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MBB161 > Craven (Spring - Kinetics) > Flashcards

Craven (Spring - Kinetics) Flashcards

1
Q

What units does KD have?

A
  • concentration
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2
Q

What is the equation for the formation of PL?

A
  • kon[P][L]
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3
Q

What is the equation for the loss of PL?

A
  • koff[PL]
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4
Q

How will a stronger binding ligand affect kon and koff?

A
  • go into binding site faster, so larger kon

- leave binding site slower, so smaller koff

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5
Q

What is the equation for Kd?

A
  • koff / kon

- [P][L] / [PL]

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6
Q

How must koff and kon change for stronger binding?

A
  • koff smaller
  • kon bigger
  • Kd smaller
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7
Q

What kind of reaction is formation of PL?

A
  • 2nd order bimolecular
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8
Q

What kind of reaction is loss of PL?

A
  • 1st order unimolecular
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9
Q

What is [P]tot?

A
  • total conc of protein

- [P] + [PL]

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10
Q

What is the equation for the fraction of bound protein?

A

[PL] / [P]tot

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11
Q

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

A
  • half
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12
Q

What is a unimolecular irreversible reaction?

A

A –> B

k on arrow

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13
Q

What does the activation free energy measure?

A
  • measures how likely it is to get to transition state
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14
Q

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

A
  • no. molecules waiting to react

- how likely molecule is to react in same given time

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15
Q

What is ‘k’ and what are its units?

A
  • 1st order rate constant

- units of per time

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16
Q

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

A

-knA

17
Q

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

A

knA

18
Q

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

A

-k[A]

19
Q

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

A

k[A]

20
Q

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

A

[U]eq / [F]eq

21
Q

What is a bimolecular irreversible reaction?

A

a + b –> c

k on arrow

22
Q

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

A
  • must collide

- collide in right orientation and (perhaps) violently enough

23
Q

What is the 1st order rate equation?

A

k[A]

24
Q

What is the 2nd order rate equation?

A

k[A][B]

25
Q

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

A
  • 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
26
Q

What does the Michaelis-Menten equation show?

A
  • rate of prod of product

- “velocity”

27
Q

What is kcat and what is it units?

A
  • catalytic constant

- units of time

28
Q

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

A
  • [S]&raquo_space; Km

- to ensure get max poss rate of product formation

29
Q

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

A
  • how well substrate binds to enzyme

- smaller the value, the better it binds substrate

30
Q

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

A
  • Km will increase
31
Q

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

A
  • measure of how well enzyme does chemistry and how easily it releases problems
  • bigger kcat means does chemistry better
32
Q

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

A
  • kcat will increase
33
Q

What is a competitive inhibitor?

A
  • molecule that can bind into active site and blocks substrate binding completely
34
Q

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

A
  • higher conc of substrate
  • increased Km
  • kcat same
35
Q

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

A
  • 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)

MBB161 (6 decks)

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