Yes and no. Muscle cells do both aerobic and anaerobic respiration to produce energy. A by product of anaerobic respiration is lactic acid, which is the stuff that makes your muscles sore after a workout.
Well trained athletes have more energy stores in their muscle cells, and are better at taking in oxygen, but even their muscles will still do some anaerobic respiration because it's faster and the muscles can do more work.
Here's more info: http://en.wikipedia.org/wiki/Cellular_re鈥?/a>
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