The three macronutrients from the food you eat — carbohydrates, fats, and proteins — provide energy. However, your body must metabolize, or break down, these large molecules into a form that the cells can use. Exercise increases metabolic rate; therefore, the body must utilize these fuel sources to maximize energy production. Although the muscles use all three macronutrients for cellular energy, it prefers carbohydrate. However, your body has limited carbohydrate stores, so long-duration exercise will cause your body to rely on fat as well. Protein only contributes a significant amount of energy during periods of prolonged exercise or long-term starvation and is a relatively inefficient energy source.
Carbohydrates, fats and proteins are energy substrates with chemical bonds between the many molecules. Chemical pathways in the muscle cell break these chemical bonds and create several smaller molecules, which the cell can use to synthesize ATP. The breakdown rate and energy yield is different among the energy substrates. This, along with substrate availability, influences the muscle cell's preference during exercise.
Carbohydrate and Fat Utilization
Carbohydrate, stored in muscle and liver as glycogen, is your muscles' preferred fuel source during exercise. ATP formation from glycogen breakdown is rapid and efficient, and carbohydrate is the only fuel source used for high-intensity anaerobic metabolism. Fat, stored as triglycerides in fat cells and in between muscle fiber, takes much longer to break down than carbohydrate. Additionally, its breakdown requires more oxygen per ATP produced, so it is less efficient. However, glycogen stores are very limited compared to fat stores: Your body only stores about 2,500 calories as glycogen, but you likely have at least 70,000 calories stored as fat. Therefore, low-intensity exercise burns a high proportion of fat to conserve muscle glycogen for higher-intensity exercise, which requires quick fuel supply.
Your body usually relies on protein for less than 10 percent of total energy expenditure. The liver can break the amino acids in protein down to glucose, which can travel through the blood to the muscles to be used for energy. Additionally, enzymes can break certain amino acids into intermediate molecules that can enter ATP-producing pathways. However, this amino acid breakdown results in excess nitrogen that the body must use ATP to remove. Therefore, using protein for energy is inefficient and since a main source of protein is from your muscle tissue, excess breakdown may lead to muscle wasting.
The use of each of the three macronutrients during exercise will depend on your fuel status before and during exercise. If your muscle glycogen stores are depleted when you start, you will use a larger proportion of fat and protein. Conversely, if you begin well-fueled and consume carbohydrates during a prolonged exercise bout, you will use these readily available ingested carbohydrates and less of your fat and protein stores. Additionally, the body does not ever use one substrate exclusively during exercise or at rest -- all three macronutrients supply energy, although the relative proportions of each vary.