Let's talk about
the peptide bond. Now, proteins are
formed from the folding of polypeptide chains. And polypeptide
chains are formed by linking amino acids together. And these links are
called peptide bonds. So before we can work our way
up to the fully-formed and functional protein, we have
to start at the very beginning by forming a peptide bond
between the first two amino acids. So let's review the structure
of an amino acid really quickly. Here we have our backbone. We have our amino group,
our carboxylic acid group. Here is our alpha carbon. And then, the r
represents our side chain. Now, peptide bonds are
formed by the nucleophilic addition-elimination reaction
between the carboxyl group of one amino acid and the amino
group of another amino acid. So let me show you what
that looks like here. Let's have another amino
acid drawn right here. So the electron pair
on the amino group of the second amino
acid comes over to form a bond with the carbonyl
carbon of the first amino acid. You give off a water
molecule in the process, and then you get your
newly-formed dipeptide. And here is our
newly-formed peptide bond. Now, remember that a
peptide bond is just an amide bond that is formed
between two amino acids. And you should also
make note of the fact that this bond is a rigid
and planar bond that is stabilized by
resonance delocalization of this nitrogen's electrons
to this carbonyl oxygen. So we can draw that out here. Remember that there is
a lone pair of electrons on this nitrogen
that can move here. And then, these electrons will
move to this oxygen atom, which also has its own two
lone pairs of electrons. So it can also be
represented like this. And we'll have the
formation of a double bond here and then an extra lone
pair on the oxygen atom. So as you can see,
the peptide bond with this resonance
delocalization of electrons has a lot of double
bond character. And because of this
double-bond-like character, the peptide bond is a
very rigid and planar one. But don't confuse
this with thinking that an entire polypeptide chain
would be a rigid-like structure because-- even
though there isn't much rotation about the
peptide bond-- you do still have for free rotation about
these alpha carbon atoms here. So now, here we can see
we have a dipeptide. And if we kept adding amino
acids along in a chain here, we would have a polypeptide. Now, if we take a closer look
at the backbone of this chain, we can see that there
is a pattern formed by the atoms that
form this backbone. And here, you have a nitrogen
atom, the alpha carbon, and a carbonyl carbon. And then, it repeats
with the nitrogen atom, the alpha carbon, and
a carbonyl carbon. And you get a pattern
that looks like this. And each time you
add a new amino acid, the pattern just repeats. So that, whatever length
of your polypeptide chain, you always start out
with a nitrogen atom and you always end with
the carbonyl carbon. And so this end of the backbone
of the polypeptide chain is called the amino
or N terminal. And then, this end of
a polypeptide chain is called the C terminal. And then once, within
a polypeptide chain, each amino acid is
called a residue. So that's the formation
of a peptide bond and a polypeptide chain. So now how do we go about
breaking this peptide bond to get two amino acids again? Let's give ourselves just
a little bit more room here to work, and we'll redraw a
bond between two amino acids as a peptide bond here. And remember that here is
our peptide bond-- just to highlight it for you. And we can break
this peptide bond in a process called hydrolysis. So if we have hydrolysis
of this peptide bond, then we go back to forming
two free amino acids. The hydrolysis of a peptide
bond is helped along by two common means,
and those two means are with the help
of strong acids or with proteolytic enzymes. So when we use strong acids,
we call this acid hydrolysis. And acid hydrolysis,
when combined with heat, is a nonspecific way of
cleaving peptide bonds. So say you have a long
polypeptide chain. And then, you throw
this polypeptide into a pot with
some strong acid, and then turn up the stove
to add a little heat. Then, you would just end up with
a jumbled up mix of amino acids as each of the peptide
bonds gets cleaved. So the other way of
cleaving a peptide bond is with proteolysis. And proteolysis is
a specific cleavage of the peptide bond with the
help of a special protein, an enzyme called a protease. So unlike acid hydrolysis,
proteolytic cleavage is a specific process. And you can choose
which peptide bonds you cleave because proteases are
pretty picky about where they will cut, and many
of them will only cleave peptide bonds between
certain specific amino acids. One example of this is
with the protease trypsin. Trypsin only cleaves
on the carboxyl side of basic amino acids,
like arginine and lysine. And interestingly,
this is the same enzyme that is produced by our
pancreas to help us digest food. So now say we have the
following polypeptide chain-- and it can be any old,
arbitrary polypeptide chain-- and say we add trypsin
to the environment that this polypeptide
chain is in. And here I'm just
representing the amino acids as their abbreviated form. Now with the
addition of trypsin, where would this polypeptide
chain be cleaved? Well, remember that
trypsin cleaves on the C terminus of
arginine and lysine. Here we have an
arginine, and this would be considered the
C terminal of arginine, since it's closest
to the C terminal of the polypeptide chain. So we would get cleavage here. And then, likewise,
we would have cleavage on the C terminal
of this lysine residue here. And so with this particular
polypeptide chain, you would end up with
three different fragments after the addition
of trypsin since it cleaves in these
very specific places. And there are many other
examples of specific proteases that cleave in at certain
parts of polypeptide chains. And you probably
don't really need to memorize which proteases
cleave after which amino acids, but you should probably
remember that they are just specific means of
breaking a peptide bond-- unlike acid hydrolysis
over here, which is a very nonspecific way
of cleaving a peptide bond.