Basic Biology - Molecules of life - Proteins

Proteins have a complex 3D structure

Proteins are chains of 20 different types of amino acids, which in principle can be joined together in any linear order, sometimes called poly-peptide chains. This sequence of amino acids is known as the primary structure, and it can be represented as a string of 20 different symbols (i.e., a word over the common alphabet of 20 letters). Information about various protein sequences and the functional roles of the respective proteins, can be found in UniProtKB/Swiss-Prot database.

UniProtKB/Swiss-Prot is a joint project between the EBI and the Swiss Institute of Bioinformatics (SIB). The length of the protein molecule can vary from few to many thousands of amino-acids. For example insulin is a small protein and it consists of 51 amino acids, while titin has ~28,000 amino acids. Although the primary structure of a protein is linear, the molecule is not straight, and the sequence of the amino acids affects the folding.

There are two common substructures often seen within folded chains - alpha-helices and beta-strands. They are typically joined by less regular structures, called loops. These three are called secondary structure elements.

As the result of the folding, parts of a protein molecule chain come into contact with each other and various attractive or repulsive forces (hydrogen bonds, disulfide bridges, attractions between positive and negative charges, and hydrophobic and hydrophilic forces) between such parts cause the molecule to adopt a fixed relatively stable 3D structure. This is called tertiary structure. In many cases the 3D structure is quite compact.