A chloroplast is a photosynthetic organelle whose internal membranes separate different stages of photosynthetic chemistry.

Inside the chloroplast, flattened membrane sacs called thylakoids form a specialized internal membrane system. The aqueous space inside a thylakoid is the thylakoid lumen. The aqueous region outside the thylakoids but inside the chloroplast inner envelope is the stroma.

Many plant chloroplasts stack thylakoids into structures called grana, connected by unstacked membrane regions. The essential functional distinction, however, is the membrane boundary between lumen and stroma rather than the stack shape itself.

The thylakoid membrane creates two chemically distinguishable sides

A membrane can restrict free mixing between aqueous compartments. The thylakoid membrane therefore allows the lumen and stroma to maintain different ion concentrations and molecular compositions.

It also provides an oriented surface in which membrane proteins can be arranged so that a process occurring on one side has a different consequence from the same process occurring on the other.

This orientation becomes crucial in photosynthesis because light-driven electron-transfer machinery is embedded in the thylakoid membrane, whereas enzymes that incorporate carbon dioxide into organic molecules operate mainly in the stroma.

The geometry can be represented as

stroma
       stromal face
================ thylakoid membrane ================
       lumenal face
thylakoid lumen

Two coupled reaction environments

The chloroplast therefore contains two major photosynthetic environments:

• thylakoid membrane and lumen: the compartment system used for light-driven electron transfer and transmembrane gradient formation;
• stroma: the aqueous compartment used for carbon-assimilation chemistry.

The important organizing principle is compartmentation: the thylakoid membrane lets photosynthesis convert oriented molecular events into a stored difference between two compartments, while the stroma provides a separate environment for fixed-carbon chemistry.