Energy-dependent hydrogen bonds in supercoiled DNA

By: James V. Kohl | Published on: January 2, 2017

(click to enlarge)

Most biological macromolecules are homochiral, and enzymes help to maintain this state of affairs; for example, checkpoints ensure that only l-amino acids are incorporated into proteins during translation.

The fixation of the only achiral amino acid, glycine in position 6 of the gonadotropin releasing hormone decapeptide protein links the nutrient energy-dependent pheromone-controlled physiology of reproduction from yeasts to humans. That fact about RNA-mediated protein folding chemistry is missing from the chirality check, It also is missing from representations of the anti-entropic virucidal force that biophysically constrains all biodiversity by protecting all organized genomes from virus-driven energy theft and genomic entropy.
That’s why theories of evolution have no explanatory power. An unknown force of nature must be included the theories for comparison to Schrodinger’s claims in What is Life? (pp. 73 and 74)

Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight.)

See for comparison: Force of nature gave life its asymmetry

…even demonstrating how a common physical phenomenon would have favoured left-handed amino acids over right-handed ones would not tell us that this was how life evolved…

The fact that there is no explanation for how life evolved outside the context of an unknown force of nature can be placed into the context of the energy-dependent creation of all differentiated cell types in all living genera.
See: RNA G-quadruplexes are globally unfolded in eukaryotic cells and depleted in bacteria (2016) by Junjie U. Guo and David P. Bartel,

Owing to the extensive hydrogen-bonding and base-stacking interactions, RG4 structures can be very stable, with in vitro melting temperatures well exceeding physiological temperatures. This stability typically depends on the presence of K+, which is the optimal size to bind at the center of two stacked G-quartets…

They fail to mention that energy-dependent hydrogen-atom transfer in DNA base pairs in solution must be linked to the stability of supercoiled DNA. Instead, the unfolding of the RNA G-quadruplexes was reported as: RNA Sequences Don’t Predict In Vivo Transcript Structure

Interactions between nucleotides can turn sections of transcripts into loops, bends, and knots, some of which have regulatory functions in the cell.

See for comparison: Electrolytes induce long-range orientational order and free energy changes in the H-bond network of bulk water. K+ is an important electrolyte in the context of interactions in solutions. That fact was reported as: A single ion impacts a million water molecules. The fact that the interactions between nucleotides are pH-dependent makes it important to consider what happens when slight changes in the cell types of species-specific tissues occur in the context of nutrient stress or social stress.
The stress causes changes in protein folding that predictably links energy-dependent interactions between nucleotides from natural selection for codon optimaility to fixation of RNA-mediated amino acid substitutions and healthy longevity? If pH does not facilitate energy-dependent codon optimality, a change in pH may predict a change in the structure of functional proteins, which can effect biophysically constrained cell type differentiation.
See for instance: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

Unfortunately, the nutrient energy-dependent interactions between nucleotides and amino acids, which are the building blocks of proteins, are typically not considered in the context of virus-driven energy theft, which has been linked from viral latency to all pathology via transgenerational epigenetic inheritance in species from archaea to humans.
See for instance: Epigenetics and Genetics of Viral Latency
… viral latency is responsible for life-long pathogenesis and mortality risk…
My comment to The Scientist on RNA Sequences Don’t Predict In Vivo Transcript Structure :

See also: MicroRNAs: Genomics, Biogenesis, Mechanism, and Function (2004) by David P. Bartel

…about a quarter of the human miRNA genes) are in the introns of pre-mRNAs. These are preferentially in the same orientation as the predicted mRNAs…

For comparison, see: From Fertilization to Adult Sexual Behavior

… epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans… Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species.

Hydrogen-atom energy-dependent changes in base pairs have since been linked from RNA-mediated protein folding chemistry to all biophysically constrained cell type differentiation in all living genera via amino acid substitutions.

The RNA-mediated fixation of amino acids links autophagy from the innate immune system to supercoiled DNA. Virus-driven energy theft has been linked to all pathology via changes in the microRNA/messenger RNA balance. The changes link fertilization to adult sexual behavior. See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems.
See also, the other publications by David P. Bartel
2016 Impact of MicroRNA Levels, Target-Site Complementarity, and Cooperativity on Competing Endogenous RNA-Regulated Gene Expression
Excerpt:

…we assumed that (1) molecular species are well mixed within the cytosol and their concentrations are not influenced by cell growth and division; (2) each mRNA and miRNA is produced at a constant rate, and unbound mRNAs and miRNAs undergo constant first-order decay; (3) upon association with a miRNA, the mRNA degradation rate increases, regardless of the site type; and (4) miRNA binding is reversible, and upon miRNA dissociation the mRNA degradation rate reverts to its original value. We also assumed that the Michaelis constant (KM) describing mRNA degradation with respect to the miRNA-mRNA complex is well approximated by the complex dissociation constant (KD), and that both bound and unbound mRNA are translated.

Simply put, they seem to have assumed that energy-dependent changes in the microRNA/messenger RNA balance need not be considered in the context of any model of biologically-based cause and effect.
See for comparison: 2014 Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
Abstract excerpt:

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man.

The clear difference between the assumptions made by Bartel (and others like him) and the facts about energy-dependent biophysically constrained RNA-mediated protein folding chemistry make it pointless for serious scientists to discuss experimental evidence of biologically-based cause and effect with anyone who does not agree that it is energy-dependent and biophysically constrained by the physiology of energy-dependent reproduction in all living genera.
See also: How the elite control the masses
Control involves giving the masses partial information, which is what Bartel and others appear to be doing in attempts to promote evolutionary theories.

See for comparison ( December 30, 2016 at 5:37pm):

Peter Berean wrote:

James, I have no problem with “energy-dependent RNA-mediated amino acid substitutions” … however, that does not show that energy = information.

And, neither does the article about “construction of phylogenetic trees”…

My recommendation is DO take the advice of your brothers in Christ… And correct your views and models accordingly.

IF you do so, you could actually have more people believe what you have to say about your models.

The comment about taking advice from my “brothers in Christ” is a classic. It comes from someone who may never understand anything about energy-dependent hydrogen bonds in supercoiled DNA, or how energy as information must be linked to all biodiversity.

Peter Berean is only one among many who are biologically uninformed. Their masses are not told that virus-driven energy theft can be linked to all pathology in the context of conserved molecular mechanisms, which have been detailed by all serious scientists. Peter Berean may think that his faith in God and/or his brothers in Christ will save him from his ignorance.

That may be true, but it may also not apply to those who have been told the truth and continue to ignore it. People like that encourage others to ignore the truth about energy-dependent hydrogen bonds in supercoiled DNA. The truth is that if you don’t know where that energy came from, you are no better off than any other theorist or atheist.

That makes this Chirality Check a reality check, and makes this a lie: “…checkpoints ensure that only l-amino acids are incorporated into proteins during translation.”

See: Evolution of constrained gonadotropin-releasing hormone ligand conformation and receptor selectivity as cited in Evolution of gonadotropin-releasing hormone (GnRH) structure and its receptor

When the chiral amino acid (Ala) in position six of Ciona I GnRH was substituted with the achiral glycine or with d-Ala, which enhances the type II’ β-turn conformation, there was a marked increase in the binding affinity of the peptides at the vertebrate GnRH receptor (Barran et al., 2005).

The substitution of achiral glycine and the increased binding affinity were placed into the following context in the Evolution of gonadotropin-releasing hormone (GnRH) structure and its receptor:

The discovery of the fact that one decapeptide molecule, among the GnRHs, was constructed perfectly at the beginning of 400 million years evolution and that it is not possible to improve its physiological potency using the any natural amino acid is, in my opinion, important, fascinating and beautiful.

The claim about 400 million years of evolution has not been substantiated by experimental evidence of biologically-based cause and effect and virus-driven energy theft was not considered in the context of the invention of neo-Darwinian theory.
The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis…
[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent…. Evolution was defined as “changes in gene frequencies in natural populations.” The accumulation of genetic mutations was touted to be enough to change one species to another…. Assumptions, made but not verified, were taught as fact.
See also: Spectrum of Antimatter Observed for First Time

The Standard Model predicts that there should have been equal amounts of matter and antimatter in the primordial Universe after the Big Bang, but today’s Universe is observed to consist almost entirely of ordinary matter. This motivates physicists to carefully study antimatter, to see if there is a small asymmetry in the laws of physics that govern the two types of matter.

Without the anti-entropic energy of the sun, the laws of physics could not be linked from chemistry to molecular epigenetics, which must link energy-dependent autophagy from the innate immune system to supercoiled DNA. If not, you are left with the magic of emergence and evolution instead of the fact that Life is physics and chemistry and communication in the context of energy as information.
In 2016, scientists collectively failed to link the anti-entropic virucidal energy of the sun to autophagy and all biophysically constrained biodiversity via the physiology of reproduction in all living genera. They also failed to link virus-driven energy theft from the negative supercoiling of DNA to all pathology.
Instead, most scientific successes are examples of politicized science. Congratulations to those who are willing to place politicized science into the context of their theories. The theories make their World a better place for other theorists to live in. Serious scientists, for comparison, will remember the theorists who failed to make the Chirality Check a reality check.

Energy-dependent hydrogen bonds in supercoiled DNA

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