The origins of mitochondria, chloroplasts, ER, and the cell nucleus can explain the topological relationships of these intra-cellular compartments in eucaryotic cells.
(A) A possible pathway for the evolution of the cell nucleus and the ER. In some bacteria the single DNA molecule is attached to an invagination of the plasma membrane. Such an invagination in a very ancient procaryotic cell could have rearranged to form an envelope around the DNA, while still allowing the DNA access to the cell cytosol (as is required for DNA to direct protein synthesis). This envelope is presumed to have eventually pinched off completely from the plasma membrane, producing a nuclear compartment surrounded by a double membrane.
As illustrated, the nuclear envelope is penetrated by communicating channels called nuclear pore complexes. Because it is surrounded by two membranes that are in continuity where they are penetrated by these pores, the nuclear compartment is topologically equivalent to the cytosol; in fact, during mitosis the nuclear contents mix with the cytosol. The lumen of the ER is continuous with the space between the inner and outer nuclear membranes and topologically equivalent to the extracellular space.
(B) Mitochondria (and plastids) are thought to have originated when a bacterium was engulfed by a larger pre-eucaryotic cell. They retain their autonomy. This may explain why the lumens of these organelles remain isolated from the membrane traffic that interconnects the lumens of many other intracellular compartments.