 24

metal ion catalysis

Answer 24

metal ions alter their redox state to participate in oxidation/reduction reactions
acts as an electrophilic catalysts by stabilizing a negative charge in a reaction intermediate
generates a nucleophile by increasing the acidity of a neighboring molecule

Question 25

catalysis by approximation and orientation

Answer 25

in reactions with 2+ substrates, the active site brings the substrates together in an optimal proximity and orientation for the reaction to occur

Question 26

protease

Answer 26

enzyme that breaks down proteins and peptides

Question 27

common features of proteases

Answer 27

active water or another nucleophile
polarize the peptide carbonyl group
stabilize a tetrahedral intermediate

Question 28

V0

Answer 28

the initial velocity of the enzyme-catalyzed reaction

Question 29

Km

Answer 29

the substrate concentration where the reaction rate is half of the maximum rate
is ALWAYS larger than Kd

Question 30

Vmax

Answer 30

maximum reaction rate at a given enzyme concentration

Question 31

Kd

Answer 31

dissociation constant for the substrate in an enzyme-catalyzed reaction

Question 32

Kcat

Answer 32

the number of reactions catalyzed in an active site per unit time when the enzyme is saturated with substrate

Question 33

what is defined as catalytic efficiency?

Answer 33

Kcat/Km

larger value = larger substrate preference

Question 34

inhibitor

Answer 34

molecule that interferes with catalysis

types: reversible, irreversible

Question 35

reversible inhibitors

Answer 35

inhibitors that dissociate from the enzyme when finished
types: competitive, uncompetitive, noncompetitive
are more commonly found

Question 36

competitive inhibitor

Answer 36

competes with the substrate directly for binding in the enzyme’s active site
often structurally similar to the substrate
increases the Km, but not the Vmax

Question 37

uncompetitive inhibitor

Answer 37

binds to the enzyme-substrate complex

decreases the Km and Vmax

Question 38

noncompetitive inhibitor

Answer 38

binds either to the enzyme or the enzyme-substrate complex, DOESN’T PREVENT THE SUBSTRATE FROM BINDING
doesn’t change the Vm, but decreases the Vmax

Question 39

irreversible inhibitors

Answer 39

modify the enzyme or cofactor by forming new covalent bonds
do NOT dissociate from the enzyme when finished
types: group-specific reagents, affinity labels, suicide inhibitors

Question 40

group-specific reagents

Answer 40

react with the side chains of specific amino acids

Question 41

affinity labels

Answer 41

substances can be chemically modified to generate specific covalent labeling agents that react with active site groups in an enzyme

Question 42

suicide inhibitor

Answer 42

a chemically modified substrate that begins to react with an enzyme like the substrate, but forms a highly reactive intermediate that covalently modifies an amino acid in the active site

Question 43

allosteric regulation

Answer 43

regulation of enzyme or protein activity by binding of a molecule at a site other than the active site