When we are engaged in intense physical activity such as running or riding a bike, the muscles need energy to function and they get this from aerobic respiration.
They will quickly run out of the oxygen required to sufficiently use aerobic respiration however and will turn to anaerobic respiration which can produce energy in the absence of oxygen.
As the body uses anaerobic respiration however, lactic acid is produced and builds up in the muscles. It is this lactic acid that leads to the muscles feeling sore.
