BCHM 201

GENERAL BIOCHEMISTRY I
AMINO ACID CHEMISTRY

Mr. Jalil I. James

COURSE OUTLINE
• Amino acids; Alpha amino acids; Amino acids as zwitterions
• Classification of amino acids;
• Amino acids of special significance in protein structure;
• Reactions of amino acids: Quantitative and qualitative.
• Amino acids not used in protein synthesis; the peptide bond
 Amino acids
Introduction
• Hundreds (over 300) of amino acids occur in nature
• Only 20 proteinogenic amino acids are included in the genetic code and therefore
regularly found in protein

• The process in turn is controlled by DNA, the genetic material of the cell.
After the synthesis of proteins, some of the incorporated amino acids
undergo modifications to form their derivative

• Amino acids and their derivatives form components of lipids (serine in

phospholipids), serve as neurotransmitters or their precursors, function as
important components of food, others form precursors for metabolites etc.
 Amino acids
• Amino acids (2-aminocarboxylic acids) are a group of organic
compounds containing two functional groups amino and
carboxyl.
• The amino group (-NH2) is basic while the carboxyl group (-COOH)
is acidic in nature
• The amino acids are termed -amino acids, if both the
carboxyl and amino groups are attached to the same carbon
atom, as depicted below
• lf a carbon atom is attached to four different groups, it is
asymmetric and therefore exhibits optical isomerism.
• The -amino acids (except glycine) possess four distinct groups held by C-
carbon
• The -carbon atom represents a chiral center i.e there are two
different enantiomers (L- and D- amino acids).
• In nature it is almost exclusively L-amino acids that are found. D-
amino acid occur in bacteria, peptide antibiotic etc.
Structures of the 20 amino acids
Glycine

Alanine

Valine

Leucine

isoleucine
Serine

Threonine

Cysteine

Methionine
Aspartic acid

Asparagine

Glutamic acid

Glutamine
Lysine

Arginine

Histidine
Phenylalanine

Tyrosine

Tryptophan

Proline
Classification of Amino acids
Amino acids can be classified based on
• structure and chemical nature
• Polarity
• nutritional requirement
• metabolic Fate
• their ability to be incorporated into protein
Classification based on structure and chemical
nature
• Amino acids with aliphatic side chain.
Amino acids containing hydroxyl (-OH) group.
Amino acids containing sulfur group.
Acidic amino acids and their amides
Basic Amino acids
 Aromatic Amino acids

Imino acid
Classification based on Polarity
The polarity of amino acids reflects its functional role in
protein structure. They can be sub-divided into two namely
• Non-polar amino acids
Also called hydrophobic amino acids. They have no charge on their ‘R’
group. The ‘R’ group can be either of Alkyl groups (with an alkyl
chain) or Aromatic groups. E.g. Glycine, Alanine, Valine, Methionine,
Leucine, Isoleucine, Proline, Phenylalanine, Tryptophan.
• Polar amino acids
If the side chains of amino acid contain different polar groups like
amines, alcohols or acids they are polar in nature. These are also
known as Hydrophilic amino acids. These are further divided into
three categories.
Acidic amino acids: e.g. Aspartic acid and glutamic acid
Basic: e.g. histidine, lysine and arginine
Neutral: e.g. serine, threonine, asparagine, glutamine, cysteine,
tyrosine
Classification based on nutritional requirement
• On the basis of their need to the human body and their availability in the
human body amino acids can be classified as
1. Essential
These are the acids that cannot be synthesized in our bodies. We must rely on food
sources to obtain these amino acids. They are Leucine, Isoleucine, Lysine, Theorine,
Methionine, Phenylalanine, Valine, Tryptophan.
2. Semi-essential
Arginine and Histidine are considered semi essential because they can be synthesised
by adults and not growing children
3. Non-essential
These acids are synthesized in our bodies itself and we need not rely on outside
sources for them. They are either produced in our bodies or obtained from protein
breakdown. They include glycine, alanine,serine, cysteine, aspartate,asparagine,
glutamate, glutamine,tyrosine and proline.
Classification based on metabolic fate
The carbon skeleton of amino acids can serve as a precursor for
the synthesis of glucose (glycogenic) or fat (ketogenic) or both.
From metabolic view point, amino acids are divided into three
groups
1. Glycogenic amino acids : These amino acids can serve as precursors
for the formation of glucose or glycogen. e.g. alanine, aspartate,
glycine, methionine etc.
2. Ketogenic amino acids : Fat can be synthesized from these amino
acids. Two amino acids leucine and lysine are exclusively ketogenic.
3. Mixed Glycogenic and ketogenic amino acids : The four amino acids
isoleucine, phenylalanine, tryptophan, tyrosine are pre-cursors for
synthesis of glucose as well as fat.
Classification based on their ability to be
incorporated into protein
• Proteinogenic: These are amino acids included into the genetic
code, they can be incorporated into a protein structure. All the
20 amino acids are example
• Non-Proteinogenic: These are amino acids that cannot be
incorporated into protein structure. They arise as a result of
metabolic reactions, enzymatic modifications of amino acid
residues in proteins, the biogenic amines are synthesized from -
amino acids by decarboxylation. Examples are Ornithine,
Citrulline, DOPA (3,4-dihydroxyphenylalanine), Selenocysteine
etc.
Examples of non-proteinogenic amino acids and their functions
Properties of Amino acids
• Physical Properties
Solubility: Soluble in water and insoluble in organic solvents
Melting point: They generally have high melting points (above 200
oC)

Taste: some have sweet taste (Gly, Val, Ala). Monosodium

Glutamate (Ajinomoto) is used as a flavouring agent to increase
the taste in food industry.
Optical properties: All the amino acids except glycine possess
optical isomers due to the presence of asymmetric carbon atom.
Some amino acids also have a second asymmetric carbon e.g.
isoleucine, threonine. The structure
of L- and D-amino acids are as that of L and D-glyceraldehyde
• Amino acids as ampholytes: Amino acids contain both acidic (-COOH)
and basic (- NH2) groups. They can donate a proton or accept a
proton,hence amino acids are regarded as ampholytes

Zwitterion or a dipolar ion is an ion with a positive and negative

electrical charge at different locations within a molecule. As the
molecule contains two opposite charges, it is electrically neutral. In solid
state amino acids acts exist in the dipolar or zwitterion form.
The amino acids rarely exist in a neutral form with free carboxylic (-
COOH) and free amino (- NH2) groups. In strongly acidic pH (low pH),
the amino acid is positively charged (cation) while in strongly alkaline pH
(high pH), it is negatively charged (anion). Each amino acid has a
characteristic pH (e.g. leucine, pH 6.0) at which it carries both positive
and negative charges and exists as zwitterion. The pH at which a
molecule (amino acid) exist as a zwitterion or dipolar ion and carries no
net charge is called the Isoelectric pH. (pI).
Existence of an amino acid as cation, anion and zwitterion
Chemical properties of amino acids

• The chemical properties of amino acids are often due to the presence
of the two functional groups
• Reactions due to -COOH group
1. Amino acids form salts (-COONa) with bases and esters (-COOR')
with alcohols.
2. Decarboxylation: Amino acids undergo decarboxylation to produce
corresponding amines.
3. Reaction with ammonia: The carboxyl group of dicarboxylic amino
acids reacts with NH3 to form amide
Aspartic acid + NH3 Asparagine
Glutamic acid + NH3 Glutamine
Reactions due to -NH2 group
1. The amino groups behave as bases and combine with acids (e.g. HCl) to form
salts (-NH3+Cl-)

2. Reaction with ninhydrin: The -amino acids react with ninhydrin to form a purple, blue or pink
colour complex (Ruhemann's purple).
Amino acid + Ninhydrin Keto acid + NH3 + CO2 + Hydrindantin
Hydrindantin + NH3 + Ninhydrin Ruhemann's purple

Ninhydrin reaction is effectively used for the quantitative determination of amino

acids and proteins. (Note : Proline and hydroxyproline give yellow colour with ninhydrin).

3. Colour reactions of amino acids: Amino acids can be identified by specific colour reactions.

4. Transamination : Transfer of an amino group from an amino acid to a keto acid to form a new
amino acid is a very important reaction in amino acid metabolism

5. Oxidative deamination: The amino acids undergo oxidative deamination to liberate free ammonia