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An autophagosome is the membrane-enclosed carrier formed around macroautophagy cargo. Enclosing a mitochondrion does not immediately digest it: subsequent delivery must expose the cargo to digestive enzymes in lysosomes.^[ref]

Autophagy delivers a biological cell's own material for digestion and recycling in lysosomes. Macroautophagy is the enclosing-carrier route illustrated here; other forms deliver cargo differently. The cargo's internal origin distinguishes this route from uptake by endocytosis.^[ref]

A lysosome is an acidic digestive and recycling organelle: one surrounding lipid bilayer encloses a lysosomal lumen containing acid hydrolases. These enzymes break down proteins, nucleic acids, carbohydrates and lipids by hydrolysis. Cargo can originate outside the biological cell, entering through endocytosis, or within its own cytoplasm, delivered through autophagy. Digestion therefore serves both disposal and reuse.^[ref]

An endosome sorts endocytosed cargo: some returns to the cell membrane, while some proceeds toward lysosomes. An autophagosome instead encloses material already in the cytoplasm. Both routes bring cargo into contact with digestive enzymes; neither implies that every internalized molecule is destroyed.^[ref]

Enzyme supply is a different itinerary from cargo disposal. Secretory protein routing and protein targeting deliver newly made digestive enzymes through the endoplasmic reticulum, Golgi apparatus and trans-Golgi network toward lysosomes.^[ref] The existing membrane transport and differential centrifugation articles explain the boundary-crossing and separation principles used below.

A proteasome is a different digestive machine: a protein complex without a surrounding lipid bilayer, acting on individual proteins in the cytosol and cell nucleus. Many targets carry ubiquitin chains. A lysosome accepts a much broader range of cargo, including material delivered inside an autophagosome. Thus an unwanted soluble protein and an unwanted mitochondrion pose different disposal problems; a proteasome does not swallow an intact mitochondrion.^[ref]

In macroautophagy, a portion of cytoplasm, potentially including an organelle, is enclosed in an autophagosome before delivery to a lysosome. Sequestration precedes digestion.^[ref]