Your body produces energy by reacting various biological molecules with oxygen. Since biological molecules are almost always based on a carbon backbone, this usually ends up reacting carbon with oxygen, which produces carbon dioxide.
The textbook example is [glucose](https://en.wikipedia.org/wiki/Glucose) (C6H12O6), which is “burned” by reacting it with oxygen:
C6H12O6 + 6 O2 -> 6 CO2 + 6 H2O
but the same basic idea applies to all sorts of things your body can burn for energy.
The carbon ultimately comes from the food you eat. That food is either plants themselves, or animals that ate plants, so we can trace it further to plants, which capture carbon from the atmosphere as part of photosynthesis. Ultimately, carbon goes around in a loop from being captured by plants, plants being eaten by animals, and animals burning that carbon for fuel. This is (part of) the [carbon cycle](https://en.wikipedia.org/wiki/Carbon_cycle); any given carbon atom in the atmosphere is recycled by this process roughly every five or ten years on average.
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