Wednesday, March 23, 2022

About prebiotic counterparts of tRNA and metabolic machinery

The question about the prebiotic counterparts of tRNA and tRNA-amino acid pairing stimulates also questions about the prebiotic counterpart of metabolic machinery.

What can one say about pre-tRNA?

What could be the prebiotic counterpart of tRNA?

  1. DtRNA should have a molecular counterpart. The simplest guess is that it corresponds to an RNA type codon appearing in tRNA but somehow differing from it. Pre-tRNA could simply be the (AAC-H)3' end of the acceptor stem with AAC replaced with XYZ, where ZYZ denotes the codon part of tRNA. The addition of a hydrogen atom would relate pre-tRNA codon to ordinary RNA codon.
  2. The bond energy for the pre-tRNA-AA pair as the energy of the ester bond would be about .5 eV, which corresponds to the metabolic energy quantum. Energy is therefore required to "charge" pre-tRNA. This requires metabolic energy and in the absence of ATP machinery, the energy should come from its predecessor. What prebiotic metabolism could be, will be discussed in the next section.
  3. If this step works, the polymerization of tRNAs involving the transformation of the ester bond of pre-tRNA-AA to AA-AA peptide bond can occur spontaneously since the peptide bond has bond energy of order .1 eV. This would give rise to polypeptides. This process would be like a translation process for RNA but without an RNA template and therefore the outcome would be random. Also the RNA polymerization in this manner can be considered, now however the RNA-RNA valence bond has considerably higher bond energy.
  4. If DRNA-RNA sequences are formed, they might be transformed to AA sequences by pre-translation process using pre-tRNA and resonance mechanism pairing DRNAs and dark counterparts of pre-tRNA-AA pairs. This would define the pre-translation process.
What could the prebiotic metabolic machinery be?

Metabolic machinery should have a prebiotic counterpart and have .5 eV as metabolic energy quantum.

  1. Could the splitting of a hydrogen bond with bond energy about .5 eV provide the energy needed in the formation of pre-tRNA-AA ester bond? IR photons are most effective in causing Pollack effect in water: could also they induce pre-tRNA-AA pairing? Both options would require the presence of water. In principle, the proposed mechanism could lead to a generation of water molecules (the energy of O-H bond is 4.81 eV) already at temperatures of few Kelvin.
  2. Could MB somehow provide the metabolic energy quantum? Gravitational flux tubes are in a central role in the TGD inspired quantum biology. Iit was observed (see this) that the gravitational binding energy of a nucleon in the gravitational field of Earth is .67 eV. This is somewhat larger than the metabolic energy quantum. A dark proton at a distance of about .34 RE, RE Earth radius, from the surface of Earth has gravitational binding energy of .5 eV.

    The bond energy of the hydrogen bond is .5 eV. Could it correspond to the reduction of the gravitational binding energy due to the delocalization of a dark proton to a gravitational flux tube? Could the hydrogen bond become dark with heff= hgr or could the proton of the ordinary hydrogen bond be dark?

    The transformation of a dark proton at the gravitational flux tube of MB to an ordinary proton implies a localization having interpretation as falling to the surface of Earth. Could this provide the metabolic energy quantum?

    For a dark variant of hydrogen bond a gravitational flux tube between atoms should form a very long loop at which the gravitationally dark proton would reside. This kind of picture about dark flux tubes associated with gauge interactions has been suggested earlier. For instance, color flux tubes assignable to nuclear protons could extend to distances of order of atomic size.

  3. The observation that gravitational binding energy equals hydrogen bond energy inspires the question whether the ordinary hydrogen bond is dark in a gravitational sense. The delocalization of proton charge to a very long scale would mean that in short scales the hydrogen bonded atom pair has an effective negative charge so that this does not work.

    This observation however suggests that phosphate ionization could be interpreted as a formation of a dark hydrogen bond. Phosphate is electronegative and forms hydrogen bonds. This would explain why phosphate ions have such a central role in metabolism. Effective ionization serves as the signature of the delocalization. Also other electronegative ions could play the role of phosphate and arsenite has done this in some bacterial systems (see this).

    The pre-biotic counterpart of metabolic machinery should have involved phosphate ions or some other electronegative ions forming dark hydrogen bonds.

  4. For electrons the gravitational binding energy at height .34 RE is about .25 meV. This corresponds to the energy of photons in the microwave background. Could this define a second metabolic energy quantum important in scales by a factor mp/me≈ 211 longer than nanoscale about 1 nm assignable to DNA. This is the length scale of the cell nucleus, microtubules and axons. Intriguingly, the minimal fluctuations of membrane potentials correspond to the so-called miniature end plate potentials .4 mV (see this).

    Metal ions could be atoms with gravitational delocalization of the valence electrons and some of them could serve as analogs of metabolic recurrencies. Some metal ions could take the role of metabolic quantum. Fe++, Ca++, and Mg++ are bosonic ions and are of special importance on living matter. They would be neutral in the scale of gravitational flux tubes.

  5. What would be the size scale Lgr of the gravitational flux tubes? The first estimate is as the Bohr radius Lgr=rn= n2 aB,gr= n2 Λgr,m for the orbit particle in 1/r gravitational potential of Earth. Λgr,m= GM/v0 is gravitational Compton length, which for v0=c is one half of Schwartschild radius of Earth and about .45 cm. For dark cyclotron photons, the wavelength is λ= 1/fc= m/ZeBend. The identification rn≈ λ gives an estimate for the value of n. fc=10 Hz for Fe++ would give for v0=c the estimate λ ≈ 2π RE and n≈ 6× 104.
This picture allows us to reconsider a long-standing question relating to the notion of MB with an onion-like layered structure. What could this sentence mean quantitatively?
  1. The gravitational magnetic body could be a layered structure containing the Bohr orbits with Bohr radii rn ∝ n2 of particles in the gravitational field of Earth. Particles with different masses would concentrate at the same orbits. One would have the shell structure of the ordinary atom.
  2. Flux sheets with a cylindrical rotational symmetry containing the orbits can be considered. These surfaces should be realized as preferred extremals of the action and should be minimal surfaces in H=M4× CP2. As closed surfaces they cannot define minimal surfaces of the Euclidean 3-space E3. Indeed, soap bubbles are not minimal surfaces but require a constant pressure difference between interior and exterior. The analog of pressure difference would be non-trivial and dynamic 1-D projection of 4-D surface to CP2 (see this). The liberation of metabolic energy quantum would be analogous to a transition of hydrogen atom to a lower energy state.
See the article Hen and egg problems of biology from TGD point of view or the chapter Molecular Signalling from the TGD Point of View.

For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.

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