Enzyme Kinetics 1 and 2

Question 1

frequent drug target

Answer 1

enzymes, enzyme activity

Question 2

why enzymes

Answer 2

biological reactions are too slow

(sucrose -> CO2 + H20 + energy

Question 3

what are enzymes?

Answer 3

biological catalyst

alters RATE of reaction, not direction or products

Question 4

enzyme characteristics

Answer 4

primarily proteins with specific structures and active sites formed when the protein folds into its three dimensional shape

Question 5

why highly ordered active site

Answer 5

makes for enzyme specificity, only bind specific substrates

Question 6

coenzyme

Answer 6

small molecule that participates in a rxn by donating or accepting a chemical group (a pseudosubstrate)

it is changed and used up in the rxn

Question 7

enzyme cofactor

Answer 7

small molecules that are not changed in the enzymatic rxn, often metal ions

Question 8

metal ions as cofactors

Answer 8

may change oxidation state and be rapidly recycled to active form

Question 9

prosthetic group

Answer 9

tightly bound coenzyme or cofactor

Question 10

six classifications of enzymes

Answer 10

oxidoreductases
transferases
hydrolases
lysases
...
...

Question 11

review of reaction equilibria

Answer 11

S P with associated delta-G

Question 12

Keq of enzyme rxn

Answer 12

[product]/[substrate] at equilibrium

[enzyme] is not included since not consumed

Question 13

transition state theory

Answer 13

suggests a high energy state between substrate and product with equal probability to go forward or backward
exists for time on the order of a molecular vibration, about 10^-13 second

Question 14

how enzyme “works”

Answer 14

lowers energy of transition state between substrate and product

Question 15

energetics of enzyme rxn coordinate

Answer 15

delta-G for rxn is unchanged

delta-G-cat much less than delta-G-uncat, i.e., transition state energy is much lower

Question 16

velocity of rxn

Answer 16

V = k[S]
where k=(kT/h)exp(-delta-G**/RT)

k in kT term is Boltzmann constant

Question 17

lock and key model of enzyme substrate rxn

Answer 17

actually stabilizes substrate, makes it harder to get to transition state

Question 18

induced fit

Answer 18

stabilize the transition state, lowers the delta-G**

Question 19

effective concentration

Answer 19

effect of an enzyme to bring substrate constituents into proximity, increasing the probability of a rxn between the substrates

Question 20

alcohol dehydrogenase cofactor

Answer 20

zn

interacts directly with OH group in alcohol

Question 21

steps to measure enzymatic parameters

Answer 21

1) measure initial velocity, V0, at one [S]
2) repeat your measurement at many [S]
3) create V0 vs [S] plot

Question 22

enzyme velocity plot characteristics

Answer 22

initial plot is linear in [S]
speed levels off to reach Vmax
read Km from 1/2 Vmax

Question 23

Michaelis-Menten equation

Answer 23

relation between Km to k-1, k1, and k2
Km = (k-1 + k2)/k1

where k1 is E+S ES
and k2 is ES E+P

Question 24

Kd

Answer 24

enzyme binding affinity

Question 25

Km

Answer 25

The substrate concentration at which enzyme velocity is half the maximum

Question 26

Kcat

Answer 26

describes the rate limiting step of any enzyme catalized rxn kcat = k2 if product release is rate limiting

Question 27

turnover number Kcat

Answer 27

number of substrate molecules per enzyme per second that are turned into product

Question 28

enzyme comparison metric

Answer 28

Kcat/Km larger means more efficient processing

Question 29

two classes of enzyme inhibitors

Answer 29

reversible and irreversible

Question 30

irreversible enzyme inhibition

Answer 30

covalent bonding, destroy active site activity

Question 31

competitive inhibition

Answer 31

reversibly bind to enzyme

Question 32

uncompetitive inhibition

Answer 32

bind only to ES complex

Question 33

Lineweaver-Burk plot

Answer 33

double reciprocal plot of | 1/V0 vs 1/[S]

Question 34

Lineweaver-Burk relation

Answer 34

1/V0 = Km/Vmax x 1/[S] + 1/Vmax

Question 35

Lineweaver-Burk characteristics

Answer 35

Slope = Km/Vmax

Question 36

competitive inhibitor

Answer 36

competes with substrate to bind the enzyme active site

Question 37

competitive inhibitor characteristics

Answer 37

Kcat is unaffected while the apparent Km increases as [I] increases

Question 38

Ritonavir

Answer 38

competitively inhibits HIV protease

Question 39

Methotrexate

Answer 39

common cancer drug, competitively inhibits dihydrofolate reductase, a key enzyme in nucleotide biosyntheses

Question 40

uncompetitive inhibitor characteristics

Answer 40

bind to a different site from the substrate active site | only binds to ES complex, prevents forward rxn

Question 41

mixed inhibitors

Answer 41

bind at a different site from active site, but can bind to E or ES

Question 42

penicillin

Answer 42

irreversible inhibitor that prevents synthesis of peptidoglycans, an integral part of bacterial cell wall

Question 43

mechanisms of enzyme regulation

Answer 43

allosteric regulation covalent modification of the enyme binding of another regulatory protein proteolytic cleavage of the enzyme to activate it

Question 44

when to affect sequence of enzyme processes

Answer 44

earlier is better, get the first step blocked

Question 45

what to use to block enzyme process

Answer 45

end product is good, abundance => shut down production

Question 46

enzyme regulation via protoenzymes

Answer 46

zymogens -> enzyme via post-translational modification such as cleavage (think chymotrypsin)