Revise Nucleic acids for IB Biology (A1.2)

The monomer (repeating unit) of a nucleic acid is the nucleotide. Each nucleotide has three parts joined together: a pentose (five-carbon) sugar in the centre, a phosphate group attached to the 5' carbon of that sugar, and a nitrogenous base attached to the 1' carbon. The sugar differs between the two nucleic acids: DNA contains deoxyribose, while RNA contains ribose. The two sugars are almost identical, but deoxyribose lacks an oxygen at the 2' carbon (it has an -H there rather than an -OH), which is the origin of the 'deoxy' in its name and part of why DNA is the more chemically stable, longer-term store.

Nucleotides join into a long chain called a polynucleotide. The phosphate on the 5' carbon of one nucleotide links to the 3' carbon (through its hydroxyl) of the next, so the sugars and phosphates form a continuous alternating backbone. Because one end of the finished strand exposes a free 5' phosphate and the other a free 3' hydroxyl, the strand has a definite direction, described as running 5' to 3'.

DNA and RNA are both polynucleotides, but three structural differences set them apart, and each difference fits their different jobs. DNA is the stable, long-term archive of genetic information; RNA is a shorter-lived working copy involved in reading out that information and making proteins. Being able to state these three contrasts precisely is a very common exam requirement.

In DNA, two polynucleotide strands wind around each other to form the famous double helix. The two sugar-phosphate backbones lie on the outside of the helix, like the side rails of a spiral ladder, while the nitrogenous bases point inwards and meet in the middle. The two strands are antiparallel: they run in opposite directions, so where one strand runs 5' to 3', its partner runs 3' to 5'. This opposite orientation is not a detail to memorise for its own sake, it is what allows the bases to line up and pair correctly all the way along the molecule.

The two strands are held together by pairing between their bases, and the pairing is not random. Adenine always pairs with thymine, and guanine always pairs with cytosine, a rule known as complementary base pairing. Each pair joins a double-ring purine to a single-ring pyrimidine, so every rung of the ladder is the same width and the helix stays uniform. The pairs are held by hydrogen bonds: two hydrogen bonds between A and T, and three between G and C. Individually these bonds are weak, but along a long molecule there are so many of them that the double helix is stable, while still able to be 'unzipped' locally when the information needs to be read or copied.

$\text{A pairs with T (2 hydrogen bonds)} \qquad \text{G pairs with C (3 hydrogen bonds)}$

Notice the division of labour between the two kinds of bond. Strong covalent bonds run ALONG each backbone, holding a single strand together; weaker hydrogen bonds run BETWEEN the two strands, holding the pair together. That combination, strong within a strand and weak between strands, is exactly what a molecule needs if it must survive intact yet be opened easily for reading and copying.

The backbone is identical in every organism, so it carries no message. The information lives in the SEQUENCE of the bases, the order in which A, G, C and T appear along a strand. With four possible bases at every position, even a short stretch of DNA can be arranged in an enormous number of ways, and it is this order that encodes the instructions for making proteins. Because the sequence has a direction, it is always read and written 5' to 3'; the same four letters in the reverse order would spell a different message, just as the letters of a word only make sense read one way.

Before the double helix was worked out, Erwin Chargaff measured the base composition of DNA from many different species. He found a consistent pattern: in every sample the amount of adenine equalled the amount of thymine, and the amount of guanine equalled the amount of cytosine, so %A = %T and %G = %C, even though the overall proportion of A-T to G-C varied from species to species. At the time this 1:1 matching was unexplained, but it becomes obvious once you know that A always pairs with T and G always pairs with C: every A on one strand is matched by a T on the other, and every G by a C. Chargaff's rules were therefore direct chemical evidence for complementary base pairing, and they let you calculate any base percentage once one is known.

The same feature that explains Chargaff's data also makes the molecule ideally suited to replication. Because each base has only one possible partner, each strand carries all the information needed to rebuild the other: it acts as a template. The weak hydrogen bonds between the base pairs allow the helix to be unzipped without breaking the strong backbone, exposing the bases so that free nucleotides can pair against each exposed strand. Since the strands are antiparallel, each is copied faithfully in the 5' to 3' direction, and the result is two identical double helices, each keeping one original strand. This is why Watson and Crick famously noted that the pairing 'immediately suggests a possible copying mechanism' for the genetic material.

The structure you have built here is the foundation for much of the rest of biology. Complementary base pairing reappears in DNA replication (A1.2 HL and beyond), in transcription where a base sequence is copied into RNA, and in translation where that sequence is read three bases at a time to build a protein. The same logic, that a fixed base pair means one strand can specify another, underpins the whole flow of genetic information. Get the double helix, antiparallel strands and base pairing secure now, and every later topic on gene expression rests on solid ground.