Definition of Peptide:
Peptides are biopolymers of amino acids in which amino acids are joined by peptide bonds. Peptides are naturally occurring biological molecules. They are short chains of amino acid monomers joined by peptide (amide) bonds. Covalent chemical bonds are created if carboxyl group of one amino acid reacts with amino group of another.
Differences between Peptide and Protein:
Proteins are also polymers of amino acids. Basic distinguishing feature between peptide and protein is in respect to molecular weight. Amino acid polymers (polypeptides) with molecular weight greater than 10000 are termed proteins while those with molecular weight less than 10000 are known as peptide. In several proteins, two or more polypeptides are related via covalent (disulfide bridge) or noncovalent hydrophobic interactions.
Peptide Bond Formation and the Nomenclature of Peptide:
i) Peptide Bond Formation:
Peptides are prepared through covalent bonding between two or more amino acids molecules. This covalent bond, peptide bond, is an amide linkage. Peptide bond is prepared by elimination of water molecule from α-carboxyl group of one amino acid and α-amino group of another as shown:
This peptide bond formation is begun via attack of lone-pair electrons of amine on carbonyl carbon of carboxyl group. If such condensation polymer comprises of 2 amino acids joined by the peptide bond, it is referred to as dipeptide. 3 amino acids can be attached by 2 peptide bonds to create tripeptide. Likewise, 4 amino acids will create tetrapeptide whereas 5 amino acids will create pentapeptide and so forth. Polymers made up of few (3-10) amino acids residues are called as oligopeptide. Term polypeptide refers to the polymer having several amino acid residues. Amino acid unit which exists as part of peptide is frequently called residue or amino acid residue, in recognition of loss of molecule of water in polymerization. Precise number of water molecule lost is one less than number of residues.
ii) Nomenclature of Peptides:
In the peptide, amino acid residue is associated to its neighbor in the head-to tail manner, creating linear polymer. End of linear polymer with the free α-amino group is N-terminus while amino acid residue at this end is known as amino terminal (or N-terminal) residue. In same way, opposite end of polymer with the free carboxyl group and its terminal amino acid are known as C-terminus and carboxyl-terminal residue respectively.
The peptide is named according to amino acid residues in it and generally starts with N-terminal residue. Therefore, pentapeptide in fig. below is named serylglycyltyrosylalanylleucine and abbreviated as ser-Gly-Tyr-Ala-Leu or SGYAL (using one-letter abbreviation).
In describing amino acid sequence of the peptide, it is expected to place amino-terminal residue at left and carboxyl-terminal residue at right. Again, residues are numbered from N-terminus with N-terminal residue as 1.
Properties of Peptide Bond/Group:
Three-dimensional structure of protein is dependent on properties of amide linkages between amino acid units. Peptide bond/peptide group has the given main properties:
i) Peptide group is a resonance hybrid of the following structures:
Apart from second and third properties mentioned below, another outcome of resonance of peptide bond is that oxygen atom gets partial negative charge and NH group partial positive charge. These opposite ends of dipole tend to relate to create hydrogen bonds which are very significant in stabilizing protein structure.
ii) It is rigid and plainer. This arises from resonance interactions.
iii) It is a partial double bond. This is also because resonance.
iv) Except in few exceptions, it supposes Trans conformation in which successive Cα atoms are on opposite sides of peptide bond joining them.
v) It is 1.32 Å in length. This value is in between that of single bond (1.49 Å) and that of double bond (1.27 Å).
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