Electron microscopy shows the chloroplast to consist of an envelope enclosing a complex of membranes, the thylakoid system often joined or stacked into grana; the lipid membranes, contrast with the background when stained with lipophilic electron dense osmium. The space between the envelope and thylakoid membranes is the chloroplast stroma. The envelope is composed of two membranes each about 5.6 nm thick separated by the intra envelope space (10 nm) with areas of high electron density which are possibly contact points between the membranes; they may be involved in transport, i.e., of proteins between cytosol and stroma. The membranes are lipid bilayers, of galactosyl glycerides and phosphatidyl choline, containing carotenoids but no chlorophyll.
The stroma contains indistinct granules and particles, mainly of proteins; the enzyme ribulose bisphosphate carboxylase (Rubisco) is the major soluble protein and may crystallize in unfavorable conditions such as water stress or air pollution. Other inclusions are products of the photosynthetic processes; for example, starch granules upto 2µm long accumulate in stroma and disturb the thylakoid membranes, and globules of lipids and plasto quinine accumulate; RNAs and DNA occur in chloroplasts which synthesize many of their constituent proteins.
The most noticeable feature of chloroplasts in electron micrographs is the thylakoid. Thylakoid membranes frequently associate into granal stacks, interconnected by pairs of membranes, called stromal thylakoids (or