A transparent-green solution of chlorophyll is made by grinding up spinach or grass leaves in acetone (in a mortar and pestle), and then filtering it through cheesecloth and course filter paper. When a bright beam of light is directed at this chlorophyll solution, a deep red glow is emitted from the test tube. The chlorophyll electrons become excited by the light energy, but have no cytochrome transport system to flow along because the chloroplast thylakoid membranes have been dissolved away. Therefore, the chlorophyll electrons give up their excited energy state by releasing energy in the form of a reddish glow. This phenomenon is known as fluorescence, and is essentially the same principle as a fluorescent light bulb. In a fluorescent light bulb, the electrons of neon gas become excited and then release their energy of activation as a white glow inside the glass tube. In an intact chloroplast with thylakoid membranes, ATP is generated by an electron flow along the cytochrome transport system. Since the electrons are being transported to other "carrier" molecules, their energy is used to generate ATP and no reddish glow is emitted. Leaves generally appear green because wavelengths of light from the red and blue regions of the visible spectrum are necessary to excite the chloroplast electrons, and unused green light is reflected. Thus, we perceive trees, shrubs and grasses as green. During the fall months when chlorophyll production ceases in deciduous trees and shrubs, the leaves turn golden yellow or red due to the presence of other pigments, such as yellow and orange carotenoids and bright red anthocyanins.

Another important ingredient for photosynthesis is also produced during the light reactions. During these light-dependent reactions of photosynthesis, a chemical called NADP (nicotinamide adenine dinucleotide phosphate) picks up two hydrogen atoms from water molecules forming NADPH₂, a powerful reducing agent that is used to convert carbon dioxide into glucose during the dark reactions of photosynthesis (also called the Calvin Cycle). When the two atoms of hydrogen join with NADP, oxygen is liberated, and this is the source of oxygen gas in our atmosphere. ATP and NADPH₂from the light reactions are used in the dark reactions of photosynthesis that take place in the stroma region of the chloroplast.

NADP (the vital coenzyme required for photosynthesis) is derived from nicotinic acid, a B-vitamin also known as niacin. Niacin prevents pellagra, a disease characterized by severe damage to the tongue, skin and digestive tract. [NAD is another vital coenzyme that carries electrons to the electron transport system in mitochondria.] Nicotine, the alkaloid in tobacco responsible for its highly addictive properties, is also derived from nicotinic acid. Nicotine is a mild stimulant of the central nervous system. In its pure form, nicotine is highly poisonous and is used as an insecticide.

In the dark reactions of photosynthesis (also known as the Calvin Cycle), carbon dioxide (CO₂) is converted into glucose through a series of complicated reactions involving ATP (adenosine triphosphate) and NADPH₂ (nicotinamide adenine dinucleotide phosphate), two essential compounds synthesized during the light reactions of daylight in the grana (thyllakoid membranes) of chloroplasts. Ordinary C-3 plants form a 3-carbon compound called phosphoglyceric acid (PGA) during the initial steps of the dark reactions. The PGA is converted into another 3-carbon compound called phosphoglyceraldehyde (PGAL). Two PGAL molecules combine to form a 6-carbon glucose molecule. The following equation shows the overall reactants and products of photosynthesis:

Chloroplast

During photosynthesis, Rubisco enzyme Used in Calvin Cycle where CO2 is converted into glucose in stroma region.

RuBisCo (rubisco) is a vital enzyme in Calvin Cycle during the dark reactions of photosynthesis. This is where CO2 (carbon dioxide) is converted into glucose in the stroma of chloroplast; the stroma region is between stacks of thyllakoid membranes called the grana. Rubisco can constitute up to 50% of the soluble protein in a leaf, and is the most abundant enzyme on earth. It is the foundation of atmospheric CO2 fixation by the biosphere. It catalyzes the addition of CO2 onto ribulose 1,5-bisphosphate (RuBP), producing 3-phosphoglycerate (PGA) which is then converted to sugars.

Plantible Foods Aqua Farm in San Marcos, California is extracting rubisco from duckweeds of the genus Lemna. The rubisco is then converted into an edible paste for cooking. Duckweeds are used as a source of rubisco because of their exponential growth rate. Rubisco is a nutritious, high protein, untapped food source for people.

Some plants adapted to hot, arid regions have a different photosynthetic mechanism called CAM photosynthesis. CAM (Crassulacean Acid Metabolism) photosynthesis is found in cacti and succulents, including the crassula family (Crassulaceae). During the hot daylight hours their stomata are tightly closed; however they still carry on vital photosynthesis as carbon dioxide gas is converted into simple sugars. During the cooler hours of darkness their stomata are open and CO₂ enters the leaf cells where it combines with PEP (phosphoenolpyruvate) to form 4-carbon organic acids (malic and isocitric acids). The 4-carbon acids are stored in the vacuoles of photosynthetic cells in the leaf. During the daylight hours the 4-carbon acids break down releasing CO₂ for the dark reactions (Calvin cycle) of photosynthesis inside the stroma of chloroplasts. The CO₂ is converted into glucose through a series of complicated reactions involving ATP (adenosine triphosphate) and NADPH₂ (nicotinamide adenine dinucleotide phosphate), the latter two compounds which were synthesized during the light reactions of daylight in the grana of chloroplasts. The adaptive advantage of CAM photosynthesis is that plants in arid regions can keep their stomata closed during the daytime, thereby reducing water loss from the leaves through transpiration; however, they can still carry on photosynthesis with a reserve supply of CO₂ that was trapped during the hours of darkness when the stomata were open. The tropical strangler Clusia rosea also has CAM photosynthesis. This unusual tree starts out as an epiphyte on other trees and then completely envelops and shades out its host. In fact, it greatly resembles strangler figs (Ficus) of tropical regions of the world.

Another interesting modification of the photosynthetic pathway is called C-4 Photosynthesis. During C-4 photosynthesis, CO₂ combines with phosphoenolpyruvate (PEP) to form a 4-carbon organic acid (oxaloacetic acid) which migrates (diffuses) to the photosynthetic bundle sheath cells surrounding the vascular bundles (veins) of the leaf. PEP essentially shuttles the CO₂ to the bundle sheath cells where it is released for the dark reactions (Calvin cycle) of photosynthesis. During hot weather the CO₂ level inside leaves is greatly reduced because the leaf stomata are closed. In ordinary C-3 plants which form a 3-carbon compound (PGA) during the initial steps of the dark reactions, photosynthesis in the leaf shuts down without a sufficient supply of CO₂. C-4 plants have a competitive advantage during hot summer days because they are able to carry on photosynthesis in the bundle sheaths where CO₂ levels are concentrated. Weedy C-4 plants such as Bermuda grass, spurges and purslane grow rapidly during hot summer days, while photosynthesis and growth in C-3 plants shuts down.

Similar electron transport systems occur in the membranes of prokaryotic bacteria. Methanogenic bacteria live in marshes, swamps and your gastrointestinal tract. In fact, they are responsible for some intestinal gas, particularly the combustible component of flatulence. They produce methane gas anaerobically (without oxygen) by removing the electrons from hydrogen gas. The electrons and H+ ions from hydrogen gas are used to reduce carbon dioxide to methane. In the reaction, the H+ ions combine with the oxygen from carbon dioxide to form water. During this process, the electrons are shuttled through an anaerobic electron transport system within the bacterial membrane which results in the phosphorylation of ADP (adenosine diphosphate) to form ATP (adenosine triphosphate). This process is much less efficient than aerobic respiration, so only two molecules of ATP (rather than 38) are formed. Desert varnish bacteria make their ATP in a similar fashion, only the electrons are coming from the aerobic oxidation of iron and manganese. A thin coating of iron or manganese oxide is deposited on the surfaces of desert boulders and rocky slopes. During the oxidation process, the electrons are shuttled through an iron-containing cytochrome enzyme system on the inner bacterial membrane. One has only to gaze at the spectacular panoramas of varnish-coated, granitic boulders throughout desert areas of the American southwest to appreciate the magnitude of this bacterial ATP production. The mechanism of ATP synthesis in prokaryotic bacteria is remarkably similar to eukaryotic cells. In addition, the circular DNA molecules of these bacteria are similar to the DNA molecules within some organelles of eukaryotic cells. In fact, some biologists believe that mitochondria and chloroplasts within eukaryotic animal and plant cells may have originated from ancient symbiotic bacteria that were once captured by other cells in the distant geologic past. This fascinating idea is called the "Endosymbiont Theory" (or "Endosymbiont Hypothesis" for those who are more skeptical).

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Plants carry on gas exchange through minute pores called stomata. Carbon dioxide from the atmosphere enters the stomata and oxygen produced by photosynthesis diffuses out of the stomata. Water molecules also escape through the stomata, especially in hot, dry weather. Water loss through the stomata is known as transpiration. If the plant loses too much water it will wilt and eventually die. To cope with this dilemma, plants have evolved paired guard cells on each side of the stoma. When the guard cells are fully turgid or expanded, they have an elongate opening (stoma) between them. The walls adjacent to the stoma are very thin and flexible, while the outer walls on the opposite sides of the stoma are much thicker and more rigid. This differential thickening causes an opening to develop when the guard cells are inflated by internal water pressure (called turgor pressure). When the guard cells lose water on a hot day, they become deflated and push together, thus closing off the stoma. This cleaver strategy prevents the plants from losing excessive water through transpiration. See the following highly magnified view of the paired guard cells:

Microscopic view of the paired guard cells and stoma on the leaf surface of spiderwort (Tradescantia). An opening or stoma develops between the inflated (turgid) guard cells due to a differential thickening of their walls. When the guard cells lose water pressure on a hot day, they deflate and push together, thus closing off the stoma and reducing water loss (transpiration) through the leaf.

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