What is the basis of allergic reactions? Of autoimmune
diseases?

Simply stated, the basis of an allergic reaction is a
hypersensitive response to an exogenous antigen
resulting in deleterious effects (McCance & Heuther,
2006). An autoimmune disease is an immune reaction
against ones own antigens resulting in damage to the
host tissue (McCance & Heuther). Multiple Sclerosis,
Myasthenia Gravis, Rheumatoid Arthritis, and Insulin
Dependent Diabetes are all autoimmune disorders. In
these cases, the body ceases to recognize oneself and
attacks itself resulting in a set of symptoms related to
the organ or tissue involved. For example, in multiple
sclerosis the CNS myelin is degraded and thus the
symptoms involve neurological disability and loss of
motor function (McCance & Heuther). 

McCance, K.L., & Huether, S. E. (2006). Pathophysiology:
The biologic basis for disease in adults and children.
Elsevier  Mosby: St. Louis.