Biomolecular Structure - Primary Structure

In biochemistry, the Primary structure of a biological molecule is the exact specification of its atomic composition and the chemical bonds connecting those atoms (including stereochemistry). For a typical unbranched, un-crosslinked biopolymer (such as a molecule of DNA, RNA or typical intracellular protein), the primary structure is equivalent to specifying the sequence of its monomeric subunits, e.g., the nucleotide or peptide sequence.

Primary structure is sometimes mistakenly termed primary sequence, but there is no such term, as well as no parallel concept of secondary or tertiary sequence. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end, while the primary structure of DNA or RNA molecule is reported from the 5' end to the 3' end.

The primary structure of a nucleic acid molecule refers to the exact sequence of nucleotides that comprise the whole molecule. Frequently the primary structure encodes motifs that are of functional importance. Some examples of sequence motifs are: the C/D and H/ACA boxes of snoRNAs, Sm binding site found in spliceosomal RNAs such as U1, U2, U4, U5, U6, U12 and U3, the Shine-Dalgarno sequence, the Kozak consensus sequence and the RNA polymerase III terminator.