Enzymes

Let us break down this definition. Biological means that they occur naturally in living things. Catalysts accelerate the rate of chemical reactions and are not consumed or 'used up' but remain unchanged. Therefore, enzymes can be reused to speed up many more reactions.

Almost all enzymes are proteins, more specifically globular proteins. From our article on proteins, you might remember that globular proteins are functional proteins. They act as enzymes, carriers, hormones, receptors, and more. They perform metabolic functions.

One example of an enzyme is the human salivary enzyme, alpha-amylase. Figure 1 shows the structure of alpha-amylase. Knowing that enzymes are proteins, spot the 3-D structure with regions coiled in α-helix and β-sheets. Remember that proteins are made up of amino acids linked together in polypeptide chains.

Fig. 1 - Ribbon diagram of the enzyme salivary alpha-amylas

Where do enzymes get their names?

You may have noticed that all enzyme names end in -ase. Enzymes get their names from the substrate or the chemical reaction they catalyse. Have a look at the table below. Reactions involving various substrates such as lactose and starch, and chemical reactions such as oxidation/reduction reactions, are catalysed by enzymes.

Table 1. Examples of enzymes, their substrates and functions.

The structure of enzymes

Like all globular proteins, enzymes are spherical in structure, with polypeptide chains folded to form the shape. The amino acid sequence (the primary structure) is twisted and folded to form a tertiary (three-dimensional) structure.

Because they are globular proteins, enzymes are highly functional. A particular area of the enzyme that is functional is called an active site. It is a slight depression on the surface of the enzyme. The active site has a small number of amino acids that can form temporary bonds with other molecules. Typically, there is only one active site on each enzyme. The molecule that can bind to the active site is called a substrate. An enzyme-substrate complex forms when the substrate temporarily binds to the active site.

How does an enzyme-substrate complex form?

Let us take a step-by-step look at how an enzyme-substrate complex forms:

1. A substrate binds to the active site and forms an enzyme-substrate complex. The substrate's interaction with the active site needs a specific orientation and speed. The substrate collides with the enzyme, i.e. it psychically comes into contact to bind.

2. The substrate converts into products. This reaction is catalysed by the enzyme, forming an enzyme-product complex.

3. The products detach from the enzyme. The enzyme is free and can be used again.

Later, you will learn that there can be one or more substrates in this process, and therefore, one or more products. For now, you must understand the difference between enzymes, substrates, and products. Have a look at the image below. Notice the formation of both enzyme-substrate and enzyme-product complexes.

Fig. 2 - A substrate binding to an enzyme forms the enzyme-substrate complex, followed by the enzyme-product complex

The induced-fit model of enzyme action

The induced-fit model of enzyme action is a modified version of an earlier lock-and-key model. The lock-and-key model assumed that both the enzyme and the substrate were rigid structures, with the substrate fitting precisely into the active site, just as a key fits into a lock. The observation of enzyme activity in reactions supported this theory and led to the conclusion that enzymes are specific to the reaction they catalyse. Have another look at figure 2. Can you see the rigid, geometric shapes that the active site and substrate supposedly had?

The scientists later found that the substrates bind to the enzymes at sites other than the active site! Consequently, they concluded that the active site is not fixed, and the shape of the enzyme changes when the substrate binds to it.

As a result, the induced-fit model was introduced. This model states that the active site forms only when the substrate binds to the enzyme. When the substrate binds, the shape of the active site adapts to the substrate. Consequently, the active site does not have an identical, rigid shape but is complementary to the substrate. These changes in the shape of the active site are called conformational changes. They maximise the enzyme's ability to act as a catalyst for a particular chemical reaction. Compare Figures 2 and 3. Can you spot the difference between the active sites and the general shapes of enzymes and substrates?

Fig. 3 - The active site changes shape when a substrate binds to it, followed by the formation of the enzyme-substrate complex

The function of enzymes

As catalysts, enzymes speed up the rate of reactions in living things, sometimes by millions of times. But how do they actually do this? They do this by lowering the activation energy.

Why do enzymes lower the activation energy and not raise it? Surely they would need more energy to make a reaction go faster? There is an energy barrier that the reaction has to 'overcome' to start. By lowering the activation energy, the enzyme allows the reactions to 'get over' the barrier faster. Imagine riding a bicycle and reaching a steep hill that you need to climb. If the hill was less steep, you could climb it easier and faster.

Enzymes allow reactions to occur at lower than average temperatures. Typically, chemical reactions occur at high temperatures. Considering that the human body temperature is about 37 °C, the energy needs to be lower to match that temperature.

In Figure 4, you can see the difference between the blue curve and the red curve. The blue curve represents a reaction occurring with the help of an enzyme (it is catalysed or accelerated by an enzyme) and therefore has lower activation energy. On the other hand, the red curve occurs without an enzyme and therefore has higher activation energy. The blue reaction is thus much faster than the red one.

Fig. 4 - The difference in activation energy between two reactions, only one of which is catalysed by an enzyme (the purple curve)

Factors affecting enzyme activity

Enzymes are sensitive to certain conditions in the body. Can enzymes, these powerful little machines, ever be altered? Do substrates bind to altered enzymes? Several factors affect enzyme activity, including temperature, pH, enzyme and substrate concentrations, and competitive and non-competitive inhibitors. They can cause the denaturation of enzymes.

Fig. 5 - Changes in external factors such as heat (2) affect the protein's 3-D structure (1), causing it to unfold (3) (the protein denatures)

Temperature changes affect the kinetic energy required to carry out reactions, especially the collision of enzymes and substrates. Too low a temperature results in insufficient energy, while too high results in denaturation of the enzyme. Changes in pH affect the amino acids in the active site. These changes break the bonds between the amino acids, causing the active site to change shape, i.e. the enzyme denatures.

Enzyme and substrate concentration affect the number of collisions between enzymes and substrates. Competitive inhibitors bind to the active site and not to the substrates. In contrast, non-competitive inhibitors bind elsewhere on the enzyme, causing the active site to change shape and become non-functional (again, denaturation).

When these conditions are optimal, the collision between enzymes and substrates is most significant. You can learn more about these factors in our article Factors Affecting Enzyme Activity.

There are thousands of enzymes involved in different pathways, where they perform different roles. Next, we will discuss some of the functions of enzymes.

The function of enzymes in catabolism

Enzymes accelerate catabolic reactions, collectively known as catabolism. In catabolic reactions, complex molecules (macromolecules) such as proteins break down into smaller molecules like amino acids, releasing energy.

In these reactions, one substrate binds to the active site, where the enzyme breaks down chemical bonds and creates two products that separate from the enzyme.

The function of enzymes in anabolism or biosynthesis

Anabolic reactions are the opposite of catabolic reactions. Together they are referred to as anabolism. A synonym for anabolism is biosynthesis. In biosynthesis, macromolecules like carbohydrates build up from their constituents, which are simple molecules such as glucose, using the energy of ATP.

In these reactions, not one but two or more substrates bind to the enzyme's active site. The chemical bond is formed between them, resulting in a single product.

Enzymes in other roles

Let's take a look at enzymes in other roles.

Cell signalling or cell communication

Chemical and physical signals are transmitted through cells and eventually trigger a cellular response. Enzymes protein kinases are essential because they can enter the nucleus and affect transcription once they receive a signal.

Muscle contraction

The enzyme ATPase hydrolyses ATP to generate energy for two proteins central to muscle contraction: myosin and actin.

Replication of viruses and spread of diseases

Both use the enzyme reverse transcriptase. After a virus inhibits host cells, reverse transcriptase makes DNA from the virus' RNA.

Gene cloning

Again, the enzyme reverse transcriptase is the main enzyme.