Protein Function: Catalysis

Question 1

What does a catalyst do?

Answer 1

Increases the rate of reaction by lowering the activation energy barrier in the absence of thermal activation

Question 2

Why don’t reactions occur instantaneously?

Answer 2

Provides an opportunity for regulation; also, reactions in cells are steady state

Question 3

Does a catalyst influence the rate of the reaction?

Answer 3

Yes

Question 4

Does a catalyst influence the position of equilibrium of a reaction?

Answer 4

No.

Question 5

Describe the slope of the rate of a reaction and the concentration of a reagent without an enzyme catalyst.

Answer 5

Linear slope

Question 6

Describe the slope of the rate of a reaction and the concentration of a reagent with an enzyme catalyst.

Answer 6

Hyperbolic slope, no longer linear

Question 7

Why would a reaction’s rate plateau when using enzymes in vitro?

Answer 7

If the enzymes become saturated with substrates, then they’re all occupied and can not increase the rate any more.

Question 8

What’s the first step of catalysis?

Answer 8

Substrate binding

Question 9

How does a catalyst act?

Answer 9

Forms a reversible complex with a substrate, stabilizing a transition state

Question 10

What does folding the catalyst do?

Answer 10

Creates a binding site where specific R groups are presented to each other; specific topology allows enzymes to have specificity.

Question 11

Is Vmax ever reached?

Answer 11

No, it is only approached.

Question 12

What is Vmax proportional to?

Answer 12

the concentration of enzymes

Question 13

What is Vmax?

Answer 13

maximum velocity of a reaction, when 100% of the enzymes are bound to a substrate

Question 14

What determines the initial rate of an enzyme catalyzed reaction?

Answer 14

Km, Vmax, and the initial substrate concentration

Question 15

What does Vmax tell us?

Answer 15

1. At high [S], reaction rates vary significantly among different enzymes.
2. Allows a calculation of kcat (the turnover number of a specific enzyme - measures how effective an enzyme is)
3. In vivo, few enzymes encounter saturating [S]; Vmax and kcat set upper bounds, enabling estimates of reaction rates in vivo.

Question 16

What does Km (Michaelis Constant) tell us?

Answer 16

measure of affinity of enzyme for substrate

Question 17

What does a high Km indicate?

Answer 17

low affinity for a substrate, may require higher substrate concentration for a reaction in vivo

Question 18

What does a low Km indicate?

Answer 18

high affinity for a substrate, may not require higher substrate concentration for a reaction in vivo

Question 19

What are the four kinds of enzyme regulation?

Answer 19

1. Substrate-Level
2. Covalent Modification (e.g. phosphorylation of Cdk)
3. Modulator Proteins
4. Allosteric

Question 20

What do modulator proteins do?

Answer 20

Bind to enzymes and either stimulate or deactivate them

Question 21

What is an allosteric effector?

Answer 21

a small molecule that regulates
the activity of an enzyme for which it is neither substrate nor immediate product

Question 22

Which kind of enzyme regulation does not obey Michaelis-Menten equation?

Answer 22

Allosteric

Question 23

How does temperature relate to the rate of the reaction? What is the rule of thumb?

Answer 23

Increased temperature increases the rate. For every 10 degrees C increase, the rate doubles (until max activity).

Question 24

Why are enzymes impacted by pH?

Answer 24

Many active sites have charged amino acid side chains and are ionizable.

Question 25

What influence does diffusion have on catalysis involving multiple enzymes?

Answer 25

Reduces the efficiency of metabolic reactions requiring multiple enzymes

Question 26

Can temperature impact pH?

Answer 26

Yes

Question 27

Can saturation occur in the cell?

Answer 27

No, only in vitro.