The Kinetics of Biochemical Reactions Flashcards
What is reaction rate?
The change in concentration of chemical states with time
In what way can the rate constant be determined?
Experimentally
What are the units for a 1st order reaction?
s-1
What are the units for a second order reaction?
M-1s-1
What are the units for a third order reaction?
M-2s-1
Why is there an exponential decay of reactants in simple 1st order reactions?
Due to the random nature of chemical reactions
What form of the rate laws are the most useful for fitting experimental data to yield rate constants?
The integrated form
How is the rate concentration calculated from half life?
k=ln2/half life
How is keq calculated?
k of the forward reaction/k of the backward reaction
When do reversible reactions approach equilibrium?
At kf + kr
How is kobs calculated?
kon + koff
What equation is used to work out affinities for simple reactions under pseudo first order conditions?
kobs= kon x [L]0 + koff
How is Kd calculated for simple reactions under pseudo 1st order conditions?
Kd= koff/kon
Describe a 2 step ligand binding scheme
- The initial rapid binding of ligand to form P•L is followed by a conformational change to form P•L* that has a tighter affinity for the ligand
In a 2 step binding scheme which reaction is usually slower?
The conformational changes (step 2)
What is step 1 in a 2 step ligand binding scheme known as?
A rapid equilibrium
What is the equation for fractional saturation in rapid equilibrium binding of a ligand?
f= [L]/ KD + [L}
If a graph of kobs vs [L] is plotted and it produces a hyperbola, what kind of reaction is being observed?
A collision and rearrangment reaction (rather than simple binding)
For reaction A —-k1—> B —-k2—->C how is average time to go from A to C calculated?
1/k1 + 1/k2
How quickly does the rate determining step occur?
It is the slowest step
In a reaction with a rate limiting step, which intermediate will become the most highly populated?
the intermediate which precedes the rate limiting step
What order are enzyme reactions?
Zero order
What are the units of a zero order reaction?
M.s-1
How is an enzyme catalysed reaction zero order?
The rate of the reaction is independent of the [substrate] when there are very few molecules of z
What affects the rate constant?
- temperature
- pressure
- solvent
For bimolecular reactions what does k reflect?
- frequency of collisions per unit of concentration
- the fraction of those collisions that lead to the formation of product
Why do very few biological reactions approach the diffusion limited rate?
- reactants must come together in a very specific orientation
- the collision must provide enough energy for the reaction to occur
What is the purpose of the arrhenius equation?
It links the rate constant to activation energy and temperature
What is the boltzmann factor?
e-Ea/RT
What is the arrheius equation?
k=Ae-Ea/RT
If Ea is much greater than RT describe the rate and energy of collisions
Few colliding molecules have sufficient energy to react, the rate is slow
If Ea is much smaller than RT describe the rate and energy of collisions
Nearly all collisions have enough energy to result in a reaction. The rate of reaction is fast
What is plotted on each of the axes of an Arrhenius plot?
- lnk is plotted on the y axis
- 1/T is plotted on the x axis
How do catalysts work?
- Decreasing activation energy
- Stabilise the transition state
- Increasing the pre-exponential factor
- Completely altering the mechanism
