Amino Acids

Mehwish Nawaz
 Amino acids
• a-Amino carboxylic acids
• These are the buildings blocks of the proteins.
• Nitrogenous molecule having both acidic (Carboxyl)
and basic (amino) groups.
• R may be as simple like H or CH3 or may be more
complex.
• Second carbon after -COOH is called the α-carbon.
• α-carbon in all the amino acids is asymmetric except in
glycine where the α-carbon is symmetric.
 Five basic parts of Amino acids
• All amino acids include five basic parts:
• A central carbon atom
• A hydrogen atom
• An amino group - consisting of a nitrogen atom
and two hydrogen atoms
• A carboxyl group - consisting of a carbon atom,
two oxygen atoms, and one hydrogen atom
• An R-group or side chain - consisting of varying
atoms
General formula of Amino acids
 Distribution of proteins
• The distribution of the 20 amino acids is not
uniform in all proteins.
• 40% by weight of fibroin and 25% by weight of
collagen are accounted for glycine.
• Fibroin is all rich in alanine (30% by weight).
• Serine and threonine predominate in casein.
• Collagen (in connective tissue), gliadin (in
wheat) and zein (in corn) are rich in proline.
 Cont..
• Human serum albumin with 585 amino acid
residues has only one tryptophan moiety.
• •Pulse lack S-containing amino acid, methionine
(Met) but contain good amount of the basic
amino acid, lysine (Lys).
• •Cereals lack lysine but have sufficient quantity
of methionine.
• •When combined, these make good the
deficiency of each other through mutual
supplementation and are therefore better utilized
in human body
 Distribution of Proteins

• Amino acids with uncharged polar side chains

are relatively hydrophilic and are usually on
the outside of the proteins, while the side
chains on non-polar amino acids tend to
cluster together on the inside.
• Amino acids with acidic or basic side chains
are very polar, and they are nearly always
found on the outside of the protein molecules
 Cont..
• Because of this asymmetry, the amino acids
(except glycine) exist in two optically active
forms : those having — NH2 group to the right
are designated as D-forms and those having —
NH2 group to the left as L-forms
• However, the two amino acids, threonine and
isoleucine have two asymmetric carbon
atoms.
 Peptide Bond
• The amino acid units are linked together through
the carboxyl and amino groups to produce the
primary structure of the protein chain.
• The bond between two adjacent amino acids is a
special type of amide bond, in which the
hydrogen atom of amino (-NH2) group is replaced
by an R radical.
• •Such a substituted amide bond is known as the
peptide bond. And the chain, thus formed, by
linking together of many amino acid units is
called a peptide chain.
Peptide Bond
 Cont..
• Each peptide chain is of considerable length and may
possess from 50 to millions of amino acid units.
• •Depending on the number of amino acid, the
peptides may be termed as a dipeptide, a tripeptide
and so on.
• •If a peptide is made up of not more than 10 amino
acids, it is called an oligopeptide ; beyond that it is a
polypeptide.
• •Polypeptides when they are made up of over 100
amino acids are, sometimes, called as macropeptides.
• •Strictly speaking, the proteins are polypeptides with
more than 100 amino acids.
 Proteinoids
• Sometimes, the word ‘proteinoids’ is used for
short polypeptides containing up to 18 amino
acids.
 N- and C-terminals
• Each amino acid in the chain is termed a residue.
• The two ends of the peptide chain are named as amino
terminal and carboxyl terminal or simply as an N-
terminal and C-terminal respectively.
• These two terminal groups, one basic and another
acidic, are the only ionizable groups of any peptide
chain except those present in the side chain.
• The terminal amino acid with the free amino group is
called as the N-terminal amino acid and the one with
the free carboxyl group at the other end as C-terminal
amino acid.
 Polypeptides Have Characteristic
Amino Acid Compositions
• When completely hydrolyzed, each type of protein
yields a characteristic proportion or mixture of the
different amino acids.
• The 20 common amino acids almost never occur in
equal amounts in a protein.
• Some amino acids may occur only once or not at all in
a given type of protein; others may occur in large
numbers.
• Complete hydrolysis alone is not sufficient for an exact
analysis of amino acid composition, because some side
reactions occur during the procedure of acid hydrolysis.
 Physical Properties of Amino acids
D/L Configuration
D :Dexter L : Left

All amino acids exist in L isomer form so they are

α-L-aminoacids
 Representation of Amino Acid
• Commonly, amino acids are represented as
follows:
D and L amino acids
 Cont..
• L and D amino acids are mirror images of each
other and are non-superimposable on each
other, just like our left and right hands. Pairs
of amino acids like these are
called enantiomers.
• Only L-amino acids are constituents of
proteins. Our body synthesizes most of its own
L-amino acids; these then get incorporated
into proteins
 Optical Properties
α Carbon is asymmetric except in Glycine
Asymmetric α Carbon is optically active
It either rotate light towards right (+/d)
dextorotatory or towards left (-/l) levorotatory
Direction of light is not related to the configuration
All naturally occuring aa are L amino acids , some
being (+/d) and others (-/l)
The optical rotation of cations, anions and Zwitter
ion are different and vary according to the pH of
solution
 Dissociation
• All Amino acid dissociate in soln

• The α- head of all amino acids is dipolar

• As they dissociate they act both as acid
/bases.
• So they amphoteric /ampholyte
• Because the resulting amino acid contains one
positive and one negative charge, it is a neutral
molecule called a zwitterion.
• In neutral solution, the COOH is ionized and the NH2
is protonated
• The resulting structures have “+” and “-” charges (a
dipolar ion, or zwitterion)
• They are like ionic salts in solution
 Isoelectric point of Amino Acids
• Isoelectric point is the point along the pH
scale where the amino acid has a net zero
charge. Form B has a net zero charge and is
called a zwitterion. Form A has a net charge of
+1, and form C has a net charge of -1
 pI depends on side chain

• The 15 amino acids with thiol, hydroxyl groups

or pure hydrocarbon side chains have pI = 5.0
to 6.5 (average of the pKa’s)
• D and E have acidic side chains and a lower pI
• H, R, K have basic side chains and higher pI
Solubility
All amino acids are more or less soluble in water/Acids/Bases
Partially soluble in organic solvents(Except proline)
Practically soluble in ether
Solubility αTemp
Melting Point
Amino acids don’t have distinct melting points
In some cases more than 300 ‘C
They destroy at or near their melting point

Taste and Odour

Most are sweet
Some are tasteless
Few are bitter
They are odourless
Classification of amino acids
1. Structure Based
1. Aliphatic
2. Aromatic
3. Heterocyclic
2. Composition Based
1. mono-amino-mono-carboxylic
2. di-amino-mono-carboxylic
3. mono-amino-di-carboxylic
4. di-amino-di-carboxylic
3. Polarity Based
1. Non-polar
2. Polar
3. Acidic and polar
4. Basic and polar
4. Nutritional requirement
1. Essential
2. Non essential
3. Semi-essential.
5. based on the composition of “-R’ side chain
1. Neutral Amino Acids (or) Simple amino acids (Gla,Ala,Val,Leu,Ile)
2. Hydroxyl Group containing amino acids (Ser , Thr)
3. Sulphar Containing amino acids (Csy , Met)
4. Acidic amino acids (Asp , Glu)
5. Basic amino acids (His,Arg, Lys)
6. Heterocyclic amino acid (Trp , His)
7. Aromatic amino acid (Phe, Tyr, Trp)
8. Imino acid: (proline, Hydroxy proline)
 Polarity Based Classification of Amino
acids
• The most useful of these
classifications is based on the polarity
of the side chains. Thus, they are
grouped into the following categories:
• Non Polar R chain (8 aa)
• Polar but Uncharged R Chain(7 aa)
• Polar +Ve Charged R chain(3 aa)
• Polar -Ve Charged R chain(2 aa)
 Nonpolar
Dispersion forces and hydrophobic effects predominate in their interactions.
They cannot H-bond with water and these side chains have a characteristic
hydrophobic effect in water.
 Polar but Uncharged R Chain
Contain functional groups that can H-bond with
water and other amino acids. Include C, H, O, N and S
atoms
 Polar -Ve Charged R chain
Contain a carboxylic acid functional group with a negative charge at
neutral pH. Can H-bond with water, can form ionic interactions, and
can also serve as nucleophiles or participate in acid-base chemistry.
 Polar +Ve Charged R chain
Nitrogen containing bases with a net positive charge at neutral
pH. Can serve as proton donors in chemical reactions, and form
ionic interactions
 Abbreviations and Codes
Alanine A, Ala Leucine L, Leu
Arginine R, Arg Lysine K, Lys
Asparagine N, Asn Methionine M,
Aspartic acid D, Asp Met
Cysteine C, Cys Phenylalanine F,
Glutamine Q, Gln Phe
Proline P, Pro
Glutamic Acid E, Glu
Glycine G, Gly Serine S, Ser
Histidine H, His Threonine T, Thr
Isoleucine I, Ile Tryptophan W,
Trp
Tyrosine Y, Tyr
Valine V, Val
 Essential and Non Essential
Amino acids
There are two types of amino acids as per the nutritional
requirement.
They are classified into essential and non-essential amino acids
Essential amino acids are those that are not synthesized by the
body and are needed in the diet.
Methionine, threonine, tryptophan, valine, isoleucine, leucine
and phenylalanine are the essential amino acids.
Non-essential amino acids are those that are synthesized in the
body and are not necessary in the diet.
Glycine, alanine, serine, cysteine, tyrosine, proline, aspartic acid
and glutamic acid are the non-essential amino acids.
Semi Essential Amino Acid
Amino acids that is required in certain conditions is known as
semi essential amino acids. Arginine and histidine are two
amino acids that are grouped as semi essential amino acid.
 Chemical properties
• Reactions due to amino group
• Reactions due to carboxyl group
• Reactions due to both amino and carboxyl
groups
• Reaction due to side chain
 Oxidative deamination
• Αn amino group is removed and
corresponding α-keto acid is formed. α -keto
acid produced is either converted to glucose
or ketone bodies or is completely oxidized.
 Transamination
• Transfer of an α amino group from an amino
acid to an α keto acid to form a new amino
acid and a corresponding keto acid.
Reaction of formaldehyde

Formaldehyde reacts with the-NH2 group

to form a methylene compound.
Reaction of formaldehyde
 Salt formation with acids
• The basic amino group reacts with mineral
acids such as HCl to form salts like
hydrochlorides.
Formation of acyl derivatives

Amino group reacts with acyl anhydride or

acyl halides such as benzoyl chloride and
give acyl amino acids like benzoyl glycine
(hippuric acid). Incidentally, this is one of the
mechanisms of detoxication in which glycine
is used and this also forms the basis of one
of the liver function tests
 Decarboxylation
• Amino acids undergo alpha decarboxylation to
form corresponding amines.
• Examples
• Glutamic acid  GABA
• Histidine  Histamine
• Tyrosine  Tyramine
Decarboxylation
 Reduction to amino alcohol
• This is achieved in presence of lithium
aluminium hydride.
 Reactions due to both amino &
carboxyl groups
• Formation of peptide bond
• Carboxyl group of an amino acid binds with
amino group of another amino acid forming a
peptide bond with the loss of one molecule of
water.
 Biological roles
• Amino acids can be metabolized to produce energy.
This is especially important during fasting, when the
breakdown of muscle protein is a major source of
energy and biosynthetic precursors.
• Some amino acids act as neurotransmitters, and some
act as starting materials for the biosynthesis of
neurotransmitters, hormones, and a wide variety of
other important biochemical compounds.
• Amino acids are the primary building blocks for
proteins