ENZYMES

ENZYMES•are biological catalyst

•are mostly proteinaceous in nature, but RNA was an early biocatalyst

•are powerful and highly specific catalysts

carbonic anhydrase

Many enzymes require co-factor for activity

Apoenzyme + co-factor = holoenzyme

NOMENCLATURE:

1. Common name- e.g. trypsin, pepsin

2. Hybrid name- e.g. sucrase

3. Systematic name: EC 2.7.4.4

example: nucleoside monophosphate kinase

ATP + NMP ADP + NDP

ENZYMES accelerate reactions by facilitating

the formation of the transition state

Active site

• is the region where the substrate binds

• contains residue that directly participate in making or breaking of bonds (formation of transition state)

• is the region where activation energy is lowered

Common features

1. Active site is a three dimensional cleft

2. Takes up a small part of the total volume of an enzyme

3. Are clefts or crevice

4. Substrates are bound to enzymes by multiple weak interactions

Two models of the Active site

1.Lock and key

2.Induced-fit

Kinetic Properties of Enzymes Michaelis-Menten

Equation

Factors Affecting Enzyme Activity

1.Temperature

2.pH

3.[S]

4.Presence of Inhibitors

•As the temperature rises, molecular motion - and hence collisions between enzyme and substrate - speed up. But as enzymes are proteins, there is an upper limit beyond which the enzyme becomes denatured and ineffective.

TEMPERATURE

pH

•The conformation of a protein is influenced by pH and as enzyme activity is crucially dependent on its conformation, its activity is likewise affected.

Kinetic Theory of Enzyme-Catalyzed Reaction

1.Effect of [E]

involves the reversible formation of an enzyme-substrate complex, which then break down to form one or more products

if [S] is constant, v is proportional to [E]

2. Effect of [S]

has profound effect on the rate of enzyme-catalyzed reaction

At low [S], rate of reaction is 1o order,

v is directly proportional to [S]

At mid [S], rate of reaction is mixed order

proportionality is changing

At high [S], rate of reaction is zero order

Michaelis-Menten Equation

Significance of KM

When V= ½ Vmax, what is [S]?

The KM of an enzyme is the

substrate concentration at which the reaction occurs at half of the maximum

rate.

There are limitations in the quantitative (i.e.

numerical) interpretation of this type of graph, known as a Michaelis plot.  The

Vmax is never really reached and therefore Vmax and

hence KM values calculated from this graph are

somewhat approximate. 

Lineweaver- Burk plot

The Effects of Enzyme Inhibitors

1.CompetitiveIn the presence of a competitive inhibitor, it takes a higher substrate concentration to achieve the same velocities that were reached in its absence. So while Vmax can still be reached if sufficient substrate is available, one-half Vmax requires a higher [S] than before and thus Km is larger

2. Non-CompetitiveWith noncompetitive inhibition, enzyme molecules that have been bound by the inhibitor are taken out of the game so

• enzyme rate (velocity) is reduced for all values of [S], including

• Vmax and one-half Vmax but

• Km remains unchanged because the active site of those enzyme molecules that have not been inhibited is unchanged.

Most Biochemical Reactions Include Multiple Substrates:

A + B P + Q

2 Classes of Multiple Substrate Reactions:

1.Sequential Displacement

2.Double Displacement

Sequential Displacement:

All substrates bind to the enzyme before any product is release

Types

• Ordered

• Random

Lactate dehydrogenase

Example of a sequential ordered mechanism

The enzyme exist as a ternary complex

Example of a Random Sequential Mechanism

Creatine kinase

Double Displacement (Ping-Pong) Reactions

-one or more products are released before all substrates bind the the enzyme

- a substituted enzyme intermediate exist

Aspartate amino transferase

Enzymes employ strategies to catalyze specific reactions

1.Covalent Catalysis- the active site contains a reactive group

2.General Acid base catalysis

3.Metal ion catalysis

4.Catalysis by approximation

1.Covalent Catalysis

Example: Chymotrypsin

A. Acylation to form the acyl-enzyme intermediate

B. Deacylation to regenerate the free enzyme

2. General Acid base catalysis

3. Metal ion catalysis- e.g. carbonic anhydrase

Regulatory Strategies:

1. Allosteric Enzyme- e.g. ATCase

2. Multiple of Enzymes:

Isoezymes or Isozymes- are homologous enzymes within a single organism that catalyze the same reaction but differ slightly in structure and in Vmax and Km

e.g. Lactate dehydrogenase (LDH)- 2 isozmic chains in humans, H (heart) and M (muscles)

3. Reversible covalent modification

4. Proteolytic activation- involves synthesis of enzymes in the ZYMOGEN form

Examples:

1. Digestive enzymes

2. Blood clotting- cascade of zymogen activations