Chapter Three

Amino Acids and Peptides

Amino Acids
Amino acid: a compound that contains
both an amino group and a carboxyl
group

-Amino acid has an amino group

attached to the carbon adjacent to
the carboxyl group
-carbon also bound to side chain
group, R
R gives identity to amino acid
Two steroisomers of amino acids
are designated L- or D-. Based on
similarity to glyceraldehdye
(Figure 3.2)

Amino Acid Structure and Properties

With the exception of glycine, all protein-derived
amino acids have at least one stereocenter (the carbon) and are chiral (stereoisomers)
the vast majority of -amino acids have the Lconfiguration at the -carbon (Proline is usually D)

Side-chain carbons in other amino acids designated

with Greek symbols, starting at a carbon (etc)
Amino acids can be referred to by three-letter or oneletter codes. Table 3.1 (KNOW THESE)

Individual Amino Acids

Group A: Nonpolar side chains- Ala, Val, Leu, Ile,
Pro. Phe, Trp, Met.
Ala, Val, Leu, Ile, Pro- contain aliphatic hydrocarbon
group. Pro has cyclic structure.
Phe- hydrocarbon aromatic ring.
Trp- Indole ring side chain, aromatic.
Met- Sulfur atom in side chain.

Amino Acids (contd)

Group B: Neutral Polar side chains- Ser, Thr, Tyr,
Cys, Glu, Asn
Ser, Thr- Side chain is polar hydroxyl group
Tyr- hydroxyl group bonded to aromatic hydrocarbon
group
Cys- Side chain contains thiol group (-SH)
Gln, Asn- contain amide bonds in side chain

Amino Acids (contd)

Group C: Acidic Side Chains: Glu, Asp
Both have a carboxyl group in side chain
Can lose a proton, forming a carboxylate ion
These amino acids are negatively charged at neutral
pH

Amino Acids (contd)

Group D: Basic side chains: His, Lys, Arg
Side chains are positively charged at pH 7
Arg-side chain is a guanidino group
His-side chain is an imidazole group
Lys-side chain NH3 group is attached to an aliphatic
hydrocarbon chain

Amino acid summary

Important structural features:
1. All 20 are -amino acids
2. For 19 of the 20, the -amino group is primary; for proline,
it is secondary
3. With the exception of glycine, the -carbon of each is a
stereocenter
4. Isoleucine and threonine contain a second stereocenter
5. 3, and 1-letter codes in Table 3.1.

Uncommon Amino Acids

Each derived from
a common amino
acid by a
modification
hydroxylysine and
hydroxyproline are
found only in a
few connective
tissues
such as collagen
thyroxine is found
only in the thyroid
gland

Ionization of Amino Acids

In amino acid, carboxyl group (-) and amino group (+) are
charged at neutral pH.
In free amino acids -carboxyl, and a-amino groups have
titratable protons. Some side chains do as well

Ionization of Amino Acids

Remember, amino acids without charged groups on side chain
exist in neutral solution as zwitterions with no net charge

Titration of Amino Acids

When an amino acid is titrated, the titration curve represents the reaction of
each functional group with the hydroxide ion

Titration of alanine with NaOH

Titration of histidine with NaOH

Acidity: -COOH Groups

The average pKa of an -carboxyl group is 2.19,
which makes them considerably stronger acids than
acetic acid (pKa 4.76)
the greater acidity of the amino acid carboxyl group is
due to the electron-withdrawing inductive effect of the NH3+ group

Basicity: -NH3+ groups

The average value of pKa for an -NH3+ group is
9.47, compared with a value of 10.76 for a 2
alkylammonium ion

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 +

writing the acid ionization constant and rearranging

terms gives (remember Ch. 2)
Ka =

[ 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

at pH 7.0, the -carboxyl group is virtually 100% in

the ionized or conjugate base form, and has a net
charge of -1
we can repeat this calculation at any pH and
determine the ratio of [-COO-] to [-COOH] and the
net charge on the -carboxyl at that pH

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 +

writing the acid ionization constant and rearranging

gives
[ -NH ]
2

[ -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

at pH 7.0, the ratio of -NH2 to -NH3 + is

approximately 1 to 1000
at this pH, an -amino group is 99.9% in the acid
or protonated form and has a charge of +1

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

Geometry of Peptide Bond

the four atoms of a peptide bond and the two alpha
carbons joined to it lie in a plane with bond angles of
120 about C and N
to account for this geometry, a peptide bond is most
accurately represented as a hybrid of two contributing
structures (resonance structures)
the hybrid has considerable C-N double bond
character and rotation about the peptide bond is
restricted
See Figure 3.10

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

Peptides with Physiological Activity

Peptides with Physiological Activity (contd)