The Kinetics of Biochemical Reactions

Question 1

What is reaction rate?

Answer 1

The change in concentration of chemical states with time

Question 2

In what way can the rate constant be determined?

Answer 2

Experimentally

Question 3

What are the units for a 1st order reaction?

Answer 3

s^-1

Question 4

What are the units for a second order reaction?

Answer 4

M^-1s^-1

Question 5

What are the units for a third order reaction?

Answer 5

M^-2s^-1

Question 6

Why is there an exponential decay of reactants in simple 1st order reactions?

Answer 6

Due to the random nature of chemical reactions

Question 7

What form of the rate laws are the most useful for fitting experimental data to yield rate constants?

Answer 7

The integrated form

Question 8

How is the rate concentration calculated from half life?

Answer 8

k=ln2/half life

Question 9

How is k_eq calculated?

Answer 9

k of the forward reaction/k of the backward reaction

Question 10

When do reversible reactions approach equilibrium?

Answer 10

At k_f + k_r

Question 11

How is k_obs calculated?

Answer 11

k_on + k_off

Question 12

What equation is used to work out affinities for simple reactions under pseudo first order conditions?

Answer 12

k_obs= k_on x [L]₀ + k_off

Question 13

How is K_d calculated for simple reactions under pseudo 1st order conditions?

Answer 13

K_d= k_off/k_on

Question 14

Describe a 2 step ligand binding scheme

Answer 14

• 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

Question 15

In a 2 step binding scheme which reaction is usually slower?

Answer 15

The conformational changes (step 2)

Question 16

What is step 1 in a 2 step ligand binding scheme known as?

Answer 16

A rapid equilibrium

Question 17

What is the equation for fractional saturation in rapid equilibrium binding of a ligand?

Answer 17

f= [L]/ K_D + [L}

Question 18

If a graph of k_obs vs [L] is plotted and it produces a hyperbola, what kind of reaction is being observed?

Answer 18

A collision and rearrangment reaction (rather than simple binding)

Question 19

For reaction A —-k₁—> B —-k₂—->C how is average time to go from A to C calculated?

Answer 19

1/k₁ + 1/k₂

Question 20

How quickly does the rate determining step occur?

Answer 20

It is the slowest step

Question 21

In a reaction with a rate limiting step, which intermediate will become the most highly populated?

Answer 21

the intermediate which precedes the rate limiting step

Question 22

What order are enzyme reactions?

Answer 22

Zero order

Question 23

What are the units of a zero order reaction?

Answer 23

M.s^-1

Question 24

How is an enzyme catalysed reaction zero order?

Answer 24

The rate of the reaction is independent of the [substrate] when there are very few molecules of z

Question 25

What affects the rate constant?

Answer 25

* temperature * pressure * solvent

Question 26

For bimolecular reactions what does k reflect?

Answer 26

* frequency of collisions per unit of concentration * the fraction of those collisions that lead to the formation of product

Question 27

Why do very few biological reactions approach the diffusion limited rate?

Answer 27

* reactants must come together in a very specific orientation * the collision must provide enough energy for the reaction to occur

Question 28

What is the purpose of the arrhenius equation?

Answer 28

It links the rate constant to activation energy and temperature

Question 29

What is the boltzmann factor?

Answer 29

e^-Ea/RT

Question 30

What is the arrheius equation?

Answer 30

k=Ae^-Ea/RT

Question 31

If Ea is much greater than RT describe the rate and energy of collisions

Answer 31

Few colliding molecules have sufficient energy to react, the rate is slow

Question 32

If Ea is much smaller than RT describe the rate and energy of collisions

Answer 32

Nearly all collisions have enough energy to result in a reaction. The rate of reaction is fast

Question 33

What is plotted on each of the axes of an Arrhenius plot?

Answer 33

* lnk is plotted on the y axis * 1/T is plotted on the x axis

Question 34

How do catalysts work?

Answer 34

* Decreasing activation energy * Stabilise the transition state * Increasing the pre-exponential factor * Completely altering the mechanism