Where does the Carbon Dioxide that we exhale come from?

It is the result from oxidizing fuel, most commonly glucose C6H12O6. The C-H, C-C, and O-H bonds are broken during oxidation and they release energy in the form of "reducing power" carried by the likes of NAD, NADP, and FAD. So the six carbon sugar glucose is oxidized, broken down, carbon by carbon to make CO2 and the H atoms go to those carriers.