An amino acid sequence is the order that amino acids join together to form peptide chains, or polypeptides. If the peptide chain is a protein, the sequence of amino acids is often called the primary structure of the protein. Due to the structure of amino acids and how they bond together, the amino acid sequence is only read in one direction and is specific for the peptide being formed.

There are over 100 different amino acids with about 20 that commonly make up proteins. All amino acids have a general structure that contains one carbon with an amino group, NH3, on one side and a carboxyl group, COOH, on the other. The amino group is basic or has a positive charge, while the carboxyl group is acidic and carries a negative charge. Most amino acids only have one of each group, making them neutral in charge. Amino acids are differentiated by the R group that is attached to the central carbon.

The R group of an amino acid is a side chain that is specific to each amino acid, which can be a variety of different chemical structures. At the most basic, the R group is replaced by a hydrogen atom, which creates the amino acid glycine. Many other more advanced chemical structures can replace the R. In tyrosine, a ring structure is attached to the carbon in place of the R group, and in lysine, it is replaced by a long hydrocarbon chain – a molecule made up of a carbon backbone with hydrogen atoms attached.

To form an amino acid sequence, peptide bonds form between the amino group of one amino acid and the carboxyl group of the other. This is an example of a condensation reaction as a molecule of water is lost when the two amino acids join together. To extend the sequence to create a polypeptide, the new amino acid is always added to the carboxyl end of the peptide chain that already exists. If a protein is being formed, hundreds and even thousands of amino acids are joined together.

Proteins are formed within cells during the process of translation. The amino acid sequence necessary for each protein is determined by the DNA found in the nucleus. During transcription, the relevant gene is transcribed to make a strand of messenger RNA, or mRNA. The mRNA moves out of the nucleus and into the cell’s cytoplasm to a ribosome, where translation takes place.

The mRNA acts as a template for which amino acids need to be joined together. For each amino acid, there is a specific triplet code of nucleotides. Based on this triplet code, transfer RNA, or tRNA, carries free amino acids from the cytoplasm to the ribosome where they are joined to the existing chain. As the mRNA is translated, the amino acids are joined to form the specific amino acid sequence for that protein.