By Levi Clancy for Student Reader on
Small chains of amino acids are known as peptides. These are biochemically very important; most hormones are peptides, and there are many peptide antibiotics. Proteins are long peptides, called polypeptides, and can sometimes consist of more than one polypeptide subunit interacting together. Some proteins have 104 amino acid residues (called residues because they are the residual aftermath of free amino acids hydrolyzed together), while others have about 5,000 and the protein titin has an exceptional 26,926 residues.
The amino acids sequence determines how the peptide will fold, and this conformation in turn determines its function. The number of potential peptides is theoretically limitless: a protein with n residues can have 20n potential sequences. However, this variability is limited by what is actual useful for the cell, and the peptide's stability and fidelity of synthesis. A peptide is named one of three ways, all beginning from the N terminus: Glycine-Alanine-Valine-etc; Gly-Ala-Val-etc; or, most commonly, GAV. A D amino acid is specified as GAD-V.
Free Amino Acid Structure
Approximate pKa of α-carboxyl of free amino acid: 2
Approximate pKa of α-amino of free amino acid: 9.5
Amino Acid Peptide Bond (aka Amine Linkage)
Approximate pKa of C-terminal carboxyl of peptide: 3
Approximate pKa of N-terminal amino of peptide: 8
Hydrolysis Reaction to form Amino Acid Peptide Bond (aka Amine Linkage)
Additional Topics and Terms
Structural analysis can be performed by a variety of techniques. A peptide sequence is determined by either of two approaches: directly from the protein, such as chemical sequencing and physical analysis techniques; or from the gene sequence, as a given codon can encode either start, stop or a single amino acid.
Amphipathic protein is a protein molecule which is having