The subunits of a protein are amino acids or to
be precise amino acid residues. An amino acid
consists of a central carbon atom (the alpha Carbon Calpha)
and an amino group (NH2), a hydrogen atom (H), a carboxy group (COOH)
and a side chain (R) which are bound to the Calpha.
Different side chains (Ri) make up different amino acids with different
physico-chemical properties. Proteins are made out of 20 amino acids
(there is a list with corresponding three- and one-lettercodes in the section
on Biological Preliminaries.
A peptide bond is formed via covalent binding of the Carbon atom of the Carboxy group
of one amino acid to the nitrogen atom of the amino group of another amino acid
Figure 1: Peptide bond linking two amino acids
A polypeptide chain is a chain of amino acid residues
linked together by peptide bonds.
The backbone of the polypeptide is given by the repeated sequence
of three atoms of each residue in the chain:
the amide N, the alpha Carbon Calpha and the Carbonyl C.
Rotations in the chain take place about the bonds in the backbone, whereat
the peptide bond usually is unflexible (see Figure 2).
The existence of an amino group (N-Terminal) at one end of the chain
and a carboxy group (C-Terminal) at the other end designs a direction
to the chain. Conventionally the beginning of a polypetide is its N-Terminal.
Figure 2: Torsion (or dihedral) angles of the backbone
A protein is a naturally occuring polypeptide with a definite 3-dimensional structure.
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