GCSE OCR Gateway Organic Chemistry C6.2h The Structure of Protein

C6.2h  To be able to recall that DNA is a polymer made from four different monomers called nucleotides and that other important naturally-occurring polymers are based on sugars and amino-acids

Naturally occurring polymers based on amino acids: Proteins

Proteins are amino acid condensation polymers.

Amino acids are the monomers of protein.

But what is an amino acid?

Amino acids contain two functional groups—an amino group —NH₂ and a carboxylic acid group —COOH

Structurally they look like this:

The group I have designated R— , the side chain, varies according to the amino acid.

Here are some examples of different amino acid side chains with different R— groups.

Note the abbreviations for each amino acid.

How do amino acids form protein?

The amino acids form protein using a condensation reaction.

The amino group and the carboxylic acid group combine to lose water and form a new type of link between the molecular residues.

The new type of link is called a peptide link (—CONH—) highlighted in green. It is also the link between molecular residues in different synthetic nylons.

This picture shows also how to write a protein structure.  By convention start with the nitrogen atom of one amino acid on the left and finish with the carbon atom of the carboxylic acid group on the right.

The different amino acids bond to each other to form a polymer or primary structure of amino acid residues.  This is just a chain of amino acid residues.

But protein formation doesn’t stop there.

Protein chains have a habit of folding up naturally and spontaneously into their lowest energy state.  These are called secondary structures.  There are two main types: α helices and β pleated sheets.  Sometimes these are colloquially called struts and plates.

Alpha helix:

Beta pleated sheet

Struts and plates form the secondary structure of most proteins.  They are held in place using different internal bonds that form between the amino acid side chains.  These bonds might be ionic, hydrogen or special disulphide bridges.

But the folding and conformations of proteins doesn’t stop there either.  Large proteins can form tertiary structures such as globules or coils or tubes.  And some go even further to form huge quaternary structures.  In the example of PCNA below we can see all four types of structure.