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Primary Structure of a Protein Primary Structure of a Protein The primary structure of peptides and proteins refers to the linear sequence of its amino acid structural units. The term "primary structure" was first coined by Linderstrøm-Lang in 1951. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end Primary Structure of a Protein Definition The primary structure of a protein refers to the number and sequence of amino acids, the constituent units of the polypeptide chain. The main mode of linkage of the amino acids in proteins is the peptide bond which links the α-carbonyl group of one amino acid residue to the α-amino group of the other. The proteins may consist either of one or of more peptide chains. Rigid and Planar Peptide bond Linus Pauling and Robert Carey demonstrated that the α-Carbons of adjacent amino acids are separated by three covalent bonds, arranged Cα -C - N - Cα. They also demonstrated that the amide C-N bond in a peptide is somewhat shorter(1.32 Å or 0.132 nm) than the C-N bond in a simple amide ((1.32 Å or 0.132 nm) and that the atoms associated with the bond are coplanar.

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This indicated a resonance or partial sharing of two pairs of electrons between the carbonyl oxygen and the amide nitrogen. (The planar peptide bond - Note that the oxygen and hydrogen atoms are on the opposite sides of the C-N bond. This is trans configuration.) The oxygen has a partial negative charge and the nitrogen a partial positive charge, setting up a small electric dipole. The four atoms of the peptide group (C, H, O, N) lie in a single plane, in such a way that the oxygen atom of the carbonyl group and the hydrogen atom of the amide nitrogen are trans to each other. Virtually, all peptide bonds in proteins occur in trans configuration. From these studies, Pauling and Corey concluded that the amide C-N bonds are unable to rotate freely because of their Partial double bond character. The backbone of a polypeptide chain can thus be separated by substituted methylene groups -CH(R)-. (The three bonds between sequential Cα carbons in a polypeptide chain - The N -Cα and Cα C bonds can be rotated, with bond angles designated Φ and Ψ respectively). The rigid peptide bonds limits the number of conformations that can be assumed by a polypeptide chain. However, rotation is permitted about the bond between the nitrogen and α - carbon atoms of the main chain (N - Cα) and between the α carbon and carbonyl carbon atoms (Cα - C). By convention, the degree of rotation at the N - Cα bond is called phi (Φ) and that between Cα C bond is called psi(Ψ). Again, by convention, both Φ and ψ are defined as 0o in the conformation in which the two peptide bonds connected to a single carbon are in the same plane.

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In principle, Φ and ψ can have any value between -180o and + 180o, but many values of Φ and ψ are prohibited by steric interference between atoms in the polypeptide backbone and the amino acid side chains. Amino Acid Analysis The amino acid analysis of a protein involves the acid-hydrolysis of amide or the peptide bonds. This is carried out by heating the peptide in 6 molar hydrochloric acid solution for 24 hours to give a solution that contains all the amino acids. This mixture is then subjected to ion-exchange chromatography, thereby separating all the amino acids present. The separation of these amino acids is based mainly on their acid-base properties.

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