What fundamental differences designate the three-domain system?

The three-domain system is based on fundamental differences in genetic and biochemical characteristics. Archaea and Bacteria are both prokaryotic but differ in their rRNA sequences, membrane lipids, and cell wall compositions. Archaea have unique lipids in their cell membranes and lack peptidoglycan in their cell walls, distinguishing them from Bacteria. Eukarya, on the other hand, are characterized by the presence of a membrane-bound nucleus and organelles, and their rRNA sequences differ significantly from those of Archaea and Bacteria. These molecular differences form the basis of the three-domain classification.