Enzymes: How They Work

Mash a raw potato and add a few drops of hydrogen peroxide, and the mixture fizzes vigorously as oxygen bubbles out. Without the potato, the peroxide would decompose so slowly you’d see nothing. The difference is an enzyme called catalase, which can break down millions of peroxide molecules every second. Enzymes like this make life possible: without them, the chemical reactions that keep you alive would run far too slowly to sustain life.

What an enzyme is

An enzyme is a biological catalyst. Like any catalyst, it:

• speeds up a chemical reaction;
• is not used up by the reaction, so one enzyme molecule can be used over and over;
• doesn’t change the overall energy change of the reaction or the position of equilibrium; it just helps the reaction get there faster.

Almost all enzymes are proteins: long chains of amino acids folded into precise three-dimensional shapes (see proteins: chains of amino acids). A few RNA molecules can also act as catalysts. They’re called ribozymes, and the ribosome itself uses RNA to join amino acids.

Enzymes are astonishingly effective. Many speed up reactions by factors of millions to billions, and some by far more. Catalase and carbonic anhydrase can each process roughly a million substrate molecules or more per second.

Key vocabulary

• Substrate: the molecule the enzyme acts on.
• Product: what the substrate is turned into.
• Active site: a small pocket or groove on the enzyme’s surface where the substrate binds and the reaction happens.
• Enzyme–substrate complex: the enzyme with the substrate bound in its active site.

The basic scheme is:

enzyme + substrate ⇌ enzyme–substrate complex → enzyme + product

The active site: shape and chemistry

The active site is formed by a small number of amino acid side chains, brought together from different parts of the folded chain. Its shape and the chemical groups lining it (charged, polar or oily) are complementary to the substrate. That’s why each enzyme is specific: it only acts on one substrate, or a small group of similar substrates.

Two models describe how substrate and enzyme fit:

• The lock-and-key model (Emil Fischer, 1894): the active site has a rigid shape that exactly matches the substrate, like a key fitting a lock.
• The induced-fit model (Daniel Koshland, 1958): the active site is flexible and changes shape slightly as the substrate binds, wrapping around it, like a glove closing on a hand.

The induced-fit model fits modern evidence better. The two are compared in lock-and-key vs induced-fit.

How enzymes speed reactions up

Every reaction needs a minimum amount of energy to start: the activation energy. Molecules must collide with enough energy, and in the right orientation, to break old bonds and make new ones. Enzymes speed reactions up by providing a different reaction pathway with a lower activation energy. They do this in several ways at once:

• Bringing substrates together in the right position and orientation, so they don’t have to rely on random collisions.
• Straining bonds in the substrate as it binds, making them easier to break.
• Providing the right chemical environment, such as acidic or basic side chains that can donate or accept protons, or a non-polar pocket that shields the reaction from water.
• Stabilising the transition state, the high-energy halfway point of the reaction. Active sites bind the transition state even more tightly than the substrate, which lowers its energy.

Naming enzymes

Most enzyme names end in -ase, often added to the name of the substrate or the type of reaction:

Enzyme	Substrate or reaction	Products
Amylase	Starch (amylose)	Maltose
Lipase	Lipids (fats)	Fatty acids + glycerol
Protease	Proteins	Peptides and amino acids
Lactase	Lactose	Glucose + galactose
Catalase	Hydrogen peroxide	Water + oxygen
DNA polymerase	Builds DNA	DNA strands

Some older names don’t follow the pattern, such as pepsin and trypsin, two digestive proteases.

What affects enzyme activity

Enzymes work best within particular conditions:

• Temperature. Activity rises as temperature increases (molecules move faster and collide more often) up to an optimum. Above that, the enzyme starts to denature: its shape, and so its active site, is lost, and activity falls sharply. Many human enzymes work best near 37 °C. See protein denaturation.
• pH. Each enzyme has an optimum pH. Changing the pH alters the charges on amino acid side chains, changing the active site’s shape and chemistry. Pepsin, in the stomach, works best at about pH 2; trypsin, in the small intestine, at about pH 8.
• Substrate concentration. More substrate means more collisions, so the rate rises, until all the active sites are busy. Then the rate levels off.
• Enzyme concentration. More enzyme means more active sites, so a faster rate, as long as there’s plenty of substrate.
• Inhibitors. Some molecules block or change the active site, slowing the enzyme down. Many medicines and poisons work this way.

Helpers: cofactors and coenzymes

Many enzymes need a small non-protein helper to work:

• Cofactors are often metal ions, such as zinc in carbonic anhydrase, iron in catalase or magnesium in many enzymes that handle ATP.
• Coenzymes are small organic molecules, many made from vitamins. For example, NAD⁺ is made from niacin (vitamin B3) and carries electrons in respiration.

This is one reason trace minerals and vitamins are essential in the diet.

Enzymes in the body

• Digestion: amylase, proteases and lipases break food down into small molecules the body can absorb.
• Respiration: a long series of enzymes releases energy from glucose step by step.
• Copying DNA: DNA polymerase builds new strands during cell division.
• Blood clotting: a cascade of enzymes turns soluble fibrinogen into insoluble fibrin.
• Detoxification: liver enzymes break down alcohol, drugs and toxins.
• Protection: catalase destroys hydrogen peroxide, a harmful by-product of metabolism.

A missing or faulty enzyme can cause disease. In lactose intolerance, too little lactase is produced; in phenylketonuria, an enzyme that processes the amino acid phenylalanine doesn’t work properly.

Enzymes in industry and everyday life

• Biological washing powders contain proteases, lipases and amylases that digest food and body-oil stains at lower washing temperatures.
• Food industry: amylases turn starch into glucose syrups; lactase makes lactose-free milk; pectinases clarify fruit juices; rennet enzymes (chymosin) curdle milk for cheese.
• Brewing and baking: enzymes in malted grain and yeast turn starch into sugars and sugars into alcohol and carbon dioxide.
• Medicine and diagnosis: glucose meters use the enzyme glucose oxidase; blood tests for liver or heart damage measure enzymes leaking from damaged cells.
• Biotechnology: DNA polymerases from heat-loving bacteria make PCR possible, the method behind DNA testing.

Common misconceptions

• “Enzymes are alive.” They’re molecules (mostly proteins), not living things.
• “Enzymes are used up in reactions.” They’re catalysts; they come out unchanged and are reused.
• “High temperature kills enzymes.” Heat denatures them: the shape is destroyed, so they stop working. They were never alive.
• “Enzymes make reactions happen that otherwise couldn’t.” They only speed up reactions that are already possible; they don’t change the energy balance.
• “The substrate and active site have the same shape.” They have complementary shapes, like matching puzzle pieces.

Key takeaways

• Enzymes are biological catalysts, almost always proteins, that speed up reactions without being used up.
• The substrate binds to the active site, whose complementary shape makes enzymes specific.
• Enzymes work by lowering activation energy: positioning substrates, straining bonds and stabilising the transition state.
• Activity depends on temperature, pH, substrate and enzyme concentration, and inhibitors.
• Many enzymes need cofactors (metal ions) or coenzymes (often from vitamins). Next, see how the substrate fits in lock-and-key vs induced-fit.