Chemistry of Amino acids
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Major concepts
1.Define amino acids &with basic structure.
2. Classify amino acids.
3. standard & the nonstandard amino acids
4. Learn three-letter abbreviations, and their single-letter code &
the occurrence of amino acids
5. Verify the Specific Roles of Some Side Chains
6. List essential amino acids, semi-essential amino acids and non-
essential amino acids
7. List general functions of amino acids.
8. Describe physical and chemical properties of amino acids
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Amino acids
• The term protein is derived from a Greek word proteios,
meaning first place.
• Berzelius ( Swedish chemist ) suggested the name proteins
to the group of organic compounds that are utmost
important to life.
• proteins are a high molecular weight . nitrogenous
macromolecules composed of many amino acids.
• Protein can be broken down into smaller monomers called
as amino acids on hydrolysis. These
• 20 amino acids are used for the synthesis of proteins by
the mRNA-directed process that occurs on ribosomes
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Amino acids…
• There are hundreds of amino acids in nature, but only
the 20 standard amino acids in different sequences and
numbers are used as building blocks of proteins in
humans
• So an indefinite number of proteins can be formed and
occur in nature.
• Thus proteins are the unbranched polymers of L- α-
amino acids.
• Amino acids are a group of organic compounds
containing two functional groups – amino and carboxyl
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AMINO ACIDS
General Structure
• All amino acids have a central carbon atom attached to a
carboxyl group, an amino group, and a hydrogen atom, as
shown in Figure I. asymmetric carbon atom
NB. the amino group is Basic and -COOH is acidic.
• R is called a side chain and can be a hydrogen, aliphatic, aromatic
or heterocyclic group
• Each amino acid has an amino group –NH2, a carboxylic acid
group– COOH and a hydrogen atom each attached to carbon
located next to the – COOH group.
• The amino acids differ from one another only in the chemical
nature of the side chain (R). 5

Amino acids…
The 20 amino acids in
proteins encoded by
DNA are shown in;
each can be
designated by a
three-letter
abbreviation and
one-letter symbol
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Table 1

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Amino acids…
Classify amino acids
1. Based on nature of side chain
1.1 Amino acids with hydrophobic properties
Non-polar amino acids: glycin, Alanine , Valine ,Leucine isoleucine ,
proline & some aromatic side chains
It contains
indole ring
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Amino acids…
1.2. Amino acids with
Hydrophilic properties on
the side chains
Polar uncharged (neutral)
amino acids:
Serine, Threonine, Tyrosine (OH
containing alcohol side group)
Methionine , Asparagine &
Glutamine
Note: Methionine can be
considered nonpolar or polar
because it has a sulfur in it.
.
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Positively charged R-group
Basic amino acids:
Arginine: It contain guanidino group and is monocarboxylic acid.
It is an intermediate in urea cycle and is precursor for nitric oxide.
Lysine: It is an essential amino acid. These are strongly polar.
Histidine :It contains imidazole ring.
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Negatively charged R-group
Acidic amino acids:
• Aspartic acid, Glutamic acid
• Are capable of forming ionic
bonds and involved in chemical
reactions
Proline
Chemically, proline is α-imino acid (not α-amino acid).
Its side chain pyrrolidine ring includes
both α-amino group and side
chain methyl group.
It forces a bend in
a polypeptide chain
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Specific Roles of Some Side Chains
• Properties of the amino acids are determined by the
functional groups in their side chains .
• In addition, the functional groups may perform some
specific roles, thereby imparting special properties to
proteins.
1. The hydroxyl groups of serine ,threonine and tyrosine
& even cysteine is exist at the catalytic sites of certain
kinds of enzyme
e.g. the enzymes that regulate energy metabolism and fuel
storage in the body.
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Specific Roles of Some Side Chains…
They can be phosphorylated, hence their charge changes from
neutral to negative, which changes the shape and function of
the enzyme proteins.
Thus, these (hydroxyl) groups are important in the regulation
of activities of these enzymes
The –OH groups of serine and threonine also similarly form
linkage with reducing end of oligosaccharide, called O-
glycosidic linkage
2. Thiol group of a cysteine can form a disulphide bond
with another cysteine through the oxidation of the two thiol
groups
The dimeric compound so formed, called cystine, is important
in cross-linking the adjacent polypeptide chains.
.
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Specific Roles of Some Side Chains ….
3. Amide bearing side chain of asparagine forms covalent
linkage with oligosaccharide unit (called N-
glycosidiclinkage) in glycoproteins
4. Aromatic side chains are responsible for the ultraviolet
absorption of most proteins, which have absorption
maxima between 275 nm and 285 nm.
Tryptophan has greater absorption in this region than the
other two aromatic amino acids.
Since nearly all proteins contain aromatic amino acids, the
amount of light absorbed at 280 nm by a protein is used as
an indirect measure of protein concentration.
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Specific Roles of Some Side Chains ….
5. Imidazole group of histidine is important in the buffering
activities of proteins.
6. Cyclic pyrrolidine group of proline introduces bend in
the peptide chain.
8. Butylammonium side chain of lysine binds with the co-
enzymes pyridoxal phosphate and biotin.
9. R group of glycine provides little stearic hindrance
because of its small size, so that proteins can bend or
rotate easily wherever glycine forms part of their structure
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Amino acids…
2. Based on nutritional requirement
a) Essential amino acids:
Essential amino acids cannot be endogenously
synthesized, and therefore, their dietary intake is essential
• Methionine, Arginine, Threonine, Tryptophan, Valine, Leucine ,
Isoleucine,, Phenylalanine, Histidine, Lysine
b)Non-essential amino acids:
The nonessential amino acids, on the other hand, can be endo-
genously synthesized in adequate quantities so as to meet the
body’s requirements.
Glutamic acid, Aspartic acid, Glutamine, Asparagine, Glycine, Alanine
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Amino acids…
(c) Semi-essential amino acids:
These are growth promoting factors since they are not
synthesized in sufficient quantity during growth of
children, pregnancy and lactating women.
 include arginine and histidine
But they are not essential for the adult individual.
Occurrence of amino acids:
All the standard amino acids mentioned above occur in
almost all proteins
Cereals are rich in acidic amino acids Asp and Glu while
collagen is rich in basic amino acids , proline and
hydroxyproline
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Amino acids…
3. Based on metabolic fate
• Glucogenic amino acids:
• Ketogenic amino acids
• Both glucogenic and ketogenic:I.
Glucogenic Amino Acids
• Those amino acids in which their carbon skeleton gets
degraded to pyrurate, α ketoglutarate, succinyl CoA,
fumrate and oxaloacetate and then converted to
Glucose and Glycogen, are called as Glucogenic amino
acids.
• These include:- Glutamic acid, Aspartic acid, Glutamine,
Asparagine, Glycine, Alanine , cysteine, tyrosine,
Arginine, Isoleucine,
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II. Ketogenic Amino Acids
• Those amino acids in which their carbon skeleton is
degraded to Acetoacetyl CoA, or acetyl CoA.
• then converted to acetone and β-hydroxy butyrate which
are the main ketone bodies are called ketogenic amino
acids.
• These includes:- leucine, and lysine.
• These amino acids have ability to form ketone bodies
which is particularly evident in untreated diabetes mellitus
in which large amounts of ketone bodies are produced by
the liver (i.e. not only from fatty acids but also from
ketogenic amino acids)
• Degradation of Leucine which is an exclusively ketogenic
amino acid makes a substantial contribution to ketone
bodies during starvation.
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III. Ketogenic and glucogenic Amino Acids
The division between ketogenic and glucogenic
amino acids is not sharp for amino acids
• (Tryptophan, phenylalanine, tyrosine and
Isoleucine are both ketogenic and glucogenic)
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Fig . Ketogenic, Glucogenic and Glucogenic-Ketogenic amino acids
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PROPERTIES OF AMINO ACIDs
A) Aminoacid are amphoteric compounds, as they contain both
acidic (COOH) and basic (NH2) groups. -NH2and-COOH groups of
amino acids are ionizable groups.
• Further, charged polar side chains of few amino acids also ionise.
• Depending on the pH of the solution these groups act as proton
donors (acids) or proton acceptors(bases).
• On the acidic side of its pI amino acids exist as a cation by
accepting a proton and on alkaline as anion by donating a proton.
• This property is called as amphoteric and therefore amino acids
are called as ampholytes.
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PROPERTIES OF AMINO ACIDs
• At a specific pH the a/ acid carries both equal number
charges and exists as dipolar ion or “Zwitterion”.
• At this point the net charge on it is zero, i.e. positive
charges and negative charges on the protein/amino acid
molecule equalizes. all the groups are ionized so , the
charges will cancel each other.
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PROPERTIES OF AMINO ACIDs…
• The net charge on an amino acid—the algebraic sum of
all the positively and negatively charged groups
present—depends upon;
– the pKa Values of its functional groups and on
– the pH of the surrounding medium.
• Altering the charge on amino acids and their derivatives
by varying the pH facilitates the physical separation of
amino acids, peptides, and proteins
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PROPERTIES OF AMINO ACIDS
B. Isomerism: Two types of isomerism are shown by amino
acids basically due to the presence of asymmetric carbon
atom
Glycine has no asymmetric carbon atom in its structure
hence is optically inactive.
(a) Stereoisomerism: All amino acids except glycine exist in
D and L isomers.
In D-amino acids – NH2 group is on the right
hand while in L- amino acids it is oriented to
the left.
Natural proteins of animals and plants
generally contain L-amino acids but D-
amino acids occur in bacteria
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PROPERTIES OF AMINO ACIDS…
(b) Optical Isomerism: All amino acids except glycine have
asymmetric carbon atom.
• all but glycine exhibit ‘optical’ activities and rotate the plane
of plane polarized light and exist as dextrorotatory (d) or
laevorotatory (l) isomers optical activity depends on the pH
and side chain
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PROPERTIES OF AMINO ACIDS…
C. Physical Properties: They are colourless, crystalline
substances, more soluble in water than in polar solvents.
Tyrosine is soluble in hot water. They have high melting point usually
more than 200°C.
They have a high dielectric constant. They possess a large dipole
moment.
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PROPERTIES OF AMINO ACIDS…
D. Chemical Properties
I. Due to Carboxylic (—COOH) Group
1. Formation of esters: They can form esters with
alcohols
2. Formation of amines by decarboxylation: Action of
specific amino acid decarboxylases, COOH group and
changes the amino acid into its amine
Fig. 6.2:Formation of amine (decarboxylation)
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II. Properties Due to Amino (–NH2) Group
1. Salt formation with acids: The basic amino group reacts with
mineral acids such as HCl to form salts like hydrochlorides (Fig.
6.4).
Fig. 6.4: Salt formation of amino acid
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III. Properties of Amino acids due to Both NH2and COOH Groups
• In addition to the property of reacting with both cation and anion,
the amino acids form chelated, co-ordination complexes with
certain heavy metals and other ions.
• These include Cu++, Co++, Mn++ and Ca++
An example of chelated complex of Ca++ and glycine is given in
below
Fig. : Chelation of glycine with Ca++ Name of compound is calcium diglycinate
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CLINICAL APPLICATION
• Chelates are non-ionic and therefore amino acids may be
used to remove calcium from bones and teeth
• It is possible that the amino acids resulting from the
breakdown of enamel and dentine could in this way form
soluble calcium complexes thereby causing a loss of calcium
and the development of caries
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Non-standard Amino Acids
• In addition to the 20 primary amino acids found in
protein, some “non-standard amino acids” are present
in small amounts in specialized structures.
• They may also occur in free or combined states and
independently play a variety of biological roles.
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Non-standard Amino Acids…
1. Non-standard amino acids found in proteins:
These amino acids are produced by specific modification of
a primary amino acid residue after the polypeptide chain has
been synthesized.
They are essential for the function of the protein.
Some examples of modified amino acids are: hydroxylysine
and hydroxyproline in collagen
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Non-standard Amino Acids…
2. Non-standard amino acids not found in proteins:
Termed non-protein amino acids, they occur in free state
in cells
e.g. Citrulline that are intermediates of urea cycle.
The most abundant amino acid in human organism,
taurine, also occurs in a free state in bile and plays an
important role in fat digestion and absorption.
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Non-standard Amino Acids..
3. Biologically active amino acids:
These amino acids are used for functions other than protein
synthesis.
Examples:
(a) as chemical messengers for communication between cells, e.g.
glycine, dopamine (tyrosine derivative), ϒ-aminobutyric acid
(glutamate derivative),
(b) as local mediator of allergic reactions, e.g. histamine
(histidine derivative), and
(c) as a hormone, e.g. thyroxine (another tyrosine derivative)
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New Amino Acids
In addition to 20 L-amino acids that take part in protein synthesis,
recently two more new amino acids described.
They are: A . Selenocysteine - 21st amino acids
B. Pyrrolysine - 22nd amino acid
A. Selenocysteine : is recently introduced as 21st amino acid.
• Selenocysteine occurs at the “active site” of several enzymes
e.g :Include: Thioredoxin reductase
Glutathione peroxidase which scavenges peroxides
B. Pyrrolysine : the 22nd Amino Acid
 Recently it has been claimed as 22nd amino acid by some
scientists
 The STOP codon UAG can code for pyrrolysine
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THANKS!!
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