All three of the basic macronutrients -- carbohydrates, fat and protein -- are used as fuel in the body. Usually, the exact fuel your body is using at any given time is a mixture of the three, but the balance changes depending upon the circumstances. Protein never plays the lead role in energy production, but even a small increase over the usual contribution can have deleterious effects over time. A proper diet can keep this from happening, but your nutritional intake must be tailored to your lifestyle.
Carbohydrates are your body's favorite fuel source, in the form of glucose and stored glycogen, because these molecules are quickly and easily converted into fuel. Glucose is your most immediate energy source, and fat provides fuel during low- to moderate-intensity activity. Intense activity forces your body to turn to your glycogen stores for faster fuel production, but when glycogen runs out, you're left with fat again. Fat takes longer to convert to fuel, so your performance will suffer. Under normal circumstances, protein only contributes about 5 to 10 percent of your body's fuel, but certain circumstances can increase protein's role.
When you perform intense activity with low glycogen stores, protein can contribute up to 15 percent of your energy. Protein breaks down in your body every day, and the pieces of the molecules that break down serve as a sub-structure upon which your body can build glucose that is used for energy. You cannot store protein the way you do carbohydrates, so it is important to eat it every day to ensure that amino acids are available to replenish the depleted proteins. If not, your body won't have enough amino acids to repair and replace damaged cells, eventually leading to a complete breakdown of body function. The most visually-apparent sign of this process is muscle loss.
Every time you use a muscle, you cause damage. Your body uses protein to repair the damage and build a little extra as protection against future stress -- you see this physically as muscle growth. If you are using up your protein as a fuel source, there won't be enough to repair any damage, let alone facilitate growth, but the damage will continue to occur. Your muscles degrade as a result, growing smaller and weaker over time. That's the reason behind the wiry physique of many distance runners -- they stress their muscles continuously, even long after their glycogen stores are depleted. Serious runners understand this, and include high amounts of protein in their diets to compensate. Muscle loss is not only about strength and appearance -- your heart is a muscle, and it's one that you definitely don't want to let degrade.
The proper diet helps you avoid muscle wasting in two ways. First, it provides enough carbohydrates that your protein is rarely called upon as a fuel source. Secondly, it provides enough protein that there is always enough amino acids for cell repair. Your individual needs depend upon your age, size and activity level, but the general guidelines say that carbohydrates should form 45 to 60 percent of your diet and protein should be between 10 and 35 percent. Endurance athletes frequently require a more precise diet to restock depleted glycogen stores and stave off muscle degradation -- the American Dietetic Association suggests up to 5.5 g of carbs and 0.9 g of protein per pound of body weight per day.