This is a tool. Those post-it notes with molecules from metabolic pathways on them.
Green are interesting endpoints.
The ribonucleic acids (as monophosohates) AMP:upper right,GMP:center right second from the edge, UMP:upper left, center right in the cluster, CMP:upper left, center left in the cluster, TMP:upper left, top of the cluster.
And some cofactors/B-vitamins:NAD/NADP/Niacin/B3, Pyridoxal Phosphate/B6:lower left, Coenzyme-A/B5:lower center edge, Thiamine/B1: center, Folate/B9:right, third from the edge Riboflavin/B2:right, green square at the edge.
Orange are some of the amino acids that are made into proteins: Aspartate:center edge top and right lower orange square, Glycine:left close to center, Histidine:right top, Tyrosine:left edge center, Phenylalanine:left edge bottom, Tryptophan:left on the lower corner square, Valine:first lower center orange square Cysteine:lower center left right member of the pair, Serine:lower center left member of the pair.
Aspartate has two because it’s an intermediate but the amino acid in protein part is more important to me. There may be other inconstancy. This is evolving
Pink are common intermediates, or junctions in pathways depending on how you want to look at it. Pink are also molecules added to reactions. Some pink start pathways and are used so often I saw them as a “pool to draw from” and not a pathway that makes the molecule (I should connect Glycolysis and the Pentose Phosphate cycle). Ribose is used to make so many things in the form of PRPP: center left third from edge. AGUCT, Tryptophan, Histidine, NAD, Folate, Riboflavin Thiamine. There’s a bunch more. Glycine is positioned as something added when making A and G
Blue are intermediates in pathways connected to something green and pink. This needs organized better. Some are missing reaction steps because I’m not working on it yet or interested in it yet. Lower center connects Coenzyme-A/B5 to Valine. AG biosynthesis stretches across the center left to right from PRPP with two pink intermediates, AIR (pink) connects to Thiamine, SAICAR (pink) connects to Histidine, IMP (pink) is an intermediate between A:AMP above and G:GMP below. I have Tryptophan lower center left in a U shape going up from Pink Erythrose-4 Phosphate (E4P) and Phospho-Enol-Pyruvate (PEP). Formate and Bicarbonate are single carbon molecules of interest.
At the moment I’m looking at the protein domain structure of purine (AG) biosynthesis and seeing what is shared with who so I can find new connections. And I’m trying to go back to an abiogenesis post which is proving challenging.
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