giovedì 2 aprile 2015

THE ORIGIN OF PROTEINS: The molecular asymmetry problem (part three)

Post n.21 English     

The device where the solution is introduced, in short, consists of a glass container, with upper and lower openings, placed at a certain height. An electrode connected to a multimeter is placed inside the container. The solution is made to flow through a diaphragm composed of Levo quartz granules or Right quartz granules, where they create micro capacitors and finally are collected in a second container. This container is placed lower than the first, and contains an electrode connected to the multimeter. The sliding solution drags with it charges from the micro capacitors, generating a potential difference between the two containers which is measured by the multimeter. First, we find the potential difference of the reference solution. Subsequently the difference of potential of the reference solution in which an L amino acid or a D amino acid was added
As we have already mentioned in the previous article, micro capacitors contain a row of about 10 molecules of water.
The purpose of these measurements were to verify Giuseppe Bianchi’s claims, Electrochemistry 1963 pag.470, states: "Species with lower dielectric constant have a tendency to be ejected from the double-layer to be replaced by species with a higher dielectric constant." In our case, the water molecules will be replaced by the amino acid molecules. Furthermore, as he emphasizes, he cited, this is a phenomenon "[...] which corresponds to a decrease in the energy of the system."
The decrease of energy is expressed in an increase of the thermal agitation of molecules of water expelled from the double layer, which is, an increase of entropy. At the same time, the amino acid molecules will be accumulated and sorted within the double electric layer. Chaos from order, a spontaneous process such as the formation of salt crystals already mentioned.
The substitution of water molecules with the amino acid molecules, then leads to a decrease of the system energy. This reduction is shown through a reduction in the electrokinetic potential, and then by the potential flow. In summary, if the solutions containing the amino acid present a potential difference lower than that of the reference solution, means that the amino acids have been subtracted from the solution and sucked-in and accumulated within the micro capacitors.
Before moving to the experimental data we have to specify the following:
A) The amino acids of the proteins of all living organisms are 20, all have the same composition, except for the R residue.

For example:
For glycine instead of R you have to put H.
For valine instead of R we must add a CH3 group.
It is therefore obvious, as illustrated by the image of some amino acids, if you change R, necessarily, both the size and the polarity of the amino acid molecule change.

To return to the metaphor of the helicoid crew, this means that in order to vary R for each amino acid the helicoid, of our hypothetical screw, the diameter and pitch changes; In conclusion, twenty amino acids for twenty different helicoid screws.
B) The quartz crystal, in the short term is insoluble in water. But prolonged contact with H2O, gives rise to a slow surface chemical reaction with the formation of silanol groups and the  -Siδ+ -Oδ- dipole is replaced by -Oδ-- Hδ+ dipoles which lower the potential.

The formation of silanol groups defines the electric field on the surface, giving rise to new electric fields and helical field lines with different amplitudes and new distances between the coils in the double electric layer.
Thus, our hypothetical screw hole has changed diameter and pitch.
This fact, as the graph shows, is manifested by a decrease of potential flow in function of time.

This decrease in potential does not occur continuously in the solution, but discretely. In particular, if you use the appliance or leave it on standby for some time, the potential is lowered with jumps of about 0,20mV. This means that on the surface of the quartz grains a number of Si-O-Si bonds are at the same energy, and at the same time react with water and giving rise to groups of silanols.

The potential flow of the capillary diaphragm of quartz in contact with the reference solution varies from a maximum of 10.10 mV to 7.50 mV. Below the potential value of 7.50mV, it isn’t stable. The flow potentials are therefore within an interval of about 2,60mV. Later, we will address the meaning and the consequences of that range.
The device for the measurement of the potential flow is connected to a Schlumberger digital multimeter. The potential flow of solutions of the following amino acids with respect to the reference solution we measured.

Val L                           10-3M            Valina
Ala L, Ala-D              10-3M            Alanina
Phe L, Phe-D            0.510-3M     Fenilalanina
Leu L, Leu D             10-3M            Leucina
Met L                         0.710-3M     Metionina
Ileu L                          10-3M            Isoleucina
Trp L                          0.810-3M     Triptofano
Pro L                          210-3M         Prolina
The amino acids have been dissolved in the reference solution.
(More information: "Prebiotic Chemistry and origin of life")

From the graph, it is clear that L amino acids solutions in capillary diaphragms of crystalline L quartz compared to the reference solution lower the potential flow only in well-determined potentials. The reduction is between 0.30 mV ± 0.05 mV for all the amino acids used.

This means that only in these specific potentials, the corresponding amino acids are sucked in and accumulated within the micro capacitors and therefore subtracted from the solution.
For example:
The potential flow of the reference solution is 9.70 mV; at this potential a solution of Ala L gives 9.40 mV.
The potential flow of the reference solution is 9.50 mV; at this potential a solution of Phe L gives 9.20 mV.
The potential flow of the reference solution is 8.70 mV; at this potential a solution of Trp L gives 8.40 mV.
At potential differences other than these, the amino acid solution gives the same potential flow of the reference solution, this means that the amino acids remain in solution, for example:
If the reference solution gives a potential of 8.70 mV and instead of Trp L, Ala L is used, the potential flow will show 8.70 mV.
If at the same potential, for example 9.70 mV for Ala L, a solution of the D-form of Ala is used, no change will be observed in potential relative to the reference solution.
The opposite is observed when a D quartz diaphragm is used.

As can be seen from the graph, D amino acids solutions, on capillary diaphragm D crystalline quartz, relative to the reference solution, lower the potential flow only at particular potentials. Such reduction is between 0.30 mV ± 0.05 mV for all the amino acids used. This means that at these potentials the corresponding D amino acids, from the solution are sucked inside the micro capacitors, for example:
The potential flow of the reference solution is 9.70 mV; at this potential Ala D solution gives 9.40 mV. If an L- form of Ala solution is used, no change is observed in potential relative to the reference solution.
Such behavior must be the logical consequence of what was said in the theoretical part.
The crystalline quartz in the double electric layer generates the helical lines of force equivalent to the bore of a screw. In the amino acid to the four different atoms or atomic groups, bound to the carbon atom in a tetrahedral structure, are associated four dipoles with a helical structure. For this reason, the amino acid is comparable to a screw. Still referring to our metaphor, if the screw finds its proper hole then the amino acid accumulate in the double electric layer; there is a decrease of the energy of the system, and a reduction of the potential can be observed. If the hole is not the right one, either the screw goes in and out right away because the hole is wider, or it doesn’t enter at all, because the hole is too tight, the potential remains constant and the amino acid don’t accumulate on the surface.
If the screw has an opposite direction, as in the case of the D-form, it cannot enter, and even in this case the potential remains constant, the amino acid remain in solution. Therefore, only at a specific potential the amino acid is accumulated in the double electric layer and removed from the solution.
The metaphor of the hole and the screw must be understood as Erwin Schrödinger, one of the fathers of quantum mechanics, states in his essay "Che cosa è la vita"1944: «In the light of current knowledge, the inheritance mechanisms are closely linked, indeed are founded on quantum theories [...]. The great revelation of the quantum theory consisted in discovering, in the book of nature, signs of discontinuity in a context in which anything other than the continuity seemed absurd [...]. Based on facts that we can not discuss here, we must admit that a small system may, for principle reasons inherent to its very nature, possesses only certain discrete amounts of energy, which are called energy levels of their system. [...]. The result is that, if a number of atomic nuclei, with all their bodyguards are to be joined to form a "system", they can’t assume, because of their nature, any arbitrary configuration among all those that can be imagined. Their nature allows them to choose only within a very large but still discrete series of "states"
Generally, we call these states with the term "levels" or "energy levels" because the value of energy is one of their most important features. [...]. Between the discrete series of states of a certain set of atoms there may be (but not necessarily), a level lower than all the others, in which the nuclei are closely spaced. In such a state the atoms constitute a molecule».
So every molecule has its own energy content defined, discrete, ie a quantum structure. But if the energy is discrete, since the bonds between the atoms are electromagnetic in nature also the electromagnetic field associated with the molecule must be discreet. And for the amino acids, the electric field associated with the molecule must also present a D or L orientation.
We will get back on these concepts.
Finally, it seems that a physical agent, quartz, in the prebiotic era, can connect deductively the separation of Destro amino acids from Levo with the fundamental principles of physics theory. It can therefore be assumed that these double electrical layers have worked as electrochemical filter, selecting and accumulating the amino acids,on the quartz surface, and then on the earth’s surface.
But we must not forget that the crystalline quartz, which is now in the wild, is 50% Destro and 50% Levo and this had to be the situation even in the prebiotic era. On the other hand we now know that, in the prebiotic era, the amino acids were 50% D and 50% L. Then, if the Levo quartz has accumulated Levo amino acids, the Destro quarz will have done the same accumulating the Destro amino acids. In these conditions, there would be L polypeptides and D polypeptides and subsequently a D life and an L-life.
But D life does not exist, in reference to amino acids only an L-life exists.
In conclusion, the results presented above cannot be taken as definitive, but as a working tool for further investigation.
So the question remains: how did Levo survive and what happened to the Destro?

                                                                 Giovanni Occhipinti

Translated by: Sydney Isae Lukee