Once these macromolecules are formed and distributed, simple diffusion – as in prokaryotic cells – is inefficient and too slow for a cell of such a large scale; a much more complex transport system is required. Due to the lipid bilayer of the organelle being impermeable to most hydrophilic molecules, it must therefore contain membrane transport proteins (sorting signal) which are responsible for the import and export of specific metabolites. In conjunction with this requirement, each organelle must have a mechanism (translocator) for importing and incorporating into the organelle these specific proteins that make the organelle so unique. The actual physical location of the various organelles, also donates to the overall success of the cell. The endoplasmic reticulum and the Golgi apparatus which are specifically devoted to the sorting and transport of proteins are found closest to the nucleus and nuclear envelop. The physical distance between these organelles is relatively short and so transport of substances is more efficient.
Another advantageous aspect of compartmentalisation is the eukaryotic cells ability to capture energy more efficiently. Again the issue of volume plays a role and even with a complex transport system in place, the rate of turnover of macromolecules is very slow compared to prokaryotic cells. Compartmentalisation however allows high concentrations of biochemical to be present within the cell, allowing for increased cell efficiency as chemical reactions occur more rapidly. These high concentrations of biochemical are found within certain organelles and not throughout the entire cell. This allows for different intracellular pH and enzyme systems to be isolated, as well as incompatible metabolic activities to be carried out simultaneously. Unlike the prokaryotic cell which must commit itself completely to one function, depending on the environment, the eukaryotic cell is able to carry out these opposing simultaneous activities independent of the cells current external environment.