Running can burn fat and muscle. Different factors determine which fuel source your body uses during running. Ideally you want your physical activity to burn fat, but under extreme circumstances, the fat available for fuel may become depleted, resulting in the burning of muscle for fuel.
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Fuel for Exercise
Your body uses fuel sources for exercise in a specific order — first carbohydrates in the form of glycogen, then fat. If exercise goes on for really long time, it turns to muscle. This may occur about two or more hours into a run.
To help support long runs like marathons, a high-carbohydrate diet is needed. It keeps the brain functioning and spares carbohydrates in the muscles, improving endurance. Increasing carbohydrates by 10 to 12 grams per day about 48 hours before the race may help prevent fatigue. Proper hydration early on during a run also helps support fuel utilization.