Introduction to Enzymes

Biological Catalysts

Life Process = Chemical Reactions

Enzymes

A B C D E FEnzyme 1 Enzyme 2 Enzyme 3 Enzyme 4 Enzyme 5

Chemical Reactions

Spontaneous and Fast

Spontaneous but Slow

Na+ + Cl- + H2OHCl + NaOH

2 H2O

ADP + Pi

2 H2 + O2

ATP + H2O

Types of Reactions

• Spontaneous Reactions: thermodynamically or energetically favorable

• Kinetically Unfavorable Reactions

• Requirement for Catalysts

– Protein Catalysts: Enzymes

– RNA Catalysts: Ribozymes

General Properties of Enzymes

• Higher reaction rates (catalytic power)

• Milder reaction conditions

• Greater reaction specificity

• Capacity for regulation

Higher Reaction Rates

Carbonic Anhydrase

105 molecules CO2 per enzyme molecule per second

107 x uncatalyzed reaction

H2CO3CO2 + H2O

Table 11-1

Catalytic Power of Some Enzymes

Mild Reaction Condition

• Physiological pH = ~7.3

• Temperature = ~37°C

Table 11-1

Greater Reaction Specificity

Glucose + ATP Glucose-6-P + ADP

Hexokinase

Fructose + ATP Fructose-6-P + ADP

Mannose + ATP Mannose-6-P + ADP

Glucose + ATP Glucose-6-P + ADP

Glucokinase

ONLY

Capacity for Regulation

• Allosteric (Regulatory) Enzymes

• Covalent Modification

– Irreversible

– Reversible

• Non-covalent Modification

Enzyme Classes

• Oxidoreductases: oxidation-reduction reactions

• Transferases: transfer of functional groups

• Hydrolases: hydrolysis reactions (cleavage and introduction of water)

• Lyases: group elimination to form double bond

• Isomerases: isomerization (intramolecular rearrangements

• Ligases (synthases): bond formation coupled with ATP hydrolysis

Enzyme Nomenclature(Usual usage: often use suffix –

ase)

• Common Name:– Useful but sometimes ambiguous

•Examples: Urease/Arginase• Exceptions to the –ase suffix:

– Trypsin/Chymotrypsin

• Systematic Name:– Substrate(s) Type of reaction-ase

Enzyme Nomenclature(Common Name versus Systematic

Name)

Aconitase

Aconitate Hydratase

EC 4.2.1.3

Enzyme Nomenclature(Common Name versus Systematic

Name)

Aconitase

Aconitate Hydratase

EC 4.2.1.3

Enzyme Nomenclature(Common Name versus Systematic

Name)

H3C CH

OH

COOH H3C C

O

COOH + NADH + H+

PyruvateLactate

+ NAD+

Lactate Dehydrogenase

L-Lactate:NAD Oxidoreductase

Enzyme Nomenclature(Common Name versus Systematic

Name)

H3C CH

OH

COOH H3C C

O

COOH + NADH + H+

PyruvateLactate

+ NAD+

Lactate Dehydrogenase

L-Lactate:NAD Oxidoreductase

Enzyme Catalysis

Substrate(s) Product(s)

Reaction Pathway (Coordinate)

Br

H

H

HO C

H

Br

H

HO C

H

H

CH3Br + OH-

CH3OH + Br-

OH- + + Br

-

Reactants "Transition State" Products

CH

H

H

Transition State Diagram

Stabilizing the transition state

Catalysts

Pathway of Enzyme Catalysis

E + S [E–S]Binding Catalysis

E + P

Enzyme–Substrate

Complex

Active Site

Substrate Specificity

• Active Site

– Lock and Key Model

– Induced Fit Model

• Stereospecificity: 3-point attachment

• Geometric Specificity: e.g. trypsin and chymotrypsin

Principle of Complementarity

• Geometric (physical) complementarity

• Electronic (chemical) complementarity

Enzyme-Substrate Complex

Binding Site

Models of Complementarity

Lock and Key Induced Fit

Enzymes are Stereospecific

Page 325

Aconitase Reaction

Prochiral Substrate Chiral Product

Figure 11-2

Stereospecificity in Substrate Binding

Enzymes Vary in Geometric Specificity

(Alcohol Dehydrogenase)

Ethanol ——> Acetaldehyde

Methanol ——> Formaldehyde

Isopropanol ——> Dimethylketone

RATE: Ethanol > Methanol > Isopropanol

Trypsin and Chymotrypsin

NH CH C

R1

NH

O

CH

R2

C

O

NH CH C

R1

O

O

CH

R2

C

O

H3N+

+_

H2O

Trypsin

NH CH C NH

O

N C

complementary binding or posit ioning site

"SPECI FI CI TY"_

+

arginine or lysine

"long + side chain"

H2O

Long positively charged side chain

Chymotrypsin

NH CH C NH

O

N C

"aromatic side chain"

"SPECI FI CI TY"

complementary binding or posit ioning site

phenylalaninetyrosinetryptophan

Hydrophobic Pocket

H2O

O Aromatic side chain

Some Enzymes Require Cofactors

Cofactors

• Simple Proteins (no cofactor)

• Protein plus Cofactor

– Apoenzyme: protein only

– Holoenzyme: protein plus cofactor

Apoenzyme + cofactor Holoenzyme

(inactive) (active)

Figure 11-3

Types of Cofactors

Organic Cofactor

PermanentlyAssociated

Transiently

Associated

Metal Ions

Figure 11-4

Coenzymes: Cosubstrates[NAD(P)+ ——> NAD(P)H + H+]

NADP+

N

OCH2

OH OH

O

OCH2

OH OPO3=

AOP

O

O–

P

O

O–

O

CNH2

O

Nucleotide

Nucleotide

NADPH

N

R

CNH2

OH H

Page 327

Coenzymes: Cosubstrates(Alcohol Dehydrogenase)

Coenzymes: Prosthetic Groups

(Cytochromes)

Cytochrome•Heme(Fe3+)

Cytochrome•Heme(Fe2+)

e–e–

Coenzymes Must be Regenerated

NAD+ NADH + H+

2H+ + 2e–

2H+ + 2e–

Heme(Fe3+) Heme(Fe2+)

e–

e–

Alcohol Dehydrogenase

Cytochromes

Cosubstrate:Different enzyme

Prosthetic group:Same enzyme

Control of Enzyme Activity

Irreversible Covalent Modification

• Zymogen Activation• Proteolysis

– Lysosomes– Proteosomes (ubiquitin)

Zymogen Activation

+

H2O

"Inactive" "Active"

Reversible Covalent Modification

PP

PP

4 ATP

4 ADP4 H2O

Phosphorylase a "active"

Phosphorylase b "inactive"

+

Phosphorylase Phosphatase

Phosphorylase Kinase4 Pi

(glucose)n-1 + glucose-1-PPhosphorylase

(glucose)n + Pi

Non-covalent Modification

Effectors or Ligands

Negative Effectors

"active"

Regulatory Site

Active Site

"inactive" orless active

I

I

+

Positive Effectors

+

"active" ormore active

"inactive" orpoorly active

++

Allosteric Proteins

positive ef f ector

negative ef f ector

no ef f ectorVo

[S]

General Properties of Enzymes

• Biological Catalysts

– Not used up in the reaction (Regenerated)

– Higher reaction rates (catalytic power)

•Within a biologically relevant time frame

– Milder reaction conditions

•Biologically appropriate conditions

– Greater reaction specificity

– Capacity for regulation

•Control of substrate and product availability