Short term: Exercise burns through the ATP and creatine phosphate stores in your muscles, and forces them to start breaking down glycogen to make more ATP through glycolysis and cellular respiration. If exercise is so vigorous that oxygen can't get to the muscles quickly enough, they will have to rely more on a process called fermentation (since they can't do respiration as much as they need to). In humans, this produces lactic acid. This will make your muscles sore later.
Long term: If you keep at it, your muscles will increase the number of mitochondria in each cell, boosting your capacity to do cellular respiration. Your muscles will also boost up their glycogen stores, which is a major cause of muscle size/mass increase. Your muscles do not get bigger by adding more cells.
I am very familiar with only one and it is also the most obvious: Micro-trauma. This is the sore feeling after physical activity and it is somewhat like tiny damages to the worked muscle. It occurs when a person hasn't exercised in a while or if that person is increasing the rigor of their workout. If the body decides that needs extra muscle to deal with the activity, it will not only treat the micro trauma, but it will also create new muscle tissue.
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