Protein structure & function

Amino acids: one backbone, twenty side chains

Proteins are polymers of amino acids. Every amino acid has the same core: a central carbon atom bonded to an amino group (–NH₂), a carboxyl group (–COOH), a hydrogen atom and a fourth group called the R group or side chain.

The R group is the only part that differs between the 20 amino acids used to build proteins, and its chemistry decides how that amino acid behaves. It helps to sort them into four groups:

• Nonpolar (hydrophobic): side chains made mostly of carbon and hydrogen, such as valine, leucine and phenylalanine. They avoid water.
• Polar, uncharged: side chains with –OH or –NH groups, such as serine and glutamine. They can hydrogen-bond with water and with each other.
• Acidic: side chains that carry a negative charge at the pH inside a cell, such as aspartate and glutamate.
• Basic: side chains that carry a positive charge at cellular pH, such as lysine and arginine.

Two amino acids are worth remembering on their own. Cysteine has a sulfur-containing side chain (–SH), and two cysteines can link covalently. Proline's side chain loops back onto its own backbone, which makes the chain kink and stiffen wherever it appears.

Primary structure: the sequence

Amino acids are joined by peptide bonds, formed by dehydration synthesis between the carboxyl group of one amino acid and the amino group of the next. A chain of them is a polypeptide. It has a direction: one end has a free amino group (the N-terminus) and the other a free carboxyl group (the C-terminus).

The exact order of amino acids is the protein's primary structure. It's set by the gene that codes for the protein. The chain itself has a repeating backbone (N–C–C–N–C–C…), with the R groups sticking out to the side.

Changing even one amino acid can matter. In sickle cell anaemia, the sixth amino acid of the haemoglobin β chain is valine instead of glutamate. Swapping a charged side chain for a hydrophobic one creates a sticky patch on the surface. When oxygen levels drop, haemoglobin molecules clump into long fibres, and red blood cells bend into a sickle shape.

Secondary structure: helices and sheets

Short stretches of the chain fold into regular, repeating shapes. These are secondary structure, and there are two main kinds:

• α-helix: the chain coils like a spring. Each backbone C=O hydrogen-bonds to the N–H of the amino acid four places further along, and the R groups point outward from the coil.
• β-pleated sheet: stretches of chain lie side by side and hydrogen-bond across to each other, forming a sheet with a folded, zigzag surface.

Tertiary structure: the whole 3-D fold

The helices, sheets and loops of a polypeptide pack together into one overall three-dimensional shape, its tertiary structure. This time the R groups do the work, through several kinds of interaction:

• Hydrophobic interactions: nonpolar side chains cluster in the protein's core, away from water.
• Hydrogen bonds between polar side chains.
• Ionic bonds (salt bridges) between positively and negatively charged side chains.
• Disulfide bridges: covalent S–S bonds between two cysteine side chains. These are the strongest links and help lock the fold in place, especially in proteins that work outside cells.

The biggest driving force is the hydrophobic effect you met in the water lesson. Water forms ordered cages around exposed nonpolar side chains. When the chain folds so that those side chains are buried together in the core, the caged water is set free, and that increase in disorder is what makes folding favourable. So a typical protein that works in water has a hydrophobic inside and a mostly polar, charged outside.

Quaternary structure: teams of chains

Some proteins are made of more than one polypeptide. How these subunits fit together is the protein's quaternary structure, and it's held by the same kinds of interaction as tertiary structure. Haemoglobin is the classic example: four subunits, two α chains and two β chains, working as one unit. Proteins with only a single polypeptide simply don't have a quaternary level.

Shape is function, and how it's lost

A protein works because of its shape. An enzyme's active site is a pocket with just the right shape and chemistry to grip its substrate. An antibody's tips fit one particular target. Change the shape and the function goes with it.

When a protein loses its folded shape, it's denatured. Heat makes the chain vibrate hard enough to break hydrogen bonds and hydrophobic packing. A change in pH adds or removes H⁺ from charged side chains, which breaks salt bridges. Some chemicals disrupt hydrogen bonds directly. That's why most human enzymes work best near body temperature and at the pH of the place they work.

Inside a crowded cell, new chains can stick to each other before they finish folding. Helper proteins called chaperones prevent this, giving the chain space to reach its correct shape. They don't supply the shape; that still comes from the sequence. Folding can also go badly wrong: prions are misfolded proteins that can make normal copies of the same protein misfold too, causing diseases such as mad cow disease.

Key terms

Amino acid

The monomer of proteins: a central carbon with an amino group, a carboxyl group, a hydrogen and an R group.

R group (side chain)

The variable part of an amino acid, which decides whether it's nonpolar, polar, acidic or basic.

Polypeptide

A chain of amino acids joined by peptide bonds.

Primary structure

The order of amino acids in a polypeptide.

Secondary structure

Local folding into α-helices and β-pleated sheets, held by backbone hydrogen bonds.

Tertiary structure

The overall 3-D shape of one polypeptide, held by R-group interactions.

Quaternary structure

The arrangement of several polypeptide subunits in one protein.

Disulfide bridge

A covalent S–S bond between the side chains of two cysteines.

Denaturation

Loss of a protein's folded shape (and function) without breaking its peptide bonds.

Chaperone

A protein that helps other proteins fold correctly by preventing them from clumping.

Check yourself

Try answering in your head before you open each answer.

• 1.Pepsin works in the stomach at about pH 2. What would you expect to happen to its activity if it were moved to the small intestine, at about pH 8, and why?Show answerHide

  Its activity would fall sharply. At the higher pH, acidic and basic side chains gain or lose H⁺, which changes their charges. Salt bridges and hydrogen bonds that held the active site in shape are disrupted, so the enzyme loses its shape and function.

• 2.A student heats an enzyme until it stops working, then says its peptide bonds must have broken. Design a simple test that could show whether the primary structure survived.Show answerHide

  Cool the enzyme slowly and see if some activity returns (as Anfinsen's ribonuclease regained activity once the chemicals were removed), or check the chain's length and sequence. If the chain is still full length, only the weak interactions of the fold were broken. For many proteins refolding fails because chains clump, so the length test is more reliable than the activity test.

• 3.An α-helix sits on the surface of a protein, with one face touching the hydrophobic core and the other face touching water. Predict which kinds of amino acid you'd find on each face.Show answerHide

  Nonpolar amino acids (such as leucine or valine) on the face toward the core, and polar or charged amino acids (such as serine, glutamate or lysine) on the face toward water. The helix itself is held by backbone hydrogen bonds; the R groups decide how it packs against the rest of the protein.