Here our coverage of this half of photosynthesis is even more 'sketchy.' The remaining part of photosynthesis occurs mostly in the stroma of the chloroplast. It is sometimes called the Calvin cycle in honor of Melvin Calvin, the biochemist who discovered the intermediates of this pathway after radioisotopes became available after World War II. He won the Nobel Prize for his work.
The reactions are also known as the carbon fixation reactions, though to be honest, only the first step of these reactions fix carbon. There was even a time...hopefully now fully out of favor...when these reactions were referred to as "dark reactions." But this name was even worse as it implied that they might operate at night or in the darkness...and that is completely false. As you shall observe below, the Calvin cycle requires the availability of NADPH from the light reactions in order to function. So the Calvin cycle operates ONLY in the light! The Calvin cycle reactions do not require light directly, so they have sometimes been called light- independent reactions. But remember, they occur only in the light when coupled to the light reactions!
Here is a crude diagram to show you the simplest form of the Calvin Cycle.
The first enzyme in this cycle, fixing carbon to to ribulose 1,5-bisphosphate, is called RuBisCO for ribulose 1,5-bisphosphate carboxylase/oxygenase. Because of its importance and relative inefficiency, up to 40% of all protein in plant cells is RuBISCO.
What makes RuBisCO inefficient? The rate of photosynthesis is usually limited not by light but by the availability of carbon dioxide for fixation by RuBisCO. The active site on RuBisCO cannot distinguish O=C=0 from O=O, and since the concentration of O2 is about 20% and CO2 is around 1%, the active site of RuBisCO is generally occupied with oxygen rather than carbon dioxide. Worse, the O of RuBisCO means that it is also an oxygenase. Oxygen is far more damaging than being a competitive inhibitor for RuBisCO's active site. When oxygen binds, it also reacts! The oxygenase reaction takes RUBP apart into CO2 rather than building trioses for sugar synthesis. The oxygen reaction pathway is known as photorespiration, but making matters worse, you get no ATP from photorespiration! So it does not help the plant in any productive way under normal circumstances. For this reason, certain plants have evolved a mechanism to more efficiently gather carbon dioxide... the C-4 reactions.
Shown here is the reaction system evolved in tropical grasses to deal with high-light, low carbon dioxide, and low water situations. The pathway here shows the C-4 cycle discovered by Hatch and Slack in sugar cane mesophyll cells at the top, which serves as a carbon dioxide pump to flood RuBisCO in bundle sheath cells and tip the balance in favor of the Calvin Cycle rather than photorespiration.
The innovation here is the evolution of a new enzyme, phosphoenolpyruvate carboxlylase (PEP carboxylase or PEPC). This enzyme attaches carbon to phosphoenolpyruvate. But rather than attempting to use O=C=O as the substrate, it uses HCO3- (bicarbonate). This is easily distinguished from oxygen gas, and so there is no competitive inhibition and certainly no photorespiration involved with PEPC. This is a very efficient enzyme!
The C-4 tropical grasses that show these features often also have what is called Kranz ('wreath' in German) anatomy. The epidermal layers show the usual features however the upper epidermis often has more stomata than the lower epidermis. The veins have the usual parallel veination, so cross sections often show very nice veins coming straight at you. The mesophyll all looks spongy and these cells are doing the C-4 reactions. The bundle sheath cells are large and have very dark chloroplasts in them doing the C-3 reactions. The flow of CO2 is very efficient, from atmosphere, through stomata, through C-4 reactions in mesophyll, through C-3 reactions in bundle sheath, followed by transport of carbohydrate in the phloem. Kranz anatomy is shown below in corn (Zea mays).
While the C-4 reactions of the mesophyll are spatially separated from the C-3 reaction in the bundle sheath, there is a second C-4 group that does this differently. In CAM (Crassulacean Acid Metabolism) plants, the C-4 and C-3 reactions are separated in time rather than in space. The mesophyll cells carry out the C-4 reactions at night and the C-3 reactions in the daylight (remember that the C-3 reactions depend completely on the light reactions!).
In the CAM plants, the C-4 reactions operating at night use energy from respiration of the previous day's accumulation of starch to drive the fixation of bicarbonate (dissolved carbon dioxide) into C-4 acids that accumulate in the vacuole. The stomata are open at night in these plants to take in the carbon dioxide to convert to bicarbonate (H2O + CO2 → H2CO3 → H+ + HCO3-.
When the sun rises, the stomata close to conserve water. The vacuole releases the C-4 acids to be converted to C-3 intermediates and carbon dioxide to swamp out the competitive inhibition of RuBisCO in the Calvin cycle in the daylight. These CAM plants are obviously well adapted to life conditions in the desert. The stomata being open only in the cool night and closed in the baking hot sun, allows for significant water savings. However this competitive edge for life in the desert comes at a cost...the use of photosynthate at night for the C-4 reactions reduces the growth rate. The cells are figuratively spinning their biochemical wheels to conserve water.