The difference between eukaryotes and prokaryotes in terms of cellular structure is significant. Eukaryotic cells have a distinct nucleus containing their DNA, along with membrane-bound organelles like mitochondria and the endoplasmic reticulum, allowing for compartmentalization of cellular functions. In contrast, prokaryotic cells lack a true nucleus and organelles; their DNA is located in a region called the nucleoid. This structural distinction has profound implications for cellular processes and organism complexity.