ATP is not stored in the body. It is continuously produced in each cell from other storage molecules, like fat or carbohydrates. There are two ways ATP is produced from these storage molecules: oxidation or fermentation. Oxidation is the preferred, more efficient method, producing around 28 ATP from a molecule of glucose. Fermentation only produces 2 ATP. The advantage of fermentation is that it does not require oxygen, and so can be used during very high intensity effort when oxygen is scarce. The trade-off is that it produces a lot of lactic acid, which inhibits fermentation, so high intensity effort can only be maintained for a short amount of time.
Fatigue after exercise occurs because you are depleting your stored energy, you are losing water to sweat, the build-up of waste products, and the general breakdown of tissues after repeated use.
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