AMINO ACID

INTRODUCTION
• Amino acid, any of a group of organic molecules that consist of a basic
amino group (―NH2), an acidic carboxyl group (―COOH), and an
organic R group (or side chain) that is unique to each amino acid.
• Amino acids, often referred to as the building blocks of proteins, are
compounds that play many critical roles in your body.
• They're needed for vital processes like the building of proteins and
synthesis of hormones and neurotransmitters.
• Amino acids are organic compounds composed of nitrogen, carbon,
hydrogen and oxygen, along with a variable side chain group.
• Your body needs 20 different amino acids to grow and function properly.
Though all 20 of these are important for your health, only nine amino acids
are classified as essential.
• These are histidine, isoleucine, leucine, lysine, methionine phenylalanine,
threonine, tryptophanand valine.
•
STRUCTURE OF AMINO ACID
TYPES OF AMINO ACIDS
 MOLECULAR PROPERTIES OF AMINO
ACID
• Size
• Solubility
• Charge
• pKa
• SIZE
• The size of amino acid is measured in molecular
weight.
• The length or diameter of a protein is given in
Armstrong.
• Generally protein separation is done based on the size
of the protein.
• Gel filtration chromatography or Size exclusive
chromatography - Smaller molecules diffuse further
into the pores of the beads and therefore move
through the bed more slowly, while larger molecules
enter less or not at all and thus move through the bed
more quickly.
• SOLUBILITY
• Amino acids are generally soluble in water and insoluble in
non-polar organic solvents such as hydrocarbons.
• This reflects the presence of the zwitterions.
• In water, the ionic attractions between the ions in the solid
amino acid are replaced by strong attractions between polar
water molecules and the zwitterions.
• This is much the same as any other ionic substance
dissolving in water.
• The extent of the solubility in water varies depending on the
size and nature of the "R" group.
• The lack of solubility in non-polar organic solvents such as
hydrocarbons is because of the lack of attraction between
the solvent molecules and the zwitterions.
• Without strong attractions between solvent and amino acid,
there won't be enough energy released to pull the ionic
lattice apart.
• CHARGE
• Amino acids have net charge. The net charge of
amino acid is zero. Gererally all amino acids are
called as zwitterions. All amino acids have a
particular pH, where the number of anions is equal to
the number of cations, which is known as isoelectric
point.
• For, example if a amino acid is having its isoelectric
point at pH 6.8, and if the pH drops all the positive
charge will accumulate on one side of the amino acid
and makes it positively charged and vice verse.
• pKa
• pKa was introduced as an index to express the acidity
of weak acids, the smaller the pKa value,the stronger
the acid.
• pKa values of amino acid side chains play an
important role in defining the pH-dependent
characteristics of a protein.
• The pH-dependence of the activity displayed
by enzymes and the pH-dependence of protein
stability, for example, are properties that are
determined by the pKa values of amino acid side
chains.
 Chemical reactivity in relation to post
translation modification
• Protein synthesis
• Post-translational modification (PTM) refers to the
covalent and generally enzymatic modification of
proteins following protein biosynthesis.
• Proteins are synthesized by ribosomes translating
mRNA into polypeptide chains, which may then
undergo PTM to form the mature protein product.
• PTMs are important components in cell signaling, as
for example when prohormones are converted to
hormones.
• Post-translational modifications can occur on the amino
acid side chains or at the protein's C- or N- termini.
• Sites that often undergo post-translational
modification are those that have a functional group
that can serve as a nucleophile in the reaction:
• the hydroxyl groups of serine, threonine, and
tyrosine;
• the amine forms of lysine, arginine, and histidine; the
thiolate anion of cysteine;
• the carboxylates of aspartate and glutamate; and the
N- and C-termini.
• the amide of asparagine is a weak nucleophile, it can
serve as an attachment point for glycans.
 TYPES OF PMT
• Glycosylation: Many proteins, particularly in eukaryotic cells, are
modified by the addition of carbohydrates, a process called
glycosylation. Glycosylation in proteins results in addition of a
glycosyl group to either asparagine, hydroxylysine, serine, or
threonine. Software for studying glycosylation by glycan structure
prediction.
• Acetylation: the addition of an acetyl group, usually at the N-
terminus of the protein.
• Alkylation: The addition of an alkyl group (e.g. methyl, ethyl).
• Methylation: The addition of a methyl group, usually at lysine or
arginine residues. (This is a type of alkylation.)
• Biotinylation: Acylation of conserved lysine residues with a biotin
appendage.
• Glutamylation: Covalent linkage of glutamic acid residues to tubulin
and some other proteins.
 CONT…
• Glycylation: Covalent linkage of one to more than 40 glycine
residues to the tubulin C-terminal tail of the amino acid sequence.
• Isoprenylation: The addition of an isoprenoid group (e.g. farnesol
and geranylgeraniol).
• Lipoylation: The attachment of a lipoate functionality.
• Phosphopantetheinylation, The addition of a 4'-phosphopantetheinyl
moiety from coenzyme A, as in fatty acid, polyketide, non-
ribosomal peptide and leucine biosynthesis.
• Phosphorylation, the addition of a phosphate group, usually to
serine, tyrosine, threonine or histidine.
• Sulfation: The addition of a sulfate group to a tyrosine.
• Selenation
• C-terminal amidation
• 1. Amino group
• Amino group modification involves the addition of a
functional group at the N terminus of the amino acid
.These modifications may alter the functions of the
protein when attached to a biochemical functional group
like acetate by changing the chemical nature of the amino
acid or by structural changes like folding, conformation
distribution, stability, activity etc.
• Types of Amino group formation:
• A) Acetylation
• Acetyaltion is an acylation (introduction of an acyl group to an organic
compound) process which involves the substitution of an organic group of
acetic acid for an active hydrogen atom at the N-terminus.
• The most widespread modification in the eukaryotes is the Acetylation of
the N-terminal α-amine group of proteins. About 50% of the proteins of
yeast and approximately 90% of the proteins in humans are modified by
this mechanism. N-α-acetyltransferase (NATs) is the enzyme responsible
for the Acetylation.
• The acetylation and deacetylation takes place on lysine
residues in the N-terminal .
• Pyroglutamate Formation
• Pyroglutamate is formed through the cyclization (ring
formation in the chemical compound) of glutamine. It is
commonly observed in antibodies that contain glutamate
or glutamine residues at their N-termini. The amino group
and the glutamate or glutamine condenses to form a five-
member ring called Pyroglutamate. This residue makes
the protein more resistant to aminopeptidases and has
many functional roles.
•
• Carboxyl group formation
• Nearly all polypeptides undergo modifications after being
translated from mRNA. Many types of these modifications
occur at the ends of the polypeptide. The C-terminus of a
protein or polypeptide is the end of the amino acid chain
terminated by a free carboxyl group (-COOH).
• Amidation
• C-Terminal amidation is a common posttranslational
modification in peptide hormones. Amidation is the addition of
an amide group to the end of the polypeptide chain .
• The amide group for C-terminal amidation is contributed by a
Glycine residue. Amidation neutralizes negative charges on
the C-terminus of the polypeptide. Peptidylglycine α-
hydroxylating monooxygenase and peptidyl α-hydroxyglycine
α-amidating lyase are two enzymes associated with amidation.
• Prenylation
• Prenylation (also isoprenylation or lipidation) is the post-translational
addition of hydrophobic molecules, called prenyl groups, to a protein. The
process of prenylation is catalyzed by three enzymes: Farnesyltransferase
and Geranylgeranyltransferase I and Geranylgeranyltransferase II .
• Hydroxyl group
• Hydroxylation is a chemical process that introduces a
hydroxyl group (-OH) into an organic compound. In
biochemistry, hydroxylation reactions are often
facilitated by enzymes called hydroxylases.