The portion of the membrane system in eukaryotic cells that is responsible for the making lipids and breaking down toxic substances is the

Smooth endoplasmic reticulum

Explanation:

The endoplasmic reticulum is a series of interconnected channels running throughout the cytoplasm. Some endoplasmic reticular have granules called ribosomes on their surfaces. The smooth endoplasmic reticulum are more specialized responsible for synthesizing and transportation of Lipids and breaking down of toxic chemicals from all parts of the cell.