Lecture # 7 How Enzymes Work, Introduction to Kinetics Flashcards Preview

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Flashcards in Lecture # 7 How Enzymes Work, Introduction to Kinetics Deck (35):
1

What is an enzyme?

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.

2

Are some enzymes proteins?

Yes

3

Are some proteins enzymes?

Yes

4

Are all enzymes proteins?

No

5

Are all proteins enzymes?

No

6

Why don't substances spontaneously combust?

Because of the inherent activation energy barriers for compounds

7

Activation Energy

The barrier to convert substrates to products.

8

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

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.

9

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

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

10

Quantifying Reaction Rates

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+.

11

The Arrhenius Equation

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

12

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

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.

13

Oxidoreductase

Transfer of electrons

14

Transferase

Transfer of functional groups

15

Hydrolase

Single Bond Cleavage (water)

16

Lyase

Bond cleavage by elimination

17

Isomerase

Intramolecular rearrangement

18

Ligase

Bond Formation (ATP dep.)

19

What are the six classes of enzymes?

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

20

What are the five mechanisms of catalysis?

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

21

Strain

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

22

Acid-Base

Mechanism of catalysis; give and take protons

23

Cage-effect

Mechanism of catalysis; binding two substrates in the correct orientation

24

Metal Ion

Mechanism of catalysis; use of redox co-factors

25

Covalent

Mechanism of catalysis; Change of reaction paths

26

Lysozyme

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

27

Citrate Synthase

Enzyme. Mechanism of catalysis is the cage effect

28

Why is the cage effect an important mechanism in catalysis?

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.

29

Chymotrypsin

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)

30

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

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

31

Draw out the Chymotrypsin mechanism

.

32

Why do we quantify enzyme kinetics?

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

33

Transition State Analogs

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

34

Why do we quantify Enzyme kinetics?

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

35

How do we perform enzyme kinetic measurements?

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

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