Your body features a variety of mechanisms for storing, retrieving and exploiting chemical energy. In particular, it has three primary energy stores: glycogen, fat and protein. During sustained aerobic exercise, blood concentrations of hormones such as glucagon and epinephrine rise, and these hormones orchestrate responses that help maintain your blood glucose at sufficient levels.
Glycogen
When you start exercising, your muscles start breaking down glycogen, a polymer of glucose molecules that serves as a readily accessible energy supply. Muscle glycogen and blood glucose are the first energy stores you retrieve during exercise. Glycogen, glucose and other sugars are called carbohydrates; during the early phases of moderate exercise, you derive as much as half of the energy you expend from oxidation of carbohydrates in your muscle tissue.
Fat
Fat is the next energy store your body mobilizes. Fat molecules are energy-rich, and fat constitutes the single largest energy reservoir in your body. During moderate-intensity exercise, the rate of fat oxidation can grow to as much as 5 or 10 times the resting rate, and fat may ultimately provide as much as half of the total energy consumed during sustained exercise. In prolonged aerobic exercise lasting more than an hour, fat becomes the primary source of energy since the body's store of carbohydrates has been depleted.
Protein
Carbohydrates and fats are the two major fuels you burn during exercise; protein plays a much more minor role. Typically, it supplies a mere 6 percent of the energy you expend during exercise. There's a good reason for this; your body needs proteins to carry out all kinds of important functions, so it can't afford to throw them away.
Considerations
Aerobic exercise is different from anaerobic exercise in that it requires a moderate but sustained level of exertion over an extended period of time. Anaerobic exercise takes place in short bursts and relies heavily on anaerobic metabolism, an alternate metabolic pathway that your muscles use when they can't get oxygen fast enough to meet their needs. During anaerobic exercise, the primary fuel source is carbohydrates. While aerobic exercise also makes use of carbohydrates, it places greater reliance on fat as a source of energy.
References
- "Lehninger Principles of Biochemistry"; David L. Nelson, et al.; 2008
- Colorado State University Extension: Nutrition for the Athlete
- "American Journal of Clinical Nutrition"; Lipid Metabolism During Endurance Exercise; Jeffrey Horowitz, et al.; 2000
- UCLA Center for Human Nutrition: Lecture 6: Fuel Utilization During Exercise



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