Clue: Con imprisoned by nasty penal system emptied part of cell (9)
Answer: ENDOPLASM
Explanation: Definition: part of cell 
DO ("con") "imprisoned by" *(penal) + **S**yste**M** 
Endoplasm is the central part of the cytoplasm of a cell, and no, I didn't know that either, but the wordplay and crossing letters make it possible to work out the solution.