Proteins
Many of the lamellar proteins are components of the chlorophyll–protein complexes described above. Other proteins include enzymes and protein-containing coenzymes. Enzymes are required as organic catalysts for specific reactions within the lamellae. Protein coenzymes, also called cofactors, include important electron carrier molecules called cytochromes, which are iron-containing pigments with the pigment portions attached to protein molecules. During electron transfer, an electron is accepted by an iron atom in the pigment portion of a cytochrome molecule, which thus is reduced; then the electron is transferred to the iron atom in the next cytochrome carrier in the electron transfer chain, thus oxidizing the first cytochrome and reducing the next one in the chain.
In addition to the metal atoms found in the pigment portions of cytochrome molecules, metal atoms also are found in other protein molecules of the lamellae. In proteins with a total molecular weight of 900,000 (based on the weight of hydrogen as one), there are 2 atoms of manganese, 10 atoms of iron, and 6 atoms of copper. These metal atoms are required for the catalytic activity of some of the enzymes important in photosynthesis. The manganese atoms are involved in water-splitting and oxygen formation. Both copper- and iron-containing proteins function in electron transport between water and the final electron-acceptor molecule of the light stage of photosynthesis, an iron-containing protein called ferredoxin. Ferredoxin is a soluble component in the chloroplasts. In its reduced form, it gives electrons directly to the systems that reduce nitrate and sulfate and via NADPH to the system that reduces carbon dioxide. A copper-containing protein called plastocyanin (PC) carries electrons at one point in the electron transport chain. PC molecules are water soluble and can move through the inner space of the thylakoids, carrying electrons from one place to another.
Quinones
Small molecules called plastoquinones are found in substantial numbers in the lamellae. Like the cytochromes, quinones have important roles in carrying electrons between the components of the light reactions. Since they are lipid soluble, they can diffuse through the membrane. They can carry one or two electrons, and, in their reduced form (with added electrons), they carry hydrogen atoms that can be released as hydrogen ions when the added electrons are passed on, for example, to a cytochrome.
Genetics
The genetic information needed for the reproduction of the photosynthetic apparatus is contained partly in the chloroplast chromosome and partly in chromosomes of the nucleus. For example, the carboxylation enzyme ribulose 1,5-bisphosphate carboxylase is a large protein molecule comprising a complex of eight large polypeptide subunits and eight small polypeptide subunits. The gene for the large subunits is located in the chloroplast chromosome, whereas the gene for the small subunits is in the nucleus. Transcription of the DNA of the nuclear gene yields messenger RNA (mRNA) that encodes the information for the synthesis of the small polypeptides. During this synthesis, which occurs on the cytosolic ribosomes, some extra amino acid residues are added to form a recognition leader on the end of the polypeptide chain. This leader is recognized by special receptor sites on the outer chloroplast membrane; these receptor sites then allow the polypeptide to penetrate the membrane and enter the chloroplast. The leader is removed, and the small subunits combine with the large subunits, which have been synthesized on chloroplast ribosomes according to mRNA transcribed from the chloroplast DNA. The expression of nuclear genes that code for proteins needed in the chloroplasts appears to be under control of events in the chloroplasts in some cases; for example, the synthesis of some nuclear-encoded chloroplast enzymes may occur only when light is absorbed by chloroplasts.