Classification of Enzymes

CH3 -C- COO-

O

CH3 -CH-COO-OH

lactate

dehydrogenase+ NADH + H + + NAD +

Pyruvate Lactate

1.Oxidoreductase

2.Transferase COO-

CH2

CH- NH3+

COO-

Aspartate

+

COO-

C= O

CH2

CH2

COO-

-Ketoglutarate

Aspartate amino

transfer ase

COO-

CH2

C= O

COO-

Oxalosuc cinate

+

COO-

C-NH3+

CH2

CH2

COO-

Glutamate

3.Hydrolase

CH3 -C-OCH2 CH2 N(CH3 ) 2

O

Acetylcholine

Acetylcholinesterease+ H2 OCH3 -C-O-

O

HOCH2 CH2 N( CH3 ) 2

Acetate Choline

4. Lyase

5. Isomerase

6. Ligase

COO-

CH2

C-COO-

CH

Aconitase

COO-

cis- Aconitate

+ H2 O

COO-

CH2

C-COO-

C-H

COO-

HO

Isocitrate

HO

CH2 OPO32 -

OH

HHO

CH2 OH

OHH

- D-Fructose-6-phosphate

O

HO

OH

OH

CH2 OPO32 -

OH

- D- Glucose-6-phosphate

Phosphohexose

isomerase

ATP + L -tyrosine + t-RNA

Ty rosine-tRNA

syntheta se L-tyro sy l-tDNA + AMP + PPi

Enzyme controlled reactions proceed 108 to 1011 times

faster than corresponding non-enzymic reactions.

Making reactions go faster

• Increasing the temperature make molecules

move faster,

• Biological systems are very sensitive to

temperature changes.

• Enzymes can increase the rate of reactions

without increasing the temperature.

• They do this by lowering the activation energy.

• They create a new reaction pathway “a short

cut”

Schematic of an Active Site

• Apoenzyme: the protein part of an

enzyme.

• Cofactor: a nonprotein portion of an

enzyme that is necessary for

catalytic function; examples are

metallic ions such as Zn2+ and Mg2+.

• Coenzyme: a nonprotein organic

molecule, frequently a B vitamin,

that acts as a cofactor.

• Substrate: the compound or

compounds whose reaction an

enzyme catalyzes.

• Active site: the specific portion of

the enzyme to which a substrate

binds during reaction.

Cofactors (simple vs. complex)

• An additional non-protein molecule that is needed by some enzymes to help the reaction

• Tightly bound cofactors are called prosthetic groups

• Cofactors that are bound and released easily are called coenzymes.

• Many vitamins are coenzymes.

Nitrogenase enzyme with Fe, Mo and ADP

cofactors

The shape and the chemical environment inside the

active site permits a chemical reaction to proceed more

easily.

Substrate of an

enzyme are the

reactants that are

activated by the

enzyme

The Lock and Key Hypothesis

• Fit between the substrate (key) and the active site of the enzyme (lock) is very precise

• Temporary structure called the enzyme-substrate complex formed

• Products have a different shape from the substrate

• Once formed, they are released from the active site

• Leaving it free to become attached to another substrate

Enzyme may

be used again Enzyme-

substrate

complex

E

S

P

E

E

P

Reaction coordinate

This explains enzyme

specificity and loss of

activity when enzymes

denature.

This explains the enzymes

that can react with a range of

substrates of similar types.

The Induced Fit Hypothesis

• Some proteins can change their shape (conformation)

• When a substrate combines with an enzyme, it induces a change in the enzyme’s conformation.

• The active site is then moulded into a precise conformation.

• Making the chemical environment suitable for the reaction

• The bonds of the substrate are stretched to make the reaction easier (lowers activation energy)

Factors Affecting Enzyme

Activity • substrate concentration

• pH

• temperature

• inhibitors

Substrate concentration: Non-enzymic

reactions

• The increase in velocity is proportional to the

substrate concentration

Reaction

velocity

Substrate concentration

Substrate concentration: Enzymic reactions

• Faster reaction but it reaches a saturation point when all the enzyme molecules are occupied.

• If you alter the concentration of the enzyme then Vmax will change too.

Reaction

velocity

Substrate concentration

Vmax

At constant substrate

concentration, increasing the

enzyme concentration,

increases the rate linearly.

(In practically all enzyme

reactions, the molar conc. of

enzyme is always much lower

than that of substrate.)

A saturation curve

A linear curve

At constant enzyme

concentration, increasing the

substrate concentration does

not increases the rate

continuously. A saturation

point is achieved.

The effect of pH

• Extreme pH levels will produce denaturation

• The structure of the enzyme is changed

• The active site is distorted and the substrate

molecules will no longer fit in it

• At pH values slightly different from the enzyme’s

optimum value, small changes in the charges of

the enzyme and it’s substrate molecules will

occur

• This change in ionisation will affect the binding

of the substrate with the active site.

The effect of temperature Q10 (the temperature coefficient) = the increase in

reaction rate with a 10°C rise in temperature.

For chemical reactions the Q10 = 2 to 3 (the rate of the reaction doubles or triples with every 10°C rise in temperature)

Enzyme-controlled reactions follow this rule as they are chemical reactions

BUT at high temperatures proteins denature

The optimum temperature for an enzyme controlled reaction will be a balance between the Q10 and denaturation.

The effect of temperature

Temperature / °C

Enzyme

activity

0 10 20 30 40 50

Q10 Denaturation

The effect of temperature

• For most enzymes the optimum temperature is

about 30°C

• Many are a lot lower,

cold water fish will die at 30°C because their

enzymes denature

• A few bacteria have enzymes that can withstand

very high temperatures up to 100°C

• Most enzymes however are fully denatured at

70°C

Organize the tiles!

When you organize these tiles, you will find a phrase describing a feature

of biological catalysts, that in fact is common to all catalysts:

• Allosterism: enzyme regulation based on an

event occurring at a place other than the active

site but that creates a change in the active site.

– An enzyme regulated by this mechanism is called

an allosteric enzyme.

– Allosteric enzymes often have multiple polypeptide

chains.

– Negative modulation: inhibition of an allosteric

enzyme.

– Positive modulation: stimulation of an allosteric

enzyme.

– Regulator: a substance that binds to an allosteric

enzyme.

• Feedback control: an enzyme-regulation process

where the product of a series of enzyme-

catalyzed reactions inhibits an earlier reaction in

the sequence.

• The inhibition may be competitive or noncompetitive.

A B C DE1 E2 E3

feedback inhibition

Inhibitors

Inhibitors are chemicals that reduce the

rate of enzymic reactions.

The are usually specific and they work at

low concentrations.

They block the enzyme but they do not

usually destroy it.

Many drugs and poisons are inhibitors of

enzymes in the nervous system.

nerve gases and pesticides, containing

organophosphorus, combine with serine

residues in the enzyme acetylcholine esterase.

Two categories of reversible inhibition:

1.) Competitive: These compete with the substrate

molecules for the active site. The inhibitor’s action is

proportional to its concentration. Resembles the

substrate’s structure closely.

Enzyme inhibitor

complex Reversible

reaction

E + I EI

2.) Non-competitive: The inhibitor

binds itself to a site other than

the active site (allosterism),

thereby changing the

conformation of the active site.

The substrate still binds but

there is no catalysis.

Examples

Cyanide combines with the Iron

in the enzymes cytochrome

oxidase.

Heavy metals, Ag or Hg,

combine with –SH groups.

These can be removed by

using a chelating agent such as

EDTA.

• Enzyme kinetics in the presence and absence of

inhibitors.

Maximum reaction rate

is the same without an

inhibitor and in the

presence of a

competitive inhibitor

(CI).

Maximum rate is

obtained at high

substrate concentration

for CI but low with no

inhibitor.

If the inhibitor is non

competitive, the

maximum rate of

reaction is lower.