Essentially, focused and sustained exercise causes metabolic and physiological adaptations that are beneficial to the human body and quality of life. This article by Chen, Zhou, Feng, and Chen was published in Nature.
An article published in PubMed (the National Library of Medicine) explains in great detail the effect of exercise on the human body. Read Section #8 Satellite Cells and Physical Activity first, but a very good explanation of the aspects of adaptation of muscles due to physical fitness training.