martedì 17 febbraio 2015

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

Post n.20 English

As we have highlighted in the previous article, amino acids exists in two forms, Destro and Levo, one a mirror image of the other. Living organisms use only the L-form, therefore life is asymmetrical.
Molecular asymmetry, as we will see applies to other compounds too, was discovered by Pasteur in 1848. Since then big steps have been made in order to understand why life uses one form and not the other and when the separation occurred.
A summary of the most significant attempts to solve the problem was made by Mario Ageno in "Lezioni di Biofisica", 1980. He anticipates the conclusion of these efforts, saying: «This issue has plagued the minds of a large number of researchers, since the times Pasteur to date and does not seem to have yet received a fully satisfying answer, that is you deductively connect molecular asymmetry existence of the biosphere with the fundamental principles from the physics or biological theory».
One of these attempts that Ageno had excluded as the assumptions were of questionable validity, was incorporated in 1990 by R. A. and R. A. Hegstrom and D. K. Kondepudi, in an article in Le Scienze, "La chiralità dell’universo". As the authors illustrate, the chemical compounds originated through electromagnetic interactions of the atoms of which they consist. During these processes, it’s said there is a conservation of parity, that is, if you form a compound its mirror image has the same chance to form.
The constituent particles of the atom, protons, neutrons and electrons, are held together by different forces. Two of these forces, the weak nuclear force and the electroweak force, do not retain parity.
In the crust of our planet, there are elements whose atoms decompose and emit radiation (radioactive decay). During radioactive decay, electrons are also emitted at high-speed, β-rays (beta). Without going into detail, the weak nuclear force is responsible for this decay, and since it does not preserve parity, more left-handed electrons than right-handed ones are emitted. When the β rays hit the chiral molecules they are decomposed, but being the majority left-handed, the rays preferentially destroy one form, leaving an excess of its mirror image. It is therefore thought that the weak nuclear force was responsible for the asymmetry of life.
It was discovered that the difference in decomposition rates is of the order of one part in 109, that is one part of 1 000 000 000 (one billion).
The second force, the electroweak force does contribute to the formation of the compounds.
Since even this force doesn’t maintain parity, it’s been calculated that during their formation, in the prebiotic era, levo amino acids had to be the most abundant than the right by the order of one in 1017, let’s save time to write a 1 followed by 17 zeros.
Even though these are tiny contributions to determine molecular asymmetry, Kondepudi and a co-worker, Nelson, tried to prove theoretically that amplification processes under certain conditions exists. He envisions a pool where competing Right and Left form and writes: «And the pool should be large enough and sufficiently well-mixed (the shuffling covers an area of ​​10 square kilometres and a depth of several meters) to eliminate the effect due to random fluctuations. If all these conditions are fulfilled, the weak nuclear force should be able, in a period between 50 000 and 100 000 years, to strongly influence the symmetry breaking process». Kondepudi and Hegstrom conclude: «We exhibited numerous models to demonstrate how a chiral asymmetry could have developed in biomolecules. [...]. However, none of them were worth indicating a particular group of prebiotic compounds with all the properties required by these models».
Ultimately, the conclusion Mario Ageno made are still relevant today.
The molecular asymmetry problem is represented by Robert M. Hazen in 2001 with an article in Scientific American, (Le Scienze): "Vita dalle rocce". As the title indicates, Hazen turns his attention to the mineral world and prefigures a single model. That is, he imagines that concentration, selection and synthesis may be occurring in small pockets of air or feldspar rocks of volcanic pumice. For these events, the author does not take into considerations deterministic events and indeed states: «The case could have produced a combination of molecules that would eventually deserved to be called “living”». Hazen tackles the molecular asymmetry problem turning his attention to the crystals of calcite, limestone and marble, because these crystals form pairs of specular faces. As he explains, the calcite crystals were immersed in a solution containing an amino acid and Right Left 50% each. After 24 hours, the crystal was extracted and washed, and the solution analyzed. The sinistrose faces of calcite mainly selected the L amino acid with an excess of 40% and vice versa.
Hazen does not pose the problem of seeking the physical causes of this phenomenon and says: «Strangely the most terraced faces were the most selective. This fact led us to predict that the edges of the terraces could force the amino acids to line up in neat rows on their respective faces». Since the faces of the crystals of the left-handed and right-handed are equal, he concludes: «It was by pure chance that the molecule destined for success developed in a crystal face that preferred the left-handed amino acids to the right-handed counterpart».
Ultimately a single model but random, so a miracle.
In 1984, it became clear that the theory of Bernal was the only theory that indicated us a credible path to understanding the origin of life and that the molecular asymmetry problem was one of the fundamental steps. Bernal, in his theory, does not indicate the physical forces in action and so, as he himself writes, it doesn’t indicate the stages of the path due to lack of necessary research. He, however, suggests a path where the laws of inert matter can penetrate those of living matter.
Yes but how? 
 A capacitor consists of two metal plates (armatures), located
at a distance of a few centimetres, one of which is positively charged and the other negatively. If the two plates are connected to a voltmeter, we will measure the potential difference of the capacitor from which one can also deuce the energy of the capacitor. 
The water, consists of hydrogen and oxygen, in small quantities is dissociated in 
H2 O ↔ H+ + OH-

 The water molecules present within them a movement of charge. In particular on the hydrogen atoms a portion of positive charge is localized δ+ and on the oxygen atom a portion of negative charge δ-. In general, molecules which have inside them a charge separation are called polar and their polarity is measured by the dielectric constant.
Imagine we have a plastic bag full of water. If it is inserted inside the capacitor, the positive part of the molecule will orient towards the negative plate of the capacitor and vice versa.
As shown by the image, the potential difference of the capacitor
decrease and consequently, also the energy of the condenser is
 In conclusion, what is important to stress in this context is as follows: Since the energy of the condenser is reduced when it is inserted a polar substance, if we slowly place this substance into the capacitor, it will be spontaneously sucked inside. A process that follows the second law of thermodynamics, like the stone that rolls down the hill when pushed.
Also the amino acid molecules exhibit a charge separation and are therefore, polar substances. In aqueous solution, they are presented as dipolar ions with a very high dielectric constant.

The question to be asked is the following: are there natural capacitors that in the prebiotic era may have sucked and accumulated within them the amino acids removing them from the solution? Certainly, they must be capacitors at a molecular level.
It was discovered that these natural capacitors exist.
Between 1890 and 1930 they have been discovered and studied, by Helmholtz, Gouy and Stern (Trattato di chmica-fisica, S. Glasstone 1963 pag.1280), double electric layers generated from silica, silicate and glass, are all substances that present residual electric surface forces. The glass, for example, initially neutral, in contact with H2O easily loses the positive ions of the surface (Na+,Ca++,...) and then remains negatively charged. If a Na+Cl- solution is put in contact with the glass, the Na+ ions originate an ion layer in the proximity of the negative part of the glass wall.
 A part of the ionic layer is firmly attached to the glass wall while the other part is spread toward the solution. We can imagine, in the spread out part, two hypothetical plates passing respectively through points A and B. Within these hypothetical plates, on the left there are more positive charges that the right and, accordingly, between points A and B there is a potential difference called electrokinetic potential. The double electric layer is then similar to a capacitor (more precisely a micro condenser) and as such was studied. The distance between A and B, for low concentrations, is of the order of 0,6x10-6cm (Giuseppe Bianchi, Electrochemistry, 1963 pag.426). Micro capacitors of this type retain a row of dipoles of about 10 molecules of water, they act at molecular distances.
So there were natural capacitors in the prebiotic era, which may have attracted and accumulated within them the amino acids removing them from the solution.
The potential between points A and B cannot be measured directly; however, forcing the solution through a capillary or a diaphragm, a portion of the spread part of the double ionic layer is dragged, while the remaining portion remains attached to the surface. These ions measured at the ends of the capillary are named: the flow potential. The flow potential of course depends on the content of the solution.
I have built an apparatus for the measurement of the potential flow. I'll spare you problems and errors as, having in mind macroscopic capacitors while operating with microscopic capacitors.
As we have seen, these micro capacitors act at molecular distances and therefore there is a problem of how to imagine the electric field inside them.
In a macroscopic capacitor like that in the figure, the electric field is uniform and is represented by parallel and equidistant force lines. In such systems, the arrangement of the charges is a uniform distribution on the two surfaces of the capacitor.

In a micro capacitor such as that described above, the + charge is not evenly
distributed on a surface but is spread, while  the negative charge still presents a fairly uniform distribution on the glass surface. As a first approximation and unconventional way we could still consider the electric field uniform and represent it with parallel and equidistant force lines.
But, we can still speak of a uniform electric field with parallel and equidistant force line, if in addition to the positive charges also the negative charges are not equally distributed on a surface?
The crystalline quartz is made from helical structures whose constituent units are tetrahedra of SiO4. These helical structures can develop, clockwise D or counter clockwise L and give origin to crystals that are the mirror image. 

When one of the forms is placed in contact with a solution, micro capacitors are generated on the surface and thus electric fields, whose force lines can’t be parallel and equidistant.
This is because:
a) The dipoles xδ+ yδ-, of the Si-O bond, don’t lie on the same plane,
b) The force lines do not have the same orientation,
c) The force lines act at small distances, i.e. at the molecular level, which leads to the fact that they belong to a helical complex.

The force lines inside a capacitor of this type, at molecular distances of the order, one could imagine a helical shape, like the hole of a right or left hand screw, according to the structure used.

The amino acids, constituents of protein, are dipolar substances presenting a group (-COO-) and an amino group (-NH3+). Their dipoles are stronger than those of water molecules. But each atom or atomic group bound to the central carbon atom, has polar covalent bonds and thus is a dipole. It is clear that if the D-form is the mirror image of the L-form, also the dipoles of the D-form will be the mirror image of the L-form dipoles. Since the carbon atom has a spatial structure, at the molecular level of the two different dipoles structures we can imagine a helical shape, just like an oriented clockwise or counter clockwise screw. 

In laboratory, in order to measure the polarity of the molecules, capacitors with high potential of the order of a few Volts, and a distance of a few centimetres between the plates are used. In these tests, we can call macroscopic, the helical nature of the dipoles of the individual molecules are not highlighted, when we measure the resultant of the dipoles.
But, if the amino acids are immersed in suitable micro capacitors generated by the quartz whereby: the hypothetical distance between the plates is of the molecular order, the electric field inside them is helical and the potential is of the order of mV (millivolts), then it must be possible to highlight the helical structure of the dipoles from their molecules.

                                                                                                Giovanni Occhipinti

Translated by: Sydney Isae Lukee

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