3 EnzymEs

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You may remember, from Key Stage 4, that catalysts are substances that can alter the rate of a chemical reaction without themselves being changed at the end of the reaction. You may also know that increasing temperature can increase the rate of many reactions, and you may recall that pH is a measure of the acidity or basicity of a solution, which is determined by the concentration of hydrogen ions in it. Before you begin this chapter you may want to remind yourself about protein structure (Chapter 2).

lEarNiNg ObJEcTivEs

In this chapter we will look at the essential roles of enzymes – biological catalysts – in controlling the metabolic reactions that take place in living organisms.

(Specification 3.1.4.2)

Enzymes make life possible because without them, the vast majority of chemical reactions that take place inside living organisms would not happen. Enzymes catalyse metabolic reactions, reducing the energy that is needed to allow these reactions to start.

Each enzyme is specific for one type of reaction, so our bodies manufacture hundreds of different enzymes. Cells can control the activity of enzymes by producing inhibitors that attach to enzyme molecules and prevent them from working. This is one of the ways by which cells can prevent a chaotic medley of reactions taking place all at the same time.

Many inhibitors are important for the day-to-day working of an organism’s body, while others are used to defend the organism from attack by other species. For example, the seeds of many plants belonging to the pea and bean family contain large quantities of protein, which provides nutrients for the growing young seedling. This high protein content makes the pea and bean seeds a tempting food for many animals. However, the seeds also contain an inhibitor that blocks the action of the protein-digesting enzyme, trypsin, so that animals that eat the seeds are unable to digest and absorb the proteins, and are likely to suffer abdominal pain. Cooking the beans destroys the inhibitor and makes them safe to eat.

Ingesting some enzyme inhibitors can have devastating consequences. Eating just small quantities of the death cap mushroom, Amanita phalloides, can be fatal, even when the mushroom has been cooked. This is because the fungus contains an inhibitor of the enzyme that catalyses the production of mRNA from a DNA template, which is the first step in protein synthesis. If this process is inhibited, the organism will die.

Not all enzyme inhibitors produced by other organisms are harmful to us. Penicillin is an inhibitor of the enzyme that helps to build and strengthen the cell walls of bacteria. The enzyme inhibitor is produced naturally by some fungi, presumably to help them to compete with and destroy bacteria that share their habitat. Penicillin is now manufactured on an industrial scale and is used as an antibiotic. Because penicillin specifically inhibits only the enzymes involved in producing bacterial cell walls, it has no direct effect on our own body cells. It is, therefore, a drug that can be used safely inside the human body.

Enzymes and chemical reactions

3.1 Biological catalysts

A huge number of chemical reactions – known as metabolic reactions – take place inside every living cell. Some of these reactions release energy, some synthesise new substances and others break down waste products. Enzymes enable these reactions to happen and, most importantly, enzymes make it possible for the reactions to happen quickly enough at body temperature.

Many chemical reactions need an input of energy to get them going and this energy is normally supplied as heat. Enzymes are catalysts. They reduce the amount of energy that is needed to get a reaction going, but they are not themselves changed at the end of the reaction. This makes them very valuable substances, not only in living organisms, but also for human use. Enzymes from yeast have for centuries been used to brew alcoholic drinks. Enzymes are also commonly added to detergents to digest food stains, and many more industrial processes in the future are likely to make use of enzymes.

Enzymes are not living things. They are proteins. The properties of proteins help to explain how enzymes work and how they lower the energy needed to get a reaction going. The protein structure of enzyme molecules does, however, make them sensitive to environmental conditions both inside and outside the body, which means that changes in temperature or pH can disrupt enzyme action. In humans, severe over-heating or getting so cold that core body temperature falls can upset the delicate balance of enzyme-controlled reactions in the body’s cells and can be fatal.

3.2 EnzymEs and chEmical rEactions

Hydrogen peroxide is a colourless liquid (it looks just like water). It has the formula H2O2. If you put some hydrogen peroxide into a flask or test tube it will gradually – very, very slowly – decompose to form water and oxygen. The equation for this reaction is:

2H2O2 → 2H2O + O2

The little bubbles of oxygen that are given off are the only evidence that this reaction is happening.

If you want to liven things up, you can add a tiny piece of fresh, raw liver to the flask. Immediately, the hydrogen peroxide begins to bubble furiously. The bubbles form a rapidly expanding froth, which climbs up the flask and may overflow (Figure 1).

What is happening when you add the liver? The liver cells, like all living cells, contain an enzyme called catalase. This enzyme catalyses the decomposition reaction shown in the equation above.

Activation energy

We have seen that hydrogen peroxide molecules will break apart to form water and oxygen, but they normally do this only very slowly. This is because the reaction needs energy to make it happen. You could speed the reaction up by heating the hydrogen peroxide. The heat energy (thermal energy) that you put in will give the hydrogen peroxide molecules more energy and make them split apart more readily. However, this is not a good idea, as the reaction can be very violent and the hydrogen peroxide is likely to explode and shatter its container.

The minimum energy needed to make a reaction start is called the activation energy. Heating raises the energy of the hydrogen peroxide, and when the activation energy is reached, the reaction takes place very rapidly. Figure 2 shows the energy changes that take place during the reaction. Before the reaction takes place, the energy of the molecules is steady. Then something happens to raise the energy level – perhaps one molecule is hit by another very hard, or perhaps they are heated up. If the molecules reach the activation energy, the reaction then takes place, leaving the product molecules at a lower energy level.

Enzymes and activation energy

Enzymes make reactions happen without having to increase the temperature. They do this by reducing the activation energy required for the reaction to take place.

Figure 3 shows the effect of an enzyme on the activation energy of the same reaction that is shown in Figure 2. You can see that the activation energy for the reaction is much lower with the enzyme than it is without the enzyme. This is just what is needed in living cells.

Cells cannot heat themselves up very much. If they could, the effects would be catastrophic because the high temperatures would damage the proteins, enzymes and other molecules from which they are made. Enzymes allow the cell’s metabolic reactions to take place at normal temperatures.

Think about this in the context of catalase. Hydrogen peroxide is produced as a by-product (in this case an unwanted product) of several different metabolic reactions. Hydrogen peroxide is a powerful oxidising agent, and it will quickly damage living cells. But because all cells contain catalase, any hydrogen peroxide is broken down almost as soon as it has been formed, in a relatively steady manner, without having to raise the temperature.

The molecule that an enzyme allows to react is called its substrate. The molecules produced at the end of the reaction are the products. The substrate for catalase is hydrogen peroxide, while water and oxygen are the products of the reaction that the enzyme catalyses.

› Enzymes are proteins that act as biological catalysts.

› Enzymes work by lowering the activation energy of a reaction, so making it possible for the reaction to happen at normal temperatures in a given organism.

3.3 how EnzymEs work

We have seen that enzymes are proteins. In fact, they are globular proteins. Their molecules are made of one or more polypeptide chains curled into a very precise three-dimensional shape.

Every enzyme molecule has an active site. This is often a ‘dent’ or ‘depression’ in the three-dimensional structure of the globular protein. The shape of the active site is very precise. It is lined with R groups (side chains) of particular amino acids that make up the polypeptide chains.

The substrate of the enzyme has a complementary shape to the active site. In a solution containing both enzyme and substrate molecules, both kinds of molecules will be in constant motion. They will often collide with one another. When a substrate molecule hits the active site on an enzyme molecule it will interact with the R groups of the amino acids lining this site. This interaction causes a small shape change in the active site, making it a perfect fit for the substrate molecule. The substrate slots into the active site and forms temporary bonds with the R groups. The combination of enzyme and substrate is called an enzyme–substrate complex (Figure 4).

This interaction also changes the shape of the substrate molecule, which stresses chemical bonds, and lowers the activation energy needed for the substrate to break apart into product molecules. The substrate splits into its product molecules, which leave the active site of the enzyme. The enzyme remains completely unchanged, and is now ready to interact with the next substrate molecule that bounces into it.

What we have just described explains how an enzyme can cause a substrate molecule to break apart. Many reactions, however, involve two substrate molecules joining together. In this case, the active site of the enzyme accommodates the two substrates side by side, holding them in exactly the right position for them to react together. The substrates combine to form a product.

This way of explaining how an enzyme works is called the induced fit model of enzyme action. ‘Induced fit’ means that the arrival of the substrate causes (induces) a small shape change in the enzyme’s active site, allowing the substrate to bind with it. You may have met the ‘lock and key’ model of enzyme activity, where the enzyme is thought of as a lock into which the substrate – the key – fits exactly. This is an older model of enzyme action. The induced fit model is a more recent model that is not completely different from the lock and key model, but is a more detailed explanation of it. You simply have to imagine a slightly flexible lock and a slightly flexible key that mould themselves to fit one another once they come into contact.

It has probably taken you several minutes to read this section (longer if you took time to look carefully at the diagram). In that time, one catalase molecule could have caused the breakdown of countless billions of hydrogen peroxide molecules. It is difficult to comprehend, but a single catalase molecule can break down more than 40 million molecules of catalase in one second. So the enzyme–substrate complex shown in Figure 4 exists for only an unimaginably short time.

QUEsTiONs

1. Enzymes are specific. A particular enzyme can catalyse only one chemical reaction. For example, catalase will only break down hydrogen peroxide. Some enzymes break only one type of bond – for example, peptidase breaks peptide bonds. Use your knowledge of how enzymes work to explain why enzymes are specific.

2. A small change in the primary structure of an enzyme molecule can prevent it from working. Use your knowledge of protein structure (Chapter 2) to explain why this is so.

KEy idEas

› An enzyme molecule has an active site into which its substrate molecule fits.

› The arrival of the substrate molecule slightly changes the shape of the active site, so that the enzyme and substrate can bind together. This is called the induced fit model.

› The temporary combination of the enzyme and substrate is called an enzyme–substrate complex.

› Enzymes can act only on their specific substrate, because only that substrate has the correct shape to bind perfectly with the enzyme’s active site.