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 alternatively intergranal connections or frets), which are in connect with the stroma on both the sides. The interface between the appressed membranes is the partition region. In C3 plants over 60 percent of the thylakoid surface is typically in the grana. The end membranes of stacked thylakoids and the ends of the grana, but not the partition regions, have direct contact with the stroma.
Thylakoid membranes vesicles in the grana are stacked and flattened, but not closed, sacs inter connected with the other membranes. The vesicles join the stromal lamellae at different points around the periphery of the granum. The structure derives from the folding and joining of separate sheets of lamellae which are interconnected and probably originate from a single point, the prolamella body, in the developing chloroplast. The thylakoid system appears to be a single interconnecting giant closed vesicle with continuous lumen, a feature of great importance in electron transport and ATP generation. Composition of the lumen is not known; but proteins, of the water-splitting complex and the light-harvesting complex for example, may occupy part of the volume and it is unlikely to be homogeneous aqueous solution of small molecules. Grana differ in extent and size between species, and with conditions during growth, for example with bright illumination, there is less granal stacking. Grana in isolated thylakoids stack and unstuck, according to the ionic concentration and light quality.
On the outer surface of stromal and of granal thylakoids in contact with the stroma, are particles of Rubisco loosely attached and easily removed.
Thylakoid membranes are ‘sided’ in construction, with the water-splitting complexes in the lumen, a PS II chlorophyll-protein complex, a cytochrome b-f complex and light harvesting complex spanning the membrane interspersed with the PSI chlorophyll-protein complex on the outer side, and finally enzymes of carbon metabolism and ATP synthesis on the outer surface. This sidedness allows thylakoids to transport electrons to the stroma from water in the lumen and accumulate protons in the lumen.
Chlorophyll- a & b occur only in thylakoid membranes and may form 5 percent of their total mass. Chlorophyll is complexed with, but not covalently bonded to proteins; the hydrophobic phytyl groups of chlorophyll may be between the membrane proteins and lipids, and the hydrophilic parts of the porphyrin ring in the protein. This would orientate pigment molecules for efficient energy capture.& transfer.
Although there is uncertainty about the chlorophyll-protein complexes in the membrane and their correspondence to their membrane particles, three main complexes contain 90 percent of the chlorophyll. One corresponds to PSI and its antenna chlorophyll-a; it is called P700 chlorophyll a complex or chlorophyll-protein complex I, CPI for short. A second is light-harvesting chlorophyll a/b-protein complex, now called light harvesting complex, LHC, which has only antenna function and no photochemical activity. The third is less well resolved but contains PSII and its antenna chlorophyll-a. It is called CPa and is the chlorophyll-protein complex serving as the internal chlorophyll-a antenna of PSII