Chemistry of amino acids

Biochemistry for medics
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Biochemistry For Medics 7/5/2012 1

Provide the monomer units from which the
long polypeptide chains of proteins are
synthesized
 L-amino acids and their derivatives
participate in cellular functions as diverse as
nerve transmission and the biosynthesis of
porphyrins, purines, pyrimidines, and urea.
Short polymers of amino acids called
peptides perform prominent roles in the
neuroendocrine system as hormones,
hormone-releasing factors,
neuromodulators, or neurotransmitters.

Each amino acid (except proline) has a
carboxyl group, an amino group and a
distinctive side chain bonded to the alpha
carbon atom. At physiological pH the
carboxyl group is dissociated forming the
negatively charged carboxylate ion(-COO-),
and the amino group is protonated(-NH3+)


 Amino acids can be classified in 4 ways:
1. Based on structure
2. Based on the side chain characters
3. Based on nutritional requirements
4. Based on metabolic fate


They are classified in three broad categories:
 Mono amino mono carboxylic acid
It is further subdivided in 5 groups:
a. Simple amino acids-example: glycine, alanine
b. Branched chain amino acids-eg: valine,leucine,isoleucine
c. Hydroxyl group containing amino acids-eg: serine, threonine
d. Sulphur containing amino acids-eg: cysteine,cystine,methionine
e. Amide group containing amino acids-e.g.- asparagine,glutamine

 Mono amino dicarboxylic acid
Example :aspartic acid, glutamic acid

 Di /poly amino mono carboxylic acid
Example : lysine,arginine


I. Aliphatic Amino Acids:
a) Mono-amino mono-carboxylic acids:
 Simple amino acids: Glycine , Alanine


Branched chain amino acids: Valine,
Leucine and Isoleucine


-OH group-containing amino acids: Serine
and Threonine


Sulfur-containing amino acids: Cysteine,
Cystine(Formed by linking of two cysteine
residues) and Methionine.


 Amide group-containing amino acids:
Glutamine and Asparagine


a) Mono-amino di-carboxylic acids: Aspartic
acid and Glutamic acid


a) Di- basic mono-carboxylic acids:
Arginine and Lysine


ii ) Aromatic amino acids-
 Phenyl alanine and tyrosine


iii) Heterocyclic Amino Acids: Tryptophan
and Histidine


iv) Imino acid- Proline


V. Derived Amino Acids:
 Non-α-amino acids
e.g.: β-alanine, γ-amino butyric acid
(GABA), δ-amino Levulinic acid

 Derived and Incorporated in tissue proteins:
e.g.: Hydroxy-proline, hydroxy-lysine

 Derived but not incorporated in tissue
proteins:
e.g.: Ornithine, Citrulline, Homocysteine,
Argino succinic acid


A. Amino acids with a non-polar side-chain:
e.g.: Alanine, Valine, Leucine, Isoleucine,
Phenylalanine, Tryptophan, Proline

Each of these amino acids has a side chain that
does not bind or give off protons or participates in
hydrogen or ionic bonds.

Side chains of these amino acids can be thought
of as “Oily” or lipid like, a property that promotes
hydrophobic interactions.


B) Amino acids with a polar but uncharged side-chain:
e.g. Serine, Threonine, Tyrosine, Cysteine,
Asparagine and Glutamine.
 These amino acids are uncharged at neutral pH,
although the side chains of cysteine and Tyrosine
can lose a proton at an alkaline pH.
Serine , Threonine and Tyrosine each contains a polar
hydroxyl group that can participate in hydrogen bond
formation.
 Side chains of Asparagine and Glutamine
contain a carbonyl group and amide group, they can
also participate in hydrogen bond formation.


C) Amino acids with a charged side-chain
a) Amino acids with a positively charged side-
chain:
The basic amino acids- Lysine, Arginine and
Histidine
b) Amino acids with a negatively charged side-
chain:
The acidic amino acids- Glutamic acid and
Aspartic acid
They are hydrophilic in nature.


I. Essential amino acids:
These amino acids cannot be synthesized in the body
and have to be present essentially in the diet.
Examples-Valine, Isoleucine, Leucine, Lysine,
Methionine, Threonine, Tryptophan and
Phenylalanine.
II. Semi-essential amino acids:
These amino acids can be synthesized in the body but
the rate of synthesis is lesser than the
requirement(e.g. during growth, repair or pregnancy)
Examples-Arginine and Histidine.
III. Non-essential amino acids:
These amino acids are synthesized in the body, thus
their absence in the diet does not adversely affect the
growth.
Examples- Glycine, Alanine, and the other remaining
amino acids.


The carbon skeleton of amino acids can be used
either for glucose production or for the production
of ketone bodies, Based on that
I. Both glucogenic and ketogenic amino acids:
Isoleucine, Tyrosine, Phenylalanine and
Tryptophan
II. Purely Ketogenic amino acids:
Leucine and Lysine
III. Purely Glucogenic amino acids:
The remaining 14 amino acids are glucogenic.
Alanine, valine ,serine, threonine, glycine,
methionine, asparagine, glutamine, cysteine, cystine,
aspartic acid, glutamic acid, histidine and arginine.


Of the over 300 naturally occurring amino
acids, 20 constitute the monomer units of
proteins. These 20 amino acids are called
the Primary or Standard amino acids.
Seleno cysteine is the 21st Amino Acid
The other are Pyroglutamate and Pyrolysine.


Each amino acid has three letter (code) and
one letter (Symbol) abbreviations-
Examples-1) Unique first letter
Cysteine- Cys- C
Histidine- His- H
2) Priority of commonly occurring amino
acids
Alanine- Ala- A (Preference over Aspartate)
 Glycine- Gly-G (Preference over
Glutamate)


3) Similar sounding names- Some one letter
symbols sound like the amino acids they
represent- Example
 Tryptophan – W (Twyptophan)
 Phenyl alanine – F
4) Letters close to initial letter
Aspartate- Asx- B( near A)
Lysine Lys- K(near L)


 Arginine- Guanidinium group
Phenyl Alanine- Benzene group
 Tyrosine- Phenol group
Tryptophan- Indole group
 Histidine- Imidazole group
Proline- Pyrrolidine
 Proline has a secondary amino group,
hence it is an imino acid.


Physical properties-
Colorless
Crystalline
May be sweet(Glycine, Alanine, Valine),
tasteless(Leucine) or bitter(Arginine,
Isoleucine). Aspartame- An artificial
sweetener contains Aspartic acid and Phenyl
alanine.
Soluble in water, acids, alkalis but insoluble
in organic solvents
High melting point(More than 200 c)
0


Amino acids can exist as ampholytes or
zwitterions in solution, depending upon pH of the
medium.
The pH at which the amino acids exist as
zwitterions, with no net charge on them is called
Isoelectric pH or Isoelectric point.
In acidic medium, the amino acids exist as cations
In alkaline medium , they exist as anions.

Due to no net charge, there is no
electrophoretic mobility at Isoelectric
pH.
Solubility and buffering capacity are
also minimum at Isoelectric pH

If HCl is added drop wise to am amino acid
solution, at a particular p H, 50 % of the
molecules are in the cationic form and 50%
are in the zwitterion form. This pH is
pK1(with regard to COOH)
If the titration is done from the Isoelectric
point with NaOH, molecules acquire the
anionic form. When 50 % of the molecules are
in the anionic form and 50% are in the
zwitterion form. This pH is pK2(with regard
to NH2)


For mono amino
mono carboxylic
amino acids-
pI = pK1+pK2
-------------
2
The buffering
action is maximum
in and around
pK1or at pK2 but is
minimum at pI


The α carbon of each amino acid is attached to
four different groups and is thus a chiral or
optically active carbon atom.
Glycine is exceptional because there are two
hydrogen substituents at the α carbon, thus it is
optically inactive.
Amino acids with asymmetric centre at the α
carbon can exist in two forms, D and L forms
that are mirror images of each other and are
called Enantiomers.
All amino acids found in proteins are of L-
configuration
D- amino acids are found in some antibiotics
and in bacterial cell walls.

1) Reactions due to amino group
2) Reactions due to carboxyl group
3) Reactions due to side chain
4) Reaction due to both amino and carboxyl
groups


 Oxidativedeamination-α amino group is removed
and corresponding α-keto acid is formed. α-keto
acid produced is either converted to glucose or
ketone bodies or is completely oxidized.
 Transamination-Transfer of an α amino group
from an amino acid to an α keto acid to form a
new amino acid and a corresponding keto acid.


Formation of carbamino compound
CO2 binds to α amino acid on the globin chain
of hemoglobin to form carbamino hemoglobin
The reaction takes place at alkaline pH and
serves as a mechanism for the transfer of
Carbon dioxide from the tissues to the lungs by
hemoglobin.


1) Decarboxylation- Amino acids undergo
alpha decarboxylation to form
corresponding amines. Examples-
Glutamic acid GABA
Histidine Histamine
Tyrosine Tyramine

2) Formation of amide linkage
• Non α carboxyl group of an acidic amino
acid reacts with ammonia by condensation
reaction to form corresponding amides
Aspartic acid Asparagine
Glutamic acid Glutamine


1) Ester formation
 OH containing amino acids e.g. serine,
threonine can form esters with
phosphoric acid in the formation of
phosphoproteins.
 OH group containing amino acid can also
form: Glycosides – by forming
 O- glycosidic bond with carbohydrate
residues.


2) Reactions due to SH group (Formation of
disulphide bonds)
Cysteine has a sulfhydryl group( SH) group and
can form a disulphide (S-S) bond with another
cysteine residue.
 The dimer is called Cystine
Two cysteine residues can connect two
polypeptide chains by the formation of interchain
disulphide chains.


3)Transmethylation
The methyl group of Methionine can be
transferred after activation to an acceptor for
the formation of important biological
compounds.


Reactions due to side chains
4)Reactions due to both amino & carboxyl
groups
Formation of peptide bond


 Incorporated in to tissue proteins
 Niacin, Serotonin and melatonin are
synthesized from Tryptophan
Melanin, thyroid hormone, catecholamines
are synthesized from Tyrosine
GABA (neurotransmitter) is synthesized
from Glutamic acid
Nitric oxide, a smooth muscle relaxant is
synthesized from Arginine.
 Act as precursors for haem, creatine and
glutathione, Porphyrins, purines and
pyrimidines.


S.No. Test Significance

1) Ninhydrin reaction Given by all Alpha amino acids

2) Xanthoproteic test Given by aromatic amino acids

3) Millon’s test Confirmatory test for Tyrosine

4) Biuret test Not given by free amino acids

5) Sakaguchi test Given by Arginine

6) Hopkins Cole reaction Confirmatory test for Tryptophan

7) Lead acetate test Given by cysteine and cystine but not
given by Methionine
8) Nitroprusside reaction Given by SH group containing amino
acids


Chemistry of amino acids

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Chemistry of amino acids