Faith writes:
Repetitive units of what? What chemically is going on there? There are some claims that parts of it DO seem to have some kind of function. And how would you know what might or might not once-upon-a-time have been there from the big nothing that is now there? I mean it LOOKS like DNA at first glance but a kind of blasted functionless DNA or something like that, right?
Hi Faith,
I will only talk about repetitive elements ("junk dna") in mammals here, because that is all I know about. But I think the same principles apply to all eukaryotes (species with nuclei).
In mammals there are two types of repetitive elements, SINES and LINES. SINES are "short interspersed elements" and LINES are "long interspersed elements". SINES are stretches of DNA around 300 nucleotide "letters" long, and LINES are stretches of DNA around 5-10,000 nucleotide "letters" long. Just to give you an idea of how small these elements are, the human genome is around 3 billion nucleotides long.
When a normal gene gets converted into a protein, it first has to be transcribed. This process involves copying each nucleotide of the gene onto a single stranded RNA. The RNA sequence is the same as the DNA sequence, but it is loose, a separate molecule, and it can leave the nucleus of the cell and travel to the protein manufacturing areas outside. The genes themselves are always trapped inside the nucleus.
There are some viruses that carry out this process in reverse. They exist as separate RNA molecules and they "reverse-transcribe" themselves into the genome itself. This just means that they insert copies of themselves into the nucleus. It's exactly the same process as turning a gene into a protein, but in reverse. In order to do so, they use an enzyme called "reverse transcriptase" which carries out the copying. The nucleotide sequence for this enzyme is part of the viral RNA molecule.
It appears that some viral sequences have got caught in a loop inside the nucleus. During infection, they reverse-transcribed themselves into the nucleus long ago. Now, they occasionally transcribe themselves from DNA into RNA, but as soon as the process is completed, reverse transcription takes place, and a new copy of their nucleotide sequence is immediately inserted randomly back into the genome. These are the LINEs. They are of viral origin but are not infectious, because they are never able to leave the nucleus. LINEs consist of a bunch of ancient viral DNA, along with a copy of the reverse transcriptase enzyme.
SINEs are little chunks of viral DNA that do not have a copy of the reverse transcriptase enzyme. They usually lie right next to a LINE, and when the LINE replicates itself, the SINE gets replicated along with it.
SINES and LINES, together, make up about 35% of the human genome. This means that around one billion of your nucleotides, in every single cell, consists of millions of copies of LINEs and SINEs.
This "junk DNA" does indeed have a function - all it does it replicate itself and insert copies of itself back into the genome.
But it doesn't have a biological function in the cell that is useful for the animal "carrier". And it doesn't contain any old remnant genes. All it contains is millions of copies of old degraded viral DNA that all look more or less identical to each other. These can sometimes cause medical problems, for example if a LINE inserts itself smack in the middle of an important functional gene. This kind of random event is associated with heart disease and developmental abnormalities during pregnancy (and probably lots of other things).
Some people consider "pseudogenes" to be junk DNA as well. These are old copies of genes that were randomly duplicated during cell division. They no longer serve any function in the cell, so just degrade over time to the point where they are barely recongisable. The number of pseudogenes is much lower than the number of SINEs and LINEs.
Hope this helps!
Mick
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