Proteins are chains of amino acids, and these chains have an
Nitrogen-terminus and a Carbon-terminus. The Nitrogen-terminus is
the end of the protein that has a nitrogen, which is available for
bonding with a free carbon of another amino acid. The
carbon-terminus is the end of the protein that has a carbon which
is available to bond with a free nitrogen of another amino
acid.
Trypsin can cleave a bond between argininel and another amino
acid or lysine and another amino acid. The reason why the
N-terminus and C-terminus is important is because enzymes either
N-terminus specific or C-terminus specific. Trypsin, for example
will cleave bonds between arginin or lysine and the amino acid it
is bonded closes to the C-terminus side (see below).
(N-terminus) Alanine--Lysine--Glycine (C-terminus) ---->
Alanine--Lysine + Glycine
In this example trypsin hydrolyzed the bond between lysine and
glycine, which was the bond on the C-terminus end. It would not
effect the bond with alanine because it is on the N-terminus
side.
