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Amino Acids
Amino acid: a compound that contains
both an amino group and a carboxyl
group
Basicity (contd)
Guanidine Group
The side chain of arginine is a considerably stronger
base than an aliphatic amine
basicity of the guanido group is attributed to the large
resonance stabilization of the protonated form relative
to the neutral form
Imidazole Group
The side chain imidazole group of histidine is a
heterocyclic aromatic amine
Ionization vs pH
Given the value of pKa of each functional group, we
can calculate the ratio of each acid to its conjugate
base as a function of pH
Consider the ionization of an -COOH
COOH + H2 O
pK a = 2.00
COO
+ H3 O +
[ H 3 O + ] [ -COO - ]
[ -COO H]
or
[ -COO - ]
[ -COO H]
Ka
[ H 3 O+ ]
Ionization vs pH (contd)
substituting the value of Ka (1 x 10-2) for the hydrogen
ion concentration at pH 7.0 (1.0 x 10-7) gives
[ -COO - ]
[ -COO H]
Ka
[ H 3 O+ ]
1.00 x 10-2
= 1.00 x 105
1.00 x 10-7
Ionization vs pH (contd)
We can also calculate the ratio of acid to conjugate
base for an -NH3+ group; for this calculation,
assume a value 10.0 for pKa
N H 3
+ H2 O
pK a = 10.00
N H 2
+ H3 O +
[ -NH 3 + ]
Ka
[H 3 O+ ]
Ionization vs pH
substituting values for Ka of an -NH3+ group and
the hydrogen ion concentration at pH 7.0 gives
[ -NH 2 ]
Ka
=
+
[H 3 O+ ]
[ -NH 3 ]
1.00 x 10 -10
= 1.00 x 10 -3
1.00 x 10 -7
Henderson-Hasselbalch Equation
We have calculated the ratio of acid to conjugate
base for an -carboxyl group and an -amino group
at pH 7.0
We can do this for any weak acid and its conjugate
base at any pH using the Henderson-Hasselbalch
equation (Ch. 2)
[conjugate base]
pH = pK a + log
[weak acid]
Isoelectric pH
Isoelectric pH, pI: the pH at which the majority of molecules
of a compound in solution have no net charge
the pI for glycine, for example, falls midway between the pKa
values for the carboxyl and amino groups
pI = 1 ( p Ka COOH + p Ka N H3 + )
2
= 1 (2.35 + 9.78) = 6.06
2
Isoelectric pH values for the 20 protein-derived amino acids are
given in Table 3.2
Electrophoresis
Electrophoresis: the process of separating
compounds on the basis of their electric charge
electrophoresis of amino acids can be carried out
using paper, starch, agar, certain plastics, and
cellulose acetate as solid supports
in paper electrophoresis, a paper strip saturated with
an aqueous buffer of predetermined pH serves as a
bridge between two electrode vessels
Peptide Bonds
Individual amino acids
can be linked by forming
covalent bonds.
Peptide bond: the
special name given to
the amide bond between
the -carboxyl group of
one amino acid and the
-amino group of
another amino acid
Peptides
peptide:
peptide the name given to a short polymer of amino
acids joined by peptide bonds; they are classified by
the number of amino acids in the chain
dipeptide:
dipeptide a molecule containing two amino acids
joined by a peptide bond
tripeptide:
tripeptide a molecule containing three amino acids
joined by peptide bonds
polypeptide:
polypeptide a macromolecule containing many
amino acids joined by peptide bonds
protein:
protein a biological macromolecule of molecular
weight 5000 g/mol or greater, consisting of one or
more polypeptide chains