EnzymesAn Introductory Presentation on the Rudiments of Biological Catalysts

EnzymesEnzymes are molecules that act as catalysts to speed up biological reactions.

The compound on which an enzyme acts is the substrate.

Enzymes can break a single structure into smaller components or join two or more substrate molecules together.

Most enzymes are proteins. Many fruits contain enzymes that are used in commercial processes. Pineapple (Ananas comosus, right) contains the enzyme papain which is used in meat tenderization processes and also medically as an anti-inflammatory agent.

EnzymesRibozymes (ribonucleic acid enzymes) are RNA molecules that are capable of catalyzing specific biochemical reactions, similar to the action of protein enzymes.

The 1982 discovery of ribozymes demonstrated that RNA can be both genetic material (like DNA) and a biological catalyst (like protein enzymes), and contributed to the RNA world hypothesis, which suggests that RNA may have been important in the evolution of prebiotic self-replicating systems.

Schematic showing ribozyme cleavage of RNA.

Enzymes

Enzyme ExamplesEnzyme Role

PepsinStomach enzyme used to break

protein down into peptides. Works at very acidic pH (1.5).

ProteasesDigestive enzymes which act on proteins in the digestive

system

AmylasesA family of enzymes which assist in the breakdown of

carbohydrates

Lipases A family of enzymes which breakdown lipids3D molecular structures for the

enzymes pepsin (top) and hyaluronidase (bottom).

Enzyme Examples One of the fastest enzymes in the body is

catalase. Catalase breaks down hydrogen peroxide, a waste product of cell metabolism, into water and oxygen. Accumulation of hydrogen peroxide is toxic so this enzyme performs an important job in the body.

Enzyme Power! All reactants need to have a certain energy

before they will react. This is like an energy barrier that it has to overcome before a reaction will occur. It is called the activation energy.

Enzymes are organic catalysts.

All catalysts lower the energy barrier, allowing the reactants (substrates) to react faster forming the products.

Enzymes do not participate in the reaction.

Reactant

Product

Without enzyme: The activation energy required is high.

With enzyme: The activation energy required is lower.

Enzymes

High

Low

Start Finish

Direction of reaction

Am

ount

of e

nerg

y st

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in

the

chem

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s

Low energy

High energy

EnzymesEnzymes have a specific region where the substrate binds and where catalysis occurs. This is called the active site. Enzymes are substrate-specific, although specificity varies from enzyme to enzyme.When a substrate binds to an enzyme’s active site, an enzyme-substrate complex is formed.

Space filling model of the yeast enzyme hexokinase. Its active site lies in the groove (arrowed)

Enzyme Active Sites

This model (above) is an enzyme called Ribonuclease S, that breaks up RNA

molecules. It has three active sites (arrowed).

Active site: The active site contains both binding and catalytic regions. The substrate is drawn to the enzyme’s surface and the substrate molecule(s) are positioned in a way to promote a reaction: either joining two molecules together or splitting up a larger one.Enzyme molecule:

The complexity of the active site is what makes each enzyme so specific (i.e. precise in terms of the substrate it acts on).

Substrate molecule:Substrate molecules are the chemicals that an enzyme acts on. They are drawn into the cleft of the enzyme.

Lock and Key ModelThe lock and key model of enzyme action, proposed earlier this century, proposed that the substrate was simply drawn into a closely matching cleft on the enzyme molecule.

Substrate

Enzyme

Products

Symbolic representation of the lock and key model of enzyme action.1. A substrate is drawn into the active sites of the enzyme.

2. The substrate shape must be compatible with the enzymes active site in order to fit and be reacted upon.

3. The enzyme modifies the substrate. In this instance the substrate is broken down, releasing two products.

Induced Fit ModelMore recent studies have revealed that the process is much more likely to involve an induced fit.

The enzyme or the reactants (substrate) change their shape slightly.

The reactants become bound to enzymes by weak chemical bonds.

This binding can weaken bonds within the reactants themselves, allowing the reaction to proceed more readily.

The enzyme changes shape, forcing the substrate molecules to combine.

Two substrate molecules are drawn into the cleft of the enzyme.

The resulting end product is released by the enzyme which returns to its normal shape, ready to undergo more reactions.

Changing the Active Site Changes to the shape of the active site will

result in a loss of function. Enzymes are sensitive to various factors such as temperature & pH.

When an enzyme has lost its characteristic 3D shape, it is said to be denatured. Some enzymes can regain their shape while in others, the changes are irreversible.

The Effect of Temperature on Enzyme Action Speeds up all reactions,

but the rate of denaturation of enzymes also increases at higher temperatures.

High temperatures break the disulphide bonds holding the tertiary structure of the enzyme together thus changing the shape of the enzyme.

This destroys the active sites & therefore makes the enzyme non – functional.

Too cold for

Enzyme to work

Too hot for Enzyme to

work

Optimum Temperatur

e for enzyme

The Effect of Temperature on Enzyme Action

The curve in the blue represents an enzyme isolated from an organism living in the artic. These cold dwelling organisms are called psychrophiles.

The curve in red represents an enzyme isolated from the digestive tract of humans.

The curve in green represents an enzyme isolated from a thermophile bacteria found growing in geothermal sea beds.

The Effect of pH on Enzyme Action Like all proteins, enzymes

are denatured by extremes of pH (acidity/alkalinity).

The green curve is for pepsin that digests proteins in the stomach.

The red curve represents the activity of arginase that breaks down arginine to ornithine & urea in the liver.

The Effect of Enzyme Concentration on Enzyme Action

Assuming that the amount of substrate is not limiting, an increase in enzyme concentration causes an increase in the reaction rate.

The Effect of Substrate Concentration on Enzyme Action

Assuming that the amount of enzyme is constant, an increase in substrate concentration causes a diminishing increase in the reaction rate.

A maximum rate is obtained at a certain concentration of substrate when all enzymes are occupied substrate (the rate cannot increase any further).

The Effect of Cofactors on Enzyme Action

Cofactors are substances that are essential to the catalytic activity of some enzymes.

Cofactors may alter the shape of enzymes slightly to make the active sites functional or to complete the reactive site.

Enzyme cofactors include coenzymes (organic molecules) or activating ions (eg. Na+, K+..)

Vitamins are often coenzymes (eg. Vit B1, Vit B6…)

The Nature of Enzyme InhibitorsEnzyme inhibitors may or may not act

reversibly:

Reversible: the inhibitor is temporarily bound to the enzyme, thereby preventing its function (used as a mechanism to control enzyme activity).

Irreversible: the inhibitor may bind permanently to the enzyme causing it to be permanently deactivated.

The Nature of Enzyme InhibitorsReversible Enzymes work in one of two

ways:Competitive inhibitors: the inhibitor

competes with the substrate for the active site, thereby blocking it and preventing attachment of the substrate.

Non-competitive: the inhibitor binds to the enzyme (but not at the active site) and alters its shape. It markedly slows down the reaction rate by making the enzyme less able to perform its function (allosteric inhibition).

Summary: Enzymes 1. Enzymes work very rapidly and help to speed

up biological reactions. 2. Enzymes can be used multiple times

(however they do degrade eventually). 3. Enzymes can work in both directions of a

chemical reaction. 4. Enzymes have optimal temperatures and pH

that they will operate. Beyond these optimum ranges they will either not work or become denatured (unfolded/breakdown).

5. Enzymes are usually specific to one particular substrate.