Talk:Prebiotic chirality

Translated from fr:Recherche:Chiralité prébiotique - Sidelight12 ^Talk 20:08, 12 February 2014 (UTC)

Mekki-Berrada Abdelali

Further thought about prebiotic chirality

Confirmation of L-Glyceraldehyde on the fixed arm

28/04/2012
The L-GA binds to the membrane in 80% (1987) in E. coli:.
Abstract:
When either 3H-labeled L-glyceraldehyde or 3H-labeled L-glyceraldehyde 3-phosphate (GAP) was added to cultures of Escherichia coli, the phosphoglycerides were labeled. More than 81% of the label appeared in the backbone of the phosphoglycerides. Chromatographic analyses of the labeled phosphoglycerides revealed that the label was normally distributed into phosphatidylethanolamine, phosphatidylglycerol, and cardiolipin. These results suggest that L-glyceraldehyde is phosphorylated and the resultant L-GAP is converted into sn-glycerol 3-phosphate (G3P) before being incorporated into the bacterial phosphoglycerides. Cell-free bacterial extracts catalyzed an NADPH-dependent reduction of L-GAP to sn-G3P. The partially purified enzyme was specific for L-GAP and recognized neither D-GAP nor dihydroxyacetone phosphate as a substrate. NADH could not replace NADPH as a coenzyme. The L-GAP:NADPH oxidoreductase had an apparent Km of 28 and 35 microM for L-GAP and NADPH, respectively. The enzyme was insensitive to sulfhydryl reagents and had a pH optimum of approximately 6.6. The phosphonic acid analog of GAP, 3-hydroxy-4-oxobutyl-1-phosphonate, was a substrate for the reductase, with an apparent Km of 280 microM.

Prebiotic Pyridoxal

16/02/2014
Synthesis of Pyridoxal at 110°C in prebiotic conditions 1999 .
Abstract:
Heating a dilute solution of NH3 and glycoaldehyde gives a large family of pyridines substituted with the same functional groups as occur in the forms of vitamin B6. Thus, vitamin B6-like molecules could have been present on the early Earth and could have been available for catalysis of primitive transamination reactions. Ethanolamine and N-methylethanolamine are also formed as major products. These are choline-like molecules, the latter of which is apparently formed by a prebiotic methylation process.

Chirality of ribose in the presence of LL-dipeptides

07/05/2012
Glycolaldehyde + DL-glyceraldehyde in the presence of LL-dipeptide gives execess of D-ribose, 44%. This, in absence of liposome..
Abstract:
Glycolaldehyde and DL-glyceraldehyde reacted in a water-buffered solution under mildly acidic conditions and in the presence of chiral dipeptide catalysts produced pentose sugars whose configuration is affected by the chirality of the catalyst. The chiral effect was found to vary between catalysts and to be largest for di-valine. Lyxose, arabinose, ribose and xylose are formed in different amounts, whose relative proportions do not change significantly with the varying of conditions. With LL-peptide catalysts, ribose was the only pentose sugar to have a significant D-enantiomeric excess (ee) (≤44%), lyxose displayed an L-ee of ≤66%, arabinose a smaller L-ee of ≤8%, and xylose was about racemic. These data expand our previous findings for tetrose sugars and further substantiate the suggestion that interactions between simple molecules of prebiotic relevance on the early Earth might have included the transfer of chiral asymmetry and advanced molecular evolution.

Polyglycine synthesis in the presence of liposome

07/05/2012
In hydrothermal conditions and not from the prebiotic pocket of oil .
Abstract:
Oligomerization of amino acids proceeded on or inside lipid vesicles as a model of prebiotic cells in a simulated hydrothermal environment. When the suspension of lipid vesicles taking up monomeric glycine underwent a sudden temperature drop by traversing from a hot (180◦C) to a cold (0◦C) region repeatedly while circulating through a closed reaction circuit, oligopeptides up to heptaglycine were formed even in the absence of condensing agents.

Prebiotic chirality reject?

29/04/2013
I mean a reject of thinking that I conducted in this article, by the following article of Shimada H and Yamagishi A (2011). There is nothing as I separate the role of the chirality of the arm carrying the amine of the chirality of glycerophosphate in my thinking. However, in the following article the authors consider that the stability of two phospholipids put together. What about the behavior of amino acids and proteins inserted into the liposomes? And even the energy point of view, it is quite obvious that the two aliphatic tails, bacteria and archaea, are different. So one of two override the other. Can be put, as I point out in my thinking, one type of tail and hétérochiralité of glycerolphosphate? I said no because the chirality of the latter must be adapted to the aliphatic tail as I explain precisely.
Abstract
Stability of heterochiral hybrid membrane made of bacterial sn-G3P lipids and archaeal sn-G1P lipids.
The structure of membrane lipids in Archaea is different from those of Bacteria and Eucarya in many ways including the chirality of the glycerol backbone. Until now, heterochiral membranes were believed to be unstable; thus, no cellular organism could have existed before the separation of the groups of life. In this study, we tested the formation of heterochiral hybrid membrane made of Bacterial sn-glycerol-3-phosphate-type polar lipid and Archaeal sn-glycerol-1-phosphate-type polar lipid using the fluorescence probe. The stability of the hybrid liposomes made of phosphatidylethanolamines or phosphatidylcholines or polar lipids of thermophilic Bacteria and polar lipids of Archaea were investigated. The hybrid liposomes are all stable compared with homochiral liposome made of dimyristoylphosphatidylethanolamine and dipalmitoylphosphatidylcholine. However, the stability was drastically changed with increasing carbon chain length. Accordingly, "chirality" may not be but chain length is important. From these results, we suggest that the heterochiral hybrid membrane could be used as the membrane lipid for the last universal common ancestor (Commonote) before the emergence of Archaea and Bacteria.

Prebiotic chemio-mecanics

28/04/2012
Preparation of the article of the same title. It will involve the study of all mechanical processes caused by chemical reactions in and on the walls of liposomes similar to the mechanical cohesion in the studied prebiotic chirality.

• Mechanical function of enzymes and proteins in general:

1. ATPase is the leading example. I shall study here,
2. Esterases and hydrolases that often are unidirectional while the reaction is reversible thermodynamicaly (in both directions). The enzyme acts in addition to its catalytic role, a mechanical role in attracting by its electromagnetic volume the substrate and not the product. One can guess that will follow the evolution, ie control of the enzyme by peptides or metabolites.
3. Oxidoreductases or isomerases, which are often in two directions. As if these catalysts require very precise positioning of substrates to involve quantum processes that are themselves reversible. This accuracy corresponds to the high energy potential of these reactions. This is very interesting quantum reversibility for the reactivity of the cell to the actions of the surrounding medium, because it is almost instantaneous compared to thermodynamic processes. With this in mind it would be interesting to study the reduction of nucleotides to désoyxnucléotides (dATP).
4. The initialization of metabolism on, and in the inner wall of the liposome: I shall continue the scenario of metabolism initialization began in the prebiotic chirality. Including the incorporation of new fatty acids in the liposome and its fission to 2 liposomes, nucleation on the internal wall of nucleotides, deoxynucleotides and amino acids to evolve enzymes, ribosomes and polymerases of transcription and replication.

The hydrostatic pressure

14/05/12
Does the lipid bilayer protects the interior of the bacteria of the hydrostatic pressure? Has anyone measured the hydrostatic pressure in the cytoplasm?
These are interesting questions to the principle of mechanical cohesion of phospholipids because they bring two essential confirmations:

1. Mechanical cohesion is a response to the hydrostatic pressure to let the hydrophilic molecules inwardly aqueous vesicles of the oil phase: enlargement of the vesicle.
2. coming closer together the 2 sheets of the liposome of the aqueous phase, with mechanical cohesion, allows it to withstand the hydrostatic pressure and thus the pressure in the cytoplasm is smaller than that of the outside. What differentiates the internal chemistry of the outside chemistry.
   

The hydrostatic pressure can be so behind the establishment of the mechanical cohesion and hence the chirality of living, as demonstrated in the article. This would strengthen the hypothesis of the origin of life in the fields of prebiotic oil (the pocket oil ) and push to experiment from abiotic oil.

The electric dipole of a phospholipid

29/04/2013
   I have not seen the electric forces in my article on the prebiotic chirality. In the first reading articles on this subject, I understand that the two dipoles of two surfaces directed towards the inside of this membrane would be sufficient to maintain its mechanical cohesion. However, the dipoles of water molecules and the interaction between heads they should change that. As the fields of research in this area has been well developed in recent years in a well-defined goal, that the passage of molecules across the membrane (pharmacopoeia). One should retain only what concerns prebiotic chirality.

Intensity of the dipole in the membrane

29/04/2013
Review de 2012 .

Angle of the head with the hydrophilic surface of the membrane

29/04/2013
The hydrophilic heads are parallel to the surface of the membrane.
NMR measurements, article 1996
Numerical simulation, article 1994 .

Interpenetration of the tails of two layers of the membrane

29/04/2013
If the strength of the dipoles was the most important factor of the membrane cohesion why two hydrophobic tails, face to face, do not they intertwine? As in an oil phase? Is the electrical repulsion of two hydrophilic heads which takes away from each other? At this point the fact to represent two separate queues suggests that there is an equilibrium and therefore this equilibrium can be broken, and where the hypothesis of prebiotic chirality (in the article) is still relevant.
Another interest that two tails do not interpenetrate, is that the two layers can slide relative to each other. This is another obstacle to the diffusion of molecules across the membrane.
Now if it involves the hydrostatic pressure (see above) we expect that the tails intertwined. But this is not the case. At 500 bar, in prokaryotes, tails remain separate and even get longer as they fight against the coming closer of the two hydrophilic heads: With my estimates after Figure 1-2 of the thesis of Badr al-Ali , the longest lipids increased from 4 to 39% of the total, while the unsaturated spend only 71 to 84%.

The rotary movement of a phospholipid in the membrane

29/04/2013
   The rotational and diffusion movements are very fast in the membrane: "La rotation axiale est très rapide, elle s'effectue avec une fréquence de l'ordre de 10⁹ à 10¹⁰ Hz pour des lipides courants. La diffusion latérale est très libre également, les coefficients de diffusion mesurés étant généralement de l'ordre de 10^-2 et 10^-9 cm².s^-1, ce qui correspond à une fréquence d'échange des positions de 10⁶ fois par seconde en moyenne."

[ The axial rotation is very fast, it takes place with a frequency of the order of 10⁹ to 10¹⁰ Hz for current lipids. The lateral diffusion is also free, diffusion coefficients measured generally being of the order of 10^-2 and 10^-9 cm².s^-1, which corresponds to a frequency of exchange of the positions of 10⁶ times per second on average.]

   Oddly rotations are given in Hz and not in revolutions per second, which is the same, but Hz is not obliged to indicate the direction. Do not be a vibration?
   Espace Science (1.4 Fluidité de la membrane) shows schematically the axial rotation with an anti-clockwise arrow as opposed to what I say in this article !! Interestingly, this site shows howover movements of paraffinic tails and the role of cholesterol in these movements: movements forced and free.