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Biochemistry > Enzyme Kinetics > Flashcards

Enzyme Kinetics Flashcards

1
Q

Enzymes

A

Substances that catalyze reactions without changing themselves (may change during reaction, but always return to their original state)
Work by lowering activation energy: stabilize transition state
Speed up rate of reaction

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2
Q

Specificity of an enzyme

A

Determined by interaction with substrate
Wide range of specificity: some cleave any peptide bond (papain), whereas some cleave only certain bonds (thrombin: cuts bonds between Arg and Gly)

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3
Q

Cofactor

A

Form complex with enzyme, allowing it to function

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4
Q

Holoenzyme

A

Enzyme and cofactor

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5
Q

Apoenzyme

A

Enzyme without cofactor

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6
Q

Prosthetic

A

A cofactor that is tightly bound to its enzyme

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7
Q

Cosubstrate

A

A cofactor that is loosely bound to its enzyme

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8
Q

Transition state

A

Structure between substrate and products
Has highest energy and is least stable
Enzymes bind to these and stabilize them

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9
Q

How the best drugs work

A

Best drugs inhibit substrate from reaching transition state: they add an inhibitor that mimics the transition state

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10
Q

The rate of product formation is proportional to…

A

Transition state formation

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11
Q

Why enzymes are necessary

A

Normally, to clear the Ea barrier, large amounts of kinetic energy that come from an increase of temperature are needed
The body can’t tolerate large increases in heat, so enzymes are needed to lower the Ea

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12
Q

Maximal velocity

A

Point at which all active sites on enzyme are occupied

Never actually reached: plot of [S] vs. reaction velocity (V not) is asymptotic

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13
Q

How to determine the active site of an enzyme

A
  1. Co-crystallography: crystallize enzyme and substrate to see binding
  2. See what enzyme reacts with
  3. Induce mutations into the enzyme and see their effect on binding
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14
Q

Spectral evidence for enzyme-substrate binding

A

Spectral changes are observed when substrate is added to enzyme, especially with color-producing reactions

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15
Q

Active site

A

Place where substrate binds to enzyme

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16
Q

Features of active site

A

3-D: folding dictates
Small part of enzyme (easily manipulated)
Specific amino acids dictate what can bind
Multiple non-covalent bonds are at work

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17
Q

Induced fit

A

Enzyme and substrate change each other to maximize binding

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18
Q

What enzymes can affect

A

Only the amount of energy needed to initiate

Never delta G

19
Q

Exergonic reaction

A

Change in delta G is negative

Spontaneous reaction

20
Q

Equilibrium

A

Delta G equals 0

Equal substrate and product formation

21
Q

Endergonic reaction

A

Change in delta G is positive

Input of free energy is needed for reaction to proceed

22
Q

Delta G and rate of reaction

A

Delta G provides no info about rate of reaction

Rate is dictated by Ea

23
Q

Free energy of reaction equation

A

Delta G= Delta G not + RT ln ([C][D])/([A][B])
Delta G not= standard free energy change at pH 7
R= gas constant
T= absolute temp

24
Q

Equilibrium constant equations

A 
Keq= ([C][D])/([A][B])
Keq= 10^(-delta G/2.303RT)
25
Q

1st order reaction equation

A

V=k[S]
k= constant in s-1
[S]= substrate concentration

26
Q

2nd order reaction equation

A

V=k[S]^2 (k is in s-1)

V=k[S1][S2] (k is in M-1 s-1)

27
Q

Michaelis constant equation

A

KM= (k-1+k2)/k1
k-1 and k2: breakdown of transition state
k1: formation of transition state

28
Q

Steady state assumption

A

Equilibrium: equal amount going to and taking away from

29
Q

Michaelis-Menton equation

A

V not= (Vmax * [S])/(KM + [S])

30
Q

Lineweaver-Burk plot

A

Plotting reciprocal of MM equation can allow measurement of V not and [S]
X intercept= -1/KM
Y intercept= 1/Vmax
Slope= KM/Vmax
Only works well if data points make good line

31
Q

Sequential reaction

A

All substrates must bind enzyme before the product is released
Can be ordered or random

32
Q

Ordered sequential reaction

A

Substrates must bind in a certain order and be released in a certain order
Enzyme undergoes conformational change

33
Q

Random sequential reaction

A

Doesn’t matter in what order substrates are bound and released
Enzyme either doesn’t undergo conformational change or undergoes small change

34
Q

Double displacement (“ping pong”) reaction

A

One or more products are released before all substrates bind

Hallmark: intermediate enzyme modification (modified until all products have been formed)

35
Q

Allosteric enzymes

A

Control from sites separate from the active site

Don’t follow MM kinetics: sigmoid rather than hyperbolic in plot of [S] vs. V not

36
Q

Reversible inhibitors

A

Can be displaced if inhibitor binds to active site
Non-covalent bonding
Used in drugs: need to inhibit some functions, but not all

37
Q

Irreversible inhibitors

A

Cannot be displaced

Covalent bonding

38
Q

Competitive inhibitor

A

Reversible inhibitor
Binds to same site as substrate
Usually looks like substrate

39
Q

Uncompetitive inhibitor

A

Reversible inhibitor
Binds to site near active site, but not active site itself
Binds when substrate is present and prevents transition to product

40
Q

Noncompetitive inhibitor

A

Reversible inhibitor
Binds to completely different site than active site
Allosteric inhibitor: changes shape of active site, disrupting substrate binding

41
Q

Reciprocal plot of competitive inhibitor

A 
No change in Vmax
KM increases (closer to 0): more substrate needed to reach 1/2 Vmax ([S]=KM)
42
Q

Reciprocal plot of uncompetitive inhibitor

A 
Vmax decreases (further from 0)
KM decreases (further from 0): less substrate needed to reach 1/2 Vmax ([S]=KM)
43
Q

Reciprocal plot of noncompetitive inhibitor

A

No change in KM: active site is still available

Smaller Vmax: substrate binding is disrupted

Biochemistry (11 decks)

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