Enzymes What are enzymes? How the confectioners make the runny yolk-like inside to chocolate eggs? The answer is : use of an enzyme What are enzymes? Enzymes are complex chemicals that control reactions in living cells. They are biochemical catalysts speeding up reactions that would otherwise happen too slowly. The chemical which an enzyme works on is called its substrate. An enzyme combines with its substrate to form a short-lived enzyme/substrate complex. Once a reaction has occurred, the complex breaks up into products and enzyme. E + S ES EP E + P The enzyme remains unchanged at the end of reaction and is free to interact again with more substrate.

The role of enzymes in an organism Many of the complex chemicals that living organisms need cannot be made in a single reaction. Instead a series of simpler reactions occur, one after another, forming a metabolic pathway. A single pathway may have many steps in which each chemical is converted to the next. A specific enzyme controls each reaction. Enzymes control cell metabolism by regulating how and when reactions occur. Using this very simple pathway as an example: A B C D The final product is substance D, the chemical needed by the living organism. The pathway needs three different enzymes and when D is no longer needed or if too much has been produced, one of the three enzymes is ‘switched off’.

The Chemical nature of enzymes Enzymes are globular proteins. They have a complex tertiary and quaternary structure in which polypeptides are folded around each other to form a roughly spherical or globular shape. The overall 3D shape of an enzyme molecule is very important: if it is altered, the enzyme cannot bind to its substrate and so cannot function. Enzyme shape is maintained by hydrogen bonds and ionic forces. Enzymes have several important properties: Enzymes are specific: each enzyme usually catalyses only one reaction. Enzymes combine with their substrates to form temporary enzyme-substrate complex. Enzymes are not altered or used up by the reactions they catalyze, so can be used again and again. Enzymes are sensitive to temperature and pH. Many enzymes need cofactors in order to function. Enzyme function may be slowed down or stopped by inhibitors.

The specificity of enzymes Two models that may explain how enzymes work are: 1) The lock and key hypothesis 2) The induced fit hypothesis The lock and key hypothesis Enzyme has a particular shape into which the substrate or substrates fit exactly. This is often referred to as the ‘lock and key’ hypothesis where the substrate is imagined being like a key whose shape is complementary to the enzyme or lock. The site where the substrate bonds in the enzyme is known as the active site and it has a specific shape. Fig: The lock and key hypothesis

2) The induced fit hypothesis The active site in many enzymes is not exactly the same shape as the substrate, but moulds itself around the substrate as the enzyme substrate complex is formed. Only when the substrate binds to the enzyme is the active site, the correct shape to catalyze the reaction. As the products of the reaction from they fit the active site less well and fall away from it. Without the substrate, the enzyme reverts to its ‘relaxed’ state, until the next substrate comes along. Fig: Diagrams to show the induced fit hypothesis of enzyme action.

Naming and classifying enzymes Although there are many different enzymes, they can be put into one of six main categories according to the type of reaction they catalyze: Oxidoreductases: These catalyze oxidation and reduction reactions. Transferases: These catalyze the transfer of a chemical group from one compound to another. Hydrolases: These catalyse hydrolysis (splitting by use of water) reactions. Most digestive enzymes are hydrolases. Lyases: these catalyze the break down of molecules by reactions that do not involved hydrolysis. Isomerases: These catalyze the transformation of one isomer into another, Ligases: These catalyze the formation of bonds between compounds, often using the free energy made available from ATP hydrolysis.

Factors affecting enzyme activity The factors that affect enzyme activity also affect the functions of the cell and ultimately the organism. Enzymes are proteins and their function is therefore affected by: Temperature pH Substrate concentration Enzyme concentration Cofactors Inhibitors

Temperature For a non-enzymatic chemical reaction, the general rule is: the higher the temperature, the faster the reaction. This same rule holds true for a reaction catalyzed by an enzyme, but only up to about 40-450C. Above this temperature, enzyme molecules begin to vibrate so violently that the delicate bonds that maintain tertiary and quaternary structure are broken, irreversibly changing the shape of the molecule. When this happens, the enzyme can no longer function and it is said to be denatured.

pH Like other proteins, enzymes are stable over a limited range of pH. Outside this range, at the extremes of pH, enzymes are denatured. Free hydrogen ions (H+) or hydroxyl ions (OH-) affect the changes on amino acid residues, distorting the 3D shape and causing an irreversible change in the proteins tertiary structure. Enzymes are particularly sensitive to changes in pH because of the great sensitivity of their active site. Even if a slight change in pH is not enough to denature the molecule, it may upset the delicate chemical arrangement at the active site and so stop the enzyme working.

Substrate concentration The rate of an enzyme-controlled reaction increases as the substrate concentration increases, until the enzyme is working at full capacity. At this point, the enzyme molecules reach their turnover number and assuming that all other conditions such as temperature are ideal, the only way to increase the speed of the reaction even more is to add more enzyme.

Enzyme concentration In any reaction catalyzed by an enzyme, the number of enzyme molecules present is very much smaller than the number of substrate molecules. When an abundant supply of substrate is available, the rate of reaction is limited by the number of enzyme molecules present. In this situation, increasing the enzyme concentration increases the rate of reaction.

Cofactors Some enzymes cannot work on their own, they need a molecule called a cofactor in order to work properly. Cofactors modify the enzyme complex so that it has the chemical properties necessary to catalyze a reaction. There are three kinds of cofactors: a) Prosthetic group: Organic molecule that is permanently attached to an enzyme. b) Coenzymes: Relatively small organic molecules are not permanently attached to the enzyme molecule. c) Metal cofactors: Inorganic metal ions that are also known as enzyme activators.

Inhibitors Inhibitors slow down or stop enzyme reaction. Usually, enzyme inhibition is a natural process, a means of switching enzymes on or off when necessary. Inhibition can be reversible and the enzyme returns to full activity once the inhibitor is removed. Drugs and poisons can inhibit particular enzymes, this type of inhibition is often non-reversible. Reversible inhibitors are either competitive or non-competitive. Competitive inhibitors Compete with normal substrate molecules to occupy the active site. A competitive inhibitor fits into the active site of the enzyme preventing the real substrate from gaining access. The inhibitor cannot be converted to the products of the reaction and so the overall rate of reaction is slowed down.

Fig: Competitive inhibitors bind reversibly to the enzyme, preventing the binding of substrate. On the other hand, binding of substrate prevents binding of the inhibitor. Substrate and inhibitor compete for the enzyme.

Non-competitive inhibitors Non-competitive inhibitors bind to the enzyme away from the active site but change the overall shape of the molecule, modifying the active site so that it can no longer turn substrate molecules into product. Non-competitive inhibition has this name because there is no competition for the active site. Fig: Non-competitive inhibition Irreversible inhibitors Irreversible inhibitors bind permanently to the enzyme, rendering it useless. For example, cyanide is an irreversible inhibitor.