What Happens When You Exercise So imagine that you start running. Here's what happens: The muscle cells burn off the ATP they have floating around in about 3 seconds. The phosphagen system kicks in and supplies energy for 8 to 10 seconds. Finally, if exercise continues, then aerobic respiration takes over.
Aerobic System (Aerobic glycolysis).wmv - YouTube NOTE: You never completely use up your fat stores but the body does begin to break down muscle to fuel prolonged physical activity after glycogen stores are depleted. (The video gets that part wrong.)