[Babcock_Hall]

Babcock hall: I see two problems here- firstly as far as I can tell the NADs and FADs dont have a role in producing CO₂ but I have not examined the mechanism in detail (if they do I'd love to know as this could be the solution). The other problem is that you only need 12e^- to reduce 6O₂ molecules at the end of the ETC. Have a look at the balanced equation:

6O₂ + 12H⁺ + 12e^- 6H₂O

So what happens to the other 12 electrons.

NAD is produced in several reactions that are oxidative decarboxylations (pyruvate dehydrogenase, isocitrate dehydrogenase, and α-ketoglutarate dehydrogenase).

[Yggdrasil]

Yggdrasil thank you for your reply.

At what point are these 6 water molecules used? I haven't spotted these on any reaction schemes I have seen (but admittedly, these are all generally massively simplified and don't show any mechanistic details). I'd love to know more.

You can see the need for water as glucose has one oxygen per carbon, but CO2 has two oxygens per carbon.  The oxygen atom in CO2 comes from water as molecular oxygen is used only in the electron transport chain to produce water.

Conceptually, you can think of glycolysis + citric acid cycle as:
C₆H₁₂O₆ + 6H₂O --> 6 CO₂ + 12H^- + 12H⁺

And the electron transport chain as:
12H^- + 12H⁺ + 6O₂ --> 12H₂O

To give the overall equation:

C₆H₁₂O₆ + 6O₂ --> 6 CO₂ + 6H₂O

Not exactly sure which exact steps are the ones that take up water (some may use water indirectly), but the fumarase reaction requires water.

[ptryon]

Ahhh I see! Isn't it interesting how it all comes together when you start to understand a chemical problem like this? Thank you to everyone who has answered. Yggdrasil, thank you. I couldn't find this anywhere I looked- but it makes perfect sense when you summarise it.