1. The Compartmentalization in Eukaryotic Cells Membranes divide the cytoplasm of eukaryotic cells into distinct compartments Tree categories in eukaryotic cells: )the endomembrane system: ER, Golgi complex, Lys secretory vesicles (2)the cytosol (3)mitochondria, chloroplasts, peroxisomes, and the nucleus Membrane-bound structures (organelles)are found in all eukaryotic cells1. The Compartmentalization in Eukaryotic Cells vMembranes divide the cytoplasm of eukaryotic cells into distinct compartments. Tree categories in eukaryotic cells: (1) the endomembrane system: ER, Golgi complex, Lys., secretory vesicles. (2) the cytosol. (3) mitochondria, chloroplasts, peroxisomes, and the nucleus. vMembrane-bound structures (organelles) are found in all eukaryotic cells