The primary structure of a protein is the sequence of amino acids in its polypeptide chain(s), joined by peptide links.Proteins are made from about 20 different amino acids, and a chain can contain hundreds of them, so an enormous number of different sequences is possible. Each protein has one particular sequence, set by the genetic code in DNA.Sequences are usually written with three-letter abbreviations, starting from the end that has the free -NH2 group, for example Gly-Ala-Ser. Gly-Ala-Ser and Ser-Ala-Gly have different primary structures and are different compounds.
The primary structure matters because it determines everything else. The side chains, their order and their properties (polar, non-polar, acidic, basic, or containing -SH) decide how the chain folds into its secondary and tertiary structure, and so decide the protein's shape and function. Changing even one amino acid can change the shape. In sickle cell anaemia, a change of one amino acid in haemoglobin changes the way the protein behaves.Worked example. How many different tripeptides could be made from the 20 amino acids if any amino acid can be used more than once? Each of the three positions has 20 choices: 20 × 20 × 20 = 8000. For a chain of 100 amino acids the number is 20100, which is vastly more than could ever be made.The primary structure can be found by partly hydrolysing the protein into short fragments, identifying them, and working out how they overlap.
The primary structure matters because it determines everything else. The side chains, their order and their properties (polar, non-polar, acidic, basic, or containing -SH) decide how the chain folds into its secondary and tertiary structure, and so decide the protein's shape and function. Changing even one amino acid can change the shape. In sickle cell anaemia, a change of one amino acid in haemoglobin changes the way the protein behaves.Worked example. How many different tripeptides could be made from the 20 amino acids if any amino acid can be used more than once? Each of the three positions has 20 choices: 20 × 20 × 20 = 8000. For a chain of 100 amino acids the number is 20100, which is vastly more than could ever be made.The primary structure can be found by partly hydrolysing the protein into short fragments, identifying them, and working out how they overlap.