Unlike eukaryotic cells, prokaryote cells lack membrane-bound organelles. However, whereas prokaryote cells are less structurally complex than eukaryotes, they are more chemically complex, since all of the prokaryote cell's biomolecules are floating around together. These biomolecules must interact only with other appropriate molecules to perform biological function.

Prokaryotic cells contain a single compartment enclosed within the cell membrane. In this space reside DNA, RNA, ribosomes and other molecules. Prokaryotes lack a defined nucleus (which is where DNA and RNA are stored in eukaryotic cells), mitochondria, ER, golgi apparatus, and so on. In addition to the lack of organelles, prokaryotic cells also lack a cytoskeleton. Recall that in addition to its role as structural support for the interior of the cell, the cytoskeleton is also involved in intracellular organelle transport. Since there are no organelles to be transported in prokaryotic cells, such a function is unnecessary.

Like the eukaryote cell, the prokaryote cell is filled with cytosol. The prokaryote cytosol is filled with enzymes, which carry out respiratory processes reserved in eukaryotes for the mitochondria. Prokaryote and eukaryote ribosomes also differ slightly, reflect minor differences in prokaryotic versus eukaryotic processing of DNA.