Molecule evolution.
First let’s accept, once and for all, one basic “fact”:
“
Considering the “time factor” is essential to understand everything we want to analyze in the universe”.
To this, I’ll add that my last post
hides a description that wasn’t done yet.
Since living organisms are produced by the interactions of different “tidal effects” between connected “gravitational effect”, we can recognize the same repeated “accretion” process that produced atoms. The difference relies only in the fact that molecule’s “accretions” are more “discreet”. “Centers of gravity” join (bound)
less “tightly” to form molecules, than when they “fall” on one another to form atoms. In other words, in molecules, it’s not the
active energetic centers of gravity that
join into one; it’s the bigger
passive “gravitational effects” that
install “communication links”.
This being defined from my last post, we can start our questioning:
How can “Molecules fields" proceed to attain the "unicellular containers” level?I’ve been able to simplify a bit, but we have to use official information as they are, before really simplifying. So let’s begin our search.
The path we must follow starts with the “molecule field” and ends to the “unicellular structure”, as shown in the next drawing:

It’s obvious that the cell didn’t appear in nature, already organized and completed. It had to be the result of an
evolution path (period) starting from the molecule. And since the universe tries
every possibilities continuously at hand, we can anticipate “
complexity” (entropy) along the path that succeeded in augmenting the stability and viability of evolving “things”; even if many of the attempts were afterward disregarded.
Fortunately, we can surmise that cells appeared first in water since they needed water to contain every of their components.
But this water, at the start, had to contain other kinds of molecules which “fabricated” the cells. So where can we begin?
First let’s take the prokaryotic cell, which must have appeared before eukaryotic cells, and try to find what part of it appeared first.

At this point, we can eliminate the capsule and all that is related to it; meaning flagellum and fimbriae.
This leaves us with the
cell wall and the
cell membrane. After a bit of research, it’s easy to understand that the cell wall’s function is to
protect the membrane. So this means that
the membrane came first before developing a protection.
The following question is, can the membrane appear before whatever it contains?
The answer is yes, because this membrane is porous and
can let pass even macromolecules.
This unicellular “container” (membrane) is full of a jelly-like fluid called
cytosol. Its viscosity is roughly the same as pure water. The cytosol consists mostly of water (70%) into which float dissolved ions, small molecules, and large water-soluble molecules.
The structure of this water in the cytosol
is not well understood; just as the structure of pure water is poorly understood, due to the ability of water
to form structures such as
water clusters through hydrogen bonds.
The next drawing shows 5 water molecules forming a
water cluster by “tidal effect”; note the surprising gradual “rotational” and “orbital”
process of the water molecules, shown during its formation:

The classic view of water in cells is that… “
about 5% of this water is strongly bound in by solutes or macromolecules as water of solvation (solvent action with molecules and ions), while the majority has the same structure as pure water. Solvation involves different types of intermolecular interactions: hydrogen bonding, and ion-dipole interactions”. As we already saw, all these events
depends on the “flowing” characteristic of the “electronic energy”.
Water can both
donate and accept hydrogen bonds; which explains why water is the main environment where cells appeared.
Naturally the cells are also contained in water; but in contrast to extracellular fluid, cytosol has a
high concentration of potassium ions and a
low concentration of sodium ions.
This low concentration of sodium ions is the result of an enzyme that
pumps sodium out of cells while
pumping potassium into cells (we don’t have to object at the existence of “pumps” in molecules, since we understand that it is the “electronic energy
density” that controls
the forming of atomic ions by the “flowing in”, or out, of an electron).
“
This pumping action uses energy from a nucleoside triphosphate called ATP”. The reality might be that this nucleoside could simply be
the “flowing surplus” of electronic energy from different atomic ions. We mustn’t forget that an “electronic energy unit” (electron) possesses a “rotation motion”.

“
For every ATP molecule that the pump uses, three sodium ions are exported and two potassium ions are imported”.
Chloride ions also exit the cell, through
selective chloride channels. The loss of sodium and chloride ions compensates for the osmotic effect (by density pressure) of the higher concentration of organic molecules inside the cell (and since everything is energy, the “density pressure” control remains to
the “tidal wave” flowing process).
The low concentration of calcium in the cytosol allows calcium ions to open calcium channels so that calcium floods into the cytosol. This sudden increase of calcium activates other signalling molecules, such as calmodulin and protein kinase C. Other ions such as chloride and potassium may also have signaling functions in the cytosol, but
these are not well understood.
As you can see, the cytosol is already quite complicated; but we’ve already cleared the process a bit. So let’s come back to the cell membrane.
The cell membrane consists of a lipid bilayer with embedded
proteins.
This protein component provides us with another step toward
the “beginning” of cells. Proteins had to appear before cells, to form cell membranes.
Proteins macromolecules, consist of one or more long chains of
amino acid residues, which permits us an additional “backward step” in time, to
amino acids.
Amino acids are organic compounds containing amine (-NH2) and carboxyl (-COOH) along with a side chain (R group) specific to each amino acid. The key elements of an amino acid are
carbon (C),
hydrogen (H),
oxygen (O), and
nitrogen (N). About 500 naturally occurring amino acids are known;
though only 20 appear in the genetic code.

These
residues are what is left
when water molecule is rejected. Which means that water molecules
are chemically implicated in their formation.
Twenty of the amino acids are encoded directly by
triplet codons (composed of three nucleotides) in the genetic code, and are known as "standard" amino acids.
A three-nucleotide codon, in a nucleic acid
sequence, specifies a single amino acid. The vast majority of genes are encoded with a single scheme. That scheme is often referred to as the genetic code; though variant codes, such as in human mitochondria, exist.
Robert W. Holley determined the structure of transfer RNA (tRNA), the adapter molecule that
facilitates the process of translating RNA into protein. Extending this work, Nirenberg and Philip Leder revealed the code's triplet nature and deciphered its codons.
So now we know that proteins originate from
RNA.
In these experiments, various combinations of mRNA (mitochondrial RNA) were passed through a filter that contained
ribosomes, those components of cells that translate RNA into protein. Unique triplets promoted the binding of specific tRNAs to the ribosome. There were, first three and then, two more “stop codons” identified which
oblige the RNA to restart another strand. The three stop codons are UAG, UGA and UAA triplets.
The
stop codon alone is not sufficient to begin the process. The real initiator of the process is the
start codon.
The start codon is the first codon of a messenger RNA (mRNA) transcript translated by a ribosome. The start codon always codes for methionine (AUG) in eukaryotes and a modified Met (fMet) in prokaryotes. The most common start codon is AUG. The start codon is often preceded by a 5' untranslated region (5' UTR). In prokaryotes this includes the ribosome binding site.
A ribosome binding site is a sequence of nucleotides upstream (5’ -> 3’) of the start codon of an mRNA transcript.
Prokaryotic ribosomes begin translation of the mRNA transcript while DNA is still being transcribed. Thus
translation and transcription are parallel processes.
So we are now
at the RNA molecule level. We already, briefly, saw this chain of nucleotides.
Generally, RNA strands are considered as “half” of the DNA strand, and appears when DNA duplicates. While this is the event description of duplication,
it’s is not the evolution explication of RNA. Logically, to obtain a DNA strand you have to “unite” two RNA strands;
which gives to RNA the priority in appearance.
RNA is a chain of nucleotides. It is found in nature as
a single-strand folded onto itself. Cellular organisms use messenger RNA (mRNA) to convey genetic information using the nitrogenous bases guanine, uracil, adenine, and cytosine (G, U, A, and C), that directs synthesis of specific proteins.
Each nucleotide in RNA contains a ribose sugar, with carbons numbered 1' through 5' (in red).

A phosphate group is attached to the 3' position of one ribose to the 5' position of the next;
which is contrary to DNA direction (5’ - > 3’).
An important structural component of RNA, that distinguishes it from DNA, is the presence of
a hydroxyl group (oxygen bonded to hydrogen) at the 2' position of the ribose sugar. The presence of this functional group causes the helix to mostly take the A-form geometry, although in single strand dinucleotide contexts, RNA can rarely also adopt the B-form most commonly observed in DNA.
A second consequence of the presence of the 2'-hydroxyl group is that in conformational flexible regions of an RNA molecule,
it can chemically attack the adjacent phosphodiester bond to cleave the backbone” (chemically” attack means “electronic energy” attack which depends on “tidal effect” as we have seen everywhere).
There are more than a 100 naturally occurring modified nucleosides. The greatest structural diversity of modifications can be found in tRNA.
The specific roles of many of these modifications in RNA are not fully understood.
The functional form of single-stranded RNA molecules, just like proteins, frequently requires a specific tertiary structure. The scaffold for this structure is provided by secondary structural elements
that are hydrogen bonds within the molecule. We have here another clear implication of “gravitational effect” with these hydrogen bounds which consist of “electronic flows” by “tidal effect”.
We will continue with RNA in the next post and try to simplify it a bit more.