AMINO ACIDS
 Building blocks of protein.
 Acts as precursors - many biologically important
molecules are derivative of amino acids.
o Example: Tyrosine (Y) is the precursor of the
hormone thyroxine and the skin pigment melanin.
 Acts as source of Sulfur – derived from the sulfur
containing amino acids.
o Example: Cysteine (C) and Methionine (M)
 Involved in many metabolic pathways such as in
Gluconeogenesis where it is involved in glucose synthesis.
 The amino acids commonly dealt with are α – amino acids
(a carboxyl group and an amine group attached to the α –
carbon).
FUNCTIONS
 For synthesis of proteins the body needs.
 Precursors of nitrogen containing compounds like N-
bases of nucleic acids (purines/ pyrimidines), porphyrins
(heme, chlorophyll), folic acid (glutamic), creatine (gly,
arg, met), glutathione (glu, cys, gly)
 Some amino acids and their derivatives function as
chemical messengers/neurotransmitters
 For glucose synthesis
 Function as buffer
 For detoxification reactions (gly, cys, met)
ANATOMY
 The name amino acid suggests that these structures have
an amine and acid group (amino acid and carboxylic acid
group).
 Since the central carbon have four (4) different groups
attached to it, it is a chiral carbon.
o Because of the tetrahedral arrangement of the
bonding orbitals around the α-carbon atom, the
four different groups can occupy two unique
spatial arrangements and thus amino acids have
two possible isomers.
 Amino acid - An organic compound that contains both an
amino (-NH2) and carboxyl (-COOH) groups attached to
same carbon atom
o The position of carbon atom is Alpha (a)
o -NH2 group is attached at alpha (a) carbon atom.
o -COOH group is attached at alpha (a) carbon
atom.
 R = side chain –vary in size, shape, charge, acidity,
functional groups present, hydrogen-bonding ability, and
chemical reactivity.
o >700 amino acids are known
o Based on common “R” groups, there are 20
standard amino acids
Side Chain
R  -Carbon Atom
H2N C COOH
-Carboxyl
-Amino H
Group
Group
 Amino acids have two (2) possible isomers;
o L and D isomers
 Nearly all amino acids in biochemistry are of the L-form (L
for life); the opposite of sugars, which nearly always
occur as the D-isomer.
 The L – designation has nothing to do with the way they
rotate polarized light but is purely structural. This is based
on the structure of L-glyceraldehyde.
 By Fischer’s convention, L and D refer only to the absolute
configuration of the four substituents around the chiral
carbon, not to optical properties of the molecule.
 The non – ionic form does not occur in significant
amounts in aqueous solutions.
 The zwitterionic form predominates at normal pH (pH =
7.4).
o At this pH, the non – ionic form has lost its
proton (hydrogen ion) and has a negative charge
with the electrons of the double bond shared
across the two O atoms.
o Also attached to the α – carbon is an amine
group that at pH = 7.4 has an extra proton and
so carries a positive charge.
o These two charges cancel each other out and
hence the net charge is dependent upon the
charge carried on their R – group.
 The amino acid residues in protein molecules are
exclusively L - isomers.
 Cells are able to specifically synthesize the L - isomers of
amino acids because the active sites of enzymes are
 asymmetric, causing the reactions they catalyze to be
stereospecific.
 All 20 of the common amino acids are α-amino acids.
 The common amino acids of proteins have been assigned
three-letter abbreviations and one-letter symbols, which
are used as shorthand to indicate the composition and
sequence of amino acids polymerized in proteins.
 They have a carboxyl group and an amino group bonded
to the same carbon atom (the α - carbon).
 They differ from each other in their side chains, or R
groups, which vary in structure, size, and electric charge,
and which influence the solubility of the amino acids in
water.
 In addition to these 20 amino acids there are many less
common ones. Some are residues modified after a
protein has been synthesized; others are amino acids
present in living organisms but not as constituents of
proteins. Important Functions of Uncommon Amino Acids
 4 – hydroxyproline
ESSENTIAL NON ESSENTIAL o A derivative of Proline, found in plant cell wall
Histidine (His) Alanine (Ala) proteins.
Isoleucine (Ile) Arginine (Arg)  5 – hydroxylysine
Leucine (Leu) Asparagine (Asn) o Found in collagen, a fibrous protein in connective
Lysine (Lys) Aspartic Acid (Asp) tissues.
Methionine (Met) Cysteine (Cys)  6 – N – methyllysine
Phenylalanine (Phe) Glutamic Acid (Glu) o Is a constituent of myosin, a contractile protein
of muscles.
Threonine (Thr) Glutamine (Gln)
Tryptophan (Trp) Glycine (Gly)   - carboxyglutamate
o Found in the blood clotting protein, prothrombin
Valine (Val) Proline (Pro)
and in certain other proteins that bind Ca2+ as
Serine (Ser)
part of their biological function.
Tyrosine (Tyr)
AMINO ACIDS NOT FOUND IN PROTEINs
 Desmosine
o A derivative of four (4) Lys residues, which is
found in the fibrous protein elastin.
o Selenocysteine
o A special case. This rare amino acid residue is
introduced during protein synthesis rather than
created through a post-synthetic modification.
o It contains selenium rather than the sulfur of
cysteine.
o Derived from serine, selenocysteine is a
constituent of just a few known proteins.
 Ornithine and Citrulline
o Deserve special note because they are key
intermediates (metabolites) in the biosynthesis
of arginine and in the urea cycle.
BIOLOGICALLY ACTIVE AMINO ACID DERIVATIVES
General Properties of  - Amino Acids
 Optical Activity
o All amino acids show optical activity except for
glycine , the rest of the amino acids contain at
least one asymmetrical carbon atom (chiral
carbon).
o Dextrorotatory (+) isomer which has the ability
to rotate the plane of polarized light to the right.
o Levorotatory (-) isomer which has the ability to
rotate the plane of polarized light to the left.
o Therefore, both isomers can rotate the plane of
polarized light by the same magnitude but in
opposite directions.
 asymmetrical carbon – it is a carbon atom that has 4
different groups attached to it.
 Among the 20 amino acids, which lack optical activity?
Glycine, because it only has H atom as R – group.
 What does possessing optical activity means? It means to
say that the amino acids in the solution is present in two
isomers.
 Acid – Base Properties of Amino Acids
o When an amino acid is dissolved in water it exist
in solution as a dipolar ion or zwitterion (German
for “hybrid ion”).
 Zwitterion can act as an acid (proton
donor).
 Zwitterion can act as a base (proton
acceptor).
o Substances having this dual nature are
amphoteric and are often called ampholytes
(from “amphoteric electrolytes”) depending on
the pH of their media.
Characteristic Titration Curves of Amino Acids
 Acid-base titration involves the gradual addition or
removal of protons.
 Amino acids vary in their acid-base properties and have
characteristic titration curves.
 The plot has two distinct stages, corresponding to
deprotonation of two different groups on glycine.
 Each of the two stages resembles in shape the titration
curve of a mono-protic acid, such as acetic acid.
 At the midpoint of any titration, a point of inflection is
reached where the pH is equal to the pKa of the
protonated group being titrated.
 pH and pKa are simply convenient notations for proton
concentration and the equilibrium constant for ionization,
respectively.
 The pKa is a measure of the tendency of a group to give
up a proton, with that tendency decreasing tenfold as the
pKa increases by one unit.
 The characteristic pH at which the net electric charge is
zero is called the isoelectric point or isoelectric pH,
designated pI.
 FIGURE 3–10 Titration of an amino acid. Shown here is
the titration curve of 0.1 M glycine at 25 C. The ionic
species predominating at key points in the titration are
shown above the graph. The shaded boxes, centered at
about pK1 2.34 and pK2 9.60, indicate the regions of
greatest buffering power.
 For glycine, the pH at the midpoint is 2.34, thus its -COOH
group has a pKa (labeled pK1) of 2.34.
 As the titration proceeds, another important point is
reached at pH 5.97.
 Here there is another point of inflection, at which removal
of the first proton is essentially complete and removal of
the second has just begun.
 At this pH glycine is present largely as the dipolar ion H3N
- CH2 - COO.
 The second stage of the titration corresponds to the
removal of a proton from the -NH3 group of glycine.
 The pH at the midpoint of this stage is 9.60, equal to the
pKa (labeled pK2) for the -NH3 group.
 The titration is essentially complete at a pH of about 12,
at which point the predominant form of glycine is H2N -
CH2 - COO.
Comparison of the titration curves of three (3) weak acids

SUMMARY
 The pKa of any functional group is greatly affected by its
chemical environment, a phenomenon sometimes
exploited in the active sites of enzymes to promote
exquisitely adapted reaction mechanisms that depend on
the perturbed pKa values of proton donor/acceptor
groups of specific residues.