In the first few seconds
Your muscles start using adenosine triphosphate (ATP), energy molecules your body makes from food.
That burst of power you feel? It's ATP converting into another high-powered molecule, adenosine diphosphate (ADP). Muscle cells—expert recyclers—will turn ADP back into ATP after the initial surge.
In the first 90 seconds
In order to unleash more ATP, your cells break down glycogen, a form of glucose fuel stored in your muscles. Cells also pull glucose directly from your blood (one reason exercise is helpful in fending off high blood sugar).
Your body gobbles more glucose, and your muscles release lactic acid—also known as the burn in the age-old workout mantra "feel the burn"—which signals the brain that you're under physical stress.
In the next few minutes
Your heart starts beating faster and directing blood toward your muscles and away from functions you don't need at the moment, such as digestion.
To make the best use of glucose, your muscle cells require an influx of oxygen. Cue heavy breathing.
As you hit your stride, your body's biggest muscle, the gluteus maximus (i.e., your butt), your legs, and your core help keep you upright, control your gait, and extend your hip joints so your feet can push off the ground.
You begin to torch calories (in general, runners work through about 100 per mile), including some that might have been stored as fat.
All this burning of glycogen and oxygen raises your body temperature. To cool you down, your circulatory system diverts blood flow to your skin, lending you a healthy flush. Your sweat glands start releasing moisture to keep you from overheating.
Within 10 minutes
If you're in decent shape, your muscles and their ATP supply are ample, and your body can efficiently shuttle oxygen and burn-fat and glucose. You feel strong.
If, however, you've been slacking on exercise, your ATP supply can't keep-up with the demand. You can't suck in or process-oxygen fast enough, and lactic acid starts to flood-your body. Every minute feels more like a slog.
After 30 minutes
Whew! It's over. As you slow to a walk, your energy demand falls and your breathing rate gradually returns to normal.
Chances are, you feel energized. Your brain has triggered a rush of the mood-elevating hormone dopamine. The effect of exercise can be so great that it can even decrease chocolate cravings. (Don't worry—even if you still indulge in the sweet stuff, you've created some room in your glycogen stockpile, so those extra calories are less likely to be converted into fat.)