Final answer:
Eukaryotic cells have a membrane-bound nucleus and numerous other organelles which prokaryotic cells do not have. These organelles allow eukaryotic cells to compartmentalize functions for increased cellular complexity and regulation.
Step-by-step explanation:
The major structure that eukaryotes have that prokaryotes don't is a membrane-bound nucleus. Eukaryotic cells have a more complex structure due to the presence of numerous membrane-bound organelles, which allow different functions to be compartmentalized in different areas of the cell. Among these organelles are the endoplasmic reticulum, Golgi apparatus, chloroplasts (in plant cells), mitochondria, and several rod-shaped chromosomes. In contrast to prokaryotic cells, which have their genetic material localized in a nucleoid region, eukaryotic cells have their genetic material enclosed within a true nucleus, surrounded by a nuclear membrane, thus ensuring greater regulation of gene expression and cellular functions.