A common concern about doing cardio especially if done on an empty stomach and high intensity, is the possibility of losing muscle. After a night of sleeping glycogen, blood glucose and insulin are low; this is an optimum environment for burning fat. Unfortunately, it may also be an optimum environment for burning muscle because carbohydrate fuel sources are low and levels of the catabolic stress hormone cortisol are high. It sounds like morning cardio might be a double-edged sword, but there are ways to avert muscle loss.
All aerobic exercise will have some effect on building muscle, but as long as you don’t overdo it, you shouldn’t worry about losing muscle. It's a fact that muscle proteins are broken down and used for energy during aerobic exercise. But you are constantly breaking down and re-building muscle tissue anyway. This process is called "protein turnover" and it’s a daily fact of life. Your goal is to tip the scales slightly in favor of increasing the anabolic side and reducing the catabolic side just enough so you stay anabolic and you gain or at least maintain muscle.
How do you build up more muscle than you break down? First, avoid excessive cardio. Aceto suggests limiting your cardio on an empty stomach to 30 minutes, and then it would be "highly unlikely that amino acids will be burned as fuel." He also mentions that "a strong cup of coffee should facilitate a shifting to burn more fat and less glycogen. If you can spare glycogen, you’ll ultimately spare protein too."
Always give your body the proper nutritional support. Losing muscle probably has more to do with inadequate nutrition than with excessive aerobics. Provide yourself with the proper nutritional support for the rest of the day, including adequate meal frequency, protein, carbohydrates and total calories, and it’s not as likely that there will be a net loss of muscle tissue over each 24-hour period.
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