The distinction between prokaryotes and eukaryotes is considered to be the most important distinction among groups of organisms. Eukaryotic cells contain membrane-bound organelles, such as the nucleus, while prokaryotic cells do not.Differences in cellular structure of prokaryotes and eukaryotes include the presence of mitochondria and chloroplasts, the cell wall, and the structure of chromosomal DNA.ukaryotes wrap their DNA around proteins called histones. Multiple proteins act together to fold and condense prokaryotic DNA. Folded DNA is then organized into a variety of conformations that are supercoiled and wound around tetramers of the HU protein.