There are differences between eukaryotic and prokaryotic cells, that allow them to be distinguished. 1) There is compartmentalisation in the eukaryotic cells, meaning the eukaryotic cells contain structures which are bound by membranes. This higher level of organisation is absent from the prokaryotic cells.2) The prokaryotic cell contains a nucleoid region where the DNA can be found, while eukaryotic cells have a nucleus for their DNA. 3) Prokaryotic cells may have structure, such as pili and flagella, which are absent in eukaryotic cells.