Eukaryotic Cell vs. Prokaryotic Cell. 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.