At the molecular level what is it about physical exercise that repairs/strengthens a body muscle (say one's shoullder)?

A muscle membrane protein called dysferlin is important for muscle repair. Deficiency of dysferlin causes muscle weakness and leads to mainly two phenotypes. They are Miyoshi myopathy with primarily distal weakness and limb-girdle muscular dystrophy type 2B (LGMD2B) with primarily proximal weakness.

Read more on dysferlinopathies here: http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=gene&part=miyoshi