CHAPTER 2

Basics of Enzymes

Life Processes
Enzyme mediated
Chemical reactions in biological systems
Spontaneous and fast
Thermodynamically or energetically favorable

HCl + NaOH

Na + Cl + H2 O

Spontaneous but slow

Kinetically unfavorable reactions

2 H2 + O2

ATP + H 2O

2 H2 O

ADP + Pi

Enzymes
Catalysts for biological reactions
Most are proteins

Lower the activation energy

Increase the rate of reaction
Activity lost if denatured
May be simple proteins
May contain cofactors such as metal ions or

organic (vitamins)

General Properties of Enzymes

Accelerate reaction for higher reaction rates

Example:

CO2 + H2O

Carbonic
anhydrase

H2 CO3

105 molecules CO2 per enzyme molecule per second

107 times faster than uncatalyzed reaction

Require milder reaction conditions

Catalytic Power of Some Enzymes

Table 11-1

General Properties of Enzymes

Possess greater reaction specificity

Capacity for regulation

Catalytic activities vary depending on the concentration of

substances & substrates

Regulatory processes involving allosteric control and variation

of the amounts of enzymes synthesized

Enzyme classifications &

Nomenclatures

Enzyme Classes
1. Oxidoreductases

2. Transferases

3. Hydrolases

Oxidation-reduction
reactions

Transfer of functional
groups

Hydrolysis reactions
(cleavage and introduction
of water)

4. Lyases

5. Isomerases

6. Ligases (synthases)

Group elimination/addition
to form double bond

Isomerization
(intramolecular
rearrangements)

Bond formation coupled

with ATP hydrolysis;
combine molecules using
ATP

Examples of Classification of
Enzymes
Oxidoreductoases

Transferases

Hydrolases

Lyases

Oxidases oxidize
Reductases - reduce

Transaminases - transfer amino groups

Kinases - transfer phosphate groups

Proteases - hydrolyze peptide bonds

Lipases - hydrolyze lipid ester bonds

Carboxylases - add CO2

Hydrolases - add H2O

Systematic Name of Enzymes

End in ase

Urease
Arginase

Identifies a reacting substance

Sucrase - reacts sucrose

Lipase - reacts lipid

Describes function of enzyme

Oxidase - catalyzes oxidation

Hydrolase - catalyzes hydrolysis

Common names of digestion enzymes still use in (degrades

proteins)

Pepsin
Trypsin
Chymotrypsin

Generation of EC Numbers
EC - Enzyme Commission
Enzymes classification system for assigning code

numbers to them
Contain 4 elements separated by points, with the
following meaning:

1st number - shows to which of the six main divisions

(classes) the enzyme belongs,
2nd - indicates the subclass
3rd - gives the sub-subclass
4th - serial number of the enzyme in its sub-subclass

Example: Aconitate hydratase, EC 4.2.1.3

Common Name vs Systematic

Name of Enzyme

Common name: Aconitase

Systematic name: Aconitate Hydratase
EC code: EC 4.2.1.3

Common Name vs Systematic

Name of Enzyme
O

OH
H3C

CH

COOH

NAD+

Lactate

H3C

COOH +

NADH

Pyruvate

Common name: Lactate Dehydrogenase

Systematic name: L-Lactate:NAD
Oxidoreductase
EC code: EC 1.1.1.27

H+

Enzyme Catalysis

Enzyme Catalysis
Accelerate interconversion to Equilibrium

Substrate(s)

Product(s)

Catalysis

Reaction Coordinate Diagram

Determine the number of reactions, intermediates

and transition states in the above reaction, A D.

Pathway of Enzyme Catalysis

E+S

Binding

[ES]

Catalysis

EnzymeSubstrate
Complex

E+P

Formation of Enzyme-Substrate
Complex

Binding Site

Figure 11-1

Formation of Enzyme-Substrate
Complex
Enzyme binding substrate
Predicted using molecular modeling technique

Enzyme Substrate Binding

Enzyme action models

Lock and Key Model

Induced Fit Model

Enzyme Action: Lock and Key

Model
An enzyme binds a substrate in a region called the

active site
Only certain substrates can fit the active site
Enzyme-substrate complex forms
Substrate reacts to form product
Product is released

Illustration of Lock and Key Model

23

P
S

E enzyme
S substrate
P product

ES complex

Enzyme Action: Induced Fit Model

Enzyme structure flexible, not rigid
Enzyme and active site adjust shape to bind

substrate
Increases range of substrate specificity
Shape changes also improve catalysis during
reaction

Illustration of Induced Fit Model

P
S

S
P

E enzyme
S substrate
P product

ES complex

Enzyme Specificty
Stereospecificity

3-point attachment

Geometric Specificity

E.g.: trypsin and chymotrypsin

Enzyme Stereospecificity
Aconitase Reaction

Prochiral Substrate

Chiral Product

Stereospecificity in Substrate Binding

Figure 11-2

Enzyme Geometric Specifcity

Trypsin and Chymotrypsin
H2O
O
NH CH

O
NH

R1

R1

R2

O
NH CH

CH

_
O

+
H 3N

O
CH

R2

Predict the class of enzyme, trypsin and chymotrypsin are,

based on the above reaction.

Enzyme Geometric Specificity:

Trypsin
H2O
O
N

NH

arginine
or
lysine

CH

NH

"long + side chain"

+
complementary binding
or positioning site

At enzyme
active site

"SPECIFICITY"

Chymotrypsin

Enzyme Geometric Specificity:

Chymotrypsin
H2O
O
N

NH

phenylalanine
tyrosine
tryptophan
Phenylalanine
Tyrosine
Tryptophan

At enzyme
active site

CH

NH

"aromatic side chain"

complementary binding
or positioning site

Hydrophobic
Pocket

"SPECIFICITY"

Enzyme Cofactors

Cofactors
A substance needed to be present in addition to an

enzyme

For a certain reaction to be catalyzed

Needed by inactive apoenzymes

To convert them into active holoenzymes

Classification of Cofactors

Cofactors

Essential ions

Activator ions
(loosely bound)

Metal ions of
metalloenzymes
(tightly bound)

Coenzymes

Cosubstrates
(loosely bound)

Prosthetic groups
(tightly bound)

Inorganic Cofactors - Essential

Ions
Mostly metal ions
Activator ions
Monovalent K, divalent Mg, Ca
Reversibly bound
Often participate in binding of substrates
Stimulate enzymes when added
Metalloenzymes
Tightly bound
More ofter - Transition metals, Fe, Zn
Less often Cu, Co
Often participate in catalytic reactions

Organic Cofactors - Coenzymes

Organic nonprotein
Group transfer reagents

Accept and donate specific chemical groups

Simple group e.g. H+, electron
Complex group e.g. large, covalently attached chemical
groups
In mammals
Dietary precursors (vitamins)
Amino acids
Coenzyme A

Organic Cofactors Coenzymes

Cosubstrates
Actually substrate
Altered in a reaction and dissociates from the active site
Original structure regenerated in a subsequent reaction

Prosthetic group
Remains bound to enzyme during reaction
Either bound to apoenzyme or active site
Must return to its original form or holoenzyme will not be active
Supply reactive groups not available on enzyme

Coenzymes
Example: Alcohol Dehydrogenase
Must be regenerated

2H+ + 2e

NAD+
2H+ + 2e

NADH + H+

Prosthetic Groups
Example: cytochromes

CytochromeHeme(Fe3+)
e

CytochromeHeme(Fe2+)