Q6(c). Natural rubber and gutta-percha; nucleic acids

Introduction. Natural rubber and gutta-percha are both 1,4-polyisoprene, -(CH₂-C(CH₃)=CH-CH₂)ₙ⁻; they differ only in the geometry of the C=C in each repeat unit. Nucleic acids are polynucleotides, the information-carrying biopolymers of the cell.

(i) Natural rubber and gutta-percha

Figure: Repeat units of 1,4-polyisoprene: the two chain CH₂ groups are cis (rubber) or trans (gutta-percha) across C=C.

In natural rubber the chain CH₂ groups are cis on each double bond. The chain bends at every unit, so the molecules cannot pack in a regular lattice; they stay as random coils with weak van der Waals contacts and a low T_g (about -70°C). When stretched the coils straighten, and when released they recoil (an entropy effect): rubber is soft and elastic. Vulcanisation with sulfur cross-links the chains and stops them flowing.

In gutta-percha the double bonds are trans. The chain is nearly linear and extended, so neighbouring chains pack closely and crystallise. Gutta-percha is hard, tough and non-elastic at room temperature, softening only on warming (about 60°C).

(ii) Nucleic acids and their primary structure

Nucleic acids (DNA and RNA) are polymers of nucleotides. Each nucleotide has three parts: a pentose sugar (2-deoxyribose in DNA, ribose in RNA), a nitrogenous base attached to C-1' of the sugar by an N-glycosidic bond (purines A, G; pyrimidines C, T in DNA, U in RNA), and a phosphate group. The nucleotides are linked by 3',5'-phosphodiester bonds between the 3'-OH of one sugar and the 5'-OH of the next. The primary structure is the sequence of bases along this sugar–phosphate backbone, read from the 5' end to the 3' end.

• Backbone: alternating sugar and phosphate; each phosphate carries a negative charge at pH 7, so nucleic acids are polyanions (acids).
• Side groups: the bases point away from the backbone; their order carries the genetic information.
• Direction: one end carries a 5'-phosphate, the other an unbonded 3'-OH.
• In RNA the 2'-OH of ribose makes the backbone easier to hydrolyse in base.

Figure: Primary structure: sugar–phosphate backbone with bases on C-1' (sequence AGC, read 5' → 3').

Conclusion. (i) Natural rubber (cis-1,4-polyisoprene) is amorphous and elastic; gutta-percha (trans-1,4-polyisoprene) packs into crystals and is hard and non-elastic. (ii) Nucleic acids are polynucleotides; their primary structure is the 5'→3' base sequence on a sugar–phosphate backbone linked by 3',5'-phosphodiester bonds.

Application. Vulcanised cis-polyisoprene is the basis of tyre rubber; sequencing the primary structure of DNA underlies genetic diagnosis, forensic DNA profiling and mRNA vaccines.