AMINO ACIDS

Assist. Prof. Dr. Pınar Siyah

Department of Biochemistry, School of Pharmacy, Bahçeşehir University

E-mail: pinar.siyah@med.bau.edu.tr
 Amino Acids
• Amino acids are the organic compounds containing amino and carboxylic groups.
• These are fundamental structural components of proteins. Amino acids have
essential nutritive value for living organisms.

© Pınar Siyah, 7 November 2022

 Structure of Amino Acid

It is an amino-carboxylic acid that is made of five components.

• Asymmetric carbon atom (C) – It is the central carbon in amino acid.

• Amino group (–NH2)
• Carboxylic group (–COOH)
• Hydrogen atom (H)
• Hydrocarbon side chain (R) – Hydrocarbon side chains provide
identity to amino acids. Side chain may contain acidic or basic groups.
It may contain hydrophilic or hydrophobic groups. These are
necessary for the steric conformation of proteins. They determine the
structure and properties of proteins.

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 Since they are nonsuperimposable mirror images of each other, the two forms represent a class of
stereoisomers called enantiomers. All molecules with a chiral center are also optically active.

© Pınar Siyah, 7 November 2022

 Nearly all biological compounds with a chiral center occur
naturally in only one stereoisomeric form, either D or L.

The amino acid residues in protein molecules are exclusively

L stereoisomers.

D-Amino acid residues have been found only in a few,

generally small peptides, including some peptides of bacterial
cell walls and certain peptide antibiotics.

It is remarkable that virtually all amino acid residues in

proteins are L stereoisomers.

© Pınar Siyah, 7 November 2022

 Important Characteristics of Amino Acids
CHIRALITY AMPHOTERIC
Amino Acids Can Act as Acids and Bases
Since amino acids have both acidic
(−NH3+) ad well as basic (−COO−)
groups, therefore , they are
amphoteric in nature.
The alpha-carbon atom is a chiral center.
ZWITTERIONS

Zwitterion ( “hybrid ion”) neutral

overall but have fully charged parts

© Pınar Siyah, 7 November 2022

 Classification of Amino Acids

Depending on various criteria, amino acids can be classified in different ways:

• Classification depending on proteinogenic property

• Classification depending on polarity of side chain
• Classification depending on chemical structure of side chain
• Classification depending on nutritional value
• Classification depending on chemical property

© Pınar Siyah, 7 November 2022

 Essential amino acids can be memorized as “TT named PVM is ILL today,” where TT stands
for threonine and tryptophan, while PVM stands for phenylalanine, valine, and
methionine, whereas ILL means isoleucine, leucine, and lysine.

20 amino
acids

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 Classification Depending on Proteinogenic Property
1. Proteinogenic amino acids
The amino acids that can be utilized for synthesis of proteins
in living organisms are called as called proteinogenic amino
acids. These amino acids are coded by DNA through triplet
codons and also called as standard amino acids.
Example: Essential and nonessential amino acids are
proteinogenic.
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2. Non-proteinogenic amino acids
The amino acids that cannot be incorporated
into structure of proteins during their
biosynthesis in body tissues are called non-
proteinogenic amino acids.
They exist in cytoplasm either as metabolites
or structural components of non-protein
compounds. They are also called as
nonstandard amino acids.
Example: Gama amino butyric acid,
hydroxyproline, ornithine, citrulline, carnitine,
glycine
 Classification
Depending on Polarity
of Side Chain
1. Hydrophobic amino acids
The hydrocarbon side chains do not react with
water molecules and are termed as non-polar side
chains.
Such amino acids are called as hydrophobic or non-
polar amino acids.
Example: valine, alanine, tyrosine, phenylalanine,
proline, tryptophan.

2. Hydrophilic amino acids

The hydrocarbon side chains have high affinity for
water molecules and are termed as polar side
chains.
Such amino acids are called as hydrophilic or polar
amino acids.
The side chains in these amino acids can be either
positively charged or negatively charged.
Example: serine, asparagine, threonine, glutamine,
histidine, tyrosine.

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 Classification Depending
on Nutritional Value
1. Essential amino acids
These amino acids are not synthesized by body tissues and have to
be supplemented with diet to fulfill their physiological demand.
They are also called as indispensable amino acids.
2. Semi-essential amino acid
It is also called as conditionally essential amino acid as its
essentiality in the body is determined by developmental stage of
children and pregnancy and lactation among women. The amino
acid has to be supplemented with diet during these conditions.
Example: as listed in Table 3.1
3. Non-essential amino acids These amino acids are synthesized in
the body and do not have to be supplemented with diet.

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Classification Depending on
Chemical Structure of Side Chain

1. Simple amino acid

The side chain has the simplest
structure in these amino acids as in
Fig. 3.16.
Example: Glycine, alanine

2. Branched chain amino acids

The side chains are short and
branched as in Fig. 3.17. Example:
Valine, isoleucine, leucine

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 3. Hydroxy amino acids
The amino acids have hydroxyl groups in side
chains as in Fig. 3.18.
Example: Serine, threonine

4. Sulfur-containing amino acids

The amino acids contain sulfur atoms in the
groups attached in side chains as in Fig. 3.19.
Example: Cysteine, methionine

5. Amide groups containing amino acids

The amino acids possess carboxy-amide groups
(R–CO–NH2–R) in the side chains as in Fig. 3.20.
Example: Asparagine, glutamine

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 6. Monoamino-dicarboxylic acids
The amino acids contain an additional carboxylic group
in the side chain and are called as monoamino-
dicarboxylic acids. These are acidic amino acids.
Example: Aspartic acid, glutamic acid

7. Diamino monocarboxylic acids

The amino acids contain additional amino group in the
side chain and are called as diamino monocarboxylic
acids. These are basic amino acids. Example: Arginine,
lysine, and a derived amino acid called as
hydroxylysine.

8. Diamino dicarboxylic acids

These amino acids contain carboxy-amide group (–
RCO–NH2–) in the side chain. Amino acids have two
amino and two carboxylic groups. These amino acids
are neutral. Example: Asparagine, glutamine

© Pınar Siyah, 7 November 2022

 9. Aromatic amino acids
The amino acids contain aromatic rings in the side
chains. They are neutral. Example: Phenylalanine,
tyrosine

10. Heterocyclic amino acids

The amino acids possess heterocyclic rings in the
side chains. It contains dissimilar atoms like
nitrogen, sulfur, or oxygen in the ring structure.
Example: Tryptophan, histidine. The amino acid
tryptophan is neutral and histidine is basic in
nature.

11. Amino acids containing amino group in side

chain
The amino acids contain amino group (–NH) in side
chains. These amino acids are basic in nature.
Example: Proline, hydroxyproline.

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 Classification Depending on Chemical Property
1. Acidic amino acids
– These amino acids have one amino and two carboxylic groups. These are
acidic in nature. Example: Monoamino dicarboxylic acids

2. Basic amino acids

– These amino acids have two amino and one carboxylic group. These are basic
in nature. Example: Arginine, histidine, lysine, and a derived amino acid named
as hydroxylysine

3. Neutral amino acids

– These amino acids have one amino and one carboxylic group. These are
neutral in reaction. Example: Aliphatic amino acids, hydroxy amino acids,
aromatic amino acids, heterocyclic amino acids, sulfur-containing amino acids,
amide-containing amino acids (dibasic dicarboxylic acids).

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 SUMMARY

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 Configuration and Conformation
• Configuration of a molecule means the
arrangement of atoms or groups within a
molecule in three-dimensional space. The
isomers are called as configurational isomers.
For example: d-amino acid and l-amino acid.
• Bond breaking
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• Conformation of a molecule means the rotation of atoms
or groups about a bond within a molecule in three-
dimensional space. The isomers are called as
conformational isomers or rotamers. For example, peptide
bond has cis and trans conformers in polypeptide chain.
• No bond breaking
 Applied
Biochemistry
Casein Phosphopeptides (CPP)
• It has been demonstrated that milk phosphor-protein, casein has a
role in the remineralization of dental enamel. Casein phosphopeptides
(CPP) are extracted from milk casein by tryptic digestion. Reynolds
(1997) observed that topically administered CPP complexes are
absorbed into the dental plaque. It has affinity for calcium and
phosphate from saliva and results into an increase in localized
concentration of calcium and phosphate over tooth surfaces.
• Casein phosphopeptides (CPP) possess specific residues in sequences.
These residues stabilize calcium and phosphate ions in oral cavity.
These ions are precipitated into amorphous calcium phosphate (ACP)
complex. The CPP molecule combines with ACP to form complexes,
CPP-ACP.
• The ACP molecules over tooth surfaces can be converted into
octacalcium phosphates. It is an intermediate of hydroxyapatite crystals
in dental enamel.
• The CPP-ACP nanoclusters are formed at pH between 5 and 9.
• The CPP-ACP complexes can inhibit growth of Streptococcus mutans
in dental plaque.
• The complexes raise oral pH which can prevent dental
demineralization.
• The ACP nano-complexes can be transformed into hydroxyapatite
crystals and help to remineralize the incipient dental carious lesion.

© Pınar Siyah, 7 November 2022

 Applied Biochemistry
Arginine
• It is an essential amino acid. Its oral health benefit has been
tried. Kleinberg (2002) proved that topical preparation
containing calcium carbonate and arginine bicarbonate gets
deposited over the open dentinal tubules. The arginine
molecule helps to block open dentinal tubules and minimizes
dental hypersensitivity.

© Pınar Siyah, 7 November 2022