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Entropy production along a single stochastic trajectory of a biomolecule isdiscussed for two different sources of non-equilibrium. For a moleculemanipulated mechanically by an AFM or an optical tweezer, entropy production(or annihilation) occurs in the molecular conformation proper or in thesurrounding medium. Within a Langevin dynamics, a unique identification ofthese two contributions is possible. The total entropy change obeys an integralfluctuation theorem and a class of further exact relations, which we prove forarbitrarily coupled slow degrees of freedom including hydrodynamicinteractions. These theoretical results can therefore also be applied to drivencolloidal systems. For transitions between different internal conformations ofa biomolecule involving unbalanced chemical reactions, we provide athermodynamically consistent formulation and identify again the two sources ofentropy production, which obey similar exact relations. We clarify theparticular role degenerate states have in such a description

Entropy Production for Mechanically or Chemically Driven Biomolecules