What major organelle are prokaryotes missing that eukaryotes have?

Nucleus

Explanation:

Prokaryotes are the organism that came earlier than eukaryotes on this earth. These prokaryotes do not have a nucleus and other membrane-bound organelles like chloroplast, mitochondria, Golgi apparatus, endoplasmic reticulum, etc.

So as prokaryotes lack membrane-bound organelle their genetic material is not enclosed in the nucleus therefore their genetic material remains in the cytoplasm of the cell while eukaryotes have membrane-bound nucleus in which their genetic material are present.

So the nucleus is the major organelle that prokaryotes are missing that eukaryotes have.