The primary sequence of a protein is the order that the amino acids it contains occur in. Proteins are chains of amino acids which are joined together into a single chain by peptide bonds (Figure 1). The order of the amino acids in the chain is a linear sequence, read along the length of these peptide bonds from the N-terminal (named for the nitrogen atom in an amine group) to the C-terminal (named for the carbon atom in a carboxylic acid group) end of the protein.

Figure 1: The formation of a peptide bond between a serine and an alanine amino acid, the order of these, in this case Ser-Ala is the primary sequence. The carboxyl group of the serine molecule forms a covalent bond with the amine group of the alanine molecule to release a single water molecule, known as condensation polymerisation. A protein is translated from the amine (N) terminus to the carboxyl (C) terminus during synthesis, and the same type of bond is formed between any combination of the 20 amino acids. A protein typically has hundreds or even thousands of amino acids in the primary sequence.

There are 20 amino acids (Table 1), which have a variety of chemical properties. They can be hydrophobic or hydrophilic, acidic, alkaline or neutral, have aromatic rings or be aliphatic, include atoms like sulfur. Proteins, as diverse molecules, have a wide range of properties, and a wide variety of amino acids that can be included to facilitate them.

Table 1: The 20 main amino acids found in proteins. Also given are the amino acid’s 1 and 3 letter codes. 1 letter codes are used in protein sequence databases, and 3 letter codes in often used in scientific literature for brevity. The structures of the amino acids are shown, as well as their chemical formulae. Amino acids are broadly categorized into hydrophobic (which tend to dislike interaction with water), polar (which interact with water, but are uncharged), acidic and basic (which are negatively and positively charged when ionized respectively, and can form electrostatic interactions). Cysteine (forming salt bridges), glycine (being very flexible) and proline (being very rigid) are all characterized as special, as they have unusual properties. Not shown here are some special amino acids, including Selenocysteine, which while found in proteins, do not occur in all organisms, and are encoded by usual mechanisms in the genetic code.

Amino Acid	3 Letter Code	1 Letter Code	Type	Structure	Formula
Alanine	Ala	A	Hydrophobic		C3H7NO2
Cysteine	Cys	C	Special		C3H7NO2S
Aspartic Acid	Asp	D	Acidic		C4H7NO4
Glutamic Acid	Glu	E	Acidic		C5H9NO4
Phenylalanine	Phe	F	Hydrophobic		C9H11NO2
Glycine	Gly	G	Special		C2H5NO2
Histidine	His	H	Basic		C6H9N3O2
Isoleucine	Ile	I	Hydrophobic		C6H13NO2
Lysine	Lys	K	Basic		C6H14N2O2
Leucine	Leu	L	Hydrophobic		C6H13NO2
Methionine	Met	M	Hydrophobic		C5H11NO2S
Asparagine	Asn	N	Polar		C4H8N2O3
Proline	Pro	P	Special		C5H9NO2
Glutamine	Gln	Q	Polar		C5H10N2O3
Arginine	Arg	R	Basic		C6H14N4O2
Serine	Ser	S	Polar		C3H7NO3
Threonine	Thr	T	Polar		C4H9NO3
Valine	Val	V	Hydrophobic		C5H11NO2
Tryptophan	Trp	W	Hydrophobic		C11H12N2O2
Tyrosine	Tyr	Y	Hydrophobic		C9H11NO3

The primary amino acid sequence can be represented as a linear sequence of letters, with each letter representing one amino acid. This has given rise to protein databases, notably the UniProtKB, where such sequences of proteins can be downloaded.

The protein sequence is inherently tied to the DNA sequence associated with it. DNA, transcribed into mRNA and translated into a primary protein sequence linking these three sequences. Each combination of 3 nucleotides (known as codons) encodes a single amino acid, so it is trivial for changes in the DNA sequences to predict changes to the protein primary sequence. It is also easy to store and analyze these sequences using computer algorithms, as they are strings.

The protein primary sequence begins the story of the structure and function of a protein. Next the protein folds into a secondary structure.