CH 2306 Lecture notes

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ENZYMES AND ENZYMOLOGY

Defination
 Enzymes are biological catalysts, catalytic proteins - speed up reactions by lowering
activation energy, orient molecules to favor reaction.
 This increases the reaction rates than random collisions would allow.
 Turnover number is the maximum number of substrate molecules an enzyme converts to
product each second this differs with enzymes.
 Each enzyme has a unique shape therefore it binds only its specific substrate(s) at the active
site and catalyzes only one specific reaction resulting in particular product(s)
 All cellular reactions are performed by enzymes and thus majority of the proteins in the
cells are enzymes.

Nomenclature of enzymes
 This is based on the nature of the reactions that the enzymes catalyze.
 There are six classes of enzymes in cells
1. Oxidoreductase – catalyze oxidation/reduction reactions
2. Transferase - transfer functional groups
3. Hydrolase – catalyze hydrolysis reactions
4. Lyase - removal of atoms without hydrolysis
5. Isomerase - rearrangement of atoms in a molecule
6. Ligase – catalyze joining of two molecules - typically named for reaction catalyzed and
substrate acted upon: e.g. DNA ligase: functions to join two pieces of DNA together

Components of an enzyme
 Most enzymes have two parts:
a) Apoenzyme - this is the protein part, it inactive by itself
b) Cofactor this is a non-protein part, usually a metal ion that makes the apoenzyme active
 Coenzyme is a cofactor that is an organic molecule rather than a metal ion

 Apoenzyme + ‘Cofactor’ = Holoenzyme (whole active enzyme)

 Metal ion cofactors form a bridge between enzyme and substrate to facilitate the reaction
while coenzymes donate or accept atoms or carry electrons to transfer to other molecules.

Examples of Coenzymes
 Two most important coenzymes:
a) NAD+ (nicotinamide adenine dinucleotide)-Carries electrons in catabolic reactions
b) NADP+ (nicotinamide adenine dinucleotide phosphate)- Carries electrons in anabolic
reactions.
 Both are derived from the B vitamin nicotinic acid
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Mechanisms of enzyme action

This follows the following steps:
1. The substrate comes into contact with the enzyme active site.
2. An enzyme substrate complex is formed.
3. The substrate molecule is altered (rearrangement, breaking down or combining with
another molecule.
4. The products are released from the active site.
5. The enzyme remains unchanged to catalyze a new reaction.

 Each enzyme acts on only one substrate, but a substrate can be acted upon by multiple
enzymes.
 Enzymes must be controlled to maintain homeostasis: two ways to control:
a) Level of synthesis (amount produced)
b) Level of activity (control cofactors, restrict access to substrate)
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Factors affecting enzyme activity

1. Temperature
Reaction rate until denaturation -Enzymes have an optimal temperature = temp at which the
enzyme catalyzes the reaction at its maximum rate -above this they become denatured (unfolded
and cannot catalyze the reaction)

2. pH
Enzymes have an optimal pH that favors the native conformation (correct folding) -pH that is too
acidic or too basic will denature the enzyme.

3. Substrate concentration
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Increasing the concentration of the substrate increases the rate until saturation. Each enzyme has a
maximum turnover number (the highest speed for converting substrate into product) -at saturation,
the active site is always full. The enzyme works at maximum speed and addition of more substrate
beyond the saturation point will not increase the reaction rate.

4. Enzyme concentration
Increasing Enzyme concentration will increase the rate of reaction, as more enzymes will
be colliding with substrate molecules. However, this will only have an effect up to a certain
concentration, where the Enzyme concentration is no longer the limiting factor.

5. Inhibitors
This is a substance that blocks enzyme function. There are three types:
A. Competitive inhibitors these are substances block the active site. They have the same shape
as the substrate thus competes for the active site thus blocking enzyme reaction with the substrate.
Some bind permanently thus killing the enzyme. This is called irreversible competitive inhibitor.
Others bind reversibly and just slow the reaction rate this is called reversible

Competitive inhibitor
B. Noncompetitive inhibitors. These do not bind the active site -binds elsewhere at the allosteric
site which is involved in regulation of enzyme function.
A reversible allosteric inhibitor will slow the reaction rate -an irreversible allosteric inhibitor will
kill the enzyme permanently.

C. Enzyme poisons
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These bind up metal ion cofactors thus preventing formation of the holoenzyme. Usually there are
many steps in a metabolic pathway to convert substrate to final product. Each step requires a
different enzyme.

Feedback inhibition / End product inhibition

This is where the product controls its own rate of formation. It occurs when the final product can
inhibit one of the enzymes in the pathway when product accumulates; the pathway is shut down
to prevent overproduction. This is common to anabolic pathways which usually functions by
reversible allosteric inhibition of the first enzyme in the pathway.