I know that after depletion of glycogen body starts to use fat for fuel. If I continue working an hour or more in this state, does my body start to use proteins for energy after a while? I have some belly fat so I don't think I am losing proteins from my muscles? Am I right?
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On average, a person has more than 80,000 calories in fat storage. You'd need to burn through this first before your body targets protein for fat storage.
Don't worry about it, proteins start getting consumed only after prolonged periods of starvation when adipose tissues are depleted. (Unless you are on a very low calorie diet.)