Levels of protein structure

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This unit uses the Jmol 3-D molecular visualisation applet.
The various levels of protein structure can also be visualised by reference to the other files on this site, especially hormone insulin, or to the oxygen storage compounds haemoglobin and myoglobin.

Primary structure 

Each 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 structure

The 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.
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!
The beta pleated sheet is another regular secondary structure, as seen in the protein fibroin in silk.

The molecular representations below can be moved around in 3 dimensions using the mouse, or modified using the buttons below.

The alpha helix

The beta pleated sheet

This shows a short section of  amino acids (10 alanines, actually) which have orientated themselves into a helix, so that >NH groups (blue+white) are in line with >C=O groups (grey+red) This graphic shows 3 layers of 5 differently coloured (fairly short) strands, forming a fairly compact sheet.

A more complex molecule: the enzyme amylase

Display options

show H bonds

trace chain

show backbone:
coloured by amino acids

secondary structure
in cartoon format
:a helices red, sheets gold

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Tertiary structure

The 3-dimensional structure of a protein's polypeptide chain or chains may be locked in place by other stronger bonds. These bonds are formed between components of  the -R groups of the amino acid residues. The types of bonds may include:

Quaternary structure

Not all proteins have a quaternary level of structure.

A protein with a quaternary structure consists of more than one practically identical sub-unit, not joined by strong bonds like those above.
A well known example is haemoglobin, which consists of 2 alpha and 2 beta chains, consisting of 141 and 146 amino acid residues respectively.
Many enzymes consist of  several sub-units, often as dimers (2 sub-units) and tetramers (4 sub-units) combined in this way.

Do not assume that quaternary means "composed of 4 sub-units" because haemoglobin is composed of 4 sub-units. It is the 4th level of  protein structure.

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