Proteins – Primary & Secondary Structures

As mentioned a couple of posts ago:

  • Proteins are polypeptides made from 20 different monomers.
  • On average contain 100-400 monomers.
  • Each monomer has an approximate molecular mass of 110.

– Monomers –> Polymers. The Primary Structure.

  • Amino Acids form peptide bonds (from the carboxylic acid group on one to the amine group on another). This releases water in a condensation reaction. The location of the peptide bond (C-N) is shown below outlined in RED.
  • When reading a sequence of Amino Acids in a protein, start at the Amino terminus (NH2 end) and read to the Carboxyl terminus at the other (COOH).
  • The sequence of amino acids is known as the primary structure of a protein.

The amino acids in chains and proteins can be post-translationally modified – eg, disulphide bridges can form between cysteine residues.

– The Secondary Structure

Assuming the following:

  1. No rotation occurs round the peptide bond (as it is partly double bonded in nature).
  2. The chain of amino acids form a rhythmical structure – forming a repeating pattern.
  3. That the maximum number of interactions from Hydrogen bonding possible are occuring, independant of the type of residue (amino acid).

Now to explain these points:

  1. As mentioned, the C-N bond is partly double bonded and so does not rotate. The bond length of a normal C-N bond is 1.49Å (angstroms, click here for more info), while the length of a normal C=N bond is 1.28Å. The length of the peptide bond is between these, at 1.28Å.
    This is due to the C-N bond resonating between single and double bonded forms, as shown above.
  2. Two different folding points exist. These are called phi and psi. A perfect helix structure (covered later) needs both phi (Φ) and psi (Ψ) to be at an angle of about -60 degrees.
  3. Hydrogen bonds occur between the C=O and H-N of other amino acids. In α helixes, the C=O: would form a hydrogen bond to the N-H 4 residues ahead in the spiral (directly above).

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