Classification, Structure and

Functions of Amino Acids

Dr. Sonia Siddiqui

Professor, Department of Biochemistry, and
Vice Principal, SPGS
Incharge Research Department, DIMC
 Central Dogma in Biological System
Transcription Translation
• Posttranslationally
DNA RNA Protein
Reverse modified proteins
Transcription • Protein-ligand
interactions

Biological phenomena
Specific covalent sequences of monomers

Noncovalent Interactions
1. Hydrogen bonds
2. Ionic Interactions
3. Hydrophobic Interactions
4. van der Waals interactions

Correct three-dimensional structures

Biological functions
 The basic structure of amino acids differ only in
the structure of the or the side chain (R-group).
Amino acids are organic compounds that contain both amino and
carboxylic acid functional groups.

L-isomer

L-isomer is normally found in proteins.

Nonionic and zwitterion forms of amino acids
The zwitterion predominates at neutral pH

Zwitterion = in German for „hybrid ion“

Week acid

Week base
 AMINO ACIDS
•Amino acids are building blocks of proteins.
•Proteins are composed of 20 different amino acid
(encoded by standard genetic code, construct proteins in
all species ).

•Their molecules containing both amino and carboxyl

groups attached to the same a-carbon (L-a-amino acids).

•Their chemical structure influences three dimensional

structure of proteins.

•They are important intermediates in metabolism

(porphyrins, purines, pyrimidines, creatin, urea etc).

•They can have hormonal and catalytic function.

•Several genetic disorders are cause in amino acid
metabolism errors (aminoaciduria - presence of amino
pKa is a measure of the tendency of a molecule or ion to keep a proton,
H+, at its ionization center(s). It is related to the ionization capabilities of
chemical species.

pI= pK1+pK2
2
 Isoelectric pH
•The isoelectronic point or isoionic point is the pH at which the amino acid does not migrate in an
electric field.
•This means it is the pH at which the amino acid is neutral, i.e. the zwitterion form is dominant.

Glycine

Aspartic Acid
A simple monoamino monocarboxyl a-amino acid
is a diprotic acid (can yield protons) when fully
protonated
 Classification of Amino Acids
Amino acids are generally divided into groups on the
basis of their side chains (R groups).
The most helpful start-point is to separate amino acids
into:

Nonpolar Neutral polar

Charged polar

1. Nonpolar amino acids

 Only carbon and hydrogen in their side chains.

 Generally unreactive but hydrophobic.
 Determining the 3-D structure of proteins (they
tend to cluster on the inside of the molecule).
 Nonpolar (Hydrophobic) R Groups
Glycine (Gly) Methionine (Met)

Alanine (Ala)

Phenylalanine (Phe)

Valine (Val)

Proline (Pro)

Leucine (Leu)

Tryptophan (Trp)

Isoleucine (Ile)
http://www.indstate.edu/thcme/mwking/amino-acids.html
 The simplest amino acid is Glycine, which has a
single hydrogen atom as its side chain.

Alanine, Valine, Leucine and Isoleucine have

saturated hydrocarbon R groups (i.e. they only
have hydrogen and carbon linked by single
covalent bonds). Leucine and Isoleucine are
isomers of each other.

Alanine Valine

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

Phenylalanine is Alanine with an extra

benzene (sometimes called a Phenyl) group on
the end. Phenylalanine is highly hydrophobic
and is found buried within globular proteins.

Methionine Phenylalanine
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 aromatic ring found in Phenylalanine.

The presence of the nitrogen group makes

Tryptophan a little less hydrophobic than
Phenylalanine.
Proline is unique amongst the amino acids –
its side chain is bonded to the backbone
nitrogen as well as to the a-carbon.

Because of this proline is technically an

imino rather than an amino acid.

The ring is not reactive, but it does restrict

the geometry of the backbone chain in any
protein where it is present.
Polar (Hydrophilic) R Groups
Serine (Ser) Cysteine (cys)

Threonine (Thr) Asparagine (Asn)

Glutamine (Gln)
Tyrosine (Tyr)

http://www.indstate.edu/thcme/mwking/amino-acids.html
Tyrosine is Phenylalanine with an extra
hydroxyl (-OH) group attached.
It is polar and very weakly acidic. Tyrosine
can play an important catalytic role in the
active site of some enzymes. Reversible
phosphorylation of –OH group in some enzymes
is important in the regulation of metabolic
pathways

Serine and Threonine play important role in

enzymes which regulate phosphorylation and
energy metabolism.
Cysteine has sulfur-containing side
group.The group has the potential to be more
reactive.It is not very polar.

Cysteine is most important for its ability to

link to another cysteine via the sulfur atoms to
form a covalent disulfide bridge, important in
the formation and maintenance of the tertiary
(folded) structure in many proteins.

COOH - CH- CH2 - HS SH- CH2- CH- COOH

NH2 NH2

S S
Asparagine and Glutamine are the amide
derivatives of Aspartate (Aspartic acid) and
Glutamate (Glutamic acid) - see below. They
cannot be ionised and are therefore
uncharged.

Asparagine Glutamine
Negatively (Nonpolar) Charged R Groups

Aspartic acid (Asp) Glutamic acid (Glu)

Two amino acids with negatively charged (i.e.

acidic) side chains - Aspartate (Aspartic acid)
and Glutamate (Glutamic acid).

These amino acids confer a negative charge

on the proteins of which they are part.
 Positively Charged R Groups
Lysine (Lys) Arginine (Arg) Histidine (His)

Lysine and Arginine both have pKs around

10.0 and are therefore always positively
charged at neutral pH.

With a pK of 6.5, Histidine can be uncharged

or positively charged depending upon its local
environment.
Histidine has an important role in the
catalytic mechanism of enzymes and explains
why it is often found in the active site.
 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
 Essential Amino Acids in Humans

• Required in diet
• Humans incapable of forming requisite
carbon skeleton

Arginine* Lysine
Histidine* Methionine
Isoleucine Threonine
Leucine Phenylalanine
Valine Tryptophan
* Essential in children, not in adults
Non-Essential Amino Acids in Humans

• Not required in diet

• Can be formed from a-keto acids by
transamination and subsequent reactions

Alanine Glycine
Asparagine Proline
Aspartate Serine
Glutamate Cysteine (from Met*)
Glutamine Tyrosine (from Phe*)
* Essential amino acids
Uncommon amino acids found
in proteins

Intermediates of biosynthesis of
arginin and in urea cycle
 Amino Acids: Atom Naming
• Organic nomenclature: start from one end
• Biochemical designation: start from
-carbon and go down the R-group
The Stereochemistry of Amino Acids
Chiral molecules existing in two forms

http://www.imb-jena.de/~rake/Bioinformatics_WEB/gifs/amino_acids_chiral.gif
The two stereoisomers of
alanine

a-carbon is a chiral center

Two stereoisomers are called

enantiomers.

The solid wedge-shaped bonds

project out of the plane of paper,
the dashed bonds behind it.

The horizontal bonds project out of

the plane of paper, the vertical
bonds behind.
 Peptides and Peptide bonds
Peptide bond in
a di-peptide

“Peptides” are
small
condensation
products of
amino acids

They are “small”

compared to
proteins (di, tri,
tetra… oligo-)
Peptide Ends are Not the Same
Numbering starts from the amino terminus
AA1 AA2 AA3 AA4 AA5
 The Three Letter Code
• Naming starts from
the N-terminus
• Sequence is written
as:
Ala-Glu-Gly-Lys

• Sometimes the one-

letter code is used:
AEGK