LECTURE ON AMINO ACIDS

Amino Acids

• Amino acids are building blocks of proteins.

• Twenty amino acids are commonly found in protein.

• The first amino acid was asparagine, discovered in 1806 and the
20th amino acid was threonine.

• All the amino acids have trivial or common names, in some cases
derived from the source from which they were first isolated.

• Asparagine was first found in asparagus, and glutamate in wheat

gluten; tyrosine was first isolated from cheese (its name is derived
from the Greek tyros, “cheese”); and glycine (Greek glykos, “sweet”)
was so named because of its sweet taste.
Structure of amino acid
 Amino acids: abbreviations and codes

Alanine A, Ala Leucine L, Leu

Arginine R, Arg Lysine K, Lys
Asparagine N, Asn Methionine M, Met
Aspartic acid D, Asp Phenylalanine F, Phe
Cysteine C, Cys Proline P, Pro
Glutamine Q, Gln Serine S, Ser
Glutamic Acid E, Glu Threonine T, Thr
Glycine G, Gly Tryptophan W, Trp
Histidine H, His Tyrosine Y, Tyr
Isoleucine I, Ile Valine V, Val
 Chirality of amino acids

• Glycine, 2-amino-acetic acid, is achiral

• In all the others, the α carbons of the amino acids are centers of chirality
• Proteins are derived exclusively from L-aminoacids
 The two stereoisomers of alanine

α-carbon is a chiral center Two

stereoisomers are called
enantiomers.
 Classification of Amino Acids

Amino acids are generally divided into groups on the basis of their side chains
(R groups). Based on the properties of R groups, in particular, their polarity, or
tendency to interact with water at biological pH (near pH 7.0) all amino acids
can be classified into following five groups:
1. Nonpolar, aliphatic R groups
2. Nonpolar, aromatic R groups
3. Polar, uncharged R groups
4. Positively charged R groups
5. Negatively charged R groups
 Nonpolar, aliphatic R groups Aromatic R groups
COO "
COO "
COO "
COO "
COO "
COO" COO"
! ! H ! ! ! !
H 3N C H H 3N C H !
C H3N C H H 3N C H H 3N C H H3N C H
H 2N CH 2
H CH3 CH CH2 CH2 CH2
H 2C CH 2
CH3 CH3 C CH
Glycine Alanine Proline Valine NH
COO "
COO "
COO "

! ! !
OH
H3N C H H3N C H H3N C H
CH2 H C CH3 CH2 Phenylalanine Tyrosine Tryptophan

CH CH2 CH2
CH3 CH3 CH3 S
Positively charged R groups
CH3
COO "
COO" COO"
Leucine Isoleucine Methionine ! ! !
H3N C H H3N C H H3N C H
CH2 CH2 CH2
Polar, uncharged R groups CH2 CH2 C NH
COO "
COO "
COO "
CH2 CH2 CH
! ! !
H3N C H H 3N C H H3N C H C N
CH2 NH H
CH2 H C OH CH2 C
!
!
NH3 NH2
OH CH3 SH NH2
Serine Threonine Cysteine Lysine Arginine Histidine

COO " COO" Negatively charged R groups

! !
H 3N C H H 3N C H COO" COO"
! !
CH2 CH2 H 3N C H H 3N C H
C CH2 CH2 CH2
H 2N O C COO" CH2
H2N O COO"
Asparagine Glutamine Aspartate Glutamate

FIGURE 3–5 The 20 common amino acids of proteins. The structural shown uncharged, its pKa (see Table 3–1) is such that a small but signifi-
formulas show the state of ionization that would predominate at pH 7.0. cant fraction of these groups are positively charged at pH 7.0. The pro-
The unshaded portions are those common to all the amino acids; the tonated form of histidine is shown above the graph in Figure 3–12b.
Nonpolar, aliphatic R Groups
The simplest amino acid is
Glycine
Glycine, which has a single
hydrogen atom as its side chain.

Alanine, Valine, Leucine and

Alanine Valine
Isoleucine have saturated
hydrocarbon R groups (i.e. they
only have hydrogen and carbon
linked by single covalent bonds).

Leucine and Isoleucine are Leucine

isomers of each other.

Isoleucine
The side chain of Methionine
includes a sulfur atom but
remains hydrophobic in
Methionine
nature.

Proline has an aliphatic side

chain with a distinctive
cyclic structure.

The secondary amino (imino)

group of proline residues is
held in a rigid conformation
that reduces the structural
flexibility of polypeptide
regions containing proline.
Phenylalanine is Alanine
with an extra benzene
(sometimes called a Phenyl)
group on the end.
Phenylalanine is highly Phenylalanine
hydrophobic and is found
buried within globular
proteins.

The hydroxyl group of

tyrosine can form hydrogen
bonds, and it is an Tyrosine
important functional group
in some enzymes. Tyrosine
is significantly more polar
than phenylalanine,
because of the tyrosine
hydroxyl group.
Tryptophan is highly hydrophobic
and tends to be found immersed
inside globular proteins.

Structurally related to Alanine, but

with a two ring (bicyclic) indole
group added in place of the single Tryptophan
aromatic ring found in
Phenylalanine.

The presence of the nitrogen group

makes Tryptophan more polar than
Phenylalanine.
Serine and Threonine
play important role in
enzymes which regulate
phosphorylation and Serine
energy metabolism.

The polarity of serine

and threonine is
contributed by their
hydroxyl groups. Threonine
Cysteine has sulfur-containing side
group. The group has the potential
to be more reactive. It is not very
polar.
Cysteine is readily oxidized to form a
covalently linked dimeric amino acid
in which two cysteine molecules or Cysteine
residues are joined by a disulfide
bond. The disulfide-linked residues
are strongly hydrophobic (nonpolar).
Disulfide bonds play a special role in
the structures of many proteins by
forming covalent links between parts
of a protein molecule or between
two different polypeptide chains.
Asparagine and Glutamine are Asparagine
the amide derivatives of
Aspartate (Aspartic acid) and
Glutamate (Glutamic acid).

Glutamine
Lysine has a second primary
amino group at the ε
position on its aliphatic
chain. Arginine has a Lysine
positively charged guanidino
group and histidine has an
imidazole group.
In many enzyme catalyzed
reactions, a His residue Arginine
facilitates the reaction by
serving as a proton
donor/acceptor.

Histidine
Two amino acids with negatively
charged (i.e. acidic) side chains -
Aspartate (Aspartic acid) and
Glutamate (Glutamic acid). Aspartate
These amino acids confer a
negative charge on the proteins
of which they are part.

Glutamate
 Classification Based on Chemical Constitution

Small amino acids – Glycine, Alanine

Branched amino acids – Valine, Leucine, Isoleucine

Hydroxy amino acids (-OH group) – Serine, Threonine

Sulfur amino acids – Cysteine, Methionine

Aromatic amino acids – Phenylalanine, Tyrosine, Tryptophan

Acidic amino acids and their derivatives – Aspartate, Asparagine,
Glutamate, Glutamine
Basic amino acids – Lysine, Arginine, Histidine
Imino acid - Proline
Thank you