Liam's write-only LJ

[Recycled mailing list post in case it's useful to anyone]

You've heard of DNA, right? DNA is the chemical that is the recording medium for your genetic code and the genetic code of all living organisms, right down to bacteria. You may have also heard it referred to as the "double helix".

Note the "living organisms" part. This is important.

DNA standard for De-oxy-ribose Nucleic Acid.

It is a chain of smaller molecules, called bases. There are 4 of these in most organisms, and their initials are C, G, T and A. A pairs to T, or T to A. G pairs with C, or C to G.

DNA is structured like a ladder: 2 long chains, that twist around each other. The twisting structure is why it's called a helix, and the fact that 2 chains twist around each other is why it's a double helix.

Think of a ladder. The chains are the vertical rails. The pairs of bases are the rungs.

Because in DNA, A only pairs with T, and G only pairs with C, if you split DNA down the middle, each side goes:

ACGTGCCTA

or something like that.

Given the way that bases match up, you can reconstruct the other half:

TGCACGGAT

This is a kind of error-checking, and that's why organisms use DNA for long-term storage.  Either half can be used to reconstruct the other.

When a cell divides, an enzyme comes along, splits the ladder in half down the middle like a zip, and then another enzyme reconstructs each side. Result, 2 matching copies, then the cell divides and each daughter cell gets a copy of their own.

To get at the info stored in DNA, an enzyme goes down the ladder looking for a marker for the bit it needs right now, which might for example say AAATTTAAATTT... that means "start here". Another bit later on says GGGCCCGGGCCC, meaning "stop here."  Then the enzype unzips the DNA after AAATTTAAATTT bit and makes a working copy, going along until it gets to GGGCCCGGGCCC then it stops.

The working copy only has 1 strand. It's half the ladder. It is not de-oxygenated. It is just RNA: Ribose Nucleir Acid.

It's for short-term working use, not long-term storage, because there is no error correction. No paired strand. So it's easier and quicker to read -- no unzipping or zipping required -- but it's prone to errors.

Right. That's DNA and RNA. A ladder structure (DNA, think "D for double"), and a working temporary copy, just reduced to half of it (think R for reduced).

Like I said, all living organisms use DNA. They have at least one strand of DNA, and encoded onto it are their genes, which tell them how to grow, how to make their special unique proteins, and so on. The genes are the constriction and operation manual for a cell.

How do you know if a cell is living? Well all living things do a bunch of stuff. They grow and move (even if just by growing, like most plants). They breathe: take gases in and emit different gases. They eat. They excrete the waste from the stuff they eat. They reproduce. They are irritable, that is, they respond to stimuli.

If it does all those -- grow, move, eat, breathe, pee and/or poop, respond and reproduce -- then it's alive.

Viruses are not alive.

Viruses are parasitic genes. They don't breathe or eat or reproduce. They float around, and then if they bump into the right kind of host cell, they get absorbed into it. Most of them have special signalling chemicals on the outside that tell the right kind of host cell "absorb me".

One they are inside, they split open and their genetic payload spills out. Then the host cell reads those genes and does what they say. The genes instruct the host cell to make copies of the virus. In most cases, the host cell is taken over completely, makes hundreds or thousands of copies of the virus until it bursts open and dies, scattering those thousands of baby viruses to infect other cells.

Repeat that enough and the host organism starts spraying viruses around in its spittle or in its pee or poop or sexual juices or whatever. Cold viruses make the lining of your nose and throat itchy so you cough and sneeze, spraying snot full of viruses everywhere. Someone else breathes them in, or swallows them, and they get infected.

The AIDS virus gets into your spunk or vaginal mucus and so it gets right onto the sexual or rectal membranes, invades those cells and starts getting copied again.

Viruses can't even reproduce themselves. They need to get the host's cells to do that for them.

So you can't kill them, because they aren't alive. They don't eat or breathe. You can extract them from someone's blood or snot or whatever, freeze them, and thaw them out years later and they become infective again.

But they mostly do have a complex capsule made of fats and proteins, protecting their genes. Damage or destroy that coat and they can't get into your cells and they are inactivated. They can't harm you any more. Soap does this quite nicely.

Complex animals, like us, have special immune systems that literally learn new threats and can then target them. So you could take just the capsules of viruses, with no genes in, or even a part of the capsule, like the protein spikes, and inject them into an animal's bloodstream, and its immune system goes "hey, that's not part of me, that's alien! Attack! Destroy! Exterminate!" And the immune system remembers this.

So, squirt a bit of the virus capsule into someone, they maybe get a mild fever, but they are now protected from the virus in future. When the real thing comes alone, with that matching capsule, the fore-warned immune system jumps on the invading virus and destroys it and you don't get sick.

Since viruses aren't alive and don't reproduce themselves, they only need a very small simple set of genes. A tiny, stripped-down, lightweight set.

And it's to their advantage to keep changing, so an organism that's seen last year's version with its distinctive capsule with a coat of protein spikes won't recognise this year's protein coat... and the new modified virus gets in, infects the host, gets into its cells and forces  them to start making millions of copies.

An error in copying DNA is called a mutation.

You are complex. You do not want errors in your genes. That would be bad. An error in your genes could give you cystic fibrosis, or muscular dystrophy, or sickle-cell anæmia, or hæmophilia, or a thousand other diseases, and if you don't get it you could pass it on to your children. As a complex organism with hundreds of thousands of genes, you do not want mutations. You just want a mixture of healthy genes, from other humans.

So you have error-checking and correction in your genes. They are recorded in double-stranded DNA for safety.

Viruses are not complex. They are very simple. Mutations are good for them. They don't have a metabolism to go wrong. Mutations help them. Random mutations might give them slightly different capsules from their ancestors, so they can infect hosts that have met their ancestors and are immune to them.

So some, but not all, viruses have switched from using double-stranded DNA to using single-stranded RNA instead. It's much more error-prone because there's no error-checking, but if you are an infective bunch of genes, that doesn't matter. So long as the slightly-mistaken copy of you is good enough to make other cells replicate it and make working copies, that's all it needs.

So transcription errors are very bad for you, but good for viruses that just want to infect you and get copied by your cells so they can infect other complex organisms with all sorts of lovely thick gooey sticky messy body fluids to carry other viruses around in, protecting them, keeping them nice and wet and protected until they can get into a new host and infect it.

And the circle of life continues. Hasa Diga Eebowai!

Nobody really knows where viruses came from. Some are super-simple. Some plant viruses are just little chains of DNA or RNA floating around unprotected, but then, plants don't have much of an immune system.

Some animal viruses are huge and complex. Some bacterial viruses are also super complex, like syringes with legs that are triggered by just the right sort of bacterial cell wall, and actively inject their genetic payload into the bacteria.

Bacteria are single cells, so each is very complicated because it has to do everything: move and eat and excrete and copy itself. They have genes too, in a single ring of DNA. No fancy multiple bundles like we have.

Bacteria have sex, too. They pinch off smaller rings of DNA and swap them. These are called plasmids. They are the way bacteria communicate and exchange genes.

It's possible some of those plasmids went rogue somehow and started making copies of themselves and spreading from cell to cell. That might be where viruses came from.

Multicellular animals and plants are far more complicated. Some of their cells can't survive alone and only live with the help of other, specialist cells.