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Proteins are an extremely important type of molecule, making up everything from your nails to the haemoglobin that carries oxygen in the blood. Proteins are very important and can be quite complicated in structure.

The Monomer: Amino Acids

For a more detailed look at amino acids, see the chemistry page amino acids.

A protein, put simply, is a special type of polymer. And the monomer of it is the amino acid. An amino acid's structure varies depending on the conditions it is in. The first image shows the amino acid as it is in crystallised form. And the image below is how it appears in nature as a zwitterion.

diagram of the amino acid

The amino acid is made up of three parts, as identified on the image. The charge of the amino acid changes depending on pH.

Low pH.An extra hydrogen on the N so it is positive.
Neutral pH.A zwitterion (both positive and negative parts).
High pH.A hydrogen is lost from the OH so it is negative.

The R-group means any molecule can replace the 'R' for instance glycine simply has an -H instead and alanine a -CH3. This is how there is so much variation in amino acids. In total there are 22 different R-groups, each with a different three letter abreviation to represent it (Asn, Glu). Different amino acids are chosen in protein synthesis.


When a number of amino acids join up they are called polypeptides. Two polypeptides are called a dipeptide, three are called a tripeptide.

Amino acids form by a condensation reaction (as carbohydrates do) producing water as a product and then make a peptide bond. The below image shows graphically how this happens.

peptide bond

Protein Structure

The structure of the protein can be divided into several different levels: primary, secondary, tertiary and quaternary. Below we go through each step-by-step.

The primary structure of the protein relates to the sequence of amino acids so isn't really the protein structure since it does not naturally stay as merely a chain of amino acids. The primary structure can also be known as the protein sequence.

The secondary structure is the most basic level of protein folding. It is made by hydrogen bonds between the carboxyl groups. There are two main types of structure formed. The first is the alpha helix this is a twirling structure like DNA. The second is the beta sheet which looks like the following:

a beta sheet, proteins

The protein's teritary structure is it's overall 3D shape and involves the R-groups as well. It is made by weak hydrogen bonds, ionic bonds (which are quite strong) and disulphide bridges (between two sulphur atoms, very strong). This is involved in creating the shape of the active site in enzymes.

And finally there is the quaternary structure this is where multiple proteins come together to make what appears to be a big mess, but which nonetheless is very important. For example haemoglobin which must have a particular shape so the iron ions can pick up oxygen to carry around the blood stream.

Structure to Function

A globular protein is a bit like a ball (e.g. haemoglobin and immunoglobin) these are used for transport, are enzymes and in membranes; since they are fluid (i.e. they can move).

A fiborous protein is long and thin, like a strand or fibre (hence the name) like myosin and cologen which make muscle and bone. These types of protein tend to be structual.

Updated: 16 May 2011