Lecture # 7 How Enzymes Work, Introduction to Kinetics

Question 1

What is an enzyme?

Answer 1

A substance made by an organism that acts as a catalyst. Enzymes lower the activation energy barrier. Most enzymes are proteins, a few RNA molecules are ribozymes, many include cofactors, or coenzymes.

Question 2

Are some enzymes proteins?

Answer 2

Yes

Question 3

Are some proteins enzymes?

Answer 3

Yes

Question 4

Are all enzymes proteins?

Answer 4

No

Question 5

Are all proteins enzymes?

Answer 5

No

Question 6

Why don’t substances spontaneously combust?

Answer 6

Because of the inherent activation energy barriers for compounds

Question 7

Activation Energy

Answer 7

The barrier to convert substrates to products.

Question 8

Are enzymes complementary to the substrate thermodynamically favorable? Why or why not?

Answer 8

They are not thermodynamically favorable. By stabilizing the substrate, the enzyme creates an even greater barrier to get the substrate to the transition state. An enzyme that is the same to the transition state puts stress on the substrate and is more thermodynamically favorable.

Question 9

Isn’t it hard to form an enzyme substrate complex if the substrate doesn’t fit well?

Answer 9

No, the bonds forming are greater than the chemical bonds already present.

Question 10

Quantifying Reaction Rates

Answer 10

1)rate constant k = d [p]/dt; rate is not affected by the total dG, but is affected by the energy barrier for the reaction dG+.

Question 11

The Arrhenius Equation

Answer 11

The relationship between dG+ and the rate constant; k = Ae^-dG+/RT

Question 12

What do we get from the Arrhenius equation? What does it mean?

Answer 12

K=Ae^-dG+/RT; A is the number of collisions per second; k is inversely and exponentially related to dG+, and directly related to T.

Question 13

Oxidoreductase

Answer 13

Transfer of electrons

Question 14

Transferase

Answer 14

Transfer of functional groups

Question 15

Hydrolase

Answer 15

Single Bond Cleavage (water)

Question 16

Lyase

Answer 16

Bond cleavage by elimination

Question 17

Isomerase

Answer 17

Intramolecular rearrangement

Question 18

Ligase

Answer 18

Bond Formation (ATP dep.)

Question 19

What are the six classes of enzymes?

Answer 19

Hot Lily (Hydrolase, Oxidoreductase, Transferase, Lyase, Isomerase, Ligase.

Question 20

What are the five mechanisms of catalysis?

Answer 20

SCCAM (Strain, Cage effect, Covalent, Acid-Base, Metal Ion)

Question 21

Strain

Answer 21

Mechanism of catalysis; stabilize ions in a high-energy pattern

Question 22

Acid-Base

Answer 22

Mechanism of catalysis; give and take protons

Question 23

Cage-effect

Answer 23

Mechanism of catalysis; binding two substrates in the correct orientation

Question 24

Metal Ion

Answer 24

Mechanism of catalysis; use of redox co-factors

Question 25

Covalent

Answer 25

Mechanism of catalysis; Change of reaction paths

Question 26

Lysozyme

Answer 26

A protective enzyme in saliva that helps to destroy bacteria by breaking polysaccharides in bacterial cell walls. Its mechanism for catalysis is strain.

Question 27

Citrate Synthase

Answer 27

Enzyme. Mechanism of catalysis is the cage effect

Question 28

Why is the cage effect an important mechanism in catalysis?

Answer 28

In solution, most molecular collisions aren’t in the correct orientation or length of contact. The cage-effect helps take two or more substrates, and puts them in the correct orientations so that reactions can occur.

Question 29

Chymotrypsin

Answer 29

Gut enzyme that breaks down proteins and peptides. It uses an acid or base (other than H+ or OH-) to add charge stress to the bound substrate. ; mechanism of catalysis (acid-base)

Question 30

What are the eight amino acids commonly used in Acid-base catalysis?

Answer 30

E, D, K, R, C, H, S, Y

Question 31

Draw out the Chymotrypsin mechanism

Answer 31

.

Question 32

Why do we quantify enzyme kinetics?

Answer 32

Kinetics determines what factors affect the rates of enzyme-catalyzed reactions. Some of those factors include (pH, temperature, ionic strength, mechanism of reactions.)

Question 33

Transition State Analogs

Answer 33

compounds that mimic the substrate, binds to and stabilizes the enzyme and decreases its activity.

Question 34

Why do we quantify Enzyme kinetics?

Answer 34

To understand the effects that enzyme concentration,substrate, product, inhibitor, activator concentrations, pH, ionic strength, temperature have on enzymatic functions.

Question 35

How do we perform enzyme kinetic measurements?

Answer 35

1) Purify and quantify the enzyme; 2) Mix the pure enzyme and pure substrates in a buffer that mimics cellular conditions 3) Record rate of substrate disappearance/ product formation as a function of time 4) plot initial velocity versus substrate concentration. 5) Change substrate concentration or other parameters