INTRODUCTION

From our genes to enzyme, blood to hairs and many endless things on earth are made up of proteins. Now the question rises what makes proteins? Answer is what we are about to discuss that is amino acid and peptide bonds so this amino acid combine through peptide bonds several times to build up very essential component of our plant that is protein.

Twenty different amino acids are commonly found in protein. The first amino acid to discovered was asparagine, in 1806. The last of the 20 to be found, threonine, was not identified until 1938.

STRUCTURE OF AMINO ACIDS

All 20 amino acids have one carboxyl group, one amino group, one hydrogen atom and one ( R) group attach to central carbon atom that is alpha carbon. Property of one amino acid differ from other is due to its R group. Changing of R side chain in amino acid allow amino acid to differ in polarity, optical property and electrical properties.

STRUCTURE OF AMINO ACIDS AND PEPTIDE, BIOMOLECULES AND STRUCTURAL BIOLOGY
FIGURE DEPICTING :- Structure of PROLINE amino acid

(A) CLASSIFICATION OF AMINO ACIDS BASED ON SIDE CHAIN POLARITY

(A) Non polar side chain

  • Among all 20 amino acid, nine amino acids contain non polar side chain. These are glycine, alaninne, valine, leucine, isoleucine, proline, methionine, phenylalanine and tryptophan.

(B) Uncharged polar side chain

  • Serine, threonine, cysteine, asparagine, glutamine and tyrosine are six amino acids contain uncharged polar side chains.

(C) Charged polar side chains

  • Lysine and arginine positively charged side chain. Amino acid aspartate and glutamate contains acidic side chain that contain negatively charged carboxyl group at physiological pH.

(B) CLASSIFICATION OF AMINO ACIDS BASED ON CHEMICAL NATURE OF SIDE CHAIN

  • Aromatic ring – phenylalanine, tryptophan and histidine
  • Butyl amino side chain – lysine
  • Maximum surface area / No alpha amino group / Imino R group- proline
  • Imidazole R group –histidine
  • Hydroxyl R group –serine, threonine
  • Sulphur R group –cysteine, methionine

(C) ABSORPTION OF UV RADIATION BY AROMATIC AMINO ACIDS

Tryptophan and tyrosine, and to a much lesser extent phenylalanine, absorb ultraviolet light. This accounts for the characteristic strong absorbance of light by most proteins at a wavelength of 280 nm.

STRUCTURE OF AMINO ACIDS AND PEPTIDE
FIGURE DEPICTING :- Tryptophan and tyrosine absorbs light at 280 nm whereas phenylalanine absorbs UV rays at 257.4 nm.

(D) ISOMERISM

All amino acids (except glycine) exist as optical isomers in dand l-forms. For all chiral compounds, stereoisomers having a configuration related to that of L-glyceraldehyde are designated L, and stereoisomers related to D-glyceraldehyde are designated D. The functional groups of L-alanine are matched with those of L-glyceraldehyde by aligning those that can be interconverted by simple, one-step chemical reactions.

Thus the carboxyl group of L-alanine occupies the same position about the chiral carbon as does the aldehyde group of L-glyceraldehyde, because an aldehyde is readily converted to a carboxyl group via a one-step oxidation.

STRUCTURE OF AMINO ACIDS AND PEPTIDE

(E) ISOELECTRIC POINT

Titration of amino acid represents the effect of pH on amino acid structure. The characteristic pH at which the net electric charge is zero is called the isoelectric point or isoelectric pH, designated pl.

STRUCTURE OF AMINO ACIDS AND PEPTIDE

Isoelectric point can be calculated as follow :-

STRUCTURE OF AMINO ACIDS AND PEPTIDE

STRUCTURE OF PEPTIDE BOND

Two amino acid molecules can be covalently joined through a bond called amide linkage, termed a peptide bond, to yield a dipeptide lead to removal of the water molecule (dehydration) from the αcarboxyl group of one amino acid and the α-amino group of another. Peptide bond formation is an example of a condensation reaction. 

STRUCTURE OF AMINO ACIDS AND PEPTIDE
FORMATION OF PEPTIDE BOND

When many amino acids are joined, the product is called a polypeptide.

RAMACHANDRAN PLOT

Peptide conformation is defined by three dihedral angles (also known as torsion angles) called ϕ (phi), ψ(psi), and ω (omega), reflecting rotation about each of the three repeating bonds in the peptide backbone. A dihedral angle is the angle at the intersection of two planes. In the case of peptides, the planes are defined by bond vectors in the peptide backbone. Two successive bond vectors describe a plane. Three successive bond vectors describe two planes. (the central bond vector is common to both, and the angle between these two planes is what we measure to describe peptide conformation).

STRUCTURE OF AMINO ACIDS AND PEPTIDE
FIGURE DEPICTING – Dihedral angles

In principle, ϕ and ψ can have any value between −180° and +180°, but many values are prohibited by steric interference between atoms in the polypeptide backbone and amino acid side chains. The conformation in which both ϕ and ψ are 0° is prohibited for this reason; this conformation is merely a reference point for describing the dihedral angles. Backbone angle preferences in a polypeptide represent yet another constraint on the overall folded structure of a protein. Allowed values for ϕ and ψ become evident when ψ is plotted versus ϕ in a Ramachandran plot introduced by G. N. Ramachandran.,

Ramachandran plots are very useful graph. They are often used to test the quality of threedimensional protein structures that are deposited in international databases. 

RAMACHANDRAN PLOT SHOWING ALLOWING ANGLES
RAMACHANDRAN PLOT SHOWING ALLOWING ANGLES

CONCLUSION

Amino acids are compounds containing carbon, hydrogen, oxygen and nitrogen. Amino acid serves as building block of protein. Proteins that are made from amino acids constitute the largest fraction (beside water) of the cell. All the amino acids are different from other in its polarity, chemical nature and also through its optical activity. Some of the amino acids are aliphatic while some are aromatic, few are positively charge while other with no charge on it, some contain sulphur while other consist of carboxyl group. This difference in structure of amino acid is responsible for different properties of proteins.

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