The essentials
DNA is a long polymer of deoxyribonucleotides. Each nucleotide has a nitrogenous base, a pentose sugar (deoxyribose) and a phosphate group. Bases are purines (adenine, guanine) or pyrimidines (cytosine, thymine; uracil replaces thymine in RNA). A base joins the 1′ carbon of the sugar by an N-glycosidic bond to form a nucleoside; adding phosphate to the 5′-OH by a phosphoester bond forms a nucleotide. Nucleotides are linked by 3′–5′ phosphodiester bonds, so a strand has a free 5′ phosphate end and a 3′-OH end.
Based on X-ray diffraction data from Maurice Wilkins and Rosalind Franklin, James Watson and Francis Crick proposed the double helix model in 1953. Its features:
- Two polynucleotide chains with a sugar–phosphate backbone and bases projecting inside.
- The chains are antiparallel (one runs 5′→3′, the other 3′→5′).
- Bases pair by hydrogen bonds: A with T (two H-bonds) and G with C (three H-bonds), so a purine always pairs with a pyrimidine and the helix has uniform width.
- The chains are coiled right-handed; the pitch is 3.4 nm with about 10 base pairs per turn, so the distance between adjacent bp is about 0.34 nm.
- Chargaff's rule: in double-stranded DNA, A = T and G = C, so purines = pyrimidines.
Packaging: if the length of human DNA (about 6.6 × 10⁹ bp) is multiplied by 0.34 nm, it comes to about 2.2 m, far longer than a nucleus. In eukaryotes, DNA wraps around a positively charged histone octamer (histones are rich in lysine and arginine) to form a nucleosome, containing about 200 bp of DNA. Nucleosomes look like "beads on a string" under the electron microscope and coil further to form chromatin fibres and chromosomes. Non-histone chromosomal (NHC) proteins help in higher-level packaging. In prokaryotes, negatively charged DNA is held with some positively charged proteins in a region called the nucleoid.
Key points
- Euchromatin: loosely packed, lightly stained, transcriptionally active.
- Heterochromatin: densely packed, darkly stained, inactive.
Common mistakes
- Histones are positively charged (basic); DNA is negatively charged because of phosphates.