• Amino Acids are the building units of proteins.
Proteins are polymers of amino acids linked
together by what is called “ Peptide bond”.
• There are about 300 amino acids occur in
nature. Only 20 of them occur in proteins.
• Each amino acid has 4 different groups
attached to α- carbon ( which is C-atom next
to COOH). These 4 groups are : amino group,
COOH gp, Hydrogen atom and side, Chain (R)
• At physiological PH (7.4), -COOH gp is
dissociated forming a negatively charged
carboxylate ion (COO-) and amino gp is
protonated forming positively charged ion
(NH3+) forming Zwitter ion
• Amino acid structures differ at the side chain (Rgroups).
• Abbreviations: three or one letter codes
• Amino acids (except glycine) have chiral centers:
• Rotate the plane of polarized light and are optically
• There are 20 commonly occurring amino acids that
make up proteins, and the order of amino acids in
proteins determines its structure and biological
• When amino acids are covalently linked to
one another, this chain can twist and fold to
form a unique three-dimensional structure
that has a specific function.
Amino Acid Structure
• Amino acids contain two functional groups, a
protonated amine and carboxylic acid in the
form of a carboxylate group.
• Amino acid carbons are named in sequence
using the Greek alphabet ( , , , , ) starting at
the carbon between the carboxyl and amino
• The carbon is also bonded to a hydrogen
atom and a larger side chain. The side chain is
unique for each amino acid.
• An amino acid, with a chiral center, has two
forms called enantiomers, which are
nonsuperimposable mirror images.
• When drawing the Fischer projection, the
carboxylate group is at the top of the structure
and the side chain (R group) is at the bottom.
• The protonated amine group can be on the
left-hand side (L form) or right-hand side (D
form) of the structure.
• The L-amino acids are the building blocks for
proteins. Some D-amino acids occur in nature,
but not in proteins.
• BUT L or D designation for an amino acid does
NOT reflect its ability to rotate plane polarized
light in a particular direction!
1 NH 3
The R group gives each amino acid its unique
identity and characteristics.
Twenty amino acids are found in most proteins.
There are nine different families of organic
compounds represented in the structures of
different amino acids. They are as follows:
Classification of amino acids
Amino acids can be classified in 4 ways:
Based on structure
Based on the side chain characters
Based on nutritional requirements
Based on metabolic fate
1)Classification based on structure
• According to number of COOH and NH2
groups i.e. according to net charge on amino
• i) Aliphatic Amino Acids
A- Monobasic, monocarboxylic amino acids i.e.
neutral or uncharged:
ii ) Aromatic amino acids
Phenyl alanine and tyrosine
iii) Heterocyclic Amino Acids:
Tryptophan and Histidine
iv) Imino acidProline: In proline, amino group enters in the ring
formation being α-imino gp so proline is an α-imino
acid rather than α-amino acid
v) Derived Amino Acids:
e.g.: β-alanine, γ-amino butyric acid (GABA),
δ-amino Levulinic acid
Derived and Incorporated in tissue proteins:
e.g.: Hydroxy-proline, hydroxy-lysine
Derived but not incorporated in tissue
e.g.: Ornithine, Citrulline, Homocysteine,
Argino succinic acid
2) Classification based on side chain
Amino Acids with a Non-polar side-chain:
e.g.: Alanine, Valine, Leucine, Isoleucine,
Phenylalanine, Tryptophan, Proline
of these amino acids has a side chain that does
not bind or give off protons or participates in
hydrogen or ionic bonds.
chains of these amino acids can be thought of
as “Oily” or lipid like, a property that promotes
B) Amino acids with a polar but
e.g. Serine, Threonine, Tyrosine, Cysteine,
Asparagine and Glutamine.
These amino acids are uncharged at neutral pH,
although the side chains of cysteine and Tyrosine
can lose a proton at an alkaline pH.
Serine , Threonine and Tyrosine each contains a
polar hydroxyl group that can participate in
hydrogen bond formation.
Side chains of Asparagine and Glutamine
contain a carbonyl group and amide group, they can
also participate in hydrogen bond formation.
C) Amino acids with a charged side-chain
a) Amino acids with a positively charged sidechain:
The basic amino acids- Lysine, Arginine and
b) Amino acids with a negatively charged
• The acidic amino acids- Glutamic acid and
• They are hydrophilic in nature.
3)- Classification based on nutritional
Essential amino acids:
These amino acids cannot be synthesized in the body and have
to be present essentially in the diet. Examples-Valine, Isoleucine,
Leucine, Lysine, Methionine, Threonine, Tryptophan and
II. Semi-essential amino acids:
These amino acids can be synthesized in the body but the rate of
synthesis is lesser than the requirement(e.g. during growth,
repair or pregnancy) Examples-Arginine and Histidine.
III. Non-essential amino acids:
These amino acids are synthesized in the body, thus their
absence in the diet does not adversely affect the growth.
Examples- Glycine, Alanine, and the other remaining amino
4)-Classification based on metabolic
The carbon skeleton of amino acids can be used either for
glucose production or for the production of ketone bodies,
Based on that
I. Both glucogenic and ketogenic amino acids:
Isoleucine, Tyrosine, Phenylalanine and Tryptophan
II. Purely Ketogenic amino acids:
Leucine and Lysine
III. Purely Glucogenic amino acids:
The remaining 14 amino acids are glucogenic. Alanine,
valine ,serine, threonine, glycine, methionine,
asparagine, glutamine, cysteine, cystine, aspartic
acid, glutamic acid, histidine and arginine.
Non standard amino acids
Of the over 300 naturally occurring amino
acids, 20 constitute the monomer units of
proteins. These 20 amino acids are called the
Primary or Standard amino acids.
Seleno cysteine is the 21st Amino Acid
The other are Pyroglutamate and
Naming of Amino acids
Each amino acid has three letter (code) and
one letter (Symbol) abbreviationsExamples-1) Unique first letter
Cysteine- Cys- C
Histidine- His- H
2) Priority of commonly occurring amino
Alanine- Ala- A (Preference over Aspartate)
Glycine- Gly-G (Preference over
Naming of Amino acids
3) Similar sounding names- Some one letter
symbols sound like the amino acids they
Tryptophan – W (Twyptophan)
Phenyl alanine – F
4) Letters close to initial letter
Aspartate- Asx- B( near A)
Lysine Lys- K(near L)
Special groups in amino acids
Arginine- Guanidinium group
Phenyl Alanine- Benzene group
Tyrosine- Phenol group
Tryptophan- Indole group
Histidine- Imidazole group
Proline has a secondary amino group,
hence it is an imino acid.
Properties of amino acids
May be sweet(Glycine, Alanine, Valine),
tasteless(Leucine) or bitter(Arginine, Isoleucine).
Aspartame- An artificial sweetener contains
Aspartic acid and Phenyl alanine.
Soluble in water, acids, alkalis but insoluble in
High melting point(More than 2000c)
Amino acids can exist as ampholytes or
zwitterions in solution, depending upon pH of the
The pH at which the amino acids exist as
zwitterions, with no net charge on them is called
Isoelectric pH or Isoelectric point.
In acidic medium, the amino acids exist as cations
In alkaline medium , they exist as anions.
Due to no net charge, there is no
electrophoretic mobility at Isoelectric pH.
Solubility and buffering capacity are also
minimum at Isoelectric pH
• pH at which amino acids exist as the zwitterion
(neutral) and carries no net charge. Thus molecule is
• The pl value can be calculated by taking the average pKa
values corresponding to the ionizable groups. For
example leucine has two ionizable groups , and its pl
value can be calculated as follows.
• Leucine exists as cation at pH below 6 and anion at pH
above 6. at the ispelectric pH leucine is found as
• Titration curve of Amino acid: in the graphical
representation of Leucine titrarion at low pH , Leucine
exists in fully protonated forms as cation. As the titration
proceeds with NaOH, Leucine loses its protons and at
isoelectric pH its become Zwitterions. Further titration
results in formation of anionic form of Leucine.
The isoelectric point (pI) of an amino acid is the pH at
which it has no net charge
Optical properties of amino acids
The α carbon of each amino acid is attached to four
different groups and is thus a chiral or optically active
Glycine is exceptional because there are two
hydrogen substituents at the α carbon, thus it is
Amino acids with asymmetric centre at the α carbon
can exist in two forms, D and L forms that are mirror
images of each other and are called Enantiomers.
All amino acids found in proteins are of Lconfiguration
D- amino acids are found in some antibiotics and in
bacterial cell walls.
1- Amination of alpha-bromocarboxylic acids provides a
straight forward method for preparing alpha- aminocarboxylic
acids. The bromoacid are conveniently prepared from
carboxylic acids by reaction with Br2 + PCl3.
Explanation of Gabriel Synthesis
• By modifying the nitrogen as a phthalimide salt the propensity of
amines to undergo multiple substitutions is removed, and a single
clean substitution reaction of 1º- and many 2º-alkylhalides takes
• Since the phthalimide substituted malonic ester has an acidic
hydrogen (colored orange) activated by the two ester groups, this
intermediate may be converted to an ambident anion and
• Finally, base catalyzed hydrolysis of the phthalimide moiety and
the esters, followed by acidification and thermal decarboxylation,
produces an amino acid and phthalic acid (not shown).
4- Resolution Method
• Resolution The three synthetic procedures described above
and many others that can be conceived, give racemic amino
acid products. If pure L or D enantiomers are desired, it is
necessary to resolve these racemic mixtures.
• A common method of resolving racemates is by diastereomeric
salt formation with a pure chiral acid or base.
• This is illustrated for a generic amino acid in the following
diagram. Be careful to distinguish charge symbols shown in
colored circles, from optical rotation signs shown in
3- Strecker Synthesis
• assembles an alpha-amino acid from ammonia (the amine
precursor), cyanide (the carboxyl precursor) and an aldehyde. This
reaction is essentially an imino analog of cyanohydrin formation.
The alpha-amino nitrile formed in this way can then be hydrolyzed
to an amino acid by either acid or base catalysis.
• Explanation of Resolution Method
• In the initial display, the carboxylic acid function contributes to
diastereomeric salt formation.
• The racemic amino acid is first converted to a benzamide derivative to
remove the basic character of the amino group.
• Next, an ammonium salt is formed by combining the carboxylic acid with an
optically pure amine, such as brucine (a relative of strychnine).
• The structure of this amine is not shown, because it is not a critical factor in
the logical progression of steps.
• Since the amino acid moiety is racemic and the base is a single enantiomer
(levorotatory in this example), an equimolar mixture of diastereomeric salts
is formed (drawn in the green shaded box).
• Diastereomers may be separated by crystallization, chromatography or other
physical manipulation and in this way one of the isomers may be isolated for
further treatment, in this illustration it is the (+):(-) diastereomer.
• Finally the salt is broken by acid treatment, giving the resolved (+)-amino
acid derivative together with the recovered resolving agent (the optically
active amine). Of course, the same procedure could be used to obtain the (-)enantiomer of the amino acid.
• Since amino acids are amphoteric, resolution could also be
achieved by using the basic character of the amine function. For
this approach we would need an enantiomerically pure chiral
acid such as tartaric acid to use as the resolving agent.
• Note that the carboxylic acid function is first esterified, so that
it will not compete with the resolving acid.
Resolution of aminoacid derivatives may also be achieved by
enzymatic discrimination in the hydrolysis of amides. For
example, an aminoacylase enzyme from pig kidneys cleaves an
amide derivative of a natural L-amino acid much faster than it
does the D-enantiomer.
• If the racemic mixture of amides shown in the green shaded box
above is treated with this enzyme, the L-enantiomer (whatever
its rotation) will be rapidly converted to its free zwitterionic
form, whereas the D-enantiomer will remain largely unchanged.
• the diastereomeric species are transition states rather than
• This separation of enantiomers, based on very different rates of
reaction is called kinetic resolution.
Reactions of amino acids
Reactions due to amino group
Reactions due to carboxyl group
Reactions due to side chain
Reaction due to both amino and carboxyl
Reactions due to amino group
Oxidative deamination-α 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
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.
Reactions due to amino group
Formation of carbamino compound
CO2 binds to α amino acid on the globin chain of
hemoglobin to form carbamino hemoglobin
The reaction takes place at alkaline pH and serves as a
mechanism for the transfer of Carbon dioxide from the
tissues to the lungs by hemoglobin.
Reactions due to carboxyl group
1) Decarboxylation- Amino acids undergo alpha
decarboxylation to form corresponding amines.
2) Formation of amide linkage
• Non α carboxyl group of an acidic amino acid reacts
with ammonia by condensation reaction to form
Reactions due to side chains
1) Ester formation
OH containing amino acids e.g. serine,
threonine can form esters with
phosphoric acid in the formation of
OH group containing amino acid can also
form: Glycosides – by forming
O- glycosidic bond with carbohydrate
Reactions due to side chains
2) Reactions due to SH group (Formation of
Cysteine has a sulfhydryl group( SH) group and
can form a disulphide (S-S) bond with another
The dimer is called Cystine
Two cysteine residues can connect two
polypeptide chains by the formation of interchain
Reactions due to side chains
The methyl group of Methionine can be
transferred after activation to an acceptor for
the formation of important biological
Reactions due to side chains
4)Reactions due to both amino & carboxyl groups
Formation of peptide bond
Special functions of Amino acids
Incorporated in to tissue proteins
Niacin, Serotonin and melatonin are
synthesized from Tryptophan
Melanin, thyroid hormone, catecholamines
are synthesized from Tyrosine
GABA (neurotransmitter) is synthesized from
Nitric oxide, a smooth muscle relaxant is
synthesized from Arginine.
Act as precursors for haem, creatine and
glutathione, Porphyrins, purines and
Colour reactions of amino acids
Given by all Alpha amino acids
Given by aromatic amino acids
Confirmatory test for Tyrosine
Not given by free amino acids
Given by Arginine
Hopkins Cole reaction
Confirmatory test for Tryptophan
Lead acetate test
Given by cysteine and cystine but not given by
Given by SH group containing amino acids
Peptides and Proteins
20 amino acids are commonly found in protein.
These 20 amino acids are linked together through “peptide bond
forming peptides and proteins (what’s the difference?).
- The chains containing less than 50 amino acids are called
“peptides”, while those containing greater than 50 amino acids
are called “proteins”.
Peptide bond formation:
α-carboxyl group of one amino acid (with side chain R1)
forms a covalent peptide bond with α-amino group of another
amino acid ( with the side chain R2) by removal of a molecule of
water. The result is : Dipeptide ( i.e. Two amino acids linked by
one peptide bond). By the same way, the dipeptide can then
forms a second peptide bond with a third amino acid (with side
chain R3) to give Tripeptide. Repetition of this process generates
a polypeptide or protein of specific amino acid sequence.
Peptide bond formation:
- Each polypeptide chain starts on the left side by free amino group of
the first amino acid enter in chain formation . It is termed (N- terminus).
- Each polypeptide chain ends on the right side by free COOH group of
the last amino acid and termed (C-terminus).
Examples on Peptides:
1- Dipeptide ( tow amino acids joined by one peptide bond):
Example: Aspartame which acts as sweetening agent being used in replacement of cane
sugar. It is composed of aspartic acid and phenyl alanine.
2- Tripeptides ( 3 amino acids linked by two peptide bonds).
Example: GSH which is formed from 3 amino acids: glutamic acid, cysteine and glycine.
It helps in absorption of amino acids, protects against hemolysis of RBC by breaking H2O2
which causes cell damage.
3- octapeptides: (8 amino acids)
Examples: Two hormones; oxytocine and vasopressin (ADH).
4- polypeptides: 10- 50 amino acids: e.g. Insulin hormone
There are four levels of protein structure (primary, secondary,
tertiary and quaternary)
The primary structure of a protein is its unique sequence of
– Lysozyme, an enzyme that attacks bacteria, consists of a
polypeptide chain of 129 amino acids.
– The precise primary structure of a protein is determined by
inherited genetic information.
– At one end is an amino acid with a free amino group the
(the N-terminus) and at the other is an amino acid with a
free carboxyl group the (the C-terminus).
High orders of Protein structure
A functional protein is not just a polypeptide chain, but one or more polypeptides
precisely twisted, folded and coiled into a molecule of unique shape (conformation).
This conformation is essential for some protein function e.g. Enables a protein to
recognize and bind specifically to another molecule e.g. hormone/receptor;
enzyme/substrate and antibody/antigen.
2- Secondary structure:
Results from hydrogen bond
formation between hydrogen of –NH
group of peptide bond and the carbonyl
oxygen of another peptide bond.
According to H-bonding there are two
main forms of secondary structure:
α-helix: It is a spiral structure resulting
from hydrogen bonding between one
peptide bond and the fourth one
β-sheets: is another form of secondary
structure in which two or more
polypeptides (or segments of the same
peptide chain) are linked together by
hydrogen bond between H- of NH- of one
chain and carbonyl oxygen of adjacent
chain (or segment).
Hydrogen bonding in α-helix: In the α-helix CO of the one amino acid residue forms H-bond
with NH of the forth one.
Supersecondary structure or Motifs :
occurs by combining secondary structure.
The combination may be: α-helix- turn- α-helix- turn…..etc
β-sheet -turn- β-sheet-turn………etc
Or: α-helix- turn- β-sheet-turn- α-helix
Turn (or bend): is short segment of polypeptides (3-4 amino acids) that connects successive
e.g. β-turn: is small polypeptide that connects successive strands of β-sheets.
• Tertiary structure is determined
by a variety of interactions (bond formation)
among R groups and between R groups and the
a. The weak interactions include:
Hydrogen bonds among polar side chains
Ionic bonds between
charged R groups ( basic and acidic amino
hydrophobic ( non polar) R
Strong covalent bonds include disulfide bridges, that form
between the sulfhydryl groups (SH) of cysteine monomers,
stabilize the structure.
Quaternary structure: results from the aggregation (combination) of two or more
polypeptide subunits held together by non-covalent interaction like H-bonds,
ionic or hydrophobic interactions.
• Examples on protein having quaternary structure:
– Collagen is a fibrous protein of three polypeptides (trimeric) that are
supercoiled like a rope.
This provides the structural strength for their role in connective tissue.
– Hemoglobin is a globular protein with four polypeptide chains (tetrameric)
– Insulin : two polypeptide chains (dimeric)
Classification of proteins
I- Simple proteins:
i.e. on hydrolysis gives only amino acids
1- Albumin and globulins: present in egg, milk and blood
They are proteins of high biological value i.e. contain all essential amino acids and easily
Types of globulins:
α1 globulin: e.g. antitrypsin: see later
α2 globulin: e.g. hepatoglobin: protein that binds hemoglobin to prevent its excretion by the
β-globulin: e.g. transferrin: protein that transport iron
γ-globulins = Immunoglobulins (antibodies) : responsible for immunity.
2- Globins (Histones): They are basic proteins rich in histidine amino acid.
They are present in :
a - combined with DNA
b - combined with heme to form hemoglobin of RBCs.
3- Gliadines are the proteins present in cereals.
4- Scleroproteins: They are structural proteins, not digested.
include: keratin, collagen and elastin.
a- α-keratin: protein found in hair, nails, enamel of teeth and outer layer of skin.
• It is α-helical polypeptide chain, rich in cysteine and hydrophobic (non polar) amino acids so
it is water insoluble.
b- collagens: protein of connective tissues found in bone, teeth, cartilage, tendons, skin and
• Collagen may be present as gel e.g. in extracellular matrix
or in vitreous humor of the eye.
• Collagens are the most important protein in mammals.
They form about 30% of total body proteins.
• There are more than 20 types of collagens, the most
common type is collagen I which constitutes about 90% of
• Structure of collagen: three helical polypeptide chains
(trimeric) twisted around each other forming triplet-helix
• ⅓ of structure is glycine, 10% proline, 10% hydroxyproline
and 1% hydroxylysine. Glycine is found in every third
position of the chain. The repeating sequence –Gly-X-Y-,
where X is frequently proline and Y is often hydroxyproline
and can be hydroxylysine.
Solubility: collagen is insoluble in all solvents and not digested.
When collagen is heated with water or dil. HCl it will be converted into gelatin which is
soluble , digestible and used as diet ( as jelly). Gelatin is classified as derived protein.
Some collagen diseases:
1- Scurvy: disease due to deficiency of vitamin C which is important coenzyme for conversion
of proline into hydroxyproline and lysine into hydroxylysine. Thus, synthesis of collagen is
decreased leading to abnormal bone development, bleeding, loosing of teeth and swollen gum.
2- Osteogenesis Imperfecta (OI): Inherited disease resulting from genetic deficiency or
mutation in gene that synthesizes collagen type I leading to abnormal bone formation in babies
and frequent bone fracture in children. It may be lethal.
C- Elastin: present in walls of large blood vessels (such as aorta). It is very important in lungs,
elastic ligaments, skin, cartilage, ..
It is elastic fiber that can be stretched to several times as its normal length.
Structure: composed of 4 polypeptide chains (tetramer), similar to collagen being having 33%
glycine and rich in proline but in that it has low hydroxyproline and absence of
Emphysema: is a chronic obstructive lung disease (obstruction of air ways) resulting from
deficiency of α1-antitrypsin particularly in cigarette smokers.
Role of α1-antitrypsin: Elastin is a lung protein. Smoke stimulate enzyme called elastase to be
secreted form neutrophils (in lung). Elastase cause
destruction of elastin of lung.
α1-antitrypsin is an enzyme (secreted from liver) and inhibit elastase and
prevent destruction of elastin. So deficiency of α1-antitrypsin especially
in smokers leads to degradation of lung and destruction of lung ( loss of
elasticity of lung, a disease called emphysema.
i.e. On hydrolysis, give protein part and non protein part and
1- Phosphoproteins: These are proteins conjugated with phosphate
group. Phosphorus is attached to oh group of serine or threonine.
e.g. Casein of milk and vitellin of yolk.
These are proteins conjugated with lipids.
Functions: a- help lipids to transport in blood
b- Enter in cell membrane structure helping lipid soluble
substances to pass through cell membranes.
proteins conjugated with sugar (carbohydrate)
e.g. – Mucin
- Some hormones such as erythropoeitin
- present in cell membrane structure
- blood groups.
4- Nucleoproteins: These are basic proteins ( e.g. histones)
conjugated with nucleic acid (DNA or RNA).
e.g. a- chromosomes: are proteins conjugated with DNA
b- Ribosomes: are proteins conjugated with RNA
5- Metalloproteins: These are proteins conjugated with metal like
iron, copper, zinc, ……
a- Iron-containing proteins: Iron may present in heme such as in
- hemoglobin (Hb)
- myoglobin ( protein of skeletal muscles and cardiacmuscle),
- catalase, peroxidases (destroy H2O2)
- tryptophan pyrrolase (desrtroy indole ring of tryptophan).
Iron may be present in free state ( not in heme) as in:
Ferritin: Main store of iron in the body. ferritin is present in liver, spleen and bone
Hemosidrin: another iron store.
Transferrin: is the iron carrier protein in plasma.
b- Copper containing proteins:
e.g. - Ceruloplasmin which oxidizes ferrous ions into ferric ions.
- Oxidase enzymes such as cytochrome oxidase.
c- Zn containing proteins: e.g. Insulin and carbonic anhydrase
d- Mg containing proteins:e.g. Kinases and phosphatases.
6-Chromoproteins: These are proteins conjugated with pigment. e.g.
- All proteins containing heme (Hb, myoglobin, ………..)
- Melanoprotein:e.g proteins of hair or iris which contain melanin.
Produced from hydrolysis of simple proteins.
e.g. - Gelatin: from hydrolysis of collagen
- Peptone: from hydrolysis of albumin