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During the Calvin cycle, it is speculated that after Ribulose bisphosphate carboxylase/oxidase carboxylate ribulose bisphosphate, a 6C molecule is created and decomposed instantaneously into two phosphoglycerates because it is extremely unstable so:

Can anyone clarify why this molecule is so unstable? and...

how we know this molecule exists?.

I did not find anything useful while researching this, perhaps I'm not looking properly or there is no debate about it.

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  • $\begingroup$ Please cite a reference for your assertion with date. On checking my copy of Berg et al there are full details of the reaction mechanism including the components of RUBISCO involved. I imagine it's a mixture of enzyme structure, chemical logic and experimental evidence, but you will need to go to the original papers if you want the details. There may be uncertainties, but if so it won't be alone. However RUBISCO has been intensively studied. $\endgroup$ – David Sep 18 '17 at 20:34
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The question of why the molecule is unstable belongs to the realm of chemistry, which is not the subject of this list. Presumably the reaction for its hydration is thermodynamically favourable and there is a reaction mechanism which allows the reaction to proceed with a low activation energy.

The question of the existence of 2-carboxy-3-keto-D-arabinitol 1,5-bisphosphate and its role as an intermediate in the RuBisCO reaction was solved in 1986 and is no longer the subject of speculation. Its synthesis was described in a paper in Phil. Trans. R. Soc. Lond. B, which is behind a pay wall, but can be found in a post on ResearchGate.

In brief, they trapped this C6 compound in a more stable form with acid, and so could characterize it chemically. Its enzymic hydrolysis could then be studied at a slower rate.

The subsequent solution of the crystal structure of RuBisCO provided further confirmation of the reaction mechanism and molecular information on the role of the enzymic groups and magnesium ion cofactor. See, for example, the review by Gutteridge and Gettenby in Cell.

So the era of speculation would appear to be long past, and the account in standard biochemical texts such as Berg et al. — shown below — would appear to be reliable.

RuBisCO reaction

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