What enzymes are and how they work

Catalysts made of protein

A living cell carries out thousands of chemical reactions. Without help, most of them would run far too slowly at body temperature. The help comes from enzymes. An enzyme is a biological catalyst. It speeds up a reaction, and it is not used up by it.

Almost all enzymes are proteins. Each is a long chain of amino acids folded into a definite three-dimensional shape, its tertiary structure. A few RNA molecules can act as enzymes too. They are called ribozymes.

A reaction and its rate

In a chemical reaction, a substrate (S) is changed into a product (P):

The rate of a reaction is the amount of product formed per unit time. A useful rule of thumb is that the rate of a reaction doubles for every $10$ °C rise in temperature, and falls to half for every $10$ °C drop.

Many reactions that a cell needs are still too slow, even when warm. Take carbon dioxide and water, which make carbonic acid:

Without an enzyme, only about $200$ molecules of carbonic acid form in an hour. The enzyme carbonic anhydrase makes about $600\,000$ molecules in a single second. That is roughly ten million times faster.

The active site

An enzyme is much larger than its substrate. The folded chain has pockets and crevices on its surface. One of them, the active site, is the place where the substrate fits.

The shape and the chemistry of the active site suit one substrate, or a few very similar ones. That is why an enzyme is specific: a lipase acts on fats, and an amylase acts on starch. If heat or acid destroys the fold of the chain, the active site is lost, and the enzyme stops working.

The picture shows the steps. The substrate binds to the active site and forms the enzyme-substrate complex (ES). The enzyme holds the substrate in a position where it can change. It passes through an unstable transition state and becomes the product. The product is held for a moment in the enzyme-product complex (EP). Then it is released:

The free enzyme, E, is unchanged. It can take up another molecule of substrate straight away. Some books show the active site as a rigid lock for the substrate's key. In many enzymes the site changes shape a little as the substrate binds, which is called induced fit, as the middle drawing shows.

Activation energy

Even a reaction that gives out energy does not start by itself. The substrate must first be pushed over an energy hill, to the transition state. The energy needed for this climb is the activation energy.

An enzyme gives the substrate an easier path. By holding the substrate in the right position, it makes the transition state easier to reach. The hill is lower, so far more molecules get over it each second. The reaction is faster.

Look at what the enzyme does not change. The substrate is at the same height before the reaction, and the product at the same height after it. So the energy given out or taken in is the same, with or without the enzyme. The enzyme only lowers the hill between them.

Try the simulation. Make the green hill lower and lower, and watch what stays still.

Try it in Python

The program works out the barrier with and without the enzyme for two reactions, and the energy change from substrate to product.

Practise with new numbers

Common mistakes

• "The enzyme is used up in the reaction." It comes out unchanged and starts again.
• "The enzyme supplies the energy." It supplies none. It only makes the climb easier.
• "An enzyme changes the energy of the product." The energies of the substrate and the product stay where they are.
• "All enzymes are proteins." Almost all are. Ribozymes are made of RNA.
• "The whole enzyme is the active site." The active site is a small pocket on the surface of a large protein.

Remember these

• An enzyme is a biological catalyst, almost always a protein. A ribozyme is an enzyme made of RNA.
• The substrate fits the active site. The shape of the site makes the enzyme specific.
• $\text{E} + \text{S} \rightleftharpoons \text{ES} \longrightarrow \text{EP} \longrightarrow \text{E} + \text{P}$.
• The activation energy is the energy needed to reach the transition state.
• An enzyme lowers the activation energy. It does not change the energy of the substrate or of the product.
• Carbonic anhydrase: about $200$ molecules an hour without it, about $600\,000$ a second with it.

Check yourself

Try each one on your own first. If you are stuck, open a hint. Then check with Show the answer.

1. What is an enzyme, and what are almost all enzymes made of?

2. What is the active site, and why does it make an enzyme specific?

3. Write the steps from the free enzyme and the substrate to the free enzyme and the product.

4. What is the activation energy, and how does an enzyme change it?

5. A reaction gives out $30$ kJ/mol without an enzyme. How much does it give out with the enzyme?