Considering the Metabolic Pathway:
http://www.genome.jp/kegg-bin/show_module?M00166
Consider the reaction R01523(the very first reaction). How is it possible to know that the compound C00199(D-Ribulose 5-phosphate) will get transformed to C01182(D-Ribulose 1,5-bisphosphate)?
What are the factors on which this transformation depends?One factor I know is structure but how does structure effect this transformation? Does two similar structured compound means that one of the compound can get transformed to the other one?
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1$\begingroup$ Cross posted chemistry.stackexchange.com/questions/32012/… $\endgroup$– user15629May 26, 2015 at 8:16
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From my answer on chemistry:
After looking at the website I found the reaction is based off of an enzyme called: phosphoribulokinase. In biological systems many reactions occur under the auspice of enzymes or proteins. These are incredibly large molecules made of an extremely long chain of amino acids which are a set of 26 or so small molecules that can 'hook' into the chain structure of a protein. Each amino acid has different properties and thus experiences different forces pulling it towards and away from other amino acids on the chain. What this means is the whole chain folds up into an extremely complex structure. For a protein to allow a reaction to occur it has a small region that the reacting molecule can hook into. There are then sets of atoms and molecules that act as scaffolds that allow atoms in the reacting molecule to be moved without the need for nearly as much energy as would be required without the scaffold. Now this is how it changes structure. Now whilst the protein can just as easily allow the molecule produced to be converted back to the original, this may be less energetically favourable which brings us to equilibrium chemistry involving dynamic forward and backward reactions. What makes this more complicated is that proteins often have separate 'hooks' for molecules to disable them. That is if a lot of substance A is around then the protein will be disabled and no longer convert B into A until more A is consumed and thus stops inhibiting the protein.
