Molecular & Cell biology Amino acids: Building blocks of Proteins Amino …oscar.iitb.ac.in/onsiteDocumentsDirectory/Gelation/Gelation/Contents/print.pdf · condensation reaction

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.

Amino acid: Building blocks of proteins

Learning ObjectiveAfter 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• Amino acids: Building blocks of Proteins

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.

Amino acid structures and properties

Molecular & Cell biology• Amino acids Building blocks

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.



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.



Serine, threonine, aspargine, glutamine & cysteine consist of polar but uncharged side chains.



These amino acids have positively charged side chains.



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.



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.

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.



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.



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.

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.



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.



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.



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.



Amino acids are the building blocks or monomers that make up proteins.

Peptide bond formation


Amino acids are oriented in a head-to-tail 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.



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.



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.


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.

2. Asymmetric centre: Except for glycine, the a-carbon atom of all other amino acids have four different groups attached to it in a tetrahedral arrangement. This carbon atom is known as an asymmetric or chiral centre and gives rise to the phenomenon of optical isomerism. There are two amino acids,


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 unpolarized light i.e. light in which the electric vector is oriented in random, unpredictable ways.

5. Unpolarized light: Light in which the orientation of the electric field vectors is random and uncorrelated is said to be unpolarized.


9. Analyzer: Part of the polarimeter device that is capable of measuring the angle of rotation by means of a rotatable lens.

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.



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.

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.

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.

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.

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.

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).

Acid base properties of amino acids



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.
