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Molecular & Cell biology
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Amino acids: Building blocks of Proteins
Amino acid: Building blocks of proteins
Amino acids constitute the basic monomeric units of
proteins, joined together by peptide bonds. The twenty
standard amino acids can be arranged in several ways giving
rise to numerous proteins having different structures and
properties.
Learning Objective
After interacting with this Learning Object, the learner will
be able to,
Describe amino acid structure and properties.
Explain isomerism and acid-base properties of amino acids.
Define peptide bond formation in amino acid.
Molecular & Cell biology
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Amino acids Building blocks
Amino acid structures and properties
Amino acids are the building blocks or
monomers that make up proteins.
They consist of a central alpha carbon
atom bonded covalently to an amino
group, a carboxyl group, a hydrogen
atom and a variable side chain, also
called the R group.
Molecular & Cell biology
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Amino acids Building blocks
Amino acid structures and properties
Amino acids are the basic monomeric
constituents of proteins found in
varying amounts depending upon the
type of protein. They are classified
based on the properties of their side
chains or R groups which vary in size,
structure and charge. The polarity of
the side chains is one of the main
basis for classification.
Molecular & Cell biology
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Amino acids Building blocks
Amino acid structures and properties
Amino
acids
having
non-polar,
aliphatic side chains include glycine,
alanine, proline, valine, leucine,
isoleucine & methionine. Essential
amino acids are those that cannot be
synthesized de novo in the organism
and therefore must be included in the
diet. Non-essential amino acids on the
other hand, can be synthesized from
various precursors.
Molecular & Cell biology
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Amino acids Building blocks
Amino acid structures and properties
Serine,
threonine,
aspargine,
glutamine & cysteine consist of polar
but uncharged side chains.
Molecular & Cell biology
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Amino acids Building blocks
Amino acid structures and properties
These amino acids have positively
charged side chains.
Molecular & Cell biology
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Amino acids Building blocks
Amino acid structures and properties
Aspartic acid and glutamic acid are polar
and negatively charged amino acids.
Tryptophan, tyrosine and phenylalanine
are all essential amino acids having an
aromatic side chain.
Molecular & Cell biology
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Amino acids Building blocks
Isomerism in amino acids
The term ‘chirality’ arises from the
Greek
term
cheir
meaning
‘handedness’. Just like the two hands
are non-superimposable mirror images
of each other, amino acid molecules
are also non-superimposable due to
their chiral -carbon centre.
Molecular & Cell biology
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Amino acids Building blocks
Isomerism in amino acids
All amino acids except glycine contain
an asymmetric centre that makes them
chiral in nature due to which they can
rotate the plane of polarized light. The
two enantiomers, designated as D and L,
rotate the plane of polarization in
opposite directions.
Molecular & Cell biology
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Amino acids Building blocks
Isomerism in amino acids
The two enantiomers of amino acids
are non-superimposable mirror image
due to the spatial arrangement of four
different groups about the chiral carbon
atom. Rotation of either isomer about
its central axis will never give rise to
the other isomeric structure.
Molecular & Cell biology
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Amino acids Building blocks
Acid-base properties of amino acids
Amino acids in acidic medium exist in the
completely protonated form carrying a net
positive charge. This can be confirmed by
means of simple paper electrophoresis.
The sample solution is applied at the
centre of the strip and current is passed
through it. The colourless amino acid
solution can be detected by spraying the
strip with ninhydrin, which gives it a
purple colour. Migration of the spot
towards the negatively charged cathode
confirms the net positive charge of the
amino acid.
Molecular & Cell biology
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Amino acids Building blocks
Acid-base properties of amino acids
All amino acids exhibit a characteristic
titration curve with distinct pK values.
0.1N NaOH is added to the acidic
amino acid solution. The cationic form
of the amino acid is gradually
converted into its neutral or zwitterionic
form by loss of a proton from its COOH
group. This can again be confirmed by
electrophoresis where there is no
migration of the sample spot.
Molecular & Cell biology
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Amino acids Building blocks
Acid-base properties of amino acids
Number of equivalents of alkali being
consumed is plotted against the pH of
the amino acid solution to obtain the
titration curve. pK1 of glycine is found
to be 2.34 i.e. it starts to lose its
carboxyl group proton at this pH.
Molecular & Cell biology
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Amino acids Building blocks
Acid-base properties of amino acids
Removal of the proton from the amino
group constitutes the second stage of
the
titration
curve.
Continued
addition of alkali to the amino acid
solution
gradually
converts
the
zwitterionic form into the anionic
form. Migration of the sample spot
towards
the
anode
during
electrophoresis confirms this.
Molecular & Cell biology
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Amino acids Building blocks
Acid-base properties of amino acids
The pK2 of an amino acid is obtained
by continued addition of alkali to the
neutral solution of the amino acid. pK2
of glycine is found to be 9.6. Some
amino acids having positively or
negatively charged side chains will
have pK1, pK2 and pKR, which
corresponds to ionization of the side
chain. These amino acids have good
buffering capacity around 1 pH unit on
either side of their pK values.
Molecular & Cell biology
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Amino acids Building blocks
Peptide bond formation
Amino acids are the building blocks or
monomers that make up proteins.
Molecular & Cell biology
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Amino acids Building blocks
Peptide bond formation
Amino acids are oriented in a head-totail fashion and linked together such
that the carboxyl group of one amino
acid combines with the amino group
of another. Two amino acids joined
together by means of such a
condensation reaction with the loss of
a water molecule forms a dipeptide.
Many such amino acids linked together
form a polypeptide.
Molecular & Cell biology
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Amino acids Building blocks
Peptide bond formation
The peptide bond is rigid due to its
partial double bond character arising
from resonance structures. However,
the bonds between the -carbon and
amino and carboxyl groups are pure
single bonds that are free to rotate.
Molecular & Cell biology
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Amino acids Building blocks
Amino acid structures & classification
1. Amino acid: The basic monomeric unit of
polypeptides and proteins. There are twenty
standard amino acids with different structures
and properties that can be combined in
multiple ways to make up the wide range of
proteins known to us. Each amino acid is also
specified by a three-letter and single letter
code.
2. a-carbon atom: The central carbon atom of
an amino acid which is covalently bonded to an
amino group (NH2), a carboxyl group (COOH), a
hydrogen atom (H) and a variable R group. The
groups are tetrahedrally arranged around this
carbon atom.
3. Side chain: The side chain or R group is
distinct for each amino acid, giving them their
unique properties. It is on the basis of this side
chain that the amino acids are classified into
various groups.
4. Amino group: This consists of an NH2 group
covalently bonded to the central carbon atom.
Depending upon the pH of the surrounding
medium, it either exists as NH2 or NH3+ . Except
for proline which has a secondary amino group, all
amino acids have only primary amino groups.
5. Carboxyl group: A COOH group covalently
bound to the central alpha carbon atom, which
exists as either COOH or COO- depending on the
pH of the surrounding medium.
Molecular & Cell biology
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Amino acids Building blocks
Isomerism in amino acids
1. Optical isomerism: Chiral molecules interact
with plane polarized light such that they rotate
the plane of polarization either in the clockwise
or counter-clockwise direction. Depending on
which direction the molecule rotates the plane
of polarization, they are designated as (+) or
dextrorotatory (d) and (-) or laevorotatory (l).
This nomenclature is not the same as the D and
L designations, which refer to the absolute
configurations specified on the basis of their
relationship with D and L glyceraldehyde.
Majority of the amino acids found in proteins
are of the l configuration.
threonine and isoleucine, that have two chiral
centres.
3. Enantiomers: Molecules with a chiral centre
have a non-superimposable mirror image and the
two forms of this molecule are known as
enantiomers. They are designated as D and L or R
(rectus) and S (sinister) depending on the
arrangement of groups around the asymmetric
carbon atom. R and S nomenclature is based on
priority of atomic numbers of atoms directly
attached to the central asymmetric centre.
4. Light source: A source of light that gives out
2. Asymmetric centre: Except for glycine, the unpolarized light i.e. light in which the electric
a-carbon atom of all other amino acids have vector is oriented in random, unpredictable ways.
four different groups attached to it in a
tetrahedral arrangement. This carbon atom is 5. Unpolarized light: Light in which the
known as an asymmetric or chiral centre and orientation of the electric field vectors is random
gives rise to the phenomenon of optical and uncorrelated is said to be unpolarized.
isomerism. There are two amino acids,
Molecular & Cell biology
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Amino acids Building blocks
Isomerism in amino acids
6. Polarizer: A polarizer is a device that is
capable of converting unpolarized light into
plane polarized light such that the
electromagnetic waves are oriented in only a
single plane.
7. Polarimeter tube: This is a part of the
polarimeter that contains a solution of the
optically active substance whose optical
activity is to be measured. The polarimeter is
an instrument that is capable of measuring the
angle of rotation of an optically active
substance.
8. Amino acid solution: The solution
containing any of the optically active amino
acids which can be either the D-isomer or the
L-isomer.
9. Analyzer: Part of the polarimeter device that is
capable of measuring the angle of rotation by
means of a rotatable lens.
Molecular & Cell biology
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Amino acids Building blocks
Acid base properties of amino acids
1. Cationic form: All amino acids exist in the
completely protonated form in acidic medium,
known as the cationic form. Both amino and
carboxyl groups are protonated here.
5. Addition of alkali: 0.1 N NaOH solution is added
in drops to the acidic amino acid solution. This
progressively converts the cationic form into
zwitterion and finally into the anionic form.
2. Zwitterionic form: The state in which the
amino acid has no net charge is known as the
zwitterion. It is neutral due to the presence of
NH3+ and COO- groups.
6. Paper electrophoresis: One of the easiest and
quickest methods to detect whether the molecule
of interest is present in its positive, negative or
neutral state. The sample is applied at the centre
of a moistened strip of filter paper and current
passed through it. Depending upon the net charge
of the molecule, it will either migrate towards the
cathode or anode or remain stationary at the
point of application. Amino acid solutions
although colourless can be detected after
electrophoresis by means of the ninhydrin
reagent which gives it a violet colour.
3. Anionic form: In a highly alkaline medium,
all amino acids exist in their anionic form due
to the presence of COO- group.
4. Amino acid in acidic medium: To obtain the
titration curve of an amino acid, it is first taken
in a highly acidic medium such that it exists
entirely in the cationic form.
Molecular & Cell biology
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Amino acids Building blocks
Acid base properties of amino acids
7. Cathode and anode: These are oppositely
charged electrodes. The cathode is negatively
charged while the anode is positively charged.
8. Sample application: The sample to be
analyzed is applied to the centre of the
electrophoresis strip after which current is
passed through it.
9. Titration curve: The number of equivalents
of alkali being consumed during the process of
addition of alkali to the amino acid solution is
plotted against pH of the solution in the flask
to yield a unique titration curve for each amino
acid. The titration curve depicted corresponds
to that of glycine.
10. pK: Negative log of the pH at which the
catonic and neutral forms inter-convert (pK1) and
neutral and anionic forms inter-convert (pK2).
Molecular & Cell biology
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Amino acids Building blocks
Peptide bond formation
1. Peptide bond: The bond formed during the
process of linking together two amino acids
with the carboxyl group of one amino acid
being linked to the amino group of another
with the concurrent loss of a water molecule.
These bonds are planar in geometry and exhibit
partial double bond character.
2. Dipeptide: Two amino acids bonded through
a peptide bond. Many such amino acids linked
together constitute a polypeptide.
3. Ψ (psi) and φ (phi): Angle of rotation about
the bond between the a-carbon atom and
carboxyl and amino groups respectively. These
angles determine which protein conformations
will be favourable.