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M2M1 > Enzyme Kinetics > Flashcards

Enzyme Kinetics Flashcards

1
Q

When a cofactor or coenzyme is tightly or even covalently bound to an enzyme, it is called a….

A

prosthetic group

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2
Q

Enzymes: covalent chemistry

A

a transient covelent bond forms between the enzyme and the substrate

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3
Q

Enzymes: general acid-base chemistry

A

amino acid side chains of the enzyme can donate or accept protons to stabilize the transition state

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4
Q

Enzymes: metal ion catlaysis

A

bound metal ions can help position teh substrate or can be powerful driving forces in redox reactions- almost 1/3 of all enzymes use a metal ion

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5
Q

Km

A

The amount of substrate needed for the enzyme velocity to be at 1/2 vmax

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6
Q

Kcat

A

The turnover number…
the number of substrate molecules converted to product in a given unit of time on a single enzyme molecule when the enzyme is saturated with substrate

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7
Q

The ratio Kcat/Km

A

enzymatic efficiency

– the larger this number the “better” the enzyme

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8
Q

Reversible inhibitors

A

Do not fundamentally alter the enzyme - act only so long as they are bound to the enzyme

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9
Q

Competitive inhibitors:

A

Bind only to the E (not ES) and compete with the S for the AS

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10
Q

What do competitive inhibitors do to the Km?

A

They raise it (because now you need more substrate to get to 1/2 vmax)

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11
Q

Uncompetitive inhibitors

A

Bind to the enzyme in a place other than the active site and only to the (ES)!

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12
Q

What do uncompetitive inhibitors do to the Km

A

change the apparent Km (lower it) because the slope does not change on the reciprocal plot (km/vmax), must lower Km by same factor as lower Vmax

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13
Q

What do uncompetetive inhibitors do to the Vmax?

A

Lowers the Vmax - because they are altering the ES - you could think of it like making the ES tighter so less likely to release

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14
Q

Mixed inhibitor

A

binds outside the active site, but can bind either E or ES

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15
Q

Mixed inhibition effect on Km and Vmax?

A

Change both Km and Vmax

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16
Q

Irreversible inhibitor

A

combine with or destroy a functional group on an enzyme that is essential for enzymes activity

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17
Q

4 mechanisms of enzyme regulation

A

allosteric
covalent modification
binding of another regulator protein
proteolytic cleavage

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18
Q

allosteric regulation

A

binding of another molecule changes the confirmation of teh enzyme and hence alters its function - often seen in feedback loop

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19
Q

covalent modification - regulation

A

phosphorylation (and other modifications) are a powerful way to change the function of an enzyme. Many enzyme are constantly being P and de-P in response to intra or extra cellular signals or conditions

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20
Q

Binding of another regulator protein - enzyme regulation

A

like allosteric regulation, small peptides can bind to enzyme and turn them on or off

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21
Q

Proteolytic cleavage - enzyme regulation

A

some enzymes are inactive when they are first made (zymogen) but once cleaved into a smaller fragment (Generally by another protein) they become active

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22
Q

What is the difference between a cofactor and coenzyme?

A

Coenzymes provide a chemical group for the reaction and are “used up”. Cofactors are not

23
Q

Coenzyme

A

small molecule bound in the enzyme that may provide a functional group

24
Q

Cofactor

A

usually metal ions bound by enzyme and used to help with chemistry

25
Q

Holoenzyme

A

enzyme + coenzyme or cofactor

26
Q

Apoenezyme

A

enzyme without coenzyme or cofactor

27
Q

How are enzymes named?

A

by what they do :)

28
Q

What determines the rate of a reaction

A

The activation energy

29
Q

Teachers opinion on lock and key vs induced fit

A

Induced fit - enzyme is complementary to the transition state (not the substrate)

30
Q

Binding favors the _________ state

A

transition

31
Q

enzymes can lower the activation energy by increasing the “Effective concentration” what does this mean

A

the confined space of the enzyme active site helps bring the substrates in close proximity so that positioned correctly

32
Q

If an enzymatic reaction results in the reduction of NAD to NADH … NAD would be conisdered a_________

A

coenzyme

33
Q

If an enzymateic reaction required zinc, e.g. alcohol dehydrogenase, zinc would be considered ________________

A

a cofactor

34
Q

If we are using an enzyme for acid / base catalysis… it likely has what in the active sight

A

a.a. with a titratable hydrogen (pka near physiologic pH)

35
Q

Michaelis Mentin Equation

A

Vo = Vmax[S] / [S] + Km where

Km = k-1 + k2 / k1

36
Q

Why is the Michaelis Mentin equation powerful?

A

We can use it to determine Km because When Vo = 1/2Vmax

Km = [s]

37
Q

What is Km

A

The substrate concentration at which the enzyme is operating at 1/2 the maximal velocity

38
Q

Kcat is used to describe what?

A

The rate limiting step of a reaction (which will be the general rate constant)

39
Q

How are Kcat, Vmax, and [E] related?

A

The Kcat (or turnover number) is equal to the maximum velocity divided by the enzyme concentration
Kcat = Vmax / E
Which makes sense because Vmax is the maximal velocity of the reaction at a given enzyme concentration…if we then divide that by by the enzyme concentration, we will get the Kcat, which is the number of molecules being made per second by a single enzyme
We could also write it as

Vmax = Kcat[E]

40
Q

What does a high Kcat mean?

A

A high Kcat means that one enzyme is able to turnover muchos molecules per unit time

41
Q

Kcat/Km usefullness

A

General description of enzymatic efficiency… takes into account both the speed of the enzyme (Kcat) and how much substrate you need to supply to get to the enzyme (Km)

42
Q

What limits enzyme

A

Diffusion of substrate around it into the active site (usually around 10^9 kcat/km) - the only thing slowing them down is how rapidly substrate is diffusing to enzyme

43
Q

Why is Michaelis Menten useful?

A

Helps us sort out the mechanism of complex enzymatic reactions

44
Q

What are the 3 types of reversible inhibitors?

A

comp.
uncomp.
mixed.

45
Q

what is the utility of Lineweaver Burke?

A

Allows us to evaluate inhibitors - determine what type

46
Q

Competetive inhibitor effect of Lineweaver Burke plot with increasing [i]

A

Increases slope (km/vmax) without changing vmax (y int)

47
Q

Competetive inhibitor effect on Kcat

A

Does not change Kcat because Kcat = Vmax/[e] and we are not changing Vmax

48
Q

Uncompetitive inhibitors … which parameters do they effect?

A

They effect all parameters
Kcat
Km
and
Vmax
However, note that they are effecting Km and Vmax by the same magnitude - lowering Km - which means they are lowering the [s] at 1/2 vmax… which is likely because we lowered vmax because we are effectively taking out enzymes - which means that even though our affinity is the same we have lowered vmax - plus we have also lowered kcat because kcat =
Vmax/[e]… we lowered Vmax but we have not in reality lowered our [e], only our effective [e] and thus, we have also lowered our kcat

49
Q

Mixed inhibitors usually affect which parameters? effect on Lineweaver Burk?

A

We are bloody chaging everything
Our slope (km/vmax) is increasing
Our x intercept is increasing (becoming less negative) (-1/km)
Our y intercept is increasing (alpha/vmax - so vmax is decreasing)
Thus, our Km is increasing, our vmax is decreasing, and our slope is increasing (km/vmax)

50
Q

Where do irreversible inhibitors usually act?

A

The active site

51
Q

In metabolic cascades, which enzyme do we usually want to target via negative feedback

A

Usually the first

52
Q

We can also have enhancers that activate enzyme

A

allosteric regulation to increase enzyme activity

53
Q

Our covalent modifcations generally reversible?

A

Yes - turn on / off

54
Q

Enzymatic regulation via proteolytic cleavage is common where?

A

digestive system

e.g. trypsinogen –> trypsin

M2M1 (7 decks)

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