Re: RNA abiogenesis question


<jjsavage@xxxxxxxxx> wrote in message news:1156460775.921232.148310@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
<snip>

And if you dont know the answer just say so, stop sounding like a tit,
making out you know the answer to a question that you dont!!! . So DONT
try to shoot him out of the air by pretending, "he doesnt understand
what hes talking about".

I didn't have to try that hard pretending when he asks whether
nucleotide activation is related to ionization.

Lol - touché. But I couldn't find a web site that explicitly said
'activated nucleotides are nucleotides with extra phosphates attached',
or anything. I probably could have looked in one of those..
whatchamacall'ems... uh, paper thingys... books.

There are some online books on biochemistry and molecular biology.
Readable with some (not excessive, IMHO) opinion). And at least
they don't throw gratuitous insults at you. ;-)

I was surprise to find you are right about finding what nucleotide
activation means just by Googling. Too bad. But since I am in
teaching mode now, I would like to point out that activating a
molecule (for example, a nucleotide) almost always means adding
something, which then will get removed later. The thing added
often involves phosphates - but sometimes it doesn't. There are
many RNA world ideas that suggest that something else besides p~p
was the original activating group.

So how is RNA made in modern-day organisms without violating
the second law of thermodynamics?

He is not asking that question, So DONT use that answer to infultrate
your BS answer.

Well, actually, that kind of was my question: how does the energy end
up in exactly the right places instead of being randomly distributed as
per the 2nd law?

And I thought I answered, but, I will admit, perhaps not clearly
enough. To take a second shot at it:

As you suggest, the RNA world scenario doesn't work if you imagine
it as happening in a homogenous world with generic energy flowing
through it. It _might_ work if the world has two kinds of places
in it - one in which nucleotides become activated somehow by the
energy, and another in which activated nucleotides become bound
together into RNA. Or it might even work if those two different
'places' were actually the same place at two different times -
during the day and at night say. There are still problems with
the scenario - you probably need catalysts, and those catalysts
either have to be very specific or else separated in space or time.

Thank you, Perplexed, for taking the time to give me a simple, thorough
answer to my question. But the hydrolysis of RNA raises a couple of
other questions for me:
1. What were the nucleotides dissolved in, if not water? I assume
they had to be in some kind of liquid for the polymerization to take
place.

Yes, a liquid or liquid crystal is needed so molecules are free to
move around. Probably water, though Steve Benner has recently
suggested that some simple nitrogen-oxygen-hydrogen molecule might
work better. I forget the name of the compound. "Aminonitrile"
maybe. It was in one of Wirt Atmar's "Lectures of the Week".

So, it is being assumed that the molecules of proto-life (like
the molecules of modern biochemistry) lived in a hostile environment;
in a medium which "wants" to destroy those molecules. So the
only proto-life molecules that have a chance are those that
can "hang-in-there" for a decent period of time, and which can
somehow contribute to reproducing themselves.

In many ways, I don't think that is an argument against the RNA
world idea. In fact, it gives it a kind of proto-biological
plausibility. As others have pointed out, the phosphodiester
bond (...~p~... in my first posting) is kinetically pretty
stable against hydrolysis - at least if the pH is near 7 and
the temperature is near 40-80C.

2. In modern cells, how do the RNAs swim from the nucleus to the
ribozomes without falling apart before they get there? Aren't cells
mostly water?

They simply diffuse there. Cells are pretty small and molecules
move pretty fast at that scale, even if they are just "wandering
around". Single-stranded molecules are fairly stable against
simple hydrolysis in the middle of a strand. Half-lifes in the
weeks, at least. (Double-stranded helical RNAs are even stabler.)
There are not - so far as I know - any enzymes in the cell that
attack in mid strand. Attacks against the end of the strand
is another issue; there are exonuclease enzymes floating around
for the express 'purpose' of breaking down miscellaneous RNA;
but mRNAs carry protection from this by carrying special 'add-ons'
at each end to discourage or stall the exonucleases.

The real problem for single-strand RNA is not hydrolysis, but
happening to twist around on itself in such a way that it performs
a 'self-lysis'. I think I read somewhere that the half-life
against this eventuality is measured in hours or less. Modern
eukaryote life defends against this by using special proteins
called SSBs. I'm not sure what prokaryotes do - they may just
rely on speed.

.

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