Enzymes notes

MDCAT Biology

Enzymes are biological catalysts, mostly proteins, that increase the rate of biochemical reactions without being used up. This chapter explains their characteristics, enzyme action, factors affecting activity, cofactors and coenzymes, and the effects of enzyme inhibitors.

Introduction and Characteristics of Enzymes

An enzyme is a biological catalyst produced by living cells. It increases the rate of a chemical reaction by lowering the activation energy. Enzymes are not consumed in the reaction and can be used repeatedly.

Most enzymes are globular proteins. Their activity depends on their specific three-dimensional shape. A small region of the enzyme, called the active site, binds the substrate and helps convert it into product.

Enzymes are biological catalysts.
Most enzymes are proteins, but some RNA molecules can also act as catalysts. Catalytic RNA is called ribozyme.
Enzymes remain chemically unchanged at the end of a reaction.
A small amount of enzyme can catalyse the conversion of a large amount of substrate.
Enzymes are highly specific. An enzyme usually acts on one substrate or on a group of closely related substrates.
The active site is formed by only a few amino acids of the enzyme.
Enzymes do not alter the overall energy difference between substrates and products. They lower the activation energy required to start the reaction.
Enzyme activity can be measured by the rate of reaction or by the amount of product formed in a given time.

Active Site and Mode of Enzyme Action

The substrate is the reactant on which an enzyme acts. It binds temporarily with the active site to form an enzyme-substrate complex, written as ES complex. The active site has a shape and chemical properties that are suitable for the substrate.

After binding, the enzyme changes the substrate into one or more products. The products leave the active site, and the free enzyme is ready to take part in another reaction.

The general sequence is: Enzyme + substrate forms ES complex, and ES complex forms enzyme + product.
The active site contains binding sites for attachment of the substrate and a catalytic site for conversion of the substrate into product.
The catalytic site converts the ES complex into product.
The lock and key model states that the active site has a fixed shape complementary to the substrate.
The induced fit model states that the active site changes its shape slightly when the substrate binds.
The induced fit model better explains the flexibility of many enzyme active sites.
Enzyme specificity depends mainly on the shape and chemical nature of the active site.
Carbonic anhydrase can hydrate up to about one million molecules of carbon dioxide per second. This shows a very high turnover number.
Turnover number is the number of substrate molecules converted into product by one enzyme molecule in one second under suitable conditions.

Classification and Functions of Enzymes

Enzymes are classified according to the type of reaction they catalyse. The names of many enzymes end in the suffix ase. For example, amylase acts on starch, lipase acts on lipids, and protease acts on proteins.

Transferases transfer a functional group from one molecule to another. Different transferases transfer different groups, such as amino, phosphate or methyl groups.

Oxidoreductases catalyse oxidation-reduction reactions.
Transferases catalyse the transfer of a functional group between molecules.
Transmethylases transfer a methyl group.
Hydrolases break chemical bonds by adding water.
Lyases remove or add groups without hydrolysis and often form double bonds.
Isomerases catalyse rearrangement of atoms within a molecule.
Ligases join two molecules, usually using energy from ATP.
Pepsin is a protein-digesting enzyme that works best in a strongly acidic medium.
Chymotrypsin works effectively near pH 7 in the medium.

Cofactors, Coenzymes and Prosthetic Groups

Some enzymes cannot function with their protein part alone. They require a non-protein component called a cofactor. The protein part is called the apoenzyme, while the complete active enzyme is called the holoenzyme.

A cofactor may be an inorganic ion or an organic molecule. Organic cofactors are called coenzymes. Most coenzymes are derivatives of vitamins and help transfer atoms or chemical groups during reactions.

Apoenzyme is the inactive protein part of an enzyme.
Holoenzyme is the complete active enzyme consisting of apoenzyme and its required cofactor.
Cofactors may be metal ions, inorganic substances or organic molecules.
Coenzymes are organic cofactors that participate in enzyme reactions.
Most coenzymes are derived from vitamins.
A prosthetic group is a non-protein part that is tightly and permanently attached to an enzyme.
A prosthetic group is usually covalently bound to the enzyme.
A cofactor that is loosely attached can separate from the enzyme and may be called a cosubstrate.
Calcium ions regulate some enzymes, including phosphoprotein phosphatase.

Effect of Temperature on Enzyme Activity

Temperature affects the movement of enzyme and substrate molecules. When temperature rises, molecules move faster and collisions become more frequent. Therefore, enzyme activity generally increases up to a particular temperature called the optimum temperature.

Above the optimum temperature, heat disrupts the bonds that maintain the enzyme's three-dimensional structure. The active site changes shape, and the enzyme loses activity. This loss of structure is called denaturation.

The optimum temperature is the temperature at which an enzyme shows its maximum activity.
The optimum temperature for enzymes in the human body is 37°C.
At low temperatures, enzymes become inactive because molecular movement is reduced.
The inactive enzyme can regain its function when the temperature is raised to a suitable level. This suitable lower temperature is called the minimum temperature in the given enzyme terminology.
Low temperature usually does not permanently denature enzymes.
At temperatures above the optimum, enzyme activity decreases because the enzyme starts to denature.
Maximum temperature refers to the temperature at which enzymes start to denature in the reaction.
The temperature activity graph usually rises to an optimum point and then falls sharply because of denaturation.
Optimum temperature is identified by the greatest percentage of product formation or the highest rate of reaction.

Effect of pH on Enzyme Activity

Each enzyme has a particular pH at which its activity is maximum. A change in pH can alter the charges on amino acids at the active site and can change the shape of the enzyme. Very high or very low pH may denature the enzyme.

Different enzymes work best at different pH values because they function in different parts of the body or in different chemical environments.

Optimum pH is the pH at which an enzyme shows maximum activity.
Pepsin has an optimum pH of about 2.0.
Pepsin works in the acidic environment of the stomach.
Arginase has an optimum pH of about 9.7.
Chymotrypsin can work at approximately pH 7 of the medium.
The activity of an enzyme usually decreases on either side of its optimum pH.
A suitable buffer helps maintain the pH required for enzyme activity.
Changes in pH can affect both the enzyme's structure and the ionisation of its active site.

Other Factors Affecting Enzyme Action

The rate of an enzyme reaction is also affected by the concentrations of enzyme and substrate. If enough substrate is available, increasing enzyme concentration increases the reaction rate because more active sites are present.

At a fixed enzyme concentration, increasing substrate concentration initially increases the reaction rate. After all active sites become occupied, the enzyme becomes saturated and the rate reaches a maximum.

Increasing enzyme concentration increases reaction rate when sufficient substrate is available.
Increasing substrate concentration increases reaction rate until all active sites are occupied.
At saturation, further increase in substrate concentration does not significantly increase the reaction rate.
Product concentration may reduce the reaction rate when product molecules interfere with the forward reaction or inhibit the enzyme.
The presence of activators may increase enzyme activity.
The presence of inhibitors may decrease or stop enzyme activity.
Temperature, pH, enzyme concentration, substrate concentration and inhibitors are major factors affecting enzyme action.
Chemical substances that regulate enzymatic activity may act as activators or inhibitors.

Enzyme Inhibitors

An inhibitor is a substance that decreases the activity of an enzyme. Some inhibitors bind temporarily, while others bind permanently or destroy the active enzyme structure. Inhibition may be reversible or irreversible.

In competitive inhibition, the inhibitor resembles the substrate and competes for the active site. In non-competitive inhibition, the inhibitor binds at a site other than the active site and changes the enzyme's structure.

A competitive inhibitor binds to the active site and prevents the substrate from binding.
Competitive inhibition can often be reduced by increasing the substrate concentration.
A non-competitive inhibitor binds to an enzyme at a site other than the active site.
Binding of a non-competitive inhibitor changes the structure of the enzyme and reduces active-site function.
In non-competitive inhibition, the extent of inhibition depends only on the concentration of the inhibitor.
Increasing substrate concentration does not usually overcome non-competitive inhibition.
Cyanide blocks the action of some enzymes by combining with their prosthetic group.
Irreversible inhibitors form a permanent association with an enzyme or permanently damage its active structure.
Reversible inhibitors can detach from the enzyme and allow activity to return.
Modern detergents may contain enzyme preparations from alkaliphiles, organisms that grow and function in alkaline conditions.

Key terms

Enzyme: An enzyme is a biological catalyst that increases the rate of a reaction without being consumed.
Catalyst: A catalyst changes the rate of a chemical reaction without undergoing permanent chemical change.
Substrate: A substrate is the reactant on which an enzyme acts.
Active site: The active site is the specific region of an enzyme where the substrate binds and the reaction occurs.
Enzyme-substrate complex: The enzyme-substrate complex is the temporary combination formed when a substrate binds to an enzyme.
Catalytic site: The catalytic site is the part of the active site that converts the bound substrate into product.
Optimum temperature: Optimum temperature is the temperature at which an enzyme shows maximum activity.
Denaturation: Denaturation is the loss of an enzyme's normal three-dimensional structure and activity.
Optimum pH: Optimum pH is the pH at which an enzyme works at its maximum rate.
Cofactor: A cofactor is a non-protein component required by some enzymes for activity.
Coenzyme: A coenzyme is an organic cofactor, usually derived from a vitamin, that helps an enzyme carry out a reaction.
Prosthetic group: A prosthetic group is a non-protein component that is tightly and permanently, usually covalently, attached to an enzyme.
Apoenzyme: An apoenzyme is the inactive protein part of an enzyme.
Holoenzyme: A holoenzyme is the complete active enzyme made of an apoenzyme and its cofactor.
Turnover number: Turnover number is the number of substrate molecules converted into product by one enzyme molecule per second.
Competitive inhibitor: A competitive inhibitor binds to the active site and competes with the substrate.
Non-competitive inhibitor: A non-competitive inhibitor binds away from the active site and changes the enzyme's structure.
Alkaliphile: An alkaliphile is an organism that grows and functions best in an alkaline environment.

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