Classes of enzyme and their cofactors

Naming and classifying enzymes

There are thousands of enzymes, and the International Union of Biochemistry sorts them by the type of reaction they carry out. Most names end in -ase. A name may come from the substrate, as in lipase for lipids, or from the reaction, as in a dehydrogenase. Every enzyme falls into one of six classes, numbered $1$ to $6$.

• 1. Oxidoreductases and dehydrogenases carry out oxidation and reduction. One substrate is oxidised and the other reduced. Examples: lactate dehydrogenase, succinate dehydrogenase.
• 2. Transferases move a group, other than hydrogen, from one substrate to another. Examples: a transaminase, which moves an amino group, and a kinase, which moves a phosphate group.
• 3. Hydrolases break ester, ether, peptide and glycosidic bonds and some others by adding water. Examples: amylase, lipase, pepsin.
• 4. Lyases break C-C, C-O and C-N bonds by means other than hydrolysis. They often leave a double bond. Examples: aldolase and the decarboxylases.
• 5. Isomerases rearrange the atoms inside a molecule. They bring about all types of isomerisation: optical, geometric and positional. Example: glucose phosphate isomerase.
• 6. Ligases join two molecules, using the energy of ATP. Examples: DNA ligase and the synthetases.

The first letters spell a handy order to remember: Oxidoreductases, Transferases, Hydrolases, Lyases, Isomerases and Ligases.

Cofactors

Some enzymes are proteins alone. Many others need a non-protein part as well, and they cannot work without it. The protein part is the apoenzyme. The non-protein part is the cofactor. Together they make the complete, active enzyme, the holoenzyme.

If the cofactor is removed, the apoenzyme has no activity. There are three kinds of cofactor.

• Prosthetic groups are organic and bound tightly to the protein part. The haem of the enzymes peroxidase and catalase is a prosthetic group. It is part of the active site. Catalase breaks down hydrogen peroxide.
• Coenzymes are organic and bound loosely. They join the enzyme only during the reaction. Many are made from vitamins. NAD and NADP contain the vitamin niacin.
• Metal ions are needed for the activity of some enzymes. They form bonds with the side chains of the protein and with the substrate, at the active site. Zinc is needed by the enzyme carboxypeptidase.

A coenzyme can be washed away from the protein, for example by dialysis, which removes small molecules. A prosthetic group cannot, because it is held so tightly.

The simulation shows why a missing cofactor matters. Each active holoenzyme needs one apoenzyme and one cofactor.

Try it in Python

The program names the class of six enzymes, one from each class.

Practise with new numbers

Common mistakes

• "A transferase moves hydrogen." Moving hydrogen belongs to the oxidoreductases. A transferase moves another group.
• "Lyases add water." Hydrolases add water. Lyases break bonds in some other way, often leaving a double bond.
• "Ligases work without energy." A ligase joins two molecules using the energy of ATP.
• "The apoenzyme is the cofactor." The apoenzyme is the protein part. The cofactor is the non-protein part.
• "A coenzyme is a protein." A coenzyme is a small organic molecule, and many come from vitamins.

Remember these

• Six classes: Oxidoreductases, Transferases, Hydrolases, Lyases, Isomerases, Ligases.
• Hydrolases use water. Lyases do not. Ligases use ATP.
• Apoenzyme + cofactor = holoenzyme.
• Prosthetic group: tight, as in the haem of catalase and peroxidase.
• Coenzyme: loose and organic, as in NAD and NADP, which contain niacin.
• Metal ion: as in the zinc of carboxypeptidase.

Check yourself

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

1. Name the six classes of enzyme in order.

2. An enzyme joins two molecules using energy from ATP. Which class is it?

3. What is the difference between an apoenzyme, a cofactor and a holoenzyme?

4. Give one example each of a prosthetic group, a coenzyme and a metal ion cofactor.

5. Why do people need niacin in their food?