Mary K. Campbell
Shawn O. Farrell
http://academic.cengage.com/chemistry/campbell
Chapter Three
Amino Acids and Peptides
Paul D. Adams University of Arkansas
Amino Acids
• Amino acid: a compound that contains
both an ____________ ____________
and a ____________ ____________
• -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 ____________, all proteinderived amino acids have at least one ____________
(the -carbon) and are ____________
(stereoisomers)
• the vast majority of -amino acids have the ________
-configuration at the -carbon (Proline is usually ___)
• 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: __________ 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 (cont’d)
• Group B: _______ _______ 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 (cont’d)
•
•
•
•
Group C: ____________ 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 (cont’d)
•
•
•
•
•
Group D: ___________ 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 ________;
for proline, it is __________
3. With the exception of ___________, the -carbon
of each is a stereocenter
4. ____________ and ____________ 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
• ___________ and
___________ are
found in only a
few connective
tissues such as
collagen
• ________ is found
only in the thyroid
gland
Ionization of Amino Acids
• In amino acids, carboxyl group (-) and amino group (+) are
________________ at neutral pH.
• In free amino acids -carboxyl, and a-amino groups have
________________ 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 _____________ 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 _________ ____________ ____________
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 (cont’d)
Guanidine Group
• The side chain of arginine is a considerably stronger
base than an ________ amine
• basicity of the guanido group is attributed to the large
________ ________ of the protonated form relative to
the neutral form
Imidazole Group
• The side chain imidazole group of ________ is a
____________ ____________ ____________
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
 C O O H +
pK a = 2.00
H2 O
 C O O
-
+
H3 O
+
• writing the acid ionization constant and rearranging
terms gives (remember Ch. 2)
Ka =
[ H 3 O + ] [  -COO
[  -COO H]
-
[  -COO
]
or
-
]
[  -COO H]
=
Ka
+
[ H 3O ]
Ionization vs pH (cont’d)
• substituting the value of Ka (1 x 10-2) for the _______
______ concentration at pH 7.0 (1.0 x 10-7) gives
[  -COO
-
]
[  -COO H]
=
Ka
+
[ H 3O ]
1.00 x 10
-2
1.00 x 10
-7
=
= 1.00 x 10
5
• at pH 7.0, the -carboxyl group is virtually ___% in
the ionized or conjugate base form, and has a net
charge of _______________
• 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 (cont’d)
• 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
[  -NH
2
]
+
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
[  -NH
2]
+
3
=
]
Ka
[H
+
O
]
3
=
1.00 x 10
-10
1.00 x 10
-7
= 1.00 x 10
-3
• 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
______ or _______ form and has a charge of ___
Henderson-Hasselbalch Equation
• We have calculated the ratio of _______________ to
____________ for an ________________ group and
an ____________ 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)
pH
= pK a + log
[conjugate base]
[weak acid]
Isoelectric pH
• Isoelectric pH, pI: the pH at which the majority of molecules
of a compound in solution have ___________________
• the pI for glycine, for example, falls midway between the pKa
values for the carboxyl and amino groups
pI =
=
1
2 ( p K a   CO O H
+
p K a  N H 3 + )
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 ____________
• 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 ____________ bond
between the _________
group of one amino acid
and the ____________
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 (____________ structures)
• the hybrid has considerable C-N ___________ bond
character and rotation about the peptide bond is
____________
• See Figure 3.10
Peptides
• ____________ : 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
• ____________ : a molecule containing two amino
acids joined by a peptide bond
• ____________ : a molecule containing three amino
acids joined by peptide bonds
• ____________ : a macromolecule containing many
amino acids joined by peptide bonds
• ____________ : 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 (cont’d)