Skip to main content
Chemistry LibreTexts

20.11: Polypeptide Chains

  • Page ID
    49620
  • [ "article:topic", "ChemPrime", "alpha carbon", "peptide bond", "authorname:chemprime", "showtoc:no" ]

    The backbone of any protein molecule is a polypeptide chain obtained by the condensation of a large number of amino acids with the elimination of water. You will recall that the amino acids are bifunctional organic nitrogen compounds containing an acid group, —COOH, and an amine group, —NH2. The amine group is attached to the carbon atom adjacent to the —COOH (the α carbon atom). The three simplest amino acids are

    Figure \(\PageIndex{1}\) Rotatable Jmol representations for three amino acids.

     

    In practice, though, these acids are usually in the form of their zwitterions, and we should write them

     

    Figure  \(\PageIndex{2}\) Zwitterionic forms of 3 amino acids.

    If these three amino acids are now condensed, water is eliminated and a simple polypeptide contaning three amino acids is obtained:

       Figure  \(\PageIndex{3}\)

    The two CO—NH bonds produced by this reaction are called peptide bonds. Notice that the peptide bond is an amide linkage. An important feature of such a peptide bond is that it is planar. This is because of the existence of two resonance structures

    In the second of these structures, there is a double bond between the carbon and the nitrogen atoms but no lone pairs around either atom. This insures that all the bonds involving the C and N atoms must lie in the same plane. The planarity of the peptide bond places considerable constraint on the conformations available to a polypeptide chain. Rotation can only occur around the single bonds involving the α carbon atoms. That is, the gray shaded areas in the polypeptide chain of Figure  \(\PageIndex{3}\) can twist relative to one another, but they must remain planar. This limitation offers important constraints which can greatly aid analysis of protein structure and of the conformations available for different polypeptide chains.

    Another important aspect of the peptide bond is the opportunity it provides for hydrogen bonding. The oxygen on the carbonyl group can bond to the hydrogen on an   group further along the chain:

    Such a bond is somewhat stronger than a normal hydrogen bond because of the partially negative character of the oxygen atom and the partially positive character of the nitrogen atom conferred by resonance structure II.

     

    Contributors