Plants are green because their cells are filled with molecules of a pigment called chlorophyll. Chlorophyll is a protein bonded to magnesium and resembles hemoglobin structurally. Chlorophyll molecules are found in organelles called chloroplast, which look suspiciously like cyanobacteria.
In 1966 Lynn Margulis, then on the faculty of the biology department at Boston University, published a paper called “The origin of mitosing eukaryotic cells,” which revived the idea that eukaryotic cells had evolved through endosymbiotic combinations of prokaryotic (bacteria) cells. Margulis’s own contribution, in addition to her review of earlier speculative work, was to actually document through observations the structural similarities between eukaryotic organelles and various bacteria.
Chloroplasts are plastids (organelles that make and store molecules) found in the cells of the Archaeoplastida, which includes plants, green and red algae and glaucophytes. These organisms are distinguished from animal cells by their lack of a centriole. Red algae are pigmented with cholorphyll a and phycobiliproteins, while green algae and plants are pigmented with chlorophyll a and b and lack phycobiliproteins. In chlorophyll b an oxygen ion is attached to the C7 carbon where an alkene group is attached in chlorophyll a.
Chlorophyll looks green because it doesn’t absorb light energy in the green portion of the spectrum well and that energy is there reflected from the surface of chlorophyll-bearing structures, making them appear green.
The energy absorbed in the blue and red portions of the light spectrum is drives a “redox” reaction, causing the “reaction center” of the molecule to donate an electron to another molecule, which in turns donates it to another, so on down a series of molecules called the “electron transport chain.”
The reaction center is “reset” to a neutral state by receiving an electron from the oxidation of water into H+ and O2, which is the source of free oxygen in the atmosphere. When this reaction evolved in cyanobacteria in the Archaean Era at least 2.5 billion years ago. Over an unknown number of years photosynthesis by cyanobacteria introduced oxygen to the atmosphere, which had previously been composed of carbon dioxide and nitrogen compounds.
The chlorophyll molecules are embedded in the membranes of thylakoids, disk-shaped suborganelles that are arranged in stacks called grana. The grana float in the stroma, a fluid inside of the chloroplast. The thylakoid membrane is the site of photosynthesis.
The electron flow described above is used to move H+ ions across the thylakoid membrane. The end of the electron transfer chain is NADH, which moves the H+ ion across the membrane from the chloroplast stroma into the thylakoid lumen in the process of becoming NAD+. This leads to a build-up of H+ ions on one side of the membrane. They re-cross at different site—where the enzyme ATP synthase is found—to induce the reaction between ADP and an inorganic phosphate to form ATP (adenosine triphosphate). ATP is an energy-rich molecule that serves as a coenzyme in the reactions that make many other molecules in the cell and in cell division (i.e. growth).
The actual making of ATP, NADH, and the production of free oxygen constitute what are called the “light dependent” or light reactions. The “light independent” or dark reactions reduce inorganic carbon dioxide (CO2) to make organic compounds like glucose (C6H1206). The dark reactions actually continue at night, but do not stop during the day. However, the antecedents from the dark reactions are created through the light reactions, so without a light interval a plant will cease absorbing making organic compounds.
The phenomenon can be seen in the cycling of atmospheric carbon dioxide in the well-known “Keeling curve” collected at Mauna Loa on the island of Hawaii. C. David Keeling of Scripps Oceanographic Institute started measuring atmospheric CO2 at Mauna Loa in 1958. The Scripps data show an annual cycle that reflects the seasonality of atmospheric CO2. As the vegetation greens up and grows in the northern hemisphere, it absorbs CO2 and reduces its concentration in the atmosphere by a few parts per million. As winter sets in and the vegetation dies back, and the light reactions slow, the amount of CO2 increases again. The amplitude of this seasonal cycle and the average value of CO2 concentration in the atmosphere have been increasing continually since 1958.