The four levels of protein structure
Primary structureEach protein is built up from a set number of amino acids, joined and shaped in a particular way.
There are 20 different types of amino acids, so for a simple dipeptide there are 400 possible combinations; 8000 combinations for a tripeptide.
Clearly the number of possible combinations is almost infinite when larger numbers of amino acids are combined to form a polypeptide.
The primary level of protein structure is not just the number and identity of the component amino acids in the protein, but the order or sequence in which the specific amino acids are combined (by condensation, forming peptide bonds) in the polypeptide chain.
Secondary structureThe polypeptide chain can fold back on itself in a number of ways. Each bond in the backbone formed by alternating amino acid central carbons and -CONH - peptide linkages can rotate completely, and so a number of shapes are possible.
It will become stabilised in a position where >NH groups (from the peptide bonds) become close enough to form hydrogen bonds with >C=O groups on another peptide bond, in another chain, or further along in the same chain.
Often, these weak interactions between several successive amino acid residues result in a coiled (helical) structure.
The usual way in which the polypeptide chain is coiled is called the alpha helix, in which interactions take place between groups 3 - 4 amino acid residues apart. Some amino acids put a kink or bend in these regions of helical structure, allowing the chain to bend back on itself and form a more globular molecular structure.
Sections of alpha-helix are often seen in larger molecules, amongst other sections of polypeptide chain which are not so ordered. Some short proteins are practically all arranged as an alpha helix. An example is glucagon.
Do not get the alpha helix confused with the double helix of DNA, or the helix formed in sections of carbohydrate molecules (e.g. amylose, amylopectin, glycogen). And do not confuse it with alpha 1,4 and 1,6 glycosidic bonds formed in those compounds!
Other types of helical structure are sometimes seen in proteins.
The beta pleated sheet is another regular secondary structure, as seen in the protein fibroin in silk, which is composed of polypeptides - long chains of amino acids - running alongside one another.
These amino acids - mostly glycine, alanine and serine - have small R groups so the side chains fit together easily and allow many long straight parallel fibres to be formed, each facing in the opposite direction to the ones above and below.
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