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A chloroplast is a photosynthetic plastid in plant and algae biological cells. The green-plant chloroplast modeled here has a chloroplast envelope surrounding chloroplast stroma and internal thylakoids. Light-dependent reactions occur at the thylakoid membrane; the Calvin cycle operates in the chloroplast stroma.^[ref]

Cyanobacteria perform oxygenic photosynthesis without chloroplasts: the prokaryotic biological cell itself contains the photosynthetic machinery. Thus chloroplast identifies an organelle, while oxygenic photosynthesis identifies a process. Endosymbiotic theory explains their historical connection; organelle protein import explains how many nuclear-encoded proteins reach the modern organelle.

The useful feature is selective separation: enzymes and substrates can share an organelle without sharing a compartment. For a constructed accessibility example, put a soluble enzyme in chloroplast stroma and its substrate in thylakoid lumen. Sharing the same chloroplast does not permit direct contact; contact requires a transport or boundary-disruption step. Placing the substrate between adjacent thylakoids instead puts it on the stromal side. The visual stack alone cannot establish chemical accessibility.

For the simplest boundary-counting model, represent surrounding cytosol, chloroplast intermembrane space, chloroplast stroma and thylakoid lumen by four vertices in a chain. Its three edges represent the outer envelope, inner envelope and thylakoid membrane, respectively. A route from cytosol to chloroplast stroma crosses two barriers; extending it into thylakoid lumen adds a third. This follows by listing the edges along the chain. Counting the two leaflets of each lipid bilayer separately would answer a different question. These counts describe this idealized geometry, not the number of protein targeting signals or the transport itinerary of every protein.

The light-dependent reactions article develops ATP, NADPH and electrochemical gradient coupling, and the Calvin cycle article develops carbon fixation bookkeeping. Their different locations make the chloroplast interesting as an organized chemical workspace. Light-independent chemical reactions still depend on supplied carriers and regulation; the name does not prescribe nighttime operation.

The space between the two chloroplast envelope membranes.

It is topologically distinct from both the chloroplast stroma and the thylakoid lumen. Naming the compartments prevents a transport measurement across one barrier from being mistaken for transport across the entire chloroplast membrane system. ^[ref]

The chloroplast stroma is the fluid compartment inside the inner chloroplast envelope membrane and outside thylakoids, containing Calvin cycle enzymes.^[ref]

A chloroplast stroma location is therefore more informative than an unspecified “inside the chloroplast” location. In the boundary model above, entering chloroplast stroma has not yet entered thylakoid lumen. Protein targeting must distinguish these destinations; a fraction containing chloroplasts does not establish which internal compartment contains a detected protein.

A stack of thylakoids.

Stacking places many thylakoid membranes in a compact region of a chloroplast. The membranes remain part of a connected internal system; the stack is a structural arrangement, whereas the thylakoid lumen is the enclosed aqueous compartment. ^[ref]

Separates chloroplast intermembrane space from chloroplast stroma.

Its selective transport systems help maintain the distinct composition of the chloroplast stroma. The thylakoid membrane is a separate internal membrane, so an imported molecule reaching the stroma has not automatically reached the thylakoid lumen. ^[ref]

Separates surrounding cytosol from chloroplast intermembrane space.

Together with the inner chloroplast envelope membrane, it defines the boundary of the chloroplast. Crossing the envelope and entering the thylakoid lumen are different transport problems because the thylakoid system supplies an additional membrane barrier. ^[ref]

A thylakoid is a membrane-enclosed sac; its thylakoid membrane contains chlorophyll and light-dependent reactions machinery. A stack is a granum.^[ref]

The membrane and its enclosed fluid answer different location questions. A soluble protein in thylakoid lumen is inside the sac; a membrane protein is embedded in its boundary and can expose different parts on the two sides. Membrane topology and organelle protein import provide the reusable language for those distinctions.

Separates thylakoid lumen from chloroplast stroma in a chloroplast.