Automatic functional annotation of predicted active sites - European ...

Chapter 1
Introduction
1.1 Proteins and functional sites
The genomic information encodes the blueprint to build an organism. The decoding and
implementation of genetic information depends on the functions of the proteins. Each protein
is the result of transcribing a gene into mRNA, which is translated into a polypeptide.
Hence, a protein is a gene product. The elementary units of a protein are the 20 natural
standard amino acids, each with four invariant parts: a central chiral alpha carbon
(Cα), an amine group (NH2), a carboxylic acid group (COOH), hydrogen (H), and a
characteristic side chain (R). Apart from the invariant amine and carboxylic acid group,
which gives every amino acid the property of a zwitterion, distinctive physicochemical
properties are defined by the side chain group. These can be polar, acidic/basic, aromatic,
bulky, conformational flexible, contain cross-linking ability, show hydrogen-bond
capability, or chemical reactivity. Figure 1.1 lists all the standard amino acids and their
common classification on the basis of the nature of the side chain group.
During biosynthesis, ribosomes catalyses the polymerisation of amino acids through
condensation and form peptide bonds between the NH2 and COOH groups of two consecutive
amino acids. The backbone (main chain) of the resulting polypeptide is the repeating
sequence of NH2-C-CO-[NH-C-CO] n -NH-C-CO. This is the primary structure of a protein
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