domenica 17 maggio 2015

THE ORIGIN OF PROTEINS: The molecular asymmetry problem (pert four)

Post n.22 English  

It seems a strange thing, as we saw in the previous article, that Levo quartz accumulates on its own surface the Levo amino acids and Destro quartz, the Destro amino acids. The obvious question is: what is the relationship between the quartz structure and molecular structure of amino acids?   None.
A beam of natural light is made from a very large number of rays whose electric vector oscillates in all directions. Schematically represented in figure 4.1a.

If such a light beam hits special crystals, called polarizing prisms, or Polaroid filters, all the rays, except one, are deflected or absorbed. The electric vector of the only outgoing beam, always oscillates in the same direction and the plane (x 'x) on which lies the propagation direction is called: the plane of the polarized light, Figure 4.1b. Similar light beams are called: linearly polarized light.
In nature there are several substances and minerals which, if crossed by a beam of polarized light, have the property to rotate the plane of polarized light, rightwards or leftwards. An analyser placed inside a device called polarimeter, whose visual field is divided into two semicircular parts, allows us to observe this deviation. This property is called optical activity and depends on the molecular structures for substances. For the crystals it depends on the crystalline structure, that is, the arrangement of atoms, ions or atomic groups within the crystal.
 In the inorganic world, the most common mineral that has optical activity is the quartz.
The quartz crystals were initially studied focussing on their outer arrangement of the faces on the crystal itself. Since comes in two different forms, one a mirror image of the other, it was assigned the morphological designation, Destro (D) and Levo (L). At the beginning of 1800s, when J. B. Biot analyzed quartz with polarized light, he did not know its internal structure, its crystal structure yet. Now, since the quartz morphologically Destro revolved right and quartz morphologically Levo, left, he gave the denomination D and L.
At the end of 1800s, X-rays were discovered. The X-ray analysis of the quartz showed that it is composed of tetrahedral structural units with the silicon atom in the centre and the oxygen atoms at the vertices.

These structural units are linked together to form right-handed and left-handed helices.

The analysis highlighted a fundamental fact: in quartz, optically and morphologically "Destro", the helixes are left-handed and in quartz optically and morphologically "Levo" the helixes are right-handed.
(Form: Rudolf Rykart, Quartz-Monographie, 1995)

So, when we say that L quartz absorbs on its surface the L amino acids, it’s actually the Right-handed quartz structure that accumulates the L amino acids.
The name assigned to Biot nevertheless benefited and is universally used.
As we said, there are several substances, such as amino acids, which in solution rotate the plane of polarized light. The same sense of rotation adopted by Biot for quartz was also adopted for substances, but was given the + sign if turned Right and - if it turned Left. This rotation has no correspondence with the designation L and D for amino acids. The denomination is related to the molecular structure that has been determined through universally accepted sequence rules, but arbitrary. There is in fact an L (+) Valine as well as the L (-) Proline.
With these clarifications, we return to our main problem.
The two molecular forms of amino acids, Destro and Levo, have the same chemical-physical properties, and it was believed that they were inseparable.
Meanwhile, through the double electrical layers we have made a first step. Quartz separates the Destro amino acids from Levo and connects deductively this separation with the fundamental principles of physics theory. But, since in reference to the amino acids, there is only an L-life, there must exist, in the inorganic world, an asymmetric substance only with an L-form that has retained and accumulated on its surface only the L amino acids.
The idea of ​​existence of an asymmetric mineral, in the inorganic way, was born from reading Encrenaz Thérèse’s article, “L’acqua nel Sistema solare”, Le Scienze (2001).
It highlighted how the water molecules are not all the same but there are of two types: ortho molecules and para molecules.
The nuclei of atoms, such as electrons, rotate around their own axis clockwise or counterclockwise. Due to this rotation, called spin, the nuclei and the electrons behave as tiny magnets.
The spin effect is most visible in the permanent magnets. In a permanent magnet, the spins of some electrons of the atoms that constitute it, all have the same orientation. Since each electron can be considered a very small magnet, the cumulative effect of all the spins gives rise, at a macroscopic level, the properties of the magnet.
The nuclei of the hydrogen atoms constituting the water present, as other atoms, nuclear spins.
 The water contains two hydrogen atoms, their spins may eventually go half in one direction and half in the opposite direction. Well it was discovered that in 75% of the water molecules of our planet, the spins of the two hydrogen atoms have the same direction of rotation, meaning, they are parallel. They are called: ortho molecules. In the remaining 25% they are antiparallel and are called para molecules.
Even pure hydrogen presents ortho molecules and para molecules with the same percentages. Although the magnetic field associated with the nuclei is very weak, several researchers have shown how, in pure hydrogen, the para hydrogen presents vapour pressure, boiling point and specific heat different from that of normal hydrogen (Samuel Glasstone, trattato di chimica fisica, 1963 page 100).
In the water molecule hydrogen is bonded to oxygen, and due to the effect of the strong electronegativity of oxygen, the hydrogen electron is moved towards oxygen.

Due to this displacement, on the hydrogen atoms from water a positive charge rises, therefore the small magnetic fields associated with nuclear spins. In para water molecules, a quarter of the water on our planet, the small magnetic fields, as indicated by the antiparallel arrows, cancel
out each other.

In the ortho water molecules, ¾ of water on our planet, the small magnetic fields are parallel

They sum up and tiny permanent magnets oriented in the same direction, rise.
Water is therefore, asymmetric.
Now, the water is the source of survival of living organisms. It was and is decisive for the evolution of the surface of our planet and, for four billion years, has stabilized the temperature within a range compatible with life. Without water the earth would be a barren rocky planet.
The spontaneous question (A question spontaneous arise): is it possible that the water asymmetry played a role in the asymmetry of the molecules essential for life?
Apparently, the two types of asymmetry seem different, one a magnetic type and the other of a structural type. But the molecular structures are formed by atoms linked through electrical interactions, and so both asymmetries are of electromagnetic origin. How these two asymmetries were able to interact is not simple to understand, but this cannot prevent some experimental attempt. The history of science is full of phenomena whose theory has been understood long after their discovery.
The asymmetry of water, however, may not have acted directly on the choice of the asymmetry of life. If we put in water a racemic amino acid, that is 50% Destro and 50% Levo, no deviation of the plane of the polarized light is observed. The water does not have a particular preference for one of two forms.
But then, how may it have led to this decision?
As Miller has shown, the primitive atmosphere was the site of synthesis of the amino acids that were dragged by the rain on the planet's surface. Amino acids, as water, were then distributed across the planet's surface. The water’s asymmetry must, therefore, have acted on a substance that was also distributed across the planet's surface. One of the minerals that was and is present almost everywhere is silica. Silica is also one of the clay components, and so we fall under the Bernal theory.
Quartz is an important component of the earth's crust, but even more important are the silicates that cover over 90% of the earth's crust.
Metamorphic rocks are sediments of silicate that have suffered environmental damage.
The clayey minerals, diffused on the whole surface of the planet, are silicate rocks which have undergone such metamorphosis reacting with H2O and CO2 (carbon dioxide or carbon dioxide). Clay is one of the components of farmlands. One of the components of this metamorphosis is amorphous silica or silica gel. In nature amorphous silica often gives rise to a mineral called opal. The X-ray analysis showed that it is always present in the tetrahedral structural unit and contains microcrystals of tridymite and cristobalite, referred to as crystallites, which are polymorphic forms of quartz. The oldest opal also contains microcrystals of quartz and in fact, with the passage of geological Eras, it is transformed into chalcedony which is a mass of microcrystalline quartz.
The X-ray analysis showed the presence tetrahedral structural unit and also microcrystals of cristobalite in amorphous silica prepared in the laboratory and dried (silica gel). The amorphous silica, in the laboratory, is obtained by reacting, in aqueous solution, sodium silicate (soluble glass) and hydrochloric acid.

Na2SiO3 +2HCl + H2O → 2NaCl + H4SiO4 (ortho silicic acid)

The ortho silicic acid thus obtained polymerize and gives rise to first colloidal silica (sol).

The colloidal silica particles (sol) are not visible and do not stay long in suspension in the solution. After several minutes, they slowly aggregate to form flakes, visible to the naked eye, which precipitate giving rise to a precipitate of amorphous silica (gel). The formation of the colloid is not instantaneous. From H4SiO4 a certain amount of colloid slowly forms an amorphous silica aggregates while another colloid begins to form. The concentration of the colloid in the solution is not always constant.
The formation of silicic acid in nature follow different chemical reactions, but the formation of the sol before and then the gel is identical to the experiments in the laboratory.

As already mentioned, the amorphous silica is one of the components of the metamorphosis of the rocks and is spread practically all over the entire surface of the planet. The silica that precedes the amorphous silica is the colloidal silica. Like all colloids, it is not even visible under the optical microscope. However, even if invisible, the particles are still very large and therefore have very large surfaces. A colloid in solution is then considered a two-phase system, which has the same properties of a liquid in contact with a surface. On the surface of the particle in contact with the liquid medium we can have, phenomena of adsorption, formation of the electrical double layer, etc.
There are no known polarimeter observation researches of siliceous solutions. To be kept in mind, however, that until the 90s the most used polarimeters had a sensitivity of 0.1 degrees, with 10cm polarimeter tubes and a manual slide. With these polarimeters, it was impossible to bring out small deviations of the plane of polarized light. The new digital polarimeters with an automatic slide (type Polax-2L), have 20cm polarimeter tubes in a horizontal position. The deviation of the plane of polarized light is then doubled. They also have a sensitivity of 0.05 degrees and thus also the sensitivity is doubled.
Measurements of the water glass solutions, at various concentrations and times, were made with the polarimeter Polax-2L.
Once the technique was standardized, it was observed that such solutions have optical activity.
In particular, the silica in solution rotates the plane of polarized light to the left.
This deviation will disappear after about 5-10 minutes.
The fact that after a certain time the deviation of the plane of polarized light disappears, this means that the colloid is to have such a characteristic. The amorphous silica, which subsequently is formed by the aggregation of the colloidal particles, forms a cloudy solution without any deflection of polarized light. The addition of ethyl alcohol to the solution substantially increases the deviation of the polarized light. It is well known that ethyl alcohol retards the aggregation of the colloidal particles and so the concentration in the solution is temporarily increased. (Procedure and data: "Prebiotic Chemistry and origin of life")
It therefore appears that, even if of short life, we are in the presence of an asymmetric mineral: the colloidal silica.
As already stated, the amorphous silica presents microcrystals of tridymite and cristobalite.

 The colloidal silica, which precedes the amorphous silica, rotates the plane of polarized light to the left. It therefore seems that the orthosilicic acid, polymerizing, forms, during its brief existence as a colloid, helical structures of Levo quartz type. These structures are transformed into microcrystals of tridymite and cristobalite in amorphous silica and, after geological years, into chalcedony quartz crystals.
Now, if the colloidal silica in aqueous solution gives rise to helical structures, they are as likely to form both Destro and Levo structures. If the structures are only Levo type, this can only be due to the asymmetry of the water.
But how does the water asymmetry determine the asymmetry of the colloidal silica?
And then, is this the missing link to solving the asymmetry molecular problem, of living organisms?

Giovanni Occhipinti

Translated by: Sydney Isae Lukee

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