Protein (Part-I)

Introduction: Proteins perform multiple functions in a cell and they are the factors to control several events.They are the building blocks and work as enzyme to participate in metabolic reactions of the organism.  

Peptide Bonds: Proteins are polymers of amino acids, joined by the covalent bonds, known as pepide bond. A peptide bond is formed between carboxyl group of first and amino group of second amino acid with release of water (Figure 32.1, A,B). it is a dehydration synthesis or condensation reaction. The peptide bond has partial double bond character due to resonance and C-N bond is not free to rotate. But the bond between N-Cα and C-Cα can be able to rotate through dihedral angles designated by φ (phi) and ψ (psi). These angles can be able to rotate from -180 to +180 with few restriction. The Indian scientist G.N. ranchandran has determined the possible φ (phi) and ψ (psi) for a particular amino acid by synthesizing tripeptide with the amino of interest in the the middle. Based on these calculations, he has constructed Ramchandran plot to define the region of allowed rotation for amino acids present in a protein structure and proposed to use this to validate the 3-D structure of a protein model (Figure 32.1, C).

Amino Acids: As discussed earlier, proteins are madeup of amino acids joined by peptide bonds. Each protein can be broken into the constituents amino acids by a variety of methods to study the free amino acids. Twenty different amino acids are found in protein. The first amino acid discovered was asparagines in 1806. The name of amino acids were trivial or classical or in few cases derived from the food source from which they were isolated first. For examples; Asparagine was isolated from asparagus, glutamate from wheat gluten, tyrosine from cheese (greek tyros, cheese) and glycine has derived its name due to sweet taste (greek Glycos; sweet). 

   
Amino acids share common structure:  All 20 amino acids are α-amino acids with a common structure. Each amino acid has a carboxyl group and amine group attached to the primary carbon (the α-carbon). They differ from each other in terms of side chain or R group (Figure 32.2, A). The side chain varies in structure, chemical nature and that has influence on the over all property of amino acid. Except Glycine, each carbon is attached to the four different groups; making it a chiral centre to give streoisomers. There are two common forms of streoisomers called as enantiomers found in the amino acids. These are non-superimposable mirror images to each other, for example, L and D-alanine as given in Figure 32.2, B.