Craven (Spring - Kinetics)

Question 1

What units does KD have?

Answer 1

• concentration

Question 2

What is the equation for the formation of PL?

Answer 2

• kon[P][L]

Question 3

What is the equation for the loss of PL?

Answer 3

• koff[PL]

Question 4

How will a stronger binding ligand affect kon and koff?

Answer 4

• go into binding site faster, so larger kon

- leave binding site slower, so smaller koff

Question 5

What is the equation for Kd?

Answer 5

• koff / kon

- [P][L] / [PL]

Question 6

How must koff and kon change for stronger binding?

Answer 6

• koff smaller
• kon bigger
• Kd smaller

Question 7

What kind of reaction is formation of PL?

Answer 7

• 2nd order bimolecular

Question 8

What kind of reaction is loss of PL?

Answer 8

• 1st order unimolecular

Question 9

What is [P]tot?

Answer 9

• total conc of protein

- [P] + [PL]

Question 10

What is the equation for the fraction of bound protein?

Answer 10

[PL] / [P]tot

Question 11

How many protein molecules will be bound when free ligand conc = KD?

Answer 11

• half

Question 12

What is a unimolecular irreversible reaction?

Answer 12

A –> B

k on arrow

Question 13

What does the activation free energy measure?

Answer 13

• measures how likely it is to get to transition state

Question 14

What does the no. of molecules that react in a given time depend on?

Answer 14

• no. molecules waiting to react

- how likely molecule is to react in same given time

Question 15

What is ‘k’ and what are its units?

Answer 15

• 1st order rate constant

- units of per time

Question 16

What is the rate of change of molecules in state A? (unimolecular irreversible)

Answer 16

-knA

Question 17

What is the rate of change of molecules in state B? (unimolecular irreversible)

Answer 17

knA

Question 18

What is the rate of change of [A]? (unimolecular irreversible)

Answer 18

-k[A]

Question 19

What is the rate of change of [B]? (unimolecular irreversible)

Answer 19

k[A]

Question 20

How is the equilibrium constant calculated for the ratio of folded to unfolded protein?

Answer 20

[U]eq / [F]eq

Question 21

What is a bimolecular irreversible reaction?

Answer 21

a + b –> c

k on arrow

Question 22

What must happen for ‘A’ and ‘B’ to react in a bimolecular irreversible reaction?

Answer 22

• must collide

- collide in right orientation and (perhaps) violently enough

Question 23

What is the 1st order rate equation?

Answer 23

k[A]

Question 24

What is the 2nd order rate equation?

Answer 24

k[A][B]

Question 25

Is a v low conc of enzyme experimentally good, and why?

Answer 25

- makes reaction slower and easier to follow - cheaper - no worries about solubility - amount of S bound in Es complexes so small, we can write [S]free ~ [S]total added

Question 26

What does the Michaelis-Menten equation show?

Answer 26

- rate of prod of product | - "velocity"

Question 27

What is kcat and what is it units?

Answer 27

- catalytic constant | - units of time

Question 28

If you have an expensive enzyme what do you want in terms of [S] and Km and why?

Answer 28

- [S] >> Km | - to ensure get max poss rate of product formation

Question 29

What is Km a measure of and what does a smaller value mean?

Answer 29

- how well substrate binds to enzyme | - smaller the value, the better it binds substrate

Question 30

What happens to Km if enzyme mutated (and negatively affected)?

Answer 30

- Km will increase

Question 31

What is kcat a measure of and what does a bigger value mean?

Answer 31

- measure of how well enzyme does chemistry and how easily it releases problems - bigger kcat means does chemistry better

Question 32

What happens to kcat if enzyme mutated (and negatively affects residues key for chemistry)?

Answer 32

- kcat will increase

Question 33

What is a competitive inhibitor?

Answer 33

- molecule that can bind into active site and blocks substrate binding completely

Question 34

How can you stop competitive inhibitor from binding to active site and how does this affect Km/kcat?

Answer 34

- higher conc of substrate - increased Km - kcat same

Question 35

What are the affects to Km/kcat that allosteric molecules can have?

Answer 35

- might make binding worse, increase Km (inhibition) - might make binding better, decrease Km (activator) - might make chem worse, decrease kcat (inhibition) - might make chem better, increase kcat (activator)