Directionality: Polynucleotide strands have a distinct orientation defined by the carbon atoms of the sugar. The 5' end terminates with a phosphate group on the fifth carbon, while the 3' end terminates with a hydroxyl group (–OH) on the third carbon.
Antiparallel Orientation: In a DNA double helix, the two strands run in opposite directions ( and ). This alignment is crucial for the stability of the helix and the accessibility of genetic information during replication.
Chemical Bonding: The 'backbone' of the strand is held together by strong covalent phosphodiester bonds, while the two strands are held together by relatively weak hydrogen bonds between complementary nitrogenous bases.
| Feature | DNA | RNA |
|---|---|---|
| Sugar | Deoxyribose | Ribose |
| Bases | A, G, C, T | A, G, C, U |
| Strands | Double-stranded (Helix) | Usually single-stranded |
| Function | Genetic storage | Protein synthesis/Regulation |
Sugar Chemistry: Ribose has a hydroxyl group (–OH) on the 2' carbon, whereas deoxyribose has a hydrogen atom (–H), making DNA more chemically stable than RNA.
Base Substitution: RNA uses Uracil (U) instead of Thymine (T). Both are pyrimidines and pair with Adenine, but Uracil is energetically less expensive to produce.
Identify the Ends: Always look for the free phosphate group to identify the 5' end and the free hydroxyl group for the 3' end in diagrams.
Bond Recognition: Distinguish between the covalent phosphodiester bonds (vertical backbone) and the hydrogen bonds (horizontal rungs). Exams often ask which bond is broken during heat-induced denaturation (it is the hydrogen bonds).
Nucleotide vs. Base: Never refer to DNA as a polymer of bases. It is a polymer of nucleotides. A base is only one-third of the monomer unit.
Verify Complementarity: When given a sequence, ensure you check both the base pairing (A-T, C-G) and the antiparallel direction (5' matches with 3').
