Craven Equations

Question 1

give an equation showing the bimolecular formation of a protein-ligand complex from a protein and ligand

Answer 1

[P][L]=[PL]

Question 2

give an equation showing the unimolecular formation of protein and ligand from a protein-ligand complex

Answer 2

[PL]=[P]x[L]

Question 3

give another name for unimolecular and bimolecular reactions

Answer 3

unimolecular: 1st order reaction
bimolecular: 2nd order reaction

Question 4

give the rate equations of uni and bimolecular reactions

Answer 4

uni: rate of production of B=k[A]
bi: rate of production of C=k[A][B]

Question 5

give 2 equations that define kD (the dissociation constant) using a the equation [P][L][PL]

Answer 5

kOFF/kON = kD
[PL]eq/[P]eq[L]eq = kD

Question 6

give an equation showing the relationship between rate, reactants and products at equilibrium (using the equation: [P][L][PL])

Answer 6

kON[P][L]=kOFF[PL]

Question 7

does a strongly bound ligand have a smaller or larger kD value?

Answer 7

smaller
using the equation: kOFF/kON = kD it can be seen that a strongly bound ligand will have:
- a small kOFF because the rate of the product leaving the enzyme is v slow
- a large kON because the rate of the substrate binding the enzyme is very quick

Question 8

how can the ratio of [S] to Km be altered to give a maximal rate of product formation?

Answer 8

if [S]&raquo_space; Km then the rate of product formation will be at its maximum (according to the equation [S]/[S]+Km)

Question 9

define Km

Answer 9

affinity an enzyme has for its substrate (units of concentration)

Question 10

what does a high Km signify?

Answer 10

that the enzyme binds its substrate with low affinity

Question 11

give the equation that gives the fraction of bound protein (using the system [P][L][PL]). give the equal form of this equation using [L] and kD

Answer 11

fraction of bound protein [P] = [PL]/[P]tot

fraction of bound protein [L]/[L]+kD

Question 12

when kD = [free ligand] state the concentration of [protein]tot

Answer 12

when [L]free=kD:
the amount of time a ligand is bound = the amount of time a ligand is free
Therefore [P]tot=0.5

Question 13

give the Michaelis Menton equation

Answer 13

Rate of production of product = kcat x [E]tot x [S]/[S] +Km

Question 14

define Vmax

Answer 14

the maximal rate of reaction when the enzyme is saturated with substrate

Question 15

define kcat

Answer 15

rate at which a single enzyme molecule will make product if its always supplied with substrate so AS is never empty - essentially: how good the enzyme is at its chemistry ie a large kcat means the enzyme does its chemistry ‘better’

Question 16

describe the relationship of Km and Vmax with an equation

Answer 16

Km=Vmax/2
Km is the affinity the enzyme has for its substrate. Therefore at half Vmax, if the concentration of [S] is ‘high’, then lots of substrate is required to saturate the enzyme, and it has a low affinity for its substrate/ligand.

Question 17

describe the relationship of Vmax, [E]tot and kcat with an equation

Answer 17

Vmax=kcat x [E]tot

Question 18

give the equation to work out the free energy change associated with moving one mole of molecules from one concentration (Ca) to another (Cb)

Answer 18

ΔG=RTxln(Cb/Ca)

replace RT with KbT to find the energy change associated with moving one molecule

Question 19

give the equation to work out the free energy change associated with forming one mole of product(s) from its constitutive elements

Answer 19

ΔG=ΔG°+RTxln([P]/[R])

replace RT with KbT to find the energy change associated with forming one molecule

Question 20

give the equation to work out the standard free energy change associated with forming one mole of product(s) from its constitutive elements when the reaction is at equilibrium

Answer 20

as ΔG = 0 because the reaction is at zero:
ΔG° = -RTln([P]/[R])
(replace RT with KbT to find the energy change associated with forming one molecule)

Question 21

does ΔG or ΔG° determine a reactions’ spontaneity?

Answer 21

ΔG

Question 22

define equilibrium constant using an equation

Answer 22

Keq=[P]/[R] = Kf/Kr

Question 23

do enzymes affect ΔG and Keq?

Answer 23

enzymes cannot change the equilibrium constant, the change the rate at which this value is obtained. Equilibrium position is a function only of the ΔG difference between reactants and products

Question 24

give the equation to work out the free energy change associated with moving one mole of charged particles across a membrane

Answer 24

ΔG = RTln(Cb/Ca) + FΔV
F = Na x charge of an electron

Question 25

give the equation to work out the free energy change associated with moving one charged molecule of across a membrane

Answer 25

ΔG = KbTln(Cb/Ca) + eΔV

Question 26

when Γ>K does the the reaction (in the Γ system) favour the reactants or the products?

Answer 26

if Γ is bigger than K then the ratio of [P]/[R] has got to be larger ([P] being bigger). As the [P] is higher compared to the equilibrium system, the reactants are favoured

Question 27

give the equation to work out kinetic energy (KE)

Answer 27

KE=1/2mv^2

Question 28

give the equation for the KE of a simple molecule eg water

Answer 28

KbT

Question 29

give the equation for work done

Answer 29

force x distance moved

Question 30

give the equation to work out free energy from the relationship between the mass action ratio (Γ) and the equilibrium constant

Answer 30

ΔG=RTln(Γ/K)

Question 31

name the 3 effects that contribute to the free energy change when H+ ions flow through the ATP synthase machinery

Answer 31

-ΔG: ion flow from low conc to high conc ionic repulsive forces of H+ within the intermembrane space +ΔG: increasing concentrations of ATP on membrane, pushing away from equilibrium