User:Pukar Baniya/sandbox 1

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You may include any references to papers as in: the use of JSmol in Proteopedia ^[1] or to the article describing Jmol ^[2] to the rescue.

Function

The atmospheric carbon dioxide is reduced to form an organic compound in the light-independent reaction or the Calvin cycle in the chloroplast. This phenomenon occurs in stroma, which is where the is located. The process of reducing carbon dioxide is known as CO2 assimilation or carbon fixation. During this process, the atmospheric carbon dioxide is condensed with rubisco to form . This molecule then goes through the Calvin cycle to contribute carbon to form a glucose molecule. For each cycle, one carbon is added to form glucose, and the rubisco is regenerated. Hence, rubisco helps us in creating essential organic carbon from the inorganic carbon dioxide. This reaction carried by rubisco is highly exergonic, with a change in Gibbs free energy of about negative 12.4 Kcal/mol. This glucose is then used to produce sucrose. Sucrose is used as the energy source in plants and is stored for later use as starch.

Reaction rate and specificity

While the significance of rubisco is exceptionally high, it is very inefficient. Relative to other enzymes, rubisco catalyzes reactions at a relatively sluggish rate. On average, rubisco catalyzes three carbon dioxide molecules per second. While usually, an enzyme can process up to thousand molecules per second. To compensate for its speed, plants build up vast amounts of rubisco. Most of the chloroplast consists of this protein. This high concentration of the enzyme in every photosynthetic plant has awarded rubisco for being the most abundant enzyme on earth. The is meant to bind carbon oxide as its substrate. However, due to similar chemical properties and size, oxygen molecules can also easily fit their active site. This ability to bind both carbon and oxygen makes rubisco both a carboxylase and an oxygenase. Therefore the atmospheric carbon dioxide that enters through stomata competes with oxygen produced via photosynthesis for the active site of rubisco. When rubisco binds with oxygen, photorespiration occurs. This process is very costly because it forms one molecule of 3-phosphoglycerate and one molecule of , a metabolically useless product. This binding with O2 does not result in carbon fixation, so the cell has to use a significant amount of cellular energy to salvage the carbons from 2-phosphoglycolate. This lack of specificity has raised many questions? CO2 and O2 are clearly different when it comes to size. So why haven't rubisco evolved to differentiate between these two molecules? There are only hypotheses for these questions without an accurate answer. One of the most compelling hypotheses is that rubisco and carbon dioxide was present in the earth's atmosphere before oxygen. Therefore, there was not any selective pressure when oxygen was not present. In today's environment, the concentration of oxygen far exceeds the concentration of carbon dioxide. As the temperature of the environment increases, the ratio of O2 to CO2 increases. This increases the probability for a plant to favour photorespiration. To overcome this disadvantage, some plants like C4 and CAM have developed different strategies. For a C4 plant, CO2 fixation and rubisco activity are spatially separated. While the CAM plants temporally separated rubisco activity and CO2 capture.^[3]

Relevance

The inefficiency in rubisco has opened a door for possible changes that we could do via genetic engineering to make it more effective. By increasing the efficiency of this enzyme, we could solve many serious world problems such as the "greenhouse" effect of increasing the concentration of CO2 in our atmosphere resulting in climate change. The CO2 concentration has constantly been increasing in the past 50 years, and this causes a temperature rise. As we have learnt, this increase in temperature favours photorespiration making the enzyme more ineffective. If we could increase the specificity of rubisco to bind CO2, this crisis could be solved. Also, the world population is growing at an even faster rate. The world food crisis could be better handled if we could increase the rate of carbon fixation. These potential solutions have attracted many researchers and scientists to perform experiments on rubisco. ^[4]

Structural highlights

Rubisco has two distinct forms; the first type is found in algae, vascular plants, and cyanobacteria. The second form is found in certain photosynthetic bacteria. The first form of the rubisco found in most of the plants is responsible for the production of biomass from CO2. They are a large protein with a size of approximately 500,000 Da. They have a complex structure that contains , each containing a catalytic site and a regulatory site. It also contains eight identical small subunits whose functions are still unidentified. These subunits are bound to each other via disulfide bonds. In general, enzymes with multiple chains operate through the interaction between these chains, the process known as allostery. However, rubisco's active site operates independently of one another. The active sites of rubisco are arranged around a . The ion is held in place with the help of three amino acids; Asp, Glu, and carbamoyl Lys. The magnesium is responsible for bringing in the reactants to the active site and polarizing the CO2. This polarization enables the five-carbon enediolate to perform a nucleophilic attack on CO2. The resulting six-carbon intermediate then breaks down to produce 3-phosphoglycerate. In order for rubisco to operate, it needs two molecules of carbon dioxide. The extra carbon is attached firmly to the end of the lysine sidechain. This extra CO2 acts as an "activator" for the enzyme, which is different from the CO2 molecules that are fixed in the Calvin cycle. The activator acts as a switch; during the day, it attaches to rubisco, which turns the enzyme "on", and it is removed at night, turning the enzyme "off". ^[5]

The eight subunits in rubisco each have a large and a small . These subunits form an isolated pair and are arranged in . The interface of these paired large subunits contains two active sites. When we look at a single subunit, we can observe alpha helices and beta sheets. These form alpha-beta barrels, which is the dominant structure in these large subunits.