Science is complex. It’s understandable that scientists will develop a jargon, a specialized language of their discoveries. But this forms a frustrating and completely unnecessary barrier to public understanding. In this series of posts I explain fundamental processes in molecular biology, the better to breach that jargon-wall.

A cell must replicate its DNA before it divides. The structure of DNA, famously discovered by Watson and Crick, makes it a perfect molecule for encoding our genetic information. The letters of our genetic code comprise four different nucleotide molecules; adenine, thymine, cytosine and guanine. These are frequently abbreviated to A, T, C, and G. A DNA molecule is made up of two strands of polynucleotides (i.e. long strands of A, T, C, and G), coiled around each other to form the famous “double helix” structure. Just as in film photography, the negative of a photograph is the same image with its colors reversed, so too in DNA. In its sequence of nucleotide letters, each DNA strand is a “photo-negative” mirror of the other. The “A” on one strand always pairs with a “T” on the other, while “G” always pairs with “C”; a sequence like “ GATTACA ” on one strand is mirrored as “ CTAATGT ” on the other, each letter binding to its partner, zipping the strands together into a single 2-metre-long molecule. This pairing, a pairing that arises straightforwardly from the laws of Chemistry, is the key to the DNA molecule’s marvelous ability to copy itself. For each strand when unzipped from its partner grows back its missing complement, automatically creating two identical DNA molecules where once was but one.

A strand of DNA has directionality; its ends are known as the 5′ (“5 prime”) end and the 3′ (“3 prime”) end. The numbers refer to the position of the carbon atom in the deoxyribose molecules terminating the strand. Because the two strands of a DNA molecule are complementary mirrors of each other, their ends complement too: when zipped together, the 3’ end of one is the 5’ end of its partner. A DNA molecule replicates by unzipping its two strands. The now lone 3’-5’ strand grows a copy of its forsaken 5’-3’ partner; the original 5’-3’ strand meanwhile recreates its missing 3’-5’ complement. For a quick introduction to the structure of DNA, check out this YouTube video:

This directionality matters because DNA replication takes place via an enzyme known as DNA polymerase. Molecules of this enzyme start at one end of a DNA double helix and ‘walk’ along the double strand, one enzyme molecule per strand, faithfully copying our genetic code letter by letter. But the biochemical versatility of DNA polymerase is strictly limited; the molecule can construct a new strand in only one direction; the 5′ to 3′ direction. Therefore, although DNA replication is straightforward for one of the DNA strands (the 5′ to 3′ strand), the process duplicating the other strand (the 3′ to 5′ strand) is more complicated. While the 5’ to 3’ strand is replicated in one continuous string, the 3’ to 5’ strand is duplicated in segments.

Replication begins with the unwinding of a section of the DNA double helix by an enzyme known as DNA Helicase*. Helicase acts like a zip slider, unzipping a section of the DNA double helix, allowing the rest of the DNA replication enzymes to access this starting site, then moves on down the double helix, splitting another length of the strands apart.

Meanwhile DNA polymerases move along the now-unzipped strands, recreating the strands’ absent partners. The process that builds a new 3’-5’ strand is particularly contorted. An enzyme known as primase reads the template DNA and initiates the synthesis of very short complementary RNA fragments. DNA polymerase uses these RNA fragments as molds to synthesize fragments of DNA in between the RNA fragments. The RNA fragments are then removed and the fragments of DNA are joined together by another enzyme, DNA ligase.

The end replication problem

The limitations of the polymerase enzyme come to a head at the end of DNA replication, when, travelling along the template 5’-3’ strand, the enzyme at last reaches the strand’s 3’ riboxyl end. The DNA polymerase enzyme requires RNA fragments to begin replication, and there is nothing for such a fragment to attach to at the 3’ end of the DNA strand. Therefore, with every round of replication, a small fragment of the DNA is lost from the end of the chromosome, since it cannot be replicated. The cell solves this problem by having telomeres at the ends of chromosomes, where they prevent the loss of valuable genetic information by acting as a disposable buffer. Over time, with each successive round of DNA replication, the telomeric DNA shortens until finally there is no more disposable buffer, at which point the cell stops dividing and enters senescence. For a visualisation of the end replication problem check out this YouTube video:



The winding problem

DNA helicase itself encounters obstacles as it unzips its way down a DNA molecule. As the DNA helicase enzyme unwinds the DNA, it builds up tension because the DNA is forced to rotate ahead of the replication point. It is possible to imagine this by twisting two ropes together and then pulling them apart; the closed end will coil tighter, because one twist is added for each twist that is pulled out. This YouTube video illustrates the problem:

Eventually DNA replication stops because the DNA cannot be unwound anymore; the remaining DNA is too tightly twisted. In order to release this tension to allow DNA replication to proceed, enzymes known as DNA topoisomerases cut the DNA periodically to release the tension and then splice it back together.

DNA replication is a carefully regulated process that allows our genetic material to be copied each time a cell divides. Many different enzymes coordinate their functions in order to carry out this process in a seamless manner. DNA polymerase is not error free, and any errors that are introduced are dealt with through elaborate DNA repair pathways whose story is fascinating and the pivot of advanced medical therapies — but that is another article, another day.

*hence the origin of the corny joke “I’ll be your Helicase and unzip your genes”