Energy "Rules":
The total amount of energy remains the same (energy is not created or destroyed)
Energy is contained in objects
Energy can move from one object to another [Transfer]
Energy is of different forms and can change from one form to another [Transformation]
Energy "Rules" in the context of biological systems and chemical reactions:
Chemical energy is stored in a substance (the molecules) of an object, not the object as a whole.
Chemical energy transfers happen when molecules rearrange (when substances change)
The matter (atoms) of the molecules does not transform into energy, and energy does not transform into the material. In all chemical reactions, rearrangements of molecules happen, but the same amount of material is present before the transformation as there is after the transformation.
Often, each time chemical energy is transferred in living systems, some of it is concurrently transformed into thermal energy.