1.
Metabolic pathway
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In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell. The reactants, products, and intermediates of a reaction are known as metabolites. In a metabolic pathway, the product of one acts as the substrate for the next. These enzymes often require dietary minerals, vitamins, and other cofactors to function, different metabolic pathways function based on the position within a eukaryotic cell and the significance of the pathway in the given compartment of the cell. For instance, the citric cycle, electron transport chain. In contrast, glycolysis, pentose phosphate pathway, and fatty acid biosynthesis all occur in the cytosol of a cell, the two pathways complement each other in that the energy released from one is used up by the other. The degradative process of a catabolic pathway provides the required to conduct a biosynthesis of an anabolic pathway. In addition to the two distinct metabolic pathways is the pathway, which can be either catabolic or anabolic based on the need for or the availability of energy. The end product of a pathway may be used immediately, initiate another metabolic pathway or be stored for later use, metabolic pathways are often considered to flow in one direction. Although all chemical reactions are reversible, conditions in the cell are often such that it is thermodynamically more favorable for flux to flow in one direction of a reaction. For example, one pathway may be responsible for the synthesis of an amino acid. One example of an exception to rule is the metabolism of glucose. Glycolysis results in the breakdown of glucose, but several reactions in the pathway are reversible. Glycolysis was the first metabolic pathway discovered, As glucose enters a cell, metabolic pathways are often regulated by feedback inhibition. Some metabolic pathways flow in a cycle wherein each component of the cycle is a substrate for the subsequent reaction in the cycle, the net reaction is, therefore, thermodynamically favorable, for it results in a lower free energy for the final products. A catabolic pathway is a system that produces chemical energy in the form of ATP, GTP, NADH, NADPH, FADH2, etc. from energy containing sources such as carbohydrates, fats. The end products are carbon dioxide, water, and ammonia. Coupled with an reaction of anabolism, the cell can synthesize new macromolecules using the original precursors of the anabolic pathway
2.
Eukaryote
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A eukaryote is any organism whose cells contain a nucleus and other organelles enclosed within membranes. Eukaryotes belong to the taxon Eukarya or Eukaryota, the presence of a nucleus gives eukaryotes their name, which comes from the Greek εὖ and κάρυον. Eukaryotic cells also contain other membrane-bound organelles such as mitochondria and the Golgi apparatus, in addition, plants and algae contain chloroplasts. Eukaryotic organisms may be unicellular or multicellular, only eukaryotes form multicellular organisms consisting of many kinds of tissue made up of different cell types. Eukaryotes can reproduce asexually through mitosis and sexually through meiosis and gamete fusion. In mitosis, one cell divides to produce two identical cells. In meiosis, DNA replication is followed by two rounds of division to produce four daughter cells each with half the number of chromosomes as the original parent cell. These act as sex cells resulting from genetic recombination during meiosis, the domain Eukaryota appears to be monophyletic, and so makes up one of the three domains of life. The two other domains, Bacteria and Archaea, are prokaryotes and have none of the above features, eukaryotes represent a tiny minority of all living things. However, due to their larger size, eukaryotes collective worldwide biomass is estimated at about equal to that of prokaryotes. Eukaryotes first developed approximately 1. 6–2.1 billion years ago, in 1905 and 1910, the Russian biologist Konstantin Mereschkowsky argued three things about the origin of nucleated cells. Firstly, plastids were reduced cyanobacteria in a symbiosis with a non-photosynthetic host, secondly, the host had earlier in evolution formed by symbiosis between an amoeba-like host and a bacteria-like cell that formed the nucleus. Thirdly, plants inherited photosynthesis from cyanobacteria, the split between the prokaryotes and eukaryotes was introduced in the 1960s. The concept of the eukaryote has been attributed to the French biologist Edouard Chatton, the terms prokaryote and eukaryote were more definitively reintroduced by the Canadian microbiologist Roger Stanier and the Dutch-American microbiologist C. B. van Niel in 1962. In his 1938 work Titres et Travaux Scientifiques, Chatton had proposed the two terms, calling the bacteria prokaryotes and organisms with nuclei in their cells eukaryotes. However he mentioned this in one paragraph, and the idea was effectively ignored until Chattons statement was rediscovered by Stanier. In 1967, Lynn Margulis provided microbiological evidence for endosymbiosis as the origin of chloroplasts and mitochondria in cells in her paper. In the 1970s, Carl Woese explored microbial phylogenetics, studying variations in 16S ribosomal RNA and this helped to uncover the origin of the eukaryotes and the symbiogenesis of two important eukaryote organelles, mitochondria and chloroplasts
3.
Archaea
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The Archaea constitute a domain and kingdom of single-celled microorganisms. These microbes are prokaryotes, meaning that they have no cell nucleus or any other membrane-bound organelles in their cells, Archaea were initially classified as bacteria, receiving the name archaebacteria, but this classification is outdated. Archaeal cells have unique properties separating them from the two domains of life, Bacteria and Eukaryota. The Archaea are further divided into multiple recognized phyla, classification is difficult because the majority have not been isolated in the laboratory and have only been detected by analysis of their nucleic acids in samples from their environment. Archaea and bacteria are generally similar in size and shape, although a few archaea have very strange shapes, such as the flat, other aspects of archaeal biochemistry are unique, such as their reliance on ether lipids in their cell membranes, including archaeols. Archaea use more energy sources than eukaryotes, these range from organic compounds, such as sugars, to ammonia, metal ions or even hydrogen gas. Salt-tolerant archaea use sunlight as a source, and other species of archaea fix carbon, however, unlike plants and cyanobacteria. Archaea reproduce asexually by fission, fragmentation, or budding, unlike bacteria and eukaryotes. They are also found in the colon, oral cavity. Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet, Archaea are a major part of Earths life and may play roles in both the carbon cycle and the nitrogen cycle. No clear examples of archaeal pathogens or parasites are known, one example is the methanogens that inhabit human and ruminant guts, where their vast numbers aid digestion. Methanogens are also used in production and sewage treatment, and enzymes from extremophile archaea that can endure high temperatures. For much of the 20th century, prokaryotes were regarded as a group of organisms and classified based on their biochemistry, morphology. For example, microbiologists tried to classify based on the structures of their cell walls, their shapes. In 1965, Emile Zuckerkandl and Linus Pauling proposed instead using the sequences of the genes in different prokaryotes to work out how they are related to each other and this approach, known as phylogenetics, is the main method used today. Archaea were first classified as a group of prokaryotes in 1977 by Carl Woese. These two groups were named the Archaebacteria and Eubacteria and treated as kingdoms or subkingdoms, which Woese. Woese argued that group of prokaryotes is a fundamentally different sort of life
4.
Bacteria
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Bacteria constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a number of shapes, ranging from spheres to rods, Bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, and only half of the bacterial phyla have species that can be grown in the laboratory. The study of bacteria is known as bacteriology, a branch of microbiology, There are typically 40 million bacterial cells in a gram of soil and a million bacterial cells in a millilitre of fresh water. There are approximately 5×1030 bacteria on Earth, forming a biomass which exceeds that of all plants, Bacteria are vital in many stages of the nutrient cycle by recycling nutrients such as the fixation of nitrogen from the atmosphere. The nutrient cycle includes the decomposition of bodies and bacteria are responsible for the putrefaction stage in this process. In March 2013, data reported by researchers in October 2012, was published and it was suggested that bacteria thrive in the Mariana Trench, which with a depth of up to 11 kilometres is the deepest known part of the oceans. Other researchers reported related studies that microbes thrive inside rocks up to 580 metres below the sea floor under 2.6 kilometres of ocean off the coast of the northwestern United States. According to one of the researchers, You can find microbes everywhere—theyre extremely adaptable to conditions, the vast majority of the bacteria in the body are rendered harmless by the protective effects of the immune system, though many are beneficial particularly in the gut flora. However several species of bacteria are pathogenic and cause diseases, including cholera, syphilis, anthrax, leprosy. The most common fatal diseases are respiratory infections, with tuberculosis alone killing about 2 million people per year. In developed countries, antibiotics are used to treat infections and are also used in farming, making antibiotic resistance a growing problem. Once regarded as constituting the class Schizomycetes, bacteria are now classified as prokaryotes. Unlike cells of animals and other eukaryotes, bacterial cells do not contain a nucleus and these evolutionary domains are called Bacteria and Archaea. The ancestors of modern bacteria were unicellular microorganisms that were the first forms of life to appear on Earth, for about 3 billion years, most organisms were microscopic, and bacteria and archaea were the dominant forms of life. In 2008, fossils of macroorganisms were discovered and named as the Francevillian biota, however, gene sequences can be used to reconstruct the bacterial phylogeny, and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage. Bacteria were also involved in the second great evolutionary divergence, that of the archaea, here, eukaryotes resulted from the entering of ancient bacteria into endosymbiotic associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea
5.
Isoprenoids
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Most are multicyclic structures that differ from one another not only in functional groups but also in their basic carbon skeletons. These lipids can be found in all classes of living things, about 60% of known natural products are terpenoids. Plant terpenoids are used extensively for their qualities and play a role in traditional herbal remedies. Terpenoids contribute to the scent of eucalyptus, the flavors of cinnamon, cloves, and ginger, the color in sunflowers. The steroids and sterols in animals are produced from terpenoid precursors. Sometimes terpenoids are added to proteins, e. g. to enhance their attachment to the cell membrane, terpenes are hydrocarbons resulting from the condensation of several 5-carbon isoprene units. The isoprene unit has the formula CH2=CCH=CH2, terpenoids can be thought of as modified terpenes, wherein methyl groups have been moved or removed, or oxygen atoms added. The Salkowski test can be used to identify the presence of terpenoids, meroterpenes are any compound, including many natural products, having a partial terpenoid structure. There are two pathways that create terpenoids, Many organisms manufacture terpenoids through the HMG-CoA reductase pathway. The reactions take place in the cytosol, the pathway was discovered in the 1950s. It was discovered in the late 1980s, pyruvate and glyceraldehyde 3-phosphate are converted by DOXP synthase to 1-deoxy-D-xylulose 5-phosphate, and by DOXP reductase to 2-C-methyl-D-erythritol 4-phosphate. IPP and DMAPP are the end-products in either pathway, and are the precursors of isoprene, monoterpenoids, diterpenoids, carotenoids, chlorophylls, synthesis of all higher terpenoids proceeds via formation of geranyl pyrophosphate, farnesyl pyrophosphate, and geranylgeranyl pyrophosphate. Although both pathways, MVA and MEP, are exclusive in most organisms, interactions between them have been reported in plants and few bacteria species. It is a material for synthesis of vitamin A. List of antioxidants in food List of phytochemicals in food Nutrition Phytochemistry Secondary metabolites IUPAC nomenclature of terpenoids
6.
Cholesterol
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Cholesterol, from the Ancient Greek chole- and stereos followed by the chemical suffix -ol for an alcohol, is an organic molecule. Cholesterol enables animal cells to dispense with a wall, thereby allowing animal cells to change shape rapidly. In addition to its importance for cell structure, cholesterol also serves as a precursor for the biosynthesis of steroid hormones, bile acid. Cholesterol is the principal sterol synthesized by all animals, in vertebrates, hepatic cells typically produce the greatest amounts. It is absent among prokaryotes, although there are exceptions, such as Mycoplasma. François Poulletier de la Salle first identified cholesterol in solid form in gallstones in 1769, however, it was not until 1815 that chemist Michel Eugène Chevreul named the compound cholesterine. Furthermore, it can be absorbed directly from animal-based foods, a human male weighing 68 kg normally synthesizes about 1 gram per day, and his body contains about 35 g, mostly contained within the cell membranes. Typical daily cholesterol dietary intake for a man in the United States is 307 mg, most ingested cholesterol is esterified, and esterified cholesterol is poorly absorbed. The body also compensates for any absorption of cholesterol by reducing cholesterol synthesis. For these reasons, cholesterol in food, seven to ten hours after ingestion, has little and it is also important to recognize, however, that the concentrations measured in the samples of blood plasma vary with the measurement methods used. Cholesterol is recycled in the body, the liver excretes it in a non-esterified form into the digestive tract. Typically, about 50% of the excreted cholesterol is reabsorbed by the small intestine back into the bloodstream, plants make cholesterol in very small amounts. Plants manufacture phytosterols, which can compete with cholesterol for reabsorption in the intestinal tract, when intestinal lining cells absorb phytosterols, in place of cholesterol, they usually excrete the phytosterol molecules back into the GI tract, an important protective mechanism. Cholesterol, given that it composes about 30% of all cell membranes, is required to build. The membrane remains stable and durable without being rigid, allowing cells to change shape. In this structural role, cholesterol also reduces the permeability of the membrane to neutral solutes, hydrogen ions. Within the cell membrane, cholesterol also functions in intracellular transport, cell signaling, cholesterol is essential for the structure and function of invaginated caveolae and clathrin-coated pits, including caveola-dependent and clathrin-dependent endocytosis. The role of cholesterol in endocytosis of these types can be investigated by using methyl beta cyclodextrin to remove cholesterol from the plasma membrane, in multiple layers, cholesterol and phospholipids, both electrical insulators, can facilitate speed of transmission of electrical impulses along nerve tissue
7.
Heme
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Not all porphyrins contain iron, but a substantial fraction of porphyrin-containing metalloproteins have heme as their prosthetic group, these are known as hemoproteins. Hemoproteins have diverse functions including the transportation of diatomic gases, chemical catalysis, diatomic gas detection. The heme iron serves as a source or sink of electrons during electron transfer or redox chemistry, in peroxidase reactions, the porphyrin molecule also serves as an electron source. In the transportation or detection of gases, the gas binds to the heme iron. During the detection of gases, the binding of the gas ligand to the heme iron induces conformational changes in the surrounding protein. Hemoproteins achieve their remarkable diversity by modifying the environment of the heme macrocycle within the protein matrix. For example, the ability of hemoglobin to effectively deliver oxygen to tissues is due to amino acid residues located near the heme molecule. Hemoglobin reversibly binds to oxygen in the lungs when the pH is high, when the situation is reversed, hemoglobin will release oxygen into the tissues. This phenomenon, which states that hemoglobins oxygen binding affinity is inversely proportional to both acidity and concentration of carbon dioxide, is known as the Bohr effect. There are several biologically important kinds of heme, The most common type is heme B, other important types include heme A, isolated hemes are commonly designated by capital letters while hemes bound to proteins are designated by lower case letters. Cytochrome a refers to the heme A in specific combination with membrane protein forming a portion of cytochrome c oxidase, the following carbon numbering system of porphyrins is an older numbering used by biochemists and not the 1–24 numbering system recommended by IUPAC which is shown in the table above. Heme l is the derivative of heme B which is attached to the protein of lactoperoxidase, eosinophil peroxidase. The addition of peroxide with the glutamyl-375 and aspartyl-225 of lactoperoxidase forms ester bonds between amino acid residues and the heme 1- and 5-methyl groups, respectively. Similar ester bonds with two methyl groups are thought to form in eosinophil and thyroid peroxidases. Heme l is one important characteristic of animal peroxidases, plant peroxidases incorporate heme B, lactoperoxidase and eosinophil peroxidase are protective enzymes responsible for the destruction of invading bacteria and virus. Thyroid peroxidase is the enzyme catalyzing the biosynthesis of the important thyroid hormones, because lactoperoxidase destroys invading organisms in the lungs and excrement, it is thought to be an important protective enzyme. Heme m is the derivative of heme B covalently bound at the site of myeloperoxidase. Heme m contains the two ester bonds at the heme 1- and 5-methyls as in heme l found in other mammalian peroxidases, myeloperoxidase is present in mammalian neutrophils and is responsible for the destruction of invading bacteria and viruse
8.
Coenzyme Q10
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Coenzyme Q10, also known as ubiquinone, ubidecarenone, coenzyme Q, and abbreviated at times to CoQ10 /ˌkoʊ ˌkjuː ˈtɛn/, CoQ, or Q10 is a coenzyme that is ubiquitous in the bodies of most animals. It is a 1, 4-benzoquinone, where Q refers to the chemical group and 10 refers to the number of isoprenyl chemical subunits in its tail. This fat-soluble substance, which resembles a vitamin, is present in most eukaryotic cells and it is a component of the electron transport chain and participates in aerobic cellular respiration, which generates energy in the form of ATP. Ninety-five percent of the bodys energy is generated this way. Therefore, those organs with the highest energy requirements—such as the heart, liver, there are three redox states of CoQ10, fully oxidized, semiquinone, and fully reduced. There are two factors that lead to deficiency of CoQ10 in humans, reduced biosynthesis, and increased use by the body. Biosynthesis is the source of CoQ10. Biosynthesis requires at least 12 genes, and mutations in many of them cause CoQ deficiency, CoQ10 levels also may be affected by other genetic defects. The role of statins in deficiencies is controversial, some chronic disease conditions also are thought to reduce the biosynthesis of and increase the demand for CoQ10 in the body, but there are no definite data to support these claims. Usually, toxicity is not observed with high doses of CoQ10, a daily dosage up to 3600 mg was found to be tolerated by healthy as well as unhealthy persons. Some adverse effects, however, largely gastrointestinal, are reported with high intakes. The observed safe level risk assessment method indicated that the evidence of safety is strong at intakes up to 1200 mg/day, although CoQ10 may be measured in blood plasma, these measurements reflect dietary intake rather than tissue status. Currently, most clinical centers measure CoQ10 levels in cultured skin fibroblasts, muscle biopsies, culture fibroblasts can be used also to evaluate the rate of endogenous CoQ10 biosynthesis, by measuring the uptake of 14C-labelled p-hydroxybenzoate. CoQ10 shares a biosynthetic pathway with cholesterol, the synthesis of an intermediary precursor of CoQ10, mevalonate, is inhibited by some beta blockers, blood pressure-lowering medication, and statins, a class of cholesterol-lowering drugs. Statins can reduce levels of CoQ10 by up to 40%. CoQ10 is not approved by the U. S. Food and it is sold as a dietary supplement. In the U. S. supplements are not regulated as drugs, how CoQ10 is manufactured is not regulated and different batches and brands may vary significantly. A2004 laboratory analysis by ConsumerLab. com of CoQ10 supplements on the found that some did not contain the quantity identified on the product label
9.
Steroid hormone
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A steroid hormone is a steroid that acts as a hormone. Steroid hormones can be grouped into two classes, corticosteroids and sex steroids, within those two classes are five types according to the receptors to which they bind, glucocorticoids, mineralocorticoids, androgens, estrogens, and progestogens. Vitamin D derivatives are a closely related hormone system with homologous receptors. They have some of the characteristics of true steroids as receptor ligands, Steroid hormones help control metabolism, inflammation, immune functions, salt and water balance, development of sexual characteristics, and the ability to withstand illness and injury. The term steroid describes both hormones produced by the body and artificially produced medications that duplicate the action for the naturally occurring steroids, the natural steroid hormones are generally synthesized from cholesterol in the gonads and adrenal glands. These forms of hormones are lipids and they can pass through the cell membrane as they are fat-soluble, and then bind to steroid hormone receptors to bring about changes within the cell. Steroid hormones are generally carried in the blood, bound to specific carrier proteins such as sex hormone-binding globulin or corticosteroid-binding globulin, further conversions and catabolism occurs in the liver, in other peripheral tissues, and in the target tissues. A variety of synthetic steroids and sterols have also been contrived, most are steroids, but some non-steroidal molecules can interact with the steroid receptors because of a similarity of shape. Some synthetic steroids are weaker or stronger than the natural steroids whose receptors they activate, some examples are sex hormone-binding globulin, corticosteroid-binding globulin, and albumin. Most studies say that hormones can affect cells when they are not bound by serum proteins. This idea is known as the free hormone hypothesis and this idea is shown in Figure 1 to the right. One study has found that these complexes are bound by megalin, a membrane receptor. The hormone then follows a pathway of action. This process is shown in Figure 2 to the right, the role of endocytosis in steroid hormone transport is not well understood and is under further investigation. In order for steroid hormones to cross the lipid bilayer of cells they must overcome barriers that would prevent their entering or exiting the membrane. Gibbs free energy is an important concept here and these hormones, which are all derived from cholesterol, have hydrophilic functional groups at either end and hydrophobic carbon backbones. These energy barriers and wells are reversed for hormones exiting membranes, Steroid hormones easily enter and exit the membrane at physiologic conditions. They have been shown experimentally to cross membranes near a rate of 20 μm/s, though it is energetically more favorable for hormones to be in the membrane than in the ECF or ICF, they do in fact leave the membrane once they have entered it
10.
HMG-CoA reductase
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HMG-CoA reductase is the rate-controlling enzyme of the mevalonate pathway, the metabolic pathway that produces cholesterol and other isoprenoids. This enzyme is thus the target of the widely available cholesterol-lowering drugs known collectively as the statins, more recent evidence shows it to contain eight transmembrane domains. In humans, the gene for HMG-CoA reductase is located on the arm of the fifth chromosome. Related enzymes having the function are also present in other animals, plants. The main isoform of HMG-CoA reductase in humans is 888 amino acids long and it is a polytopic transmembrane protein. It contains two domains, an N-terminal sterol-sensing domain, which binds sterol groups. Cholesterol binding at this region inhibits the activity of the catalytic domain, a C-terminal catalytic domain, namely the 3-hydroxy-3-methyl-glutaryl-CoA reductase domain. This domain is required for the enzymatic activity of the protein. Isoform 2 is 835 amino acids long and this variant is shorter because it lacks an exon in the middle region. This does not affect any of the aforementioned domains, HMGCR catalyses the conversion of HMG-CoA to mevalonic acid, a necessary step in the biosynthesis of cholesterol. Click on genes, proteins and metabolites below to link to respective articles, drugs that inhibit HMG-CoA reductase, known collectively as HMG-CoA reductase inhibitors, are used to lower serum cholesterol as a means of reducing the risk for cardiovascular disease. These drugs include rosuvastatin, lovastatin, atorvastatin, pravastatin, fluvastatin, pitavastatin, red yeast rice extract, one of the fungal sources from which the statins were discovered, contains several naturally occurring cholesterol-lowering molecules known as monacolins. The most active of these is monacolin K, or lovastatin, HMG-CoA reductase is active when blood glucose is high. The basic functions of insulin and glucagon are to maintain glucose homeostasis and it can be noted that blocking of isoprenoid synthesis by statins has shown promise in treating a mouse model of multiple sclerosis, an inflammatory autoimmune disease. HMG-CoA reductase is an important developmental enzyme, inhibition of its activity and the concomitant lack of isoprenoids that yields can lead to germ cell migration defects as well as intracerebral hemorrhage. Regulation of HMG-CoA reductase is achieved at several levels, transcription, translation, degradation and phosphorylation, transcription of the reductase gene is enhanced by the sterol regulatory element binding protein. This protein binds to the regulatory element, located on the 5 end of the reductase gene. When SREBP is inactive, it is bound to the ER or nuclear membrane with another protein called SREBP cleavage-activating protein, when cholesterol levels fall, SREBP is released from the membrane by proteolysis and migrates to the nucleus, where it binds to the SRE and transcription is enhanced
11.
Mevalonate
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Mevalonic acid is a key organic compound in biochemistry. The name is a contraction of dihydroxymethylvalerolactone, the carboxylate anion of mevalonic acid, which is the predominant form in biological environments is known as mevalonate, and is of major pharmaceutical importance. Drugs such as the stop the production of mevalonate by inhibiting HMG-CoA reductase. Mevalonic acid is soluble in water and polar organic solvents. It exists in equilibrium with its form, called mevalonolactone. Mevalonic acid is a precursor in the biosynthetic pathway known as the pathway that produces terpenes. Mevalonic acid is the precursor of isopentenyl pyrophosphate, that is in turn the basis for all terpenoids. Mevalonic acid is chiral and the -enantiomer is the one that is biologically active
12.
Decarboxylation
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Decarboxylation is a chemical reaction that removes a carboxyl group and releases carbon dioxide. Usually, decarboxylation refers to a reaction of acids, removing a carbon atom from a carbon chain. The reverse process, which is the first chemical step in photosynthesis, is called carboxylation, enzymes that catalyze decarboxylations are called decarboxylases or, the more formal term, carboxy-lyases. The term decarboxylation literally means removal of the COOH and its replacement with a hydrogen, the term relates the state of the reactant and product. Decarboxylation is one of the oldest organic reactions, since it often entails simple pyrolysis, heating is required because the reaction is less favorable at low temperatures. Yields are highly sensitive to conditions, in retrosynthesis, decarboxylation reactions can be considered the opposite of homologation reactions, in that the chain length becomes one carbon shorter. Metals, especially copper compounds, are usually required, such reactions proceed via the intermediacy of metal carboxylate complexes. Decarboxylation of aryl carboxylates can generate the equivalent of the corresponding aryl anion, alkanoic acids and their salts do not always undergo decarboxylation readily. Exceptions are the decarboxylation of beta-keto acids, α, β-unsaturated acids, and α-phenyl, α-nitro, such reactions are accelerated due to the formation of a zwitterionic tautomer in which the carbonyl is protonated and the carboxyl group is deprotonated. Typically fatty acids do not decarboxylate readily, reactivity of an acid towards decarboxylation depends upon stability of carbanion intermediate formed in above mechanism. Many reactions have been named after workers in organic chemistry. The Barton decarboxylation, Kolbe electrolysis, Kochi reaction and Hunsdiecker reaction are radical reactions, the Krapcho decarboxylation is a related decarboxylation of an ester. In ketonic decarboxylation a carboxylic acid is converted to a ketone, hydrodecarboxylations involve the conversion of a carboxylic acid to the corresponding hydrocarbon. This is conceptually the same as the general term decarboxylation as defined above except that it specifically requires that the carboxyl group is. The reaction is common in conjunction with the malonic ester synthesis. The reaction involves the base of the carboxyl group, a carboxylate ion. Where reactions entail heating the carboxylic acid with concentrated hydrochloric acid, in these cases, the reaction is likely to occur by initial addition of water and a proton. Upon heating, Δ9-Tetrahydrocannabinolic acid decarboxylates to give the psychoactive compound Δ9-Tetrahydrocannabinol, when cannabis is heated in vacuum, the decarboxylation of tetrahydrocannabinolic acid appears to follow first order kinetics
13.
Haloferax volcanii
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In taxonomy, Haloferax volcanii is a species of organism in the genus Haloferax in the Archaea. Microbiologist Benjamin Elazari Volcani first discovered Haloferax volcanii, a self-named extremophile, H. Haloferax volcanii is noteworthy because it can be cultured without much difficulty, rare for an extremophile. H. volcanii is chemoorganotrophic, metabolizing sugars as a carbon source and it is primarily aerobic, but is capable of anaerobic respiration under anoxic conditions. Recently an isolate of this species was studied by researchers at University of California, Berkeley, the genome of H. volcanii consists of a large, multicopy chromosome and several megaplasmids. The genome has been sequenced and a paper discussing it was published in 2010. The molecular biology of H. volcanii has been studied for the last decade in order to discover more about DNA replication, DNA repair. The archaeal proteins used in processes are extremely similar to Eukaryotic proteins. H. volcanii undergoes prolific horizontal gene transfer through a mechanism of cell fusion. Reproduction among H. volcanii occurs asexually by binary fission and this practice is similar to that of other Archaea and, indeed, that of bacteria. H. volcanii cells have no cell wall and, like many archaea, an individual H. volcanii archaeon can vary from 1-3 micrometers in diameter. They are typically recognisable by their dished crisp shape, but are somewhat pleiomorphic so may be seen in other shapes including coccoid, H. volcanii use a salt in method to maintain osmostasis, rather than the typical compatible solutes method seen in bacteria. This method involves the maintenance of a degree of potassium ions in the cell to balance the sodium ions outside. For this reason H. volcanii has a complex ion regulation system and is chemoautotrophic, due to the salt in method cytoplasmic proteins are structured to fold in the presence of high ionic concentrations. As such they typically have a number of charged residues on the exterior section of the protein. This structure increases their stability in saline and even high temperature environments considerably, H. Isolates of H. volcanii are commonly found in high-salinity aquatic environments, such as the Dead Sea. Their precise role in the ecosystem is uncertain, but the contained within these organisms potentially serve many practical purposes. Because of their ability to maintain homeostasis in spite of the salt around them, as it is likely that H. volcanii and comparable species are ranked among the earliest living organisms, they also provide information related to genetics and evolution. The Dead Sea contains a high concentration of sodium, magnesium
14.
Enzyme
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Enzymes /ˈɛnzaɪmz/ are macromolecular biological catalysts. Enzymes accelerate, or catalyze, chemical reactions, the molecules at the beginning of the process upon which enzymes may act are called substrates and the enzyme converts these into different molecules, called products. Almost all metabolic processes in the cell need enzymes in order to occur at rates fast enough to sustain life, the set of enzymes made in a cell determines which metabolic pathways occur in that cell. The study of enzymes is called enzymology, enzymes are known to catalyze more than 5,000 biochemical reaction types. Most enzymes are proteins, although a few are catalytic RNA molecules, enzymes specificity comes from their unique three-dimensional structures. Like all catalysts, enzymes increase the rate of a reaction by lowering its activation energy, some enzymes can make their conversion of substrate to product occur many millions of times faster. An extreme example is orotidine 5-phosphate decarboxylase, which allows a reaction that would take millions of years to occur in milliseconds. Chemically, enzymes are like any catalyst and are not consumed in chemical reactions, enzymes differ from most other catalysts by being much more specific. Enzyme activity can be affected by other molecules, inhibitors are molecules that decrease enzyme activity, many drugs and poisons are enzyme inhibitors. An enzymes activity decreases markedly outside its optimal temperature and pH, some enzymes are used commercially, for example, in the synthesis of antibiotics. French chemist Anselme Payen was the first to discover an enzyme, diastase and he wrote that alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells. In 1877, German physiologist Wilhelm Kühne first used the term enzyme, the word enzyme was used later to refer to nonliving substances such as pepsin, and the word ferment was used to refer to chemical activity produced by living organisms. Eduard Buchner submitted his first paper on the study of yeast extracts in 1897, in a series of experiments at the University of Berlin, he found that sugar was fermented by yeast extracts even when there were no living yeast cells in the mixture. He named the enzyme that brought about the fermentation of sucrose zymase, in 1907, he received the Nobel Prize in Chemistry for his discovery of cell-free fermentation. Following Buchners example, enzymes are usually named according to the reaction they carry out, the biochemical identity of enzymes was still unknown in the early 1900s. Sumner showed that the enzyme urease was a protein and crystallized it. These three scientists were awarded the 1946 Nobel Prize in Chemistry, the discovery that enzymes could be crystallized eventually allowed their structures to be solved by x-ray crystallography. This high-resolution structure of lysozyme marked the beginning of the field of structural biology, an enzymes name is often derived from its substrate or the chemical reaction it catalyzes, with the word ending in -ase
15.
Transcription (biology)
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Transcription is the first step of gene expression, in which a particular segment of DNA is copied into RNA by the enzyme RNA polymerase. Both DNA and RNA are nucleic acids, which use base pairs of nucleotides as a complementary language, during transcription, a DNA sequence is read by an RNA polymerase, which produces a complementary, antiparallel RNA strand called a primary transcript. Transcription proceeds in the general steps, RNA polymerase, together with one or more general transcription factors. RNA polymerase creates a bubble, which separates the two strands of the DNA helix. This is done by breaking the bonds between complementary DNA nucleotides. RNA sugar-phosphate backbone forms with assistance from RNA polymerase to form an RNA strand, hydrogen bonds of the RNA–DNA helix break, freeing the newly synthesized RNA strand. If the cell has a nucleus, the RNA may be further processed and this may include polyadenylation, capping, and splicing. The RNA may remain in the nucleus or exit to the cytoplasm through the pore complex. The stretch of DNA transcribed into an RNA molecule is called a transcription unit, if the gene encodes a protein, the transcription produces messenger RNA, the mRNA, in turn, serves as a template for the proteins synthesis through translation. Alternatively, the gene may encode for either non-coding RNA, ribosomal RNA, transfer RNA. Overall, RNA helps synthesize, regulate, and process proteins, in virology, the term may also be used when referring to mRNA synthesis from an RNA molecule. For instance, the genome of a negative-sense single-stranded RNA virus may be template for a positive-sense single-stranded RNA and this is because the positive-sense strand contains the information needed to translate the viral proteins for viral replication afterwards. This process is catalyzed by a viral RNA replicase, the regulatory sequence before the coding sequence is called the five prime untranslated region, the sequence after the coding sequence is called the three prime untranslated region. As opposed to DNA replication, transcription results in an RNA complement that includes the nucleotide uracil in all instances where thymine would have occurred in a DNA complement, only one of the two DNA strands serve as a template for transcription. The antisense strand of DNA is read by RNA polymerase from the 3 end to the 5 end during transcription. The complementary RNA is created in the direction, in the 5 →3 direction. This directionality is because RNA polymerase can only add nucleotides to the 3 end of the growing mRNA chain and this use of only the 3 →5 DNA strand eliminates the need for the Okazaki fragments that are seen in DNA replication. This also removes the need for an RNA primer to initiate RNA synthesis, the non-template strand of DNA is called the coding strand, because its sequence is the same as the newly created RNA transcript
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Sterol regulatory element-binding protein
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Sterol regulatory element-binding proteins are transcription factors that bind to the sterol regulatory element DNA sequence TCACNCCAC. Mammalian SREBPs are encoded by the genes SREBF1 and SREBF2, SREBPs belong to the basic-helix-loop-helix leucine zipper class of transcription factors. Unactivated SREBPs are attached to the envelope and endoplasmic reticulum membranes. In cells with low levels of sterols, SREBPs are cleaved to a water-soluble N-terminal domain that is translocated to the nucleus and these activated SREBPs then bind to specific sterol regulatory element DNA sequences, thus upregulating the synthesis of enzymes involved in sterol biosynthesis. Sterols in turn inhibit the cleavage of SREBPs and therefore synthesis of additional sterols is reduced through a feed back loop. Mammalian genomes have two separate SREBP genes, SREBP-1 expression produces two different isoforms, SREBP-1a and -1c and these isoforms differ in their first exons owing to the use of different transcriptional start sites for the SREBP-1 gene. SREBP-1c was also identified in rats as ADD-1, SREBP-1c is responsible for regulating the genes required for de novo lipogenesis. SREBP-2 regulates the genes of cholesterol metabolism, SREB proteins are indirectly required for cholesterol biosynthesis and for uptake and fatty acid biosynthesis. These proteins work with asymmetric sterol regulatory element, SREBPs have a structure similar to E-box-binding helix-loop-helix proteins. However, in contrast to E-box-binding HLH proteins, a residue is replaced with tyrosine making them capable of recognizing StREs. Animal cells maintain proper levels of lipids under widely varying circumstances. For example, when cellular cholesterol levels fall below the level needed, a principal step in this response is to make more of the mRNA transcripts that direct the synthesis of these enzymes. Conversely, when there is enough cholesterol around, the cell stops making those mRNAs, as a result, the cell quits making cholesterol once it has enough. A notable feature of this regulatory feedback machinery was first observed for the SREBP pathway - regulated intramembrane proteolysis, subsequently, RIP was found to be used in almost all organisms from bacteria to human beings and regulates a wide range of processes ranging from development to neurodegeneration. A feature of the SREBP pathway is the release of a membrane-bound transcription factor. Proteolytic cleavage frees it to move through the cytoplasm to the nucleus, once in the nucleus, SREBP can bind to specific DNA sequences that are found in the control regions of the genes that encode enzymes needed to make lipids. This binding to DNA leads to the transcription of the target genes. The ~120 kDa SREBP precursor protein is anchored in the membranes of the endoplasmic reticulum, the precursor has a hairpin orientation in the membrane, so that both the amino-terminal transcription factor domain and the COOH-terminal regulatory domain face the cytoplasm
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Lipoprotein
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A lipoprotein is a biochemical assembly whose purpose is to transport hydrophobic lipid molecules in water, as in blood or ECF. Apolipoproteins are embedded in the membrane, both stabilising the complex and giving it functional identity determining its fate, thus the complex serves to emulsify the fats. Many enzymes, transporters, structural proteins, antigens, adhesins, the lipids are often an essential part of the complex, even if they seem to have no catalytic activity by themselves. To isolate transmembrane lipoproteins from their associated biological membranes, detergents are often needed, because fats are insoluble in water, these cannot be transported in blood on its own. Instead, they are attached to proteins that function as transport vehicles. The role of lipoprotein particles is to transport triacylglycerols and cholesterol in the blood all the tissues of the body. The most common being the liver and the adipocytes of adipose tissue, particles are synthesized in the small intestine and the liver, but interestingly not in the adipocytes. The lipoprotein particles have hydrophilic groups of phospholipids, cholesterol, such characteristics make them soluble in the salt water-based blood pool. Triglyceride-fats and cholesteryl esters are carried internally, shielded from the water by the phospholipid monolayer, the interaction of the proteins forming the surface of the particles determines whether triglycerides and cholesterol will be added to or removed from the lipoprotein transport particles. Regarding atheroma development and progression as opposed to regression, the key issue has always been cholesterol transport patterns, the handling of lipoprotein particles in the body is referred to as lipoprotein particle metabolism. The hepatocytes are the platform for the handling of triacylglycerols and cholesterol. While adipocytes are the storage cells for triacylglycerols, they do not produce any lipoproteins. Bile emulsifies fats contained in the chyme, then pancreatic lipase cleaves triacylglycerol molecules into two fatty acids and one 2-monoacylglycerol, enterocytes readily absorb these small molecules from the chymus. Inside of the enterocytes, fatty acids and monoacylglycerides are transformed again into triacylglycerides, then these lipids are assembled with apolipoprotein B-48 into nascent chylomicrons. These particles are secreted into the lacteals in a process that depends heavily on apolipoprotein B-48. As they circulate through the vessels, nascent chylomicrons bypass the liver circulation and are drained via the thoracic duct into the bloodstream. In the blood stream, nascent chylomicron particles interact with HDL particles resulting in HDL donation of apolipoprotein C-II, the chylomicron at this stage is then considered mature. Via apolipoprotein C-II, mature chylomicrons activate lipoprotein lipase, an enzyme on endothelial cells lining the blood vessels, LPL catalyzes the hydrolysis of triacylglycerol that ultimately releases glycerol and fatty acids from the chylomicrons
Orange nodes: carbohydrate metabolism. 
Violet nodes: photosynthesis. 
Red nodes: cellular respiration. 
Pink nodes: cell signaling. 
Blue nodes: amino acid metabolism. 
Grey nodes: vitamin and cofactor metabolism. 
Brown nodes: nucleotide and protein metabolism. 
Green nodes: lipid metabolism.