Nucleus - In eukaryotes the nucleus contains most of the DNA and also directs chemical processes of the cell. Prokaryotes do not have nuclei.Mitochondria - Most eukaryotic cells have mitochondria which are the main site of respiration in the cell. Prokaryotes do not have mitochondria.Chloroplasts - Chloroplasts are found in plant cells and contain chlorophyll. They are they main site of photosynthesis and are not found in prokaryotes.