  Master equation could be applied to model various kinds of biochemical
systems. A general theory for its time-dependent nonequilibrium thermodynamics
is rigorously derived. We not only introduce a concept of general internal
energy, but also propose an extension of the equilibrium state. Moreover, we
find out an explicit expression for the extended form of the Second Law, which
is phenomenologically stated as "the conversion of work to excess heat is
irreversible". The theory is carefully applied to several thermodynamic
processes, and its consistence with the classical thermodynamics is clearly
shown.
