Proteins

Proteins are biomacromolecules present in all organisms and have a large variety of functions. Proteins are linear chains of L-α-amino acids (Figure 9). There are 22 different amino acids that can be directly encoded for by naturally occurring genetic code.

Structure of an alpha amino acid
Figure 9 Structure of an alpha amino acid;  R represents amino-acid-specific side-chain, that is attached to the α–carbon; each side chain has different physico-chemical properties that can be exploited by proteins to perform different roles (image from Wikipedia.

To be able to perform their biological function, proteins fold into specific spatial conformations. The formation of binding pockets and local 3D structures allow proteins to create different chemical environments through which they can specifically interact with other biomacromolecules, small molecules or water. Examples of the interacting partners are: substrates, metal ions, prosthetic groups, cofactors and coenzymes.

Reversible structural changes, which create alternative structures of the same protein are referred to as different conformers. The transitions between them are called conformational changes.

Examples protein functions include:

  • Structural: offering stiffness and rigidity to fluid biological components
    • Collagen is the most abundant structural protein in mammals and forms a triple helix
  • Catalysis of chemical reactions as enzymes
    • Only a small region of an enzyme called the active site binds the substrate and contains the catalytic residues
    • Trypsin, found in the digestive system, hydrolyses proteins
  • Receptors: they usually have a ligand-binding site on the cell surface and an effector domain within the cell, which may have enzymatic activity or may undergo a conformational change
  • Channels for molecules to pass through the cell membrane, for example the potassium channel
  • Transport: proteins that bind small molecules and transport them to other locations in the cell or organism