Chapter 6.1 and 6.2: Introduction to Enzymes

CHEM 7784

Biochemistry

Professor Bensley

CHAPTER 6.1 and 6.2 Introduction to Enzymes and How

Enzymes Work

– Physiological significance of enzymes– Origin of catalytic power of enzymes– Chemical mechanisms of catalysis

Today’s Objectives: (To learn and understand the)

What are Enzymes?

• Enzymes are catalytically active biological macromolecules

• Most enzymes are globular proteins, however some RNA (ribozymes, and ribosomal

RNA) also catalyze reactions

• Study of enzymatic processes is the oldest field of biochemistry, dating back to late 1700s

Why Biocatalysis?• Higher reaction rates• Greater reaction specificity• Milder reaction conditions• Capacity for regulation

COO

OH

O COO

COO

O COO

NH2

OOCCOO

O

OH

OH

COO

NH2

COO

-

-

-

-

-

-

--

Chorismate mutase

• Metabolites have many potential pathways of decomposition

• Enzymes make the desired one most favorable

Quiz Question 29

In order to function properly, some enzymes require the presence of an additional chemical component such

as inorganic ions (Zn2+ or Fe2+). These inorganic ions are known as

for enzymes.

Quiz Question 30

Chymotrypsin is an enzyme that cleaves peptide bonds. It most likely, therefore, belongs to which class of enzymes?

a)Transferases b) Ligases

c) Isomerases d) Hydrolases

Classes of enzymes

1. Oxidoreductases = catalyze oxidation-reduction reactions (Transfer of electrons) (NADH)

2. Transferases = catalyze transfer of functional groups from one molecule to another.

3. Hydrolases = catalyze hydrolytic cleavage (transfer of functional groups to water)

4. Lyases = catalyze removal of a group from or addition of a group to a double bond, or other cleavages involving electron rearrangement.

5. Isomerases = catalyze intermolecular rearrangement.

6. Ligases = catalyze reactions in which two molecules are joined.

Enzymes named for the substrates and type of reaction

E + S ES E + Pk1

k-1

k2

k-2

E S+ E S E + P

Rate Acceleration

• The enzyme lowers the activation barrier compared to the uncatalyzed aqueous reaction

• In theory, the enzyme may also facilitate the tunneling through the barrier. This may be important for electrons.

How to Lower G?

1. Enzymes organize reactive groups into proximity

2. Enzymes bind transition states best (LargelyaH‡ effect)

Support for the Proximity Model

• The rate of anhydride formation from esters and carboxylates shows a strong dependence on proximity of two reactive groups

Support for TS Stabilization

• Structure-activity correlations in chymotrypsin substrates

Illustration of TS Stabilization Idea:Imaginary Stickase

How is TS Stabilization Achieved?

acid-base catalysis: give and take protonscovalent catalysis: change reaction pathsmetal ion catalysis: use redox cofactors, pKa

shifterselectrostatic catalysis: preferential

interactions with TS

Acid-base Catalysis: Chemical Example

Consider ester hydrolysis:

R

O

C

H

3

O

R

O

C

H

3

O

O

H

H

+

R

O

O

H

+ H-OH + + CH3OH

Water is a poor nucleophile, and methanol is a poor leaving group

Aqueous hydrolysis can be catalyzed either by acids or by bases

Enzymes can do acid and base catalysis simultaneously

Amino Acids in General Acid-Base catalysis

•The anhydride hydrolysis reaction is catalyzed by pyridine, a better nucleophile than water (pKa=5.5).

•Hydrolysis is accelerated because of charge loss in the transition state makes pyridine a good leaving group.

Covalent Catalysis: Chemical Example

CH3O

O

CH3

O

CH3O

O

CH3O

O

H+- -+

H2O

slow + 2

CH3O

O

CH3

O

N

CH3O

O

N CH3

O

OH H

N CH3

O

OHN

CH3O

O

H+

..fast

-+ +

..

+

-

-+..

Covalent Catalysis: In Enzymes• Proteases and peptidases

– chymotrypsin, elastase, subtilisin– reactive serine nucleophile

• Some aldehyde dehydrogenase– glyceraldehyde-3-phosphate dehydrogenase– reactive thiolate nucleophile

• Aldolases and decarboxylases– amine nucleophile

• Dehalogenases– carboxylate nucleophile

N

OH

ON

S

ON O

NH2

N O

O

O-

-