IMP is not a Nucleoside Monophosphate intermediate but the First Purine Nucleotide of Nature
Don't mistake a purine nucleoside monophosphate created by Purine catabolic degradation, for purine nucleotide synthesis de novo, which is the correct pathway for RNA and DNA synthesis from scratch. The difference is subtle, but the consequences huGe.
The Central Dogma Mainstream Life Scientists and Genomics have mistaken nature’s evolutionary 3.6 billion year old purine nucleotide parent-child relationships.
Current Watson-Crick believers use 5 nucleotide families, but only two purine families. Conventional wisdom teaches AMP (adenosine mono phosphate) is the parent nucleotide molecular structure because AMP is deaminated IMP to inosine to A to I mRNA post transcriptional mRNA (miRNA, piMRNa, RNAi, snoRNA and many other small RNA molecules which control human metabolism at the gene not single nucleotide pair levels.
This flow chart of human purine nucleotide synthesis gives a wrong picture of how nucleotides become the molecular substrates for nucleic acids. The picture above is used as the basis for the codon-anti-codon dna=ATGC, rna=AUGC genetic codes we have been using for 51 years (1966).
In actuality, the flow chart below is the “real way” purine nucleotides and RNA/DNA are synthesized in and by nature. The anabolic (synthesis de novo, salvage) lead to RNA and DNA. After DNA has been replicated and RNA transcribed by the CTD pol II ribozyme, and the mature mRNA transcript has been edited, spliced, uploaded or downloaded, and moves to the translation phase of protein synthesis on the ribosome, using the combined inputs of mRNA mature, tRNA, and rRNA and their multiple sub components, the right amino acid is synthesized through the creation of the peptide bond 5’NH2+ head to 3’ COOH- tail. The amino acid chain builds until 7 amino acid peptide bonds twist into an Alpha helix, the first protein structure found my scientific man i.e. Drs. L. Pauling and F. Crick co discovered this alpha protein 3d structure in 1953, and noticed how it coiled and had knobs in holes i.e. 4 knobs, 3 holes. The most hydrophobic (fear of water) amino acids i.e. leucine, alanine, serine, threonine, valine etc. were buried in the core of the heptad structure stabilized by two polar amino acids forming semi-ionic bonds through electromagnetic ionization. The leucine zipper or alpha protein is the most common motif and usually forms the basis of the higher order i.e. protein quaternary and ternary molecular structures connect by disulfide bonds.
Back to the major point, IMP (inosine monophosphate is not an intermediate nucleoside monophosphate in purine nucleotide metabolism, but actually the first purine nucleotide closed ring made by nature through and 11 step multi-enzyme pathway which eventually led to IMP cyclo- hydrogenase and the closed ring of IMP (inosine monophosphate). IMP is not an intermediate but the first of the class of nucleotide molecular structures which is today the genetic code used in genomics. AMP and GMP are both the “children” of IMP the parent purine nucleotide, not the other way around/inversion. Where the genetic code captures the catabolic degradation process while it should have used the anabolic syntheses process of IMP, synthesis de novo = from scratch; and the purine
have used the anabolic syntheses process of IMP, synthesis de novo = from scratch; and the purine synthesis salvage which is catalyzed by HGPRT and APRT. The break down of the nucleic acid molecules which signals for purine and pyrimidine catabolic degradation, starts with the ATP to IMP deamination and the excretion of toxic ammonia NH3 oxidized by xanthine oxidase to uric acid and then to the kidneys.
It is particularly noteworthy: IMP, HGPRT, Xanthine Oxidase which play key roles in purine nucleotide synthesis de novo (IMP), purine synthesis salvage (HGPRT) for the hypoxanthine and guanine families, APRT for adenosine, so the nucleotide purine pool can maintain homeostasis for further higher order functions in the genome. i.e. G7 transmembrane signaling system, the adenine and guanine binding proteins, kinases, and other nuclear nucleic acid/protein hybridizations which reach its zenith in the neocortex of homosapiens, the most complex organ of extant earth today.
So history, should be rewritten and corrected in an updated version 2.0 of the Watson-Crick-Berger Triplex 7 nucleotide genomic code. Genomic code = genetic code (ATGCU) combined with the epigenetic code (IX), 1= Inosine family, X= Xanthosine family. Therefore, we propose expanding the existing genetic code, with natural nucleotides to the genome wide (genetic + epigenetic) encoding and decoding schema which accounts for all the events of the 3.2 billion nucleotide base pairs which make up the human genome.
The above two pathways show the primary and secondary feedback purine nucleotide pathways used in purine synthesis de novo, salvage and catabolic degradation, the final step using xanthine oxidase
in purine synthesis de novo, salvage and catabolic degradation, the final step using xanthine oxidase to uric acid + NH3.
I hope this further clarifies why IMP and inosine family must be included in the suggested expanded 7 nucleotide genomic code i.e. ATUICGX, while converting the existing 5 nucleotide dna = ATGC, rna = AUGC. The expanded ATUICGX genome code will better explain the inner workings of the small molecular RNA substrates which seem to use the majority of the 98% of the human genome while the 2% of the genome which codes for Proteins, still receives the “lion’s” share of research money and scientific headcount.