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Oxidative phosphorylation or electron transport-linked phosphorylation or terminal oxidation is the metabolic pathway in which cells use enzymes to oxidize nutrients, thereby releasing chemical energy in order to produce adenosine triphosphate (ATP). In eukaryotes, this takes place inside mitochondria. Almost all aerobic organisms carry out oxidative phosphorylation. This pathway is so pervasive because it releases more energy than alternative fermentation processes such as anaerobic glycolysis.
The nitrogen cycle is the biogeochemical cycle by which nitrogen is converted into multiple chemical forms as it circulates among atmospheric, terrestrial, and marine ecosystems. The conversion of nitrogen can be carried out through both biological and physical processes. Important processes in the nitrogen cycle include fixation, ammonification, nitrification, and denitrification. The majority of Earth's atmosphere (78%) is atmospheric nitrogen, making it the largest source of nitrogen. However, atmospheric nitrogen has limited availability for biological use, leading to a scarcity of usable nitrogen in many types of ecosystems.
An electron transport chain (ETC) is a series of protein complexes and other molecules that transfer electrons from electron donors to electron acceptors via redox reactions (both reduction and oxidation occurring simultaneously) and couples this electron transfer with the transfer of protons (H+ ions) across a membrane. The electrons that transferred from NADH and FADH2 to the ETC involves 4 multi-subunit large enzymes complexes and 2 mobile electron carriers. Many of the enzymes in the electron transport chain are membrane-bound.
Nitrification is the biological oxidation of ammonia to nitrite followed by the oxidation of the nitrite to nitrate occurring through separate organisms or direct ammonia oxidation to nitrate in comammox bacteria. The transformation of ammonia to nitrite is usually the rate limiting step of nitrification. Nitrification is an important step in the nitrogen cycle in soil. Nitrification is an aerobic process performed by small groups of autotrophic bacteria and archaea.
The nitrite ion has the chemical formula NO−
2. Nitrite is widely used throughout chemical and pharmaceutical industries. The nitrite anion is a pervasive intermediate in the nitrogen cycle in nature. The name nitrite also refers to organic compounds having the –ONO group, which are esters of nitrous acid.
Photorespiration (also known as the oxidative photosynthetic carbon cycle or C2 cycle) refers to a process in plant metabolism where the enzyme RuBisCO oxygenates RuBP, wasting some of the energy produced by photosynthesis. The desired reaction is the addition of carbon dioxide to RuBP (carboxylation), a key step in the Calvin–Benson cycle, but approximately 25% of reactions by RuBisCO instead add oxygen to RuBP (oxygenation), creating a product that cannot be used within the Calvin–Benson cycle. This process lowers the efficiency of photosynthesis, potentially lowering photosynthetic output by 25% in C3 plants. Photorespiration involves a complex network of enzyme reactions that exchange metabolites between chloroplasts, leaf peroxisomes and mitochondria.
Denitrification is a microbially facilitated process where nitrate (NO3−) is reduced and ultimately produces molecular nitrogen (N2) through a series of intermediate gaseous nitrogen oxide products. Facultative anaerobic bacteria perform denitrification as a type of respiration that reduces oxidized forms of nitrogen in response to the oxidation of an electron donor such as organic matter. The preferred nitrogen electron acceptors in order of most to least thermodynamically favorable include nitrate (NO3−), nitrite (NO2−), nitric oxide (NO), nitrous oxide (N2O) finally resulting in the production of dinitrogen (N2) completing the nitrogen cycle. Denitrifying microbes require a very low oxygen concentration of less than 10%, as well as organic C for energy. Since denitrification can remove NO3−, reducing its leaching to groundwater, it can be strategically used to treat sewage or animal residues of high nitrogen content. Denitrification can leak N2O, which is an ozone-depleting substance and a greenhouse gas that can have a considerable influence on global warming.
Anammox, an abbreviation for "anaerobic ammonium oxidation", is a globally important microbial process of the nitrogen cycle that takes place in many natural environments. The bacteria mediating this process were identified in 1999, and were a great surprise for the scientific community. In the anammox reaction, nitrite and ammonium ions are converted directly into diatomic nitrogen and water.
Denitrifying bacteria are a diverse group of bacteria that encompass many different phyla. This group of bacteria, together with denitrifying fungi and archaea, is capable of performing denitrification as part of the nitrogen cycle. Denitrification is performed by a variety of denitrifying bacteria that are widely distributed in soils and sediments and that use oxidized nitrogen compounds in absence of oxygen as a terminal electron acceptor. They metabolise nitrogenous compounds using various enzymes, turning nitrogen oxides back to nitrogen gas or nitrous oxide.
Nitrobacter is a genus comprising rod-shaped, gram-negative, and chemoautotrophic bacteria. The name Nitrobacter derives from the Latin neuter gender noun nitrum, nitri, alkalis; the Ancient Greek noun βακτηρία, βακτηρίᾱς, rod. They are non-motile and reproduce via budding or binary fission. Nitrobacter cells are obligate aerobes and have a doubling time of about 13 hours.
Nitrite reductase refers to any of several classes of enzymes that catalyze the reduction of nitrite. There are two classes of NIR's. A multi haem enzyme reduces NO2− to a variety of products. Copper containing enzymes carry out a single electron transfer to produce nitric oxide.
Microbial metabolism is the means by which a microbe obtains the energy and nutrients it needs to live and reproduce. Microbes use many different types of metabolic strategies and species can often be differentiated from each other based on metabolic characteristics. The specific metabolic properties of a microbe are the major factors in determining that microbe's ecological niche, and often allow for that microbe to be useful in industrial processes or responsible for biogeochemical cycles.
Nitrate reductases are molybdoenzymes that reduce nitrate to nitrite. This reaction is critical for the production of protein in most crop plants, as nitrate is the predominant source of nitrogen in fertilized soils.
Nitrifying bacteria are chemolithotrophic organisms that include species of genera such as Nitrosomonas, Nitrosococcus, Nitrobacter, Nitrospina, Nitrospira and Nitrococcus. These bacteria get their energy from the oxidation of inorganic nitrogen compounds. Types include ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB). Many species of nitrifying bacteria have complex internal membrane systems that are the location for key enzymes in nitrification: ammonia monooxygenase, hydroxylamine oxidoreductase, and nitrite oxidoreductase.
Nitric oxide dioxygenase (EC 1.14.12.17) is an enzyme that catalyzes the conversion of nitric oxide (NO) to nitrate (NO−
3) . The net reaction for the reaction catalyzed by nitric oxide dioxygenase is shown below:
Nitric oxide is a molecule and chemical compound with chemical formula of NO. In mammals including humans, nitric oxide is a signaling molecule involved in several physiological and pathological processes. It is a powerful vasodilator with a half-life of a few seconds in the blood. Standard pharmaceuticals such as nitroglycerine and amyl nitrite are precursors to nitric oxide. Low levels of nitric oxide production are typically due to ischemic damage in the liver.
Aerobic denitrification or co-respiration the simultaneous use of both oxygen (O2) and nitrate (NO3−) as oxidizing agents, performed by various genera of microorganisms. This process differs from anaerobic denitrification not only in its insensitivity to the presence of oxygen, but also in that it has a higher potential to create the harmful byproduct nitrous oxide.
The fnr gene of Escherichia coli encodes a transcriptional activator (FNR) which is required for the expression of a number of genes involved in anaerobic respiratory pathways. The FNR protein of E. coli is an oxygen – responsive transcriptional regulator required for the switch from aerobic to anaerobic metabolism.
"Type III mutants, originally frdB, were designated fnr because they were defective in fumarate and nitrate reduction and impaired in their ability to produce gas." - Lambden and Guest, 1976 Journal of General Microbiology97, 145-160
Phytoglobins are globular plant proteins classified into the globin superfamily, which contain a heme, i.e. protoporphyrin IX-Fe, prosthetic group. The earliest known phytoglobins are leghemoglobins, discovered in 1939 by Kubo after spectroscopic and chemical analysis of the red pigment of soybean root nodules. A few decades after Kubo's report the crystallization of a lupin phytoglobin by Vainshtein and collaborators revealed that the tertiary structure of this protein and that of the sperm whale myoglobin was remarkably similar, thus indicating that the phytoglobin discovered by Kubo did indeed correspond to a globin.
Abir Ubayevich Igamberdiev is a Russian-Canadian theoretical biologist and plant scientist. He is professor at Memorial University of Newfoundland, Canada. He is most known for his research on organization of plant metabolism, for the conceptual development of foundations of theoretical biology, and for his works on history and philosophy of science.
References
- ↑ Igamberdiev AU, Baron K, Manac'h-Little N, Stoimenova M, Hill RD (September 2005). "The haemoglobin/nitric oxide cycle: involvement in flooding stress and effects on hormone signalling". Annals of Botany. 96 (4): 557–64. doi:10.1093/aob/mci210. PMC 4247025 . PMID 16027133.
- ↑ Gupta KJ, Igamberdiev AU (July 2011). "The anoxic plant mitochondrion as a nitrite: NO reductase". Mitochondrion. 11 (4): 537–43. doi:10.1016/j.mito.2011.03.005. PMID 21406251.
- ↑ Igamberdiev AU, Bykova NV, Hill RD (April 2006). "Nitric oxide scavenging by barley hemoglobin is facilitated by a monodehydroascorbate reductase-mediated ascorbate reduction of methemoglobin". Planta. 223 (5): 1033–40. doi:10.1007/s00425-005-0146-3. PMID 16341544. S2CID 10684182.
- ↑ Jokipii-Lukkari S, Kastaniotis AJ, Parkash V, Sundström R, Leiva-Eriksson N, Nymalm Y, Blokhina O, Kukkola E, Fagerstedt KV, Salminen TA, Läärä E, Bülow L, Ohlmeier S, Hiltunen JK, Kallio PT, Häggman H (June 2016). "Dual targeted poplar ferredoxin NADP(+) oxidoreductase interacts with hemoglobin 1". Plant Science. 247: 138–49. doi:10.1016/j.plantsci.2016.03.013. PMID 27095407.
- ↑ Yamasaki H, Sakihama Y (February 2000). "Simultaneous production of nitric oxide and peroxynitrite by plant nitrate reductase: in vitro evidence for the NR-dependent formation of active nitrogen species". FEBS Letters. 468 (1): 89–92. doi:10.1016/S0014-5793(00)01203-5. PMID 10683447. S2CID 35069932.
- ↑ Stöhr C, Strube F, Marx G, Ullrich WR, Rockel P (April 2001). "A plasma membrane-bound enzyme of tobacco roots catalyses the formation of nitric oxide from nitrite". Planta. 212 (5–6): 835–41. doi:10.1007/s004250000447. PMID 11346959. S2CID 19990801.
- ↑ Stoimenova M, Igamberdiev AU, Gupta KJ, Hill RD (July 2007). "Nitrite-driven anaerobic ATP synthesis in barley and rice root mitochondria". Planta. 226 (2): 465–74. doi:10.1007/s00425-007-0496-0. PMID 17333252. S2CID 8963850.