The Peptide Bond

We touched on the idea of peptides in the last couple of articles about amino acids but what are they and how do we make them?

Peptides

A peptide is a short string of amino acids joined together by peptide bonds. Peptides range in size from two (dipeptide) to three (tripeptide) amino acids strung together and beyond. When the number of amino acids in a peptide is less than 20 we call them oligopeptides and polypeptides when there are more than 20 amino acids.

The peptide bond forms between the carboxyl end of one amino acid and the amino end of another leaving a free amine group on one end of the peptide and a free carboxyl group on the other. We call these free ends the N-terminus and C-terminus respectively.

In cells peptide bonds are created during translation when mRNA is used as a template by ribosomes to generate proteins.

Peptide Notation

By convention, the N-terminus will always be shown first, and the C-terminus last. This carries forward for each of the amino acids present as well. So the peptide GLKDYE has an N-terminus that starts with a glycine (G) residue and ends with glutamate (E) on its C-terminus. While tyrosine (Y) is connected to aspartate (D) on its N side and to glutamate (E) on its C side.

Peptide Bond Formation

As with many biologically relevant synthesis reactions the bond occurs as a result of a dehydration reaction wherein a water molecule is lost while forming the peptide bond. We will continue to see this reaction type occur throughout our biochemistry review so keep an eye out for the similarities and differences between those reactions and peptide bond formation.

Since a peptide bond is just a fancy amide bond it experiences resonance as any other amide, carboxylic acid, or other carboxylic acid derivative would.

This imparts partial double bond character to the peptide bond making them especially stable and rigid. Meaning the bonds between individual amino acids are unable to rotate and will form fairly consistent structures and conformation as we will see when discussing protein structure in later topics.

Peptide Bond Destruction

While peptide bonds are especially stable it is important that our cells have a mechanism for breaking them down. After all, if we couldn’t breakdown peptides our cells would fill up with junk proteins. Not to mention the protein in chicken or any other food would be completely useless to our bodies.

In order to break the peptide bonds holding amino acids together, we have to reverse the reaction that creating them. So instead of removing water from the bond, we will be adding it in a process called hydrolysis. Hydrolysis is another common reaction within biochemistry and is the breaking apart of one molecule by the addition of water.

Specifically, hydrolytic enzymes such as trypsin and chymotrypsin are required to catalyze the cleavage of peptides into their amino acid components. When we discuss digestion later on we will touch on this process and look at how proteins are broken down and digested. Now let’s turn toward exploring really, really big peptides known as proteins.