Chapter 9: Molecular Structure of DNA and RNA

Three landmark experiments form the evidentiary core: Griffith's bacterial transformation demonstrated the existence of a transforming principle, Avery, MacLeod, and McCarty identified DNA as this principle, and Hershey and Chase conclusively showed that DNA rather than protein constitutes the hereditary molecule. The chapter then systematically examines nucleic acid architecture, detailing how nucleotides—composed of a phosphate group, pentose sugar, and nitrogenous base—link through phosphodiester bonds to form the negatively charged sugar-phosphate backbone that serves as DNA and RNA's structural scaffold. Structural distinctions between DNA and RNA reflect their different biological roles: DNA incorporates deoxyribose and thymine, while RNA contains ribose and uracil. Watson and Crick's double helix model synthesized multiple experimental streams, particularly Chargaff's base-pairing ratios, Franklin's X-ray crystallography, and chemical reasoning about hydrogen bonding. The resulting B-DNA structure exhibits antiparallel strands twisted into a right-handed helix with approximately ten base pairs per turn, where adenine pairs exclusively with thymine and guanine with cytosine through hydrogen bonds and stabilizing base stacking interactions. The major and minor grooves created by this geometry function as critical recognition sites for regulatory proteins including transcription factors and histones. The chapter acknowledges alternative conformations like Z-DNA, a left-handed variant implicated in transcriptional regulation. Finally, the discussion of RNA structure emphasizes its predominantly single-stranded character while highlighting its capacity to fold into complex three-dimensional architectures through intramolecular base pairing, generating secondary structures such as stem-loops, bulge loops, and branched junctions. Transfer RNA and ribosomal RNA exemplify how RNA's three-dimensional conformation directly determines its biochemical function within cellular machinery.