Chloroplasts are organells surrounded by double membranes: outer and inner envelopes. The inner envelope extends into the light of chloroplast (stroma) where it forms an interior membrane system called thylakoids. These membranes are organized into grana stacks, with inner spaces called lumen, which are interconnected with one another via lamellae. Curved regions at the external parts of grana are called grana margins, whereas the top and bottom parts are called grana ends.
TEM micrographs of Arabidopsis thaliana chloroplast's ultrastructure (A) and thylakoid membrane magnification (B). Legend: 1 - cell wall, 2 - grana stacks, 3 - starch granules, 4 - stroma lamellae, 5 - stroma, 6 - plastoglobules, 7- outer and inner envelopes, 8 - tonoplast, 9 - vacuole, 10 - cytoplasm.
The light reactions of photosynthesis are further divided into different regions of thylakoids, what is determined by the 3-D structure of different protein complexes. Photosystem II (PSII) with its light harvesting complex II (LHCII) are mainly found in tightly packed grana stacks, while photosystem I (PSI) with its light harvesting complex I (LHCI), NAD(P)H dehydrogenase-like complex (NDH), proton gradient regulation 5 (PGR5)/PGR5-like photosynthetic phenotype 1 (PGRL1) heterodimer, and ATP synthase (ATPase) are found in stroma-exposed lamellae. Cytochrome b6f (cyt b6f) on the other hand is distributed evenly across the membranes. Grana margins and ends are the only regions where all of major photosynthetic complexes can be found.
This spatial separation of PSII from PSI prevents the energy spillover to much faster PSI. It increases the efficiency of photosynthetic light harvesting by PSII and its antennae, enabling fine-tuning between the linear and cyclic electron flows. Furthermore, it protects PSII from photodamage caused by reactive oxygen species (ROS) produced by PSI.