Proteins

Proteins and amino acids

Proteins

Proteins are large sized molecules (macromolecules). Proteins are made up of polymers of structural units called 'amino acids'. A total of 20 different amino acids exist in proteins of animal and plants. Recently selenocysteine and pyrrolysine have been identified as 21st and 22nd amino acid from the methanogenic Archaea (Rother and Krzyck, 2010). These two unusual amino acids are involved in the proteins required in menthanogenesis. RUBISCO (ribulose bisphosphate carboxylase/oxygenase) is the most abundant protein on earth.
Proteins are involved in every aspect of cellular life. Proteins perform following functions in living organisms.
  • Proteins transport various materials across the biological membranes.
  • In the form of enzymes, proteins catalyze biochemical reactions.
  • Histone proteins are involved in the condensation of DNA into chromosomes.
  • Proteins support the movement of materials within (intracellular trafficking).
  • Proteins drive the movement of entire cells.
Structurally proteins are linear heteropolymers of amino acids. A linear chain of amino acids folds into a particular three-dimensional conformation determined by the sequence of the amino acids in the chain.

Amino acids

Amino acids are the “building blocks” for proteins. They are synthesized on the mRNA by triplet codons. Each amino residue joined to its neighboring amino acid by peptide bond (a covalent bond) to form protein. All the amino acids share basic common properties. They have following components covalently joined to the α carbon.
  1. A carboxyl group (COOH)
  2. An amino group (NH2)
  3. H-atom, and
  4. A variable side chain (R group)
All the amino acids differ from each other at the variable side chain. Glycine being simplest amino acid contains H atom as side chain.

Classification of amino acids

Amino acids can be grouped according to their R group:
  • Neutral amino acid: containing single COOH and NH2.
    (e.g. glycine, alanine, valine)
  • Acidic amino acid: with extra COOH group.
    (e.g. Glutamic acid, Aspartic acid)
  • Basic amino acid: with extra NH2 group.
    (e.g. Lysine, Arginine)
  • Sulfur containing amino acid: contain S in side chain.
    (e.g. Cysteine, methionine)
  • Aromatic amino acid: containing cyclic ring structure.
    (e.g. Phenylalanine, tryptophan, tyrosine)

Peptide bond

Carboxyl group of one amino acid joined to the NH2 group of neighboring amino acid through a substituted amide linkage, so called, peptide bond to yield dipeptide. Thus, total number of peptide bonds in 'n' amino acid is 'n-1'. Peptide bond is formed by the removal of the water molecule. Hence the process may be called as dehydration of condensation reaction.
It is the peptide bond, which determines various level of organization to produce protein.

Primary structure of proteins

Primary structure of protein consists of polypeptide chain. A polypeptide is the chain of amino acids joined by peptide bonds. Amino acids in polypeptide chain are conventionally called as amino acid 'residues'. The sequence of amino acid in polypeptide chain constitute primary structure of proteins.
It the sequence of amino acid in polypeptide chain, which determines the higher level of organization in proteins.

Secondary structure of proteins

Secondary structure refers to the local conformation of some part of a polypeptide.
The most prominent secondary structures are:
  • Alpha helix (α-helix)
  • Beta sheets (β-sheet)

Alpha helix (α-helix)

α-helices are stabilized by intrachain H- bonding, wherein the H of amino group combines with O carboxyl group at every 13th atom. It is because of intrachain H- bonding, polypeptide is twisted or coiled to form a helical structure. In this α-helix:
  • Distance (rise) between each turn (360°) of the coil is 5.4 Ã….
  • There are 3.6 amino acids per turn.
  • Distance adjacent two amino acid is therefore 1.5 Ã….
  • The ‘R’ groups are seen protruding out of the helix.
Pure α-helix structure is seen in hair protein, i.e., keratin.

Beta sheets (β-sheet)

When two or more polypeptide chains are lineup side by side, interchain H- bonds are formed between H of amino and O of carboxyl group, which stabilized the β-sheet. In β-sheets:
  • Amino acids are fully extended.
  • Distance between adjacent amino acid is 3.5 Ã….
  • The strands are either arranged in parallel or anti-parallel.
  • Anti parallel sheet is more stable because of fully co-linear H-bond.

Tertiary structure of proteins

Tertiary structures are the 3D conformation of the polypeptide chain. These are stabilized by following covalent and non-covalent interactions.
  • Hydrophobic interactions
  • Electrostatic interactions
  • Hydrogen bonds
  • van der Waals force of interaction
  • Covalent bond
    • Disulfide bridges
Tertiary structures are also referred as 'domains'.

References

First published on 13-04-2021
Last updated on 13-04-2021

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