An Alternative Interpretation of Purine Metabolism

Dear Reader: Please click on the purple link embedded in the text; it will take you to visual proof: access my picassa web album with over 100,000 "visioneering newspaper like - BIG BOLD  headlines which function as annotations-summarizing the context and conditions of actual biomolecular dynamics captured in a blended story line vector, showing up when least expected.  That is the beauty of these albums, like a like the universe of plato's idealized world only focused on the modern life sciences genome of : codes, biochemical and protein -protein; protein/RNA, nucleotide/gene, purine families of enzymes, genes, synthesis, salvage and catabolic degradation to Uric Acid. These are the themes and story lines of evolution and all it's elementary mass particles from Cosmic Dust, Carboniferous Meteorites which provided the major purines adenine, hypoxanthine, xanthine as well as uracil the pyrimidine, and several organic amino acids including many of the Inosine Wobble hydrophobic amino acids where A to I RNA editing and alternative splicing of CTD transcripts and RNA polymerase 2, the self catalytic RNA autocatalytic replicator from the much discussed RNA world hypothesis where ribozymes performed two both catalytic and information in one molecular structure probably in a viroid or crcRNA, a circular single stranded nucleotide string of genome bits of small rna molecules like miRNA etc. 

This whole project is about using my imagination to capture, first by picture or image in my mind's eye as I arranged the pictures together to tell a little story of three parts, start,action,stop unload product, start synthesis again. 

Second I am trying to put to English text, what all these pictures mean, especially when organized by standardized scientific formats. I have captured in those 100,000 stored in picassa files somewhere on google, this universe of relationship beginning with quantum physics the moving into all the non-euclidean geometries for the shapes, sizes and symmetries of all classes of crystalline structure 3D mineral based substrate as the shell protector, supplies electromagnetic field around pi electron shell volumes with the organism or subcellular organelle like the mitochondria, ribosome, lysosome, golgi apparatus as well as the nucleus, home of the genetic material of carbon based life forms, on planet earth. (Yes I do believe other intelligent life forms have formed and grown in all areas of the universe which planet earth is less than a "drop in the Pacific Ocean". 

That is basically a discussion and attempted explanation of how the conventionally annotated slide shows and other linear stories are told, due to limitations of the relatively new organ of homo sapiens, the neocortex, the most complex organ ever developed by nature.

My rather idiosyncratic picture, embedded words, scientific symbols, headlines all part of the evolution of human metabolism and nucleic acids synthesis, especially RNA with DNA playing a supporting role in providing the source mRNA code but RNA transcribing, editing, and specifications for protein and enzyme anabolic synthesis and catabolic degradation with salvage a short cut to providing purine and pyrimidine nucleotide synthesis and nucleic acid formation to make new biomolecular products. 

In our Novagon DNA model its starts with purine metabolism because that is the only natural molecular heterocyclic closed ring structure which never breaks and releases the captured photons which negatively charged electrons driving oxidative phosphorylation, ATP synthase and power for nature's nucleotide blueprints encode and decode the genius of nature from 3.6 billion years of wisdom gained from million of "trial and error" experiments, where the loser become extinct, and its successor gains addition duties, tasks, and responsibilities.)

A purine is a heterocyclic aromatic organic compound. It consists of a pyrimidine ring fused an imidazole ring. Purines, which include substituted purines and their tautomers, are the most widely occurring nitrogen-containing heterocycle in nature.

Purines and pyrimidines make up the two groups of nitrogenous bases, including the two groups of nucleotide bases. Two of the four deoxyribonucleotides and two of the four ribonucleotides, the respective building-blocks of deoxyribonucleic acid - DNA, and ribonucleic acid - RNA, are purines.

Notable purines:

There are many nat​u​rally oc​cur​ring purines. Two of the five bases in nu​cleic acids, ade​nine(2) and gua​nine (3), are purines. In DNA, these bases form hy​dro​gen bonds with their com​ple​men​- tary pyrim​idines thymine and cy​to​sine, re​spec​tively. This is called com​ple​men​tary base pair​ing. In RNA, the com​ple​ment of ade​nine is uracil in​stead of thymine.

Other no​table purines are at the top of the page.

The orange belongs in the 7 color genomic code Number 4 = Hypoxanthine/Inosine    +    Number 5 = Xanthine/Xanthosine

These are the two purines we have been advocating for to update the current 5 nucleotide genetic code (ATGCU) + epigenetic (IX) = genomic = ATUICGX.

This code can be either a six or seven but not a five only code. Inosine has to be in the genomic code; I am not certain xanthine needs to be in, but another option is to include a 4th pyrmidine = Orotine, the first closed pyrmidine ring and technically the parent pyrmidine with uracil as its child and Thymine and Cytosine direct descendants. These are issues which need resolving in my mind.

Many or​gan​isms have meta​bolic path​ways to syn​the​size and break down purines.

Purines are bi​o​log​i​cally syn​the​sized as nu​cle​o​sides (bases at​tached to ri​bose).

Wrong. They are synthesized from ATP synthase catalyzing the reaction of monophosphate. The Genomic Code should consist of sugar-phosphate + purine base = nucleotide, just as nature synthesized IMP from PRPP in purine synthesis de novo i.e. from scratch, from the beginning.

This suggests nucleotides were a new class of molecular structures and IMP was the first with a closed heterocyclic aromatic ring.

If this is true, and there is a scientific consensus it is, then

IMP is by all rights, the parent molecular structure of AMP and GMP which eventually lead to ATP and GTP (the DNA and RNA code purines).

Purines are bio​ l​ogi​c​ ally synt​hes​ ized as nu​cle​o​sides (bases att​ached to rib​ ose). This is a description of purine salvage where the closed ring is not formed again, but only the sugars and bases are metabolized.

This is obviously false since ATP powers ~approximately 96% of oxidation/reduction reactions where electronic charge and proton gradient are the electromagnetic atomic milieu which molecular reactions take place in.

The electromagnetic radiation field is like the ocean, the nucleotides are boats and ships. Nucleosides have a base pair and a sugar but no energy to contribute to the reaction. They have no phosphates (P1O4-) to catalyze the reaction whether it be a serine or serine-threonine kinase or leucine zipper or and alanine heptad polar molecule. The central dogma has misinterpreted how the genetic + epigenetic code works.

The epigenetic level of gene regulation is not even mentioned in the current 5 nucleotide Watson-Crick genetic central dogma theory paradigm.

Also false , is the notion that inosine mono phosphate and xanthosine monophosphate are toxic nucleotides and need to be removed from nucleic acid reactions.

The AMP to=IMP to XMP catabolic reaction with nitrous acid isa spontaneous deamination which rids the liver and CNS neocortex of toxic NH3 which destroys water based cells by nitrogenase dehydrogenase which rips the water molecules apart thus destabilizing the protein foundations of hydrophobic amino acids. IMP actually saves cell from neoplasms, it is dATP and dGTP which are the dangerous free radical scavenges which cannot be stopped by the immune system and it white blood cell B and T cells.

This is deeper biomolecular discussion of why the current Watson-Crick central dogma paradigm must be updated and edited for accuracy and validity of empirical facts.

Ac​cu​mu​la​tion of mod​i​fied purine nu​cleotides is de​fec​tive to var​i​ous cel​lu​lar processes, es​pe​cially those in​volv​ing DNA and RNA. To be vi​able, or​gan​isms pos​sess a num​ber of (deoxy)purine phos​pho​hy​dro​lases, which hy​drolyze these purine de​riv​a​tives re​mov​ing them from the ac​- tive NTP and dNTP pools. Deam​i​na​tion of purine bases can re​sult in ac​cu​mu​la​tion of such nu​- cleotides as ITP, dITP, XTP and dXTP.

De​fects in en​zymes that con​trol purine pro​duc​tion and break​down can se​verely alter a cell’s DNA se​quences, which may ex​plain why peo​ple who carry cer​tain ge​netic vari​ants of purine meta​bolic en​zymes have a higher risk for some types of cancer.

This is another reason IMP should be the major focus of cancer therapeutics. IMP is not the cause but a symptom of the underling dysfunctional electromagnetic/geochemical base level upon which the molecular Watson Crick sits upon. To cure disease, we have to correct the architecture and balance the particle charges of the atoms which make up the purine, pyrmidines, amino acids, and phospholipids which the building blocks of our metabolic pathways.

All Bold type text is my writing, the normal font is Wikipedia 2.