![]() ![]() The secondary structure of a nucleic acid molecule refers to the base pairing interactions within one molecule or set of interacting molecules. Structural biologists solving a new atomic-resolution structure will sometimes assign its secondary structure by eye and record their assignments in the corresponding Protein Data Bank (PDB) file. Many other less formal definitions have been proposed, often applying concepts from the differential geometry of curves, such as curvature and torsion. For example, helices can adopt backbone dihedral angles in some regions of the Ramachandran plot thus, a segment of residues with such dihedral angles is often called a helix, regardless of whether it has the correct hydrogen bonds. The secondary structure of a nucleic acid is defined by the hydrogen bonding between the nitrogenous bases.įor proteins, however, the hydrogen bonding is correlated with other structural features, which has given rise to less formal definitions of secondary 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. Secondary structure is formally defined by the hydrogen bonds of the biopolymer, as observed in an atomic-resolution structure. 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. The secondary structure of a protein is the pattern of hydrogen bonds in a biopolymer. Secondary (inset) and tertiary structure of tRNA demonstrating coaxial stacking PDB: 6TNA) Of snoRNAs, LSm binding site found in spliceosomal RNAs such as U1, U2, U4, U5, U6, U12 and U3, the Shine-Dalgarno sequence, Īnd the RNA polymerase III terminator. Some examples of such motifs are: the C/D Often, the primary structure encodes sequence motifs that are of functional importance. The nucleic acid sequence refers to the exact sequence of nucleotides that comprise the whole molecule. The primary structure of a protein is reported starting from the amino N-terminus to the carboxyl C-terminus, while the primary structure of DNA or RNA molecule is known as the nucleic acid sequence reported from the 5' end to the 3' end. 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 amino acids or nucleotides. The primary structure of a biopolymer is the exact specification of its atomic composition and the chemical bonds connecting those atoms (including stereochemistry). Main articles: Protein primary structure and Nucleic acid sequence The terms primary, secondary, tertiary, and quaternary structure were introduced by Kaj Ulrik Linderstrøm-Lang in his 1951 Lane Medical Lectures at Stanford University. This leads to several recognizable domains of protein structure and nucleic acid structure, including such secondary-structure features as alpha helixes and beta sheets for proteins, and hairpin loops, bulges, and internal loops for nucleic acids. The scaffold for this multiscale organization of the molecule arises at the secondary level, where the fundamental structural elements are the molecule's various hydrogen bonds. This useful distinction among scales is often expressed as a decomposition of molecular structure into four levels: primary, secondary, tertiary, and quaternary. The structure of these molecules may be considered at any of several length scales ranging from the level of individual atoms to the relationships among entire protein subunits. ( PDB: ADNA, 1BNA, 4OCB, 4R4V, 1YMO, 1EQZ)īiomolecular structure is the intricate folded, three-dimensional shape that is formed by a molecule of protein, DNA, or RNA, and that is important to its function. Interactive image of nucleic acid structure (primary, secondary, tertiary, and quaternary) using DNA helices and examples from the VS ribozyme and telomerase and nucleosome. ![]()
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