The primary structure of a biopolymer 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 a typical intracellular protein, or of DNA or RNA), the primary structure is equivalent to specifying the sequence of its monomeric subunits, such as peptides or nucleotides.
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) to the carboxyl terminal (C), 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. Often, the primary structure encodes sequence motifs that are of functional importance. Some examples of such motifs are: the C/D and H/ACA boxes of snoRNAs, LSm 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.
The secondary structure is the pattern of hydrogen bonds in a biopolymer. These determine the general three-dimensional form of local segments of the biopolymers, but does not describe the global structure of specific atomic positions in three-dimensional space, which are considered to be tertiary structure. Secondary structure is formally defined by the hydrogen bonds of the biopolymer, as observed in an atomic-resolution structure. In proteins, the secondary structure is defined by patterns of hydrogen bonds between backbone amine and carboxyl groups (sidechain–mainchain and sidechain–sidechain hydrogen bonds are irrelevant), where the DSSP definition of a hydrogen bond is used. In nucleic acids, the secondary structure is defined by the hydrogen bonding between the nitrogenous bases.