Monday, June 09, 2008

Evolution: DNA basics

It's been difficult to grasp the subtleties of some of the discourses on evolution without having a precise grasp of genetic biology. A general understanding can only help so far. In fact, I've found that some of the reason for my difficulties has been that much of the terminology has been used quite loosely, particularly when discussion escapes into the realms of mass communication such as journalism. In particular, the term 'gene' has been tossed about with such reckless abandon that it's all but lost useful meaning in the popular press.

Ideally, Wikipedia would always be a clarifying resource, but I've found that it's often not as clear as one might expect. In days to come, I hope to nail down some basics, starting with DNA.

Deconstructing the term DNA
Schematically, the shape of Deoxyribonucleic acid is the well-known double helix. To be literal, the name is broken down thus. An Acid by definition has hydrogen ion activity greater than that of pure water - this corresponds to a pH of less than 7 (which is neutral). Nucleic acid - mostly either DNA or RNA - is typically located within a cell's nucleus, although there are exceptions. The ribose part of the name refers to the backbone spirals - they are made of repeating groups called nucleotides, each of which is built on a nitrogen base, a phosphate, and ribose sugar. Further, in DNA the ribose sugar has an oxygen atom removed, thus the sugar is effectively deoxyribose.

These molecules are long - about 1.8 metres in humans! - but 46 of them are wrapped into each cell nucleus in our body - these are the 23 pairs of chromosomes.

The two spirals of repeating nucleotides are just infrastructure. The true value lies in the rung that connect one nucleotide to its opposite. Each nucleotide contains one of four bases, at their simplest C, G, A and T. They are paired (via hydrogen bonds) with their opposite number in one of four combinations: C with G, G with C, A with T, and T with A. There are up to 220 million of these base pairs in a human chromosome. Three base pairs in a row, called a codon, provides the blueprint for an amino acid, the building block of a protein. One codon sequence denotes the end of the DNA strand. (There are 64 possible codon sequences but only 20 amino acids, so some redundancy exists in ways of describing them.) A somewhat involved process uses the whole sequence in the manufacture of proteins, which are ultimately responsible for the development of an organism.

Before a cell divides, the two arms of the spiral separate and unwind. This requires the DNA molecule to spin at several hundred turns per second. I can't say my reading has given me a clear understanding of this process, although DNA molecules are located in specific areas of the cell nucleus, so there's unlikely to be any entanglement (and thus interference) between the different strands of DNA in a cell.

Junk DNA
Better described as non-coding DNA, this term refers to coding sections of DNA for which no function has been detected. This currently constitutes about 80% to 90% of the information stored in DNA. There's a variety of thoughts on the reason for this non-coding information. Most of it may be repetitive elements. A lot of it may be historical artifacts of evolution. It's plausible that the function of some of these sequences simply remains to be discovered. Some consider the sequences as stored away for potential future use. This is an interesting puzzle that may speak volumes on evolutionary processes. The evolutionary narrative finds demonstrated that redundant features of an organism don't tend to survive too long: carrying extra baggage costs, and the mutations that ditch unneeded baggage tend to be more successful. Either this precept doesn't apply at the DNA level, or there is some evolutionary benefit in this "junk" being maintained, which we just haven't yet fathomed.

There is some to suggest organisms habitually absorb DNA from other sources (as seen recently, bdelloid rotifers seem particularly good at this), although it's hard to say what part this plays in the mystery.

Other DNA
Mitochondrial DNA is that located outside the cell nucleus, in an organelle (an organ of the cell) called mitochondria, which are used to produce energy. This DNA is circular in shape, as is that of bacteria. In fact, it's thought that it originated from bacteria absorbed by eukaryotic cells. mDNA is inherited entirely matrilinearly; it has been found that mDNA in sperm cells have been marked for deletion. There are hundreds to thousands of copies per human cell, each with around 16,000 base pairs, which correspond to the same set of functions in most higher organisms.

Jones, S & Van Loon B (1993): Genetics For Beginners. Icon, Cambridge.
Lafferty P & Rowe J (eds, 1994): The Hutchinson Dictionary Of Science. Helicon, Oxford. [of the sources, this one has proved the most lucid, despite the brevity.]
Wikipedia: DNA, Base Pairs, Junk DNA and Mitochondrial DNA.

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