Pathophysiology is the study of the disturbance of normal mechanical, physical, and biochemical functions that a disease causes, or that cause the disease. An example, from the field of infectious disease, would be the study of a toxin released by a bacterium, and what that toxin does to the body to cause harm, in cases of sepsis. Another example is the study of the chemical changes that take place in body tissue that is undergoing inflammation.
Reference
Kumar, V., Abbas, A. and N. Fausto. 2004. Robbins & Cotran Pathologic Basis of Disease. Philadelphia: W. B. Saunders Company