Craven Equations Flashcards
give an equation showing the bimolecular formation of a protein-ligand complex from a protein and ligand
[P][L]=[PL]
give an equation showing the unimolecular formation of protein and ligand from a protein-ligand complex
[PL]=[P]x[L]
give another name for unimolecular and bimolecular reactions
unimolecular: 1st order reaction
bimolecular: 2nd order reaction
give the rate equations of uni and bimolecular reactions
uni: rate of production of B=k[A]
bi: rate of production of C=k[A][B]
give 2 equations that define kD (the dissociation constant) using a the equation [P][L][PL]
kOFF/kON = kD [PL]eq/[P]eq[L]eq = kD
give an equation showing the relationship between rate, reactants and products at equilibrium (using the equation: [P][L][PL])
kON[P][L]=kOFF[PL]
does a strongly bound ligand have a smaller or larger kD value?
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
how can the ratio of [S] to Km be altered to give a maximal rate of product formation?
if [S]»_space; Km then the rate of product formation will be at its maximum (according to the equation [S]/[S]+Km)
define Km
affinity an enzyme has for its substrate (units of concentration)
what does a high Km signify?
that the enzyme binds its substrate with low affinity
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
fraction of bound protein [P] = [PL]/[P]tot
fraction of bound protein [L]/[L]+kD
when kD = [free ligand] state the concentration of [protein]tot
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
give the Michaelis Menton equation
Rate of production of product = kcat x [E]tot x [S]/[S] +Km
define Vmax
the maximal rate of reaction when the enzyme is saturated with substrate
define kcat
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’
describe the relationship of Km and Vmax with an equation
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.
describe the relationship of Vmax, [E]tot and kcat with an equation
Vmax=kcat x [E]tot
give the equation to work out the free energy change associated with moving one mole of molecules from one concentration (Ca) to another (Cb)
ΔG=RTxln(Cb/Ca)
replace RT with KbT to find the energy change associated with moving one molecule
give the equation to work out the free energy change associated with forming one mole of product(s) from its constitutive elements
ΔG=ΔG°+RTxln([P]/[R])
replace RT with KbT to find the energy change associated with forming one molecule
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
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)
does ΔG or ΔG° determine a reactions’ spontaneity?
ΔG
define equilibrium constant using an equation
Keq=[P]/[R] = Kf/Kr
do enzymes affect ΔG and Keq?
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
give the equation to work out the free energy change associated with moving one mole of charged particles across a membrane
ΔG = RTln(Cb/Ca) + FΔV F = Na x charge of an electron
give the equation to work out the free energy change associated with moving one charged molecule of across a membrane
ΔG = KbTln(Cb/Ca) + eΔV
when Γ>K does the the reaction (in the Γ system) favour the reactants or the products?
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
give the equation to work out kinetic energy (KE)
KE=1/2mv^2
give the equation for the KE of a simple molecule eg water
KbT
give the equation for work done
force x distance moved
give the equation to work out free energy from the relationship between the mass action ratio (Γ) and the equilibrium constant
ΔG=RTln(Γ/K)
name the 3 effects that contribute to the free energy change when H+ ions flow through the ATP synthase machinery
-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
