9. Enzyme kinetics

Question 1

define exergonic reaction

Answer 1

a spontaneous reaction

Question 2

what value of delta G does an exergonic reaction have

Answer 2

negative

Question 3

describe the speed of exergonic reactions when catalysts aren’t used

Answer 3

very slow

Question 4

are most chemical reactions exergonic or endergonic

Answer 4

exergonic

Question 5

what is a catalyst

Answer 5

a substance that speeds up attainment of equilibrium of a chemical reaction

Question 6

T or F: a catalyst changes the position of the equilibrium when it’s used

Answer 6

false! it only speeds up the process

Question 7

what happens to a catalyst after a reaction is complete

Answer 7

it is recycled to participate in future reactions

Question 8

T or F: a catalyst may be temporarily changed during a reaction

Answer 8

true; but it remains unchanged in the overall process

Question 9

define catalysis

Answer 9

the increase in the rate of a chemical reaction due to the participation of a catalyst

Question 10

what are biological catalysts

Answer 10

enzymes

Question 11

what key properties do enzymes have that you don’t see in inorganic catalysts

Answer 11

high degree of substrate specificity, substantial reaction acceleration, and they function in aqueous solutions at physiological pH

Question 12

why are enzymes control points for metabolism

Answer 12

they can accelerate chemical reactions by a factor of a million or more

Question 13

what is enzyme kinetics

Answer 13

the study of reaction rates and how they respond to changes in reaction parameters

Question 14

what letter is rate represented by

Answer 14

V (ie velocity)

Question 15

in the reaction of S –> P, what does the rate represent

Answer 15

the quantity of S that disappears in a specific unit of time

Question 16

what are the units of V

Answer 16

M/s

Question 17

T or F: V (the rate) should equal the rate of appearance of P

Answer 17

true

Question 18

for a first order reaction, what is the rate formula

Answer 18

V=k[S]
where V=rate
k=rate constant
and [S]=concentration of substrate

Question 19

what are the units of k for a first order reaction

Answer 19

s^-1

Question 20

describe the reaction rate (V) in regards to k

Answer 20

higher k value = faster reaction

Question 21

for a second order reaction, what is the rate formula

Answer 21

V=k[S1][S2]

Question 22

what are the units of k for a second order reaction

Answer 22

(M^-1)(s^-1)

Question 23

what are pseudo-first order reactions

Answer 23

a second order that appears as a first when one substrate is present in far excess of the other

Question 24

what is the rate formula for a pseudo-first order reaction

Answer 24

V=k[S1][S2], but S2 is negligible

Question 25

how do we plot reaction rates?

Answer 25

[P] vs time

Question 26

from a graph of product formed over time, what formula do we use to find V

Answer 26

delta P/delta t = V = k[S]

Question 27

what is V0

Answer 27

initial velocity

Question 28

how do we find V0 from a [P] vs time graph

Answer 28

calculate the slope at time=0 (tangent line)

Question 29

describe the slope of V0 depending on different amounts of [S]

Answer 29

at low [S], V0 increases almost linearly with increases in [S] at higher [S], V0 increases by smaller and smaller increments in response to increases in [S]

Question 30

what is Vmax (in regards to [S] and V0)

Answer 30

the point where increases in [S] no longer increases V0

Question 31

what is Vmax (in regards to the reaction)

Answer 31

Vmax is the fastest rate at which it can convert substrate to product. Adding more S doesn't increase the rate

Question 32

what are k1, k2, k-1, k-2

Answer 32

k1: E+S --> ES k2: ES --> E+ P k-1: ES --> E + S k2: E+P --> ES

Question 33

which step in the formation of a product from E and S is the slow step

Answer 33

ES --> E+P

Question 34

what is another name for the slow step of a reaction

Answer 34

the rate limiting step

Question 35

what is the M-M equation

Answer 35

V0=Vmax[S]/(Km+[S])

Question 36

what are the assumptions of the M-M equation

Answer 36

there is an ES complex, each step has distinct rates, very early in the reaction there is no product (so k-2 is negligible), the second step is rate limiting, [Etotal]=[Efree]+[ES], and [ES] is constant (formation=breakdown)

Question 37

what is Km

Answer 37

the Michaelis constant

Question 38

what are the units for Km

Answer 38

M

Question 39

what formula represents Km

Answer 39

(k-1 + k2)/k1 | ES breakdown/ES formation

Question 40

what does Km represent

Answer 40

it summarizes the rates of a reaction | it's ES breakdown over ES formation

Question 41

what happens to Km when V0=1/2 Vmax

Answer 41

Km=[S]

Question 42

how do we plot using the M-M equation

Answer 42

V0 on the y axis, [S] on the x axis the curve is hyperbolic

Question 43

T or F: we can use the M-M equation for second order reactions

Answer 43

false; only first order

Question 44

when does Km=Kd

Answer 44

when k2 is limiting and can be ignored, then Km=(k-1)/k1, which is equivalent to Kd

Question 45

reminder: what is Kd

Answer 45

dissociation constant of the ES complex

Question 46

what does a low Km represent

Answer 46

strong binding affinity between E and S

Question 47

what is another name for the L-B plot

Answer 47

double reciprocal plot

Question 48

how do we derive the L-B equation

Answer 48

by inverting the M-M equation

Question 49

what is the L-B equation

Answer 49

1/V0 = (Km/Vmax)(1/[S]) + 1/Vmax

Question 50

what are the axes for the L-B plot

Answer 50

y: 1/V0 x: 1/[S]

Question 51

what are the L-B plot intercepts

Answer 51

x=0: 1/Vmax | y=0: -1/Km

Question 52

what is the benefit of using an L-B plot vs an M-M plot

Answer 52

LB plot allows a better approximation of Vmax (because it's linear, nit hyperbolic)

Question 53

what is the turnover number of an enzyme

Answer 53

the number of substrate molecules converted into product by enzyme in a unit of time when the enzyme is fully saturated with substrate

Question 54

what variable reveals the turnover number of an enzyme

Answer 54

Vmax

Question 55

what variable is the turnover rate equal to

Answer 55

k2 (which is the rate limiting step)

Question 56

what is the rate constant k2 often referred to as

Answer 56

kcat

Question 57

how can you adjust V0=k2[ES] to solve for kcat?

Answer 57

kcat=Vmax/[Etotal]

Question 58

what does kcat tell us

Answer 58

the amount of product we produce per second

Question 59

what does 1/kcat tell us

Answer 59

the time each individual reaction takes

Question 60

what rate constant is called the specificity constant

Answer 60

kcat/Km

Question 61

what does the specificity constant measure

Answer 61

the catalytic efficiency, because it takes into account both the rate of catalysis with a particular substrate (kcat) and the nature of the enzyme-substrate interaction (Km)

Question 62

why do you need both kcat and Km for the specificity constant

Answer 62

two enzymes catalyzing different reactions may have the same kcat (turnover number) but the rate of uncatalyzed reactions may be different and this the rate enhancements brought about by the enzymes may differ greatly

Question 63

what is the equation for kcat and Km

Answer 63

V0=kcat/Km x [Etotal][S]

Question 64

T or F: there is an upper limit to kcat/Km

Answer 64

true

Question 65

why is there an upper limit to kcat/Km

Answer 65

it's imposed by the rate at which E and S can diffuse together in an aqueous solution and form ES

Question 66

what is the upper limit value for kcat/Km

Answer 66

10^8 to 10^9, in the units M^1s^1

Question 67

define kinetic perfection

Answer 67

when the catalytic velocity of enzymes is only restricted by the rate at which they encounter substrate in the solution

Question 68

what are the two types of reversible inhibition

Answer 68

competitive and uncompetitive

Question 69

in competitive inhibition, where does the inhibitor bind

Answer 69

to the active site

Question 70

how do we overcome competitive inhibition

Answer 70

by adding more substrate

Question 71

if we add more substrate in competitive inhibition, will the same Vmax be reached as without the inhibitor?

Answer 71

yes

Question 72

in competitive inhibition, since the [S] needs to be increased to reach Vmax, what else is increased

Answer 72

the Km at 1/2Vmax

Question 73

by which factor will Km be increased in competitive inhibition when more S is added

Answer 73

alpha

Question 74

how does the MM equation change to account for Km being increased by a factor of a (in competitive inhibition)

Answer 74

V0= Vmax[S]/aKm + [S]

Question 75

on a graph, how can we tell if inhibition is competitive

Answer 75

using the LB plot

Question 76

what are the signs of competitive inhibition on an LB plot

Answer 76

steeper slope=more inhibitor, more inhibitor=closer x intercept is to zero

Question 77

how do you overcome uncompetitive inhibition

Answer 77

you can't. Adding more S has no effect

Question 78

T or F: adding more S to uncompetitive inhibition will overcome it

Answer 78

false; adding more S has no effect

Question 79

why can't we overcome uncompetitive inhibition by adding more S

Answer 79

the inhibitor binds at a site distinct from the active site, forming an ESI complex

Question 80

what value is reduced in uncompetitive inhibition

Answer 80

Vmax

Question 81

by which factor is Vmax reduced by in uncompetitive inhibition

Answer 81

alpha'

Question 82

which way does the equilibrium shift in uncompetitive inhibition and why

Answer 82

shifts towards ES, because the inhibitor is removing ES from the population as ESI is formed

Question 83

in uncompetitive inhibition, what is the result in the equilibrium shifting towards ES

Answer 83

it makes the enzyme appear as if it has a higher affinity for S than it really does

Question 84

in uncompetitive inhibition, what else (other than Vmax) is reduced (and why which factor)

Answer 84

[S] required to reach Vmax is reduced by alpha'

Question 85

in uncompetitive inhibition, what effect does the reduced [S] and Vmax have

Answer 85

we have a decreased Km^app value

Question 86

how does uncompetitive inhibition appear on an LB plot

Answer 86

parallel lines

Question 87

why are the lines on an LB plot parallel when there's uncompetitive inhibition

Answer 87

each line has an equally reduced slope, so all lines have the same slope = parallel

Question 88

what happens to the intercepts on an LB plot of uncompetitive inhibition when inhibition is increased

Answer 88

absolute value of the intercepts increases (ie they are more up and to the left)