Craven (Spring - Kinetics) Flashcards
What units does KD have?
- concentration
What is the equation for the formation of PL?
- kon[P][L]
What is the equation for the loss of PL?
- koff[PL]
How will a stronger binding ligand affect kon and koff?
- go into binding site faster, so larger kon
- leave binding site slower, so smaller koff
What is the equation for Kd?
- koff / kon
- [P][L] / [PL]
How must koff and kon change for stronger binding?
- koff smaller
- kon bigger
- Kd smaller
What kind of reaction is formation of PL?
- 2nd order bimolecular
What kind of reaction is loss of PL?
- 1st order unimolecular
What is [P]tot?
- total conc of protein
- [P] + [PL]
What is the equation for the fraction of bound protein?
[PL] / [P]tot
How many protein molecules will be bound when free ligand conc = KD?
- half
What is a unimolecular irreversible reaction?
A –> B
k on arrow
What does the activation free energy measure?
- measures how likely it is to get to transition state
What does the no. of molecules that react in a given time depend on?
- no. molecules waiting to react
- how likely molecule is to react in same given time
What is ‘k’ and what are its units?
- 1st order rate constant
- units of per time
What is the rate of change of molecules in state A? (unimolecular irreversible)
-knA
What is the rate of change of molecules in state B? (unimolecular irreversible)
knA
What is the rate of change of [A]? (unimolecular irreversible)
-k[A]
What is the rate of change of [B]? (unimolecular irreversible)
k[A]
How is the equilibrium constant calculated for the ratio of folded to unfolded protein?
[U]eq / [F]eq
What is a bimolecular irreversible reaction?
a + b –> c
k on arrow
What must happen for ‘A’ and ‘B’ to react in a bimolecular irreversible reaction?
- must collide
- collide in right orientation and (perhaps) violently enough
What is the 1st order rate equation?
k[A]
What is the 2nd order rate equation?
k[A][B]
Is a v low conc of enzyme experimentally good, and why?
- 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
What does the Michaelis-Menten equation show?
- rate of prod of product
- “velocity”
What is kcat and what is it units?
- catalytic constant
- units of time
If you have an expensive enzyme what do you want in terms of [S] and Km and why?
- [S]»_space; Km
- to ensure get max poss rate of product formation
What is Km a measure of and what does a smaller value mean?
- how well substrate binds to enzyme
- smaller the value, the better it binds substrate
What happens to Km if enzyme mutated (and negatively affected)?
- Km will increase
What is kcat a measure of and what does a bigger value mean?
- measure of how well enzyme does chemistry and how easily it releases problems
- bigger kcat means does chemistry better
What happens to kcat if enzyme mutated (and negatively affects residues key for chemistry)?
- kcat will increase
What is a competitive inhibitor?
- molecule that can bind into active site and blocks substrate binding completely
How can you stop competitive inhibitor from binding to active site and how does this affect Km/kcat?
- higher conc of substrate
- increased Km
- kcat same
What are the affects to Km/kcat that allosteric molecules can have?
- 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)
