Department of Chemistry

/
Biochemistry / Molecular
Biology
Objectives
•What are amino acids ?
•Structure of Amino acids
•Classification of Amino acids
•Reactions of amino acids (chemistry e.t.c.)
•Proteins functions and amino acid derivatives.
•Methods of isolation and identification
Proteins mediate virtually every process that takes place in a
cell, exhibiting an almost endless diversity of functions.
Proteins are the most abundant biological macromolecules,
occurring in all cells and all parts of cells.
Proteins are the molecular instruments through which
genetic information is expressed.
All proteins, whether from the most ancient lines of
bacteria or from the most complex forms of life, are
constructed from the same ubiquitous set of 20 amino acids,
covalently linked in characteristic linear sequences.
• Proteins are found in a wide range of sizes, from relatively
small peptides with just a few amino acid residues to huge
polymers with molecular weights in the millions.
• What is most remarkable is that cells can produce proteins
with strikingly different properties and activities by joining the
same 20 amino acids in many different combinations and
sequences. Fromthese building blocks different organisms can
make such widely diverse products as enzymes, hormones,
antibodies, transporters, muscle fibers, the lens protein of the
eye, feathers, spider webs, rhinoceros horn, milk proteins,
antibiotics, mushroom poisons, and myriad other substances
having distinct biological activities
•They are the building blocks of proteins.
•They are organic compounds, which contain two
functional groups, amino group (-NH2) and carboxyl
group (-COOH).
•The amino group is usually attached to the α-carbon
atom (next to the -COOH group).
•Amino acids present in proteins are of the α-L-type i.e.
the amino (H2N-) group is present on the left side of the
vertical formula.
Hydrogen for R,
most simple,
optically
inactive
Methyl for R, a
simple functional
group to start just
like “A” (in alanine)
starts the alphabet
Valine (V)
simple again,
but shaped
like the “V” in
its name
valine
extended by
one
methylene
lopsided
valine....?
Proline (P) 3
carbon chain to
proline’s own
nitrogen,
structurally
“special” and
found in turns
Methionine
(Met) (M)
special - starts every
protein, 3 carbons
with a thioether;
methyl-blocked
sulfhydryl...?
“sulfhydryl alanine,”
reactive, can form
disulfides
alanine with a phenol
group which you
KNOW is aromatic, the
“Y” in phenyl can
remind you which 3
amino acids with names
beginning with T (the
“T”s) are aromatics
hydroxylated
phenylalanine,
one of 3 “T”s
that has “Y” in its
name so it is an
aromatic
one of 3 “T”s with a “Y” so it is aromatic, will
“tryp” you up because it is hard to
remember,
has a 3 carbon start to N (or indole ring on
methylene)
“hydroxyl
alanine
one of 3 “T”s, without
“Y” so aliphatic (also
its symbol is the first
letter of its name like
the other aliphatics), its
“threo” parts are
methyl, hydroxyl, and
hydrogen on a single C
“carboxyl alanine”
with acidic nature
noted
by suffix “ate”, the
alphabetical ordering
of
the first letter of their
names correlates with
an increase in length
of side chain
aspartate
plus one
methylene, G
is after A
3 carbon chain
linked to a C full of
only N’s
(no H’s & C has 4
bonds) through an
N
3 carbon chain
plus one
methylene to
amino,
it lies (“Lys”)
about the 3
carbon trend
Histidine
(His) (H)
3 carbons to N and
loop back through C
‘n’ N
amide
derivative
of aspartate
amide
derivative of
glutamate
Amino acids can be classified in 4 ways:
1. Based on structure
2. Based on the side chain characters
3. Based on nutritional requirements
4. Based on metabolic fate
30 Biochemistry For Medics
They are classified in three broad categories:
• Mono amino mono carboxylic acid
It is further subdivided in 5 groups:
a. Simple amino acids-example: glycine, alanine
b. Branched chain amino acids-eg: valine,leucine,isoleucine
c. Hydroxyl group containing amino acids-eg: serine, threonine
d. Sulphur containing amino acids-eg: cysteine, cystine,
methionine
e. Amide group containing amino acids-e.g.- asparagine,
glutamine
1)Classification based on structure
• Mono amino dicarboxylic acid
Example :aspartic acid, glutamic acid
• Di /poly amino mono carboxylic acid
Example : lysine, arginine
1)Classification based on structure
1)Classification based on structure
I. Aliphatic Amino Acids:
a) Mono-amino mono-carboxylic acids:
Simple amino acids: Glycine , Alanine
1)Classification based on structure
I. Aliphatic Amino Acids:
a) Mono-amino mono-carboxylic acids:
Branched chain amino acids: Valine, Leucine and Isoleucine
1)Classification based on structure
I. Aliphatic Amino Acids:
a) Mono-amino mono-carboxylic acids:
-OH group-containing amino acids: Serine and Threonine
1)Classification based on structure
I. Aliphatic Amino Acids:
a) Mono-amino mono-carboxylic acids:
Sulfur-containing amino acids: Cysteine, Cystine(Formed by linking of
two cysteine residues) and Methionine.
1) Classification based on structure
I. Aliphatic Amino Acids:
a) Mono-amino mono-carboxylic acids:
Amide group-containing amino acids:
Glutamine and Asparagine
1) Classification based on structure
I. Aliphatic Amino Acids:
a) Mono-amino di-carboxylic acids: Aspartic acid and
Glutamic acid
1) Classification based on structure
I. Aliphatic Amino Acids:
a) Di- basic mono-carboxylic acids:
Arginine and Lysine
1) Classification based on structure
ii ) Aromatic amino acids-
Phenyl alanine and tyrosine
1)Classification based on structure
iii) Heterocyclic Amino Acids: Tryptophan and Histidine
1)Classification based on structure
iv) Imino acid- Proline
Hydroxl proline
1)Classification based on structure
V.Derived Amino Acids:
Non-α-amino acids
e.g.: β-alanine, γ-amino butyric acid
(GABA), δ-amino Levulinic acid
1) Classification based on structure
V.Derived Amino Acids:
Derived and Incorporated in tissue
proteins:
e.g.: Hydroxy-proline, hydroxy-lysine
1) Classification based on structure
V. Derived Amino Acids:
 Derived but not incorporated in tissue proteins:
e.g.: Ornithine, Citrulline, Homocysteine, Argino
succinic acid
2) Classification based on side chain characters
A. Amino acids with a non-polar side-chain:
e.g.: Alanine, Valine, Leucine, Isoleucine, Phenylalanine,
Tryptophan, Proline
Each of these amino acids has a side chain that does not
bind or give off protons or participates in hydrogen or ionic
bonds.
Side chains of these amino acids can be thought of as
“Oily” or lipid like, a property that promotes hydrophobic
interactions.
Amino acids with a non-polar side-chain:
2) Classification based on side chain characters
B) Amino acids with a polar but uncharged side-chain:
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.
Amino acids with a polar but uncharged
side-chain
2) Classification based on side chain characters
C) Amino acids with a charged side-chain
a)Amino acids with a positively charged side-chain:
The basic amino acids- Lysine, Arginine and
Histidine
b)Amino acids with a negatively charged side-chain:
The acidic amino acids- Glutamic acid and Aspartic
acid
They are hydrophilic in nature.
Amino acids with a charged side-chain
3)- Classification based on nutritional requirements
I. 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 Phenylalanine.
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 acids.
4)-Classification based on metabolic fate
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.
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 21
st
Amino Acid
The other are Pyroglutamate and Pyrolysine.
Each amino acid has three letter (code) and one
letter (Symbol) abbreviations-
Examples-1) Unique first letter
Cysteine- Cys- C
Histidine- His- H
2) Priority of commonly occurring amino acids
Alanine- Ala- A (Preference over Aspartate)
Glycine- Gly-G (Preference over Glutamate)
3) Similar sounding names- Some one letter
symbols sound like the amino acids they
represent- Example
Tryptophan – W (Twyptophan)
Phenyl alanine – F
4) Letters close to initial letter
Aspartate- Asx- B( near A)
Lysine Lys- K(near L)
Amino acid abbreviations
Arginine - Guanidiniumgroup
Phenyl Alanine- Benzene group
Tyrosine - Phenol group
Tryptophan - Indole group
Histidine - Imidazole group
Proline - Pyrrolidine
Proline has a secondary amino group, hence it
is an imino acid.
Properties of amino acids
Physical properties-
Colorless
Crystalline
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 organic
solvents
High melting point(More than 200
0
c)
Amino acids can exist as ampholytes or zwitterions in
solution, depending upon pH of the medium.
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.
If HCl is added drop wise to am amino acid solution, at
a particular pH, 50 % of the molecules are in the cationic
form and 50% are in the zwitterion form. This pH is pK1
(with regard to COOH)
If the titration is done from the Isoelectric point with
NaOH, molecules acquire the anionic form. When 50 % of
the molecules are in the anionic form and 50% are in the
zwitterion form. This pH is pK2(with regard to NH
2
)
For mono amino mono
carboxylic amino acids-
pI = pK1+pK2
-------------
2
The buffering action is
maximum in and around
pK1 or at pK2 but is
minimum at pI
pK
a
of some amino acids
The α carbon of each amino acid is attached to four different
groups and is thus a chiral or optically active carbon atom.
Glycine is exceptional because there are two hydrogen
substituents at the α carbon, thus it is optically inactive.
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 L- configuration
D- amino acids are found in some antibiotics and in bacterial
cell walls.
7/5/2012 Biochemistry For Medics 66
L & D isomers of amino acids
1) Reactions due to amino group
2) Reactions due to carboxyl group
3) Reactions due to side chain
4) Reaction due to both amino and carboxyl
groups
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 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.
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.
1) Decarboxylation- Amino acids undergo alpha decarboxylation to
form corresponding amines. Examples-
Glutamic acid GABA
Histidine Histamine
Tyrosine Tyramine
2) Formation of amide linkage
• Non α carboxyl group of an acidic amino acid reacts with ammonia
by condensation reaction to form corresponding amides
Aspartic acid Asparagine
Glutamic acid Glutamine
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 phosphoproteins.
OH group containing amino acid can also form:
Glycosides – by forming
O- glycosidic bond with carbohydrate residues.
2) Reactions due to SH group (Formation of disulphide
bonds)
Cysteine has a sulfhydryl group( SH) group and can
form a disulphide (S-S) bond with another cysteine
residue.
The dimer is called Cystine
Two cysteine residues can connect two polypeptide
chains by the formation of interchain disulphide chains.
Reactions due to side chains
3)Transmethylation
The methyl group of Methionine can be
transferred after activation to an acceptor for the
formation of important biological compounds.
4)Reactions due to both amino & carboxyl groups
Formation of peptide bond
Reactions due to side chains
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 Glutamic
acid
Nitric oxide, a smooth muscle relaxant is synthesized
from Arginine.
Act as precursors for haem, creatine and glutathione,
Porphyrins, purines and pyrimidines.
S.No. Test Significance
1) Ninhydrin reaction Given by all Alpha amino acids
2) Xanthoproteic test Given by aromatic amino acids
3) Millon’s test Confirmatory test for Tyrosine
4) Biuret test Not given by free amino acids
5) Sakaguchi test Given by Arginine
6) Hopkins Cole reaction Confirmatory test for Tryptophan
7) Lead acetate test Given by cysteine and cystine but
not given by Methionine
8) Nitroprusside reaction Given by SH group containing
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