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The Origin of Life

The origin of the first cells from simple replicators. The transition from the RNA-world to the
protein-world. The key role of RNA-splicing as a producing factory.
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Последняя редакция №0 от 12.02.15
URL: http://kb.mista.ru/article.php?id=938

The Origin of Life
Author: Stanislav Mitichkin (Russia, 2010)

Summary:
The origin of the first cells from simple replicators. The transition from the RNA-world to the
protein-world. The key role of RNA-splicing as a producing factory.

1. In the beginning there was a primordial soup, where a REPLICATOR appeared. It is already life.

It appeared very simply, naturally. Imagine the ancient Earth. It has water with various simple
organic molecules (nucleotides, amino acids), which can't replicate themselves. There are hot
springs of water nearby volcanoes. The Earth goes round the Sun and spins round its own axis, so
there are days and nights. It's enough.

And now a miracle happens.

In the water under the ultraviolet radiation the nucleotides (A, G, U, C) join together into a chain
by covalent bonds. The Sun is setting and the water is cooling. The chain stops growing and the
second chain starts assembling out of free nucleotides as bricks. They connect together by weak
hydrogen bonds according to the principle of complementarity.

A day is dawning, the Sun is warming the water up to ~80 degrees Celsius (it's a hot spring, right?)
and hydrogen bonds are broken. Now we have two separate but complementary chains. The Sun is
shinning with ultraviolet radiation and the chains are growing with next nucleotides by covalent
bonds. A night is coming and the water is cooling. The chains are again connecting complementary
bricks. And it goes on. In the night the chains connect bricks, in the day they separate. Connecting
the bricks at nights, separating at days. We have a REPLICATION by natural way.

A simple example. Let's assume we have a short RNA-chain: AGUC. Say, it appeared at day by random
combination of molecules (it is quite probable).

At night it creates a complementary chain:
AGUC
UCAG

At day the water warms, the hydrogen bonds break and it divides into two chains: AGUC and UCAG

Next night it again creates a complementary chain, but now two of them:
AGUC
UCAG
and
UCAG
AGUC.

At day they separate and start growing under the ultraviolet radiation:
AGUCAGUC
UCAGUCAG

And a replication started...

2. Then ribozymes appear.

So, the chain becomes longer and makes complementary connections to itself. The tails of the chain
join each other. Or second quarter joins the third quarter. Now we have got a secondary molecular
structure as a result. It's able to fold up and take part in catalysis. The molecule accelerates its
own replication (or do it for the unfolded neighbours)

How really it was in detail maybe no one would learn. Let's just assume that the replication
accelerated. Before we had only 2 chains around the clock, now we have 2000 chains during the same
time. Accelerating of a chemical reaction by 1000 times is a trifle. The modern protein enzymes
speed up chemical reactions by millions or hundreds of million times, but we will approach them
later.

So, the process is speeding up. The replication accelerated amazingly and it doesn't depend on day-
night cycle anymore. However it needs the energy income from the hot water and the ultraviolet
radiation of the Sun.

3. Mutations and the natural selection. We already have an ancient camera/xerox that multiplies
molecules in a Positive-Negative-Positive way. However, sometimes errors happen. Not always the
complementarity keeps on at 100%. Therefore we get a variety. The natural selection begins to act.
Only they survive who can replicate and do it FASTER. It means they have a more perfect catalytic
ability of their own replication.

4. Now let's assume one of "error" replicator's copies gained an ability to cut itself (self-
splicing). There is no any fantastic here. It is proven that some RNA molecules can cut itself.
Tested in vitro.

Let's look at intermediates results. We have a PRODUCING system, that can theoretically produce any
product in a form of RNA molecules, including such of them that have catalytic abilities (we are
interested only in such molecules, because the life itself is an amazingly accelerated chemical
reaction). This producing system, or in other words a FACTORY, started to produce (cut away from
itself) various kinds of RNA, that didn't code proteins yet. The RNA-factory gradually diversified
its assortment.

Thanks to some key events the transformation to a protein world happened slowly:

* Ribosome RNA has been produced, which makes an active center of ribosomes. It catalyzes the
forming of a peptide bond between amino acids. In the beginning it worked without any program,
connecting amino acids by chance.

* Transfer RNAs have been produced, which transport amino acids to a protoribosome and implement a
genetic code (nucleotides to amino acids). The proteins started being produced by program coded in
RNA.

* Nucleoproteins appeared, which are complexes made of RNA and proteins. They became more and more
sophisticated because of new kinds of proteins.

Ineffective ribozymes made of RNA are replaced by effective protein enzymes, produced by program,
written in RNA. It is increasing the speed and the accuracy of RNA copying, and the accuracy of
protein reproduction.

The transformation to a protein world finished. However, even today RNA takes part in the key and
vital processes in every single cell.

Then DNA appeared as a reliable storage of information.

5. RNA turns into DNA by changing one nucleotide (uracil to thymine) and one simple sugar (ribose to
deoxyribose). The single-chained RNA turns into the double-chained DNA. It increases the security of
information, its chemical resistance, and provides an opportunity to correct mistakes, restoring the
data from the second spiral by the principle of complementarity.

Gradually a protocell appears.

6. The whole factory surrounds itself by a lipid membrane and comes out of some porous mineral
structure like clay.

7. A nuclei separates itself from the rest of the cell (in eukaryotes). The protein biosynthesis
(ribosomes) moves out from the nuclei. Only DNA and RNA processing remain in the nuclei, where all
kind of RNA are being processed, including mRNA (messenger RNA) or non-coding RNA (ribosomal,
transfer, snoRNA and others).

8. A variety of proteins increases, the accuracy and speed of DNA copying grow, thanks to protein
enzymes. A protein splicing appears...

9. Different organelles (parts of a cell) appear, which made of proteins. They specialize on their
functions, taking part in the general process of replicator's copying. The main goal remains the
same — the multiplication of replicators, more accurate and faster.

An epoch of cooperation and competition comes:

10. Unicellular organisms start eating each other, the first predators appear.

11. A symbiogenesis happens, that is a merging of big unicellular creatures with small ones:
mitochondria and chloroplasts.

12. Simple multicellular organisms appear, which consist of identical or similar unicellular ones.

13. A cell specialization started by regulating of gene expression. The somatic cells are generated
to form various tissues of a multicellular organism. They have a limit of their reproduction cycle,
Hayflick limit. Gametes appear.

14. Species appear. Further read Darwin's "The origin of species".

Excuse me for I couldn't manage in a week of Creation, but two weeks are quite good, too.
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