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Carbon dioxide levels regulate breathing via the chemoreceptors in your brain, carotid arteries, and aorta. As Carbon dioxide levels go up, the pH of the cerbrospinal fluid goes down (becomes acidic) and triggers a reaction by the chemoreceptors in your brain to cause you to breath. Specifically, those receptors are located in the floor of the fourth ventricle (in your brain stem for all intents and purposes). Expelling CO2 by breathing brings your cerebrospinal fluid's pH back down to acceptable levels. The chemoreceptors in your carotid arteries and aorta respond to the partial pressures of CO2 as well as the partial pressure of oxygen. Basically, it also tells you to breath when your CO2 levels get too high. Ultimately, it looks like when you hold your breath and "run out of air", you don't actually run out of oxygen, but you accumulate too much CO2 (after all, we can make ATP without oxygen, it just makes nasty byproducts *muscles -> lactic acid* but if our pH gets too high, we don't have a real good contingency plan for fixing it quickly)

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