OVERVIEW OF AMINO ACIDS AND THEIR CLASSIFICATION.

Amino acids are the building blocks of proteins and play crucial roles in various biological
processes within the human body. They are organic compounds that are composed of an amino
group (-NH2), a carboxyl group (-COOH), a hydrogen atom (H), and a distinctive side chain (R
group) attached to a central carbon atom, known as the alpha carbon (α-carbon).

Amino Group (-NH2): The amino group consists of a nitrogen atom bonded to two hydrogen
atoms. It acts as a base and can accept a proton (H+) to form an ammonium ion (NH3+). This
ionization state allows amino acids to participate in acid-base reactions and contribute to the
overall charge of a protein or peptide.

Carboxyl Group (-COOH): The carboxyl group consists of a carbon atom double-bonded to an
oxygen atom and single-bonded to a hydroxyl group (-OH). It acts as an acid and can donate a
proton to form a carboxylate ion (-COO-). The presence of these 2 groups (amino group and
carboxyl groups) makes amino acids amphoteric.

Hydrogen Atom (H): The hydrogen atom is bonded to the alpha carbon (1st carbon). It is relatively
unreactive but contributes to the overall stability and geometry of the amino acid molecule.

Side Chain (R Group): The side chain, also known as the variable group, differs among amino
acids and determines their unique properties. It can range from a simple hydrogen atom (as in
glycine, the simplest amino acid) to complex structures containing various functional groups. The
side chain influences the amino acid's polarity, charge, hydrophobicity, and reactivity.

Classification of Amino Acids: Amino acids can be classified based on several criteria, including
their structure, properties, and essentiality for human health. The classification schemes commonly
used are as follows:
Structure-based Classification:

a. Nonpolar (hydrophobic) amino acids: These amino acids have nonpolar R groups, making them
insoluble in water. They cluster together in the interior of proteins, away from water-based
environments. Examples are glycine, alanine, valine, leucine, isoleucine, phenylalanine, tyrosine,
tryptophan and methionine.

b. Polar (hydrophilic) amino acids: These amino acids have polar R groups that contain functional
groups capable of forming hydrogen bonds with water molecules. Examples include serine,
threonine, cysteine, tyrosine, asparagine, glutamine, and histidine.
c. Charged amino acids: Charged amino acids can be further divided into:

Acidic amino acids: These amino acids possess a carboxyl group in their side chain, making them
negatively charged at physiological pH. Examples include aspartic acid (aspartate) and glutamic
acid (glutamate).

Basic amino acids: These amino acids contain an amino group in their side chain, conferring a
positive charge at physiological pH. Examples include lysine, arginine, and histidine.
Essential and Non-Essential Amino Acids:

a. Essential amino acids: These amino acids cannot be synthesized by the human body and must
be obtained through the diet.

1. Histidine: Histidine is essential during periods of growth and development. It plays a role
in the synthesis of histamine, a neurotransmitter, and is also involved in hemoglobin
production.
2. Isoleucine: Isoleucine is involved in muscle metabolism, immune function, and
hemoglobin synthesis. It is important for energy regulation and the maintenance of healthy
blood sugar levels.
3. Leucine: Leucine is primarily involved in protein synthesis, muscle growth, and repair. It
also plays a role in regulating blood sugar levels and energy production.
4. Lysine: Lysine is important for collagen production, which is crucial for the health of
connective tissues, skin, and bones. It is also involved in the absorption of calcium and the
synthesis of carnitine, a molecule involved in energy production.
5. Methionine: Methionine is essential for protein synthesis and is a precursor for various
important molecules, including glutathione, which has antioxidant properties. It is also
involved in the metabolism of lipids and the production of other sulfur-containing
compounds.
6. Phenylalanine: Phenylalanine is a precursor for several important molecules, including
neurotransmitters like dopamine, epinephrine, and norepinephrine. It is also involved in
the synthesis of tyrosine, another amino acid with diverse physiological functions.
7. Threonine: Threonine is involved in the synthesis of proteins, antibodies, and collagen. It
also plays a role in maintaining the balance of nitrogen in the body and supporting proper
immune function.
8. Tryptophan: Tryptophan is a precursor for serotonin, a neurotransmitter that regulates
mood, sleep, and appetite. It is also involved in the synthesis of niacin (vitamin B3), which
is important for energy production and the health of the nervous system.
9. Valine: Valine is involved in muscle metabolism, tissue repair, and the maintenance of
proper nitrogen balance in the body. It also contributes to energy production and supports
the functioning of the immune system.

b. Non-essential amino acids: These amino acids can be synthesized by the human body through
various metabolic pathways and are not required to be obtained through the diet. Examples include
alanine, arginine, asparagine, aspartate, cysteine, glutamate, glycine, proline, tyrosine and serine.

CLASSIFICATION BASED ON THEIR METABOLIC FATE

Glucogenic Amino Acids: These amino acids can be converted into glucose through various
metabolic pathways. The carbon skeletons of these amino acids are used for gluconeogenesis, the
synthesis of new glucose molecules. They include: Alanine, Arginine, Asparagine, Aspartic acid,
Cysteine, Glutamic acid, Glutamine, Glycine, Histidine, Methionine, Proline, Serine, Valine and
Threonine.
Ketogenic Amino Acids: These amino acids can be metabolized to form ketone bodies, which
can serve as an alternative fuel source for certain tissues, especially the brain, during periods of
prolonged fasting or low carbohydrate intake. Ketogenic amino acids are Leucine and Lysine.

Glucogenic and Ketogenic Amino Acids: Some amino acids are both glucogenic and ketogenic,
meaning they can be converted into glucose and ketone bodies. These amino acids include
Isoleucine, Phenylalanine, Tryptophan and Tyrosine.

PROPERTIES OF AMINO ACIDS

Polarity: The polarity of an amino acid is determined by the nature of its side chain.

Amphoteric: Amino acids possess both acidic and basic properties due to the presence of the
carboxyl and amino groups. This characteristic allows amino acids to act as buffers.

Isoelectric Point (pI): The isoelectric point of an amino acid is the pH at which the molecule
carries no net electrical charge. At this pH, the amino acid exists as a zwitterion, with the amino
group protonated and the carboxyl group deprotonated. The pI varies for each amino acid and is
important for understanding their behavior in various biochemical processes, such as protein
separation techniques and protein-protein interactions.

A zwitterion is a molecule that has both a positive and a negative charge within the same molecule,
making it electrically neutral overall. In the case of amino acids, the presence of both an amino
group (-NH2) and a carboxyl group (-COOH) allows them to exist as zwitterions. At physiological
pH, which is around 7.4, the carboxyl group of the amino acid is deprotonated (-COO-) and carries
a negative charge, while the amino group is protonated (-NH3+) and carries a positive charge. This
results in a dipolar ion with a net neutral charge, known as a zwitterion. The presence of these
charges allows for ionic interactions with other molecules in biological systems.

Hydrophobicity and Hydrophilicity: The hydrophobicity or hydrophilicity of an amino acid

Reactivity and Functional Groups: Cysteine contains a thiol (-SH) group that can form disulfide
bonds (-S-S-) with other cysteine residues, contributing to stabilizing the protein structure and
structural integrity.

Serine, threonine, and tyrosine can undergo phosphorylation, influencing protein activity and
signaling pathways.

Methionine contains a methyl thiol group (-CH2-S-CH3) as part of its side chain that allows it to
participate in methylation reactions, where it donates its methyl group to various biomolecules,
such as DNA, proteins, and neurotransmitters. Methylation reactions play crucial roles in gene
expression regulation, protein function modulation, and neurotransmitter synthesis.

Histidine has an imidazole ring in its side chain. The imidazole ring in histidine can exist in two
protonation states, depending on the pH of the environment. At lower pH (acidic conditions), the
imidazole ring is protonated, carrying a positive charge. At higher pH (basic conditions), the
imidazole ring is deprotonated, carrying no net charge. This pH sensitivity allows histidine to act
as a proton donor or acceptor, making it essential for enzyme catalysis, aids in protein structure
stabilization in various physiological processes and act as a buffer in biological system.

Isomerism
Some amino acids can exist in different isomeric forms, L and D forms, due to the presence of
chiral carbon atoms (attached to 4 other atoms) in the structure. L Serine and D Serine are shown
below.
Aromaticity
Some amino acids possess a conjugated ring of atoms (ring structure) resulting in enhanced
stability and unique chemical behavior