The primary structure of a protein

The primary structure of a protein is the sequence of amino acids in its polypeptide chain: which amino acids it has, and in what order. The amino acids are joined by peptide bonds, made in condensation reactions. The primary structure matters because it decides everything else: how the chain folds, the protein's 3D shape and so its job. Change one amino acid and the whole protein can stop working.

What is the primary structure of a protein?

OpenStax defines it in one line: the unique sequence of amino acids in a polypeptide chain is its primary structure. A protein made of one chain has one primary structure; one made of several chains, such as insulin, has a sequence for each.

Amino acids are often written with three-letter abbreviations, as in the diagram, which shows an example sequence. Every chain has a free amino group at one end (the N-terminus) and a free carboxyl group at the other (the C-terminus), so a sequence is always read in one direction.

Amino acids: the monomers

AQA's A-level specification describes amino acids as the monomers proteins are made from. Each has a central carbon atom bonded to four things:

AQA notes that the twenty amino acids common in all organisms differ only in their side group. The R groups give each amino acid its character: some are charged, some are polar and some are non-polar, and cysteine's contains a sulfur atom.

Peptide bonds and condensation

Two amino acids join when the carboxyl group of one reacts with the amine group of the next. A molecule of water is removed, so it is a condensation reaction, and the new bond between the carbon of one and the nitrogen of the next is a peptide bond. AQA's terms: two amino acids make a dipeptide; many make a polypeptide. Breaking a peptide bond needs water added back, which is hydrolysis.

amino acid + amino acid → dipeptide + water

Where the sequence comes from

The primary structure is set by a gene. AQA defines a gene as a base sequence of DNA that codes for the amino acid sequence of a polypeptide, with each triplet of three bases coding for one amino acid. During protein synthesis, the base sequence is copied into mRNA and translated, codon by codon, into a chain of amino acids. Try it in the DNA Translator, or see the codon chart guide.

How primary structure decides the shape

AQA asks you to relate the primary, secondary, tertiary and quaternary structure of proteins to their function. Each level is built on the one before:

Because the bonds in the tertiary structure form between R groups, the position of each amino acid in the sequence decides where the chain folds and what it bonds to. Disulfide bridges, for example, only form between cysteines, so where the cysteines sit in the sequence matters. OpenStax notes that disulfide bonds are the only covalent bonds that form as the protein folds. That is why an enzyme's active site, or an antibody's binding site, depends on the primary structure. See enzymes and antibodies.

Haemoglobin is AQA's example of a protein with a quaternary structure. OpenStax describes it as four chains, two α and two β, each about 150 amino acids long.

When the primary structure changes

A mutation in a gene can change one amino acid in the primary structure, and that can change the protein's shape. OpenStax gives sickle cell anaemia as the example: in the β chain of haemoglobin, the amino acid at position six is normally glutamate (glutamic acid), and in sickle cell haemoglobin it is replaced by valine. One change in a chain of 147 amino acids alters how the haemoglobin molecules behave.

Not every change matters. Because the genetic code is degenerate, some mutations don't change the amino acid at all, and a change to a similar amino acid away from the active site may have little effect. Name the kind of mutation, then press Mark to check it in the genetics course.

Denaturation doesn't change the primary structure

Heat, a change in pH or some chemicals can break the hydrogen and ionic bonds that hold a protein's shape. OpenStax describes this as denaturation: the protein loses its shape without losing its primary sequence. The peptide bonds stay intact, which is a useful point to make in exam answers about enzymes.

Worked examples

Example 1: counting peptide bonds in insulin

OpenStax describes insulin as two chains: an A chain of 21 amino acids and a B chain of 30, linked by disulfide bonds. How many peptide bonds does it have, and how many water molecules were removed making them?

1. A chain of n amino acids has n − 1 peptide bonds between them.
2. A chain: 21 − 1 = 20. B chain: 30 − 1 = 29.
3. Total: 20 + 29 = 49 peptide bonds, and one water molecule was removed for each, so 49 water molecules.
4. The disulfide bonds joining the chains are not peptide bonds, so they aren't counted.

Example 2: how many sequences are possible?

With 20 amino acids to choose from at each position, a chain of 3 amino acids can have 20 × 20 × 20 = 20³ = 8000 different primary structures. A chain of just 10 has 20¹⁰, about 1.0 × 10¹³. That huge number of possible sequences is why proteins can have so many different shapes and jobs.

Common mistakes

• Saying the primary structure is the shape. It is the sequence; the shape comes from the secondary and tertiary structure.
• Saying hydrogen bonds hold the primary structure. Peptide bonds do. Hydrogen bonds belong to the higher levels.
• Forgetting the water. Forming a peptide bond releases water; breaking one by hydrolysis uses water.
• Counting peptide bonds as the number of amino acids. It is one fewer per chain.
• Saying denaturing breaks peptide bonds. It breaks the bonds holding the shape; the sequence is unchanged.
• "Different R groups" without saying why it matters. Link the R groups to the bonds they form and so to the shape.

Proteins are in the first year of A-level Biology, so practise them on today's A-level Biology: Year 1 short timed paper. The biuret test for proteins is covered in food tests, and the sugar equivalent of the peptide bond in disaccharides.

Read next

Biology · Biological moleculesStarch, glycogen and cellulose: structure and functionThe structure of starch, glycogen and cellulose: alpha and beta glucose, glycosidic bonds, branching, microfibrils, and how each fits its function.