1.
Melting point
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The melting point of a solid is the temperature at which it changes state from solid to liquid at atmospheric pressure. At the melting point the solid and liquid phase exist in equilibrium, the melting point of a substance depends on pressure and is usually specified at standard pressure. When considered as the temperature of the change from liquid to solid. Because of the ability of some substances to supercool, the point is not considered as a characteristic property of a substance. For most substances, melting and freezing points are approximately equal, for example, the melting point and freezing point of mercury is 234.32 kelvins. However, certain substances possess differing solid-liquid transition temperatures, for example, agar melts at 85 °C and solidifies from 31 °C to 40 °C, such direction dependence is known as hysteresis. The melting point of ice at 1 atmosphere of pressure is close to 0 °C. In the presence of nucleating substances the freezing point of water is the same as the melting point, the chemical element with the highest melting point is tungsten, at 3687 K, this property makes tungsten excellent for use as filaments in light bulbs. Many laboratory techniques exist for the determination of melting points, a Kofler bench is a metal strip with a temperature gradient. Any substance can be placed on a section of the strip revealing its thermal behaviour at the temperature at that point, differential scanning calorimetry gives information on melting point together with its enthalpy of fusion. A basic melting point apparatus for the analysis of crystalline solids consists of an oil bath with a transparent window, the several grains of a solid are placed in a thin glass tube and partially immersed in the oil bath. The oil bath is heated and with the aid of the melting of the individual crystals at a certain temperature can be observed. In large/small devices, the sample is placed in a heating block, the measurement can also be made continuously with an operating process. For instance, oil refineries measure the point of diesel fuel online, meaning that the sample is taken from the process. This allows for more frequent measurements as the sample does not have to be manually collected, for refractory materials the extremely high melting point may be determined by heating the material in a black body furnace and measuring the black-body temperature with an optical pyrometer. For the highest melting materials, this may require extrapolation by several hundred degrees, the spectral radiance from an incandescent body is known to be a function of its temperature. An optical pyrometer matches the radiance of a body under study to the radiance of a source that has been previously calibrated as a function of temperature, in this way, the measurement of the absolute magnitude of the intensity of radiation is unnecessary. However, known temperatures must be used to determine the calibration of the pyrometer, for temperatures above the calibration range of the source, an extrapolation technique must be employed
2.
Caenorhabditis elegans
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Caenorhabditis elegans is a free-living, transparent nematode, about 1 mm in length, that lives in temperate soil environments. The name is a blend of the Greek caeno-, rhabditis, in 1900, Maupas initially named it Rhabditides elegans, Osche placed it in the subgenus Caenorhabditis in 1952, and in 1955, Dougherty raised it to the status of genus. C. elegans is an unsegmented pseudocoelomate, and lacks a respiratory and it possesses gut granules which emit a brilliant blue fluorescence, a wave of which is seen at death in a death fluorescence. The majority of these nematodes are hermaphrodites, males have specialised tails for mating that include spicules. In 1963, Sydney Brenner proposed research into C. elegans primarily in the area of neuronal development, in 1974, he began research into the molecular and developmental biology of C. elegans, which has since been extensively used as a model organism. C. elegans was the first multicellular organism to have its genome sequenced, and as of 2012. It is the species of its genus. C. elegans is unsegmented, vermiform, and bilaterally symmetrical and it has a cuticle, four main epidermal cords, and a fluid-filled pseudocoelom. It also has some of the organ systems as larger animals. About one in an individuals is male and the rest are hermaphrodites. The basic anatomy of C. elegans includes a mouth, pharynx, intestine, gonad, like all nematodes, they have neither a circulatory nor a respiratory system. When a wave of dorsal/ventral muscle contractions proceeds from the back to the front of the animal, when wave of contractions is initiated at the front and proceeds posteriorly along the body, the animal is propelled forwards. Because of this bias in body bends, any normal living, moving individual tends to lie on either its left side or its right side when observed crossing a horizontal surface. A set of ridges on the sides of the body cuticle. The pharynx is a muscular food pump in the head of C. elegans and this grinds food and transports it directly to the intestine. A set of valve cells connects the pharynx to the intestine, after digestion, the contents of the intestine are released via the rectum, as is the case with all other nematodes. No direct connection exists between the pharynx and the canal, which functions in the release of liquid urine. Males have a single-lobed gonad, a vas deferens, and a tail specialized for mating, hermaphrodites have two ovaries, oviducts, spermatheca, and a single uterus
3.
Drosophila melanogaster
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Drosophila melanogaster is a species of fly in the family Drosophilidae. The species is generally as the common fruit fly or vinegar fly. It is typically used because it is a species that is easy to care for, has four pairs of chromosomes, breeds quickly. D. melanogaster is a common pest in homes, restaurants, flies belonging to the family Tephritidae are also called fruit flies. This can cause confusion, especially in Australia and South Africa, the D. melanogaster lifespan is about 30 days at 29 °C. The developmental period for D. melanogaster varies with temperature, as with many ectothermic species, the shortest development time,7 days, is achieved at 28 °C. Development times increase at higher temperatures due to heat stress, under ideal conditions, the development time at 25 °C is 8.5 days, at 18 °C it takes 19 days and at 12 °C it takes over 50 days. Under crowded conditions, development time increases, while the emerging flies are smaller, females lay some 400 eggs, about five at a time, into rotting fruit or other suitable material such as decaying mushrooms and sap fluxes. The eggs, which are about 0.5 mm long, the resulting larvae grow for about 4 days while molting twice, at about 24 and 48 h after hatching. During this time, they feed on the microorganisms that decompose the fruit, the mother puts feces on the egg sacs to establish the same microbial composition in the larvaes guts which has worked positively for herself. Then the larvae encapsulate in the puparium and undergo a four-day-long metamorphosis, the female fruit fly prefers a shorter duration when it comes to sex. Males, on the hand, prefer it to last longer. Males perform a sequence of five behavioral patterns to court females, first, males orient themselves while playing a courtship song by horizontally extending and vibrating their wings. Soon after, the positions itself at the rear of the females abdomen in a low posture to tap. Finally, the male curls its abdomen and attempts copulation, females can reject males by moving away, kicking, and extruding their ovipositor. Copulation lasts around 15–20 minutes, during which males transfer a few hundred, females store the sperm in a tubular receptacle and in two mushroom-shaped spermathecae, sperm from multiple matings compete for fertilization. A last male precedence is believed to exist in which the last male to mate with a female sires about 80% of her offspring and this precedence was found to occur through both displacement and incapacitation. The displacement is attributed to sperm handling by the fly as multiple matings are conducted and is most significant during the first 1–2 days after copulation
4.
Yeast
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Yeasts are eukaryotic, single-celled microorganisms classified as members of the fungus kingdom. The yeast lineage originated hundreds of millions of years ago, and 1,500 species are currently identified and they are estimated to constitute 1% of all described fungal species. Yeast sizes vary greatly, depending on species and environment, typically measuring 3–4 µm in diameter, most yeasts reproduce asexually by mitosis, and many do so by the asymmetric division process known as budding. Yeasts, with their growth habit, can be contrasted with molds. Fungal species that can take both forms are called dimorphic fungi and it is also a centrally important model organism in modern cell biology research, and is one of the most thoroughly researched eukaryotic microorganisms. Researchers have used it to information about the biology of the eukaryotic cell. Other species of yeasts, such as Candida albicans, are opportunistic pathogens, yeasts have recently been used to generate electricity in microbial fuel cells, and produce ethanol for the biofuel industry. Yeasts do not form a taxonomic or phylogenetic grouping. The budding yeasts are classified in the order Saccharomycetales, within the phylum Ascomycota, the word yeast comes from Old English gist, gyst, and from the Indo-European root yes-, meaning boil, foam, or bubble. Yeast microbes are probably one of the earliest domesticated organisms, archaeologists digging in Egyptian ruins found early grinding stones and baking chambers for yeast-raised bread, as well as drawings of 4, 000-year-old bakeries and breweries. In 1680, Dutch naturalist Anton van Leeuwenhoek first microscopically observed yeast, but at the time did not consider them to be living organisms, researchers were doubtful whether yeasts were algae or fungi, but in 1837 Theodor Schwann recognized them as fungi. In 1857, French microbiologist Louis Pasteur proved in the paper Mémoire sur la fermentation alcoolique that alcoholic fermentation was conducted by living yeasts and not by a chemical catalyst. Pasteur showed that by bubbling oxygen into the yeast broth, cell growth could be increased, by the late 18th century, two yeast strains used in brewing had been identified, Saccharomyces cerevisiae and S. carlsbergensis. S. cerevisiae has been sold commercially by the Dutch for bread-making since 1780, while, around 1800, in 1825, a method was developed to remove the liquid so the yeast could be prepared as solid blocks. The industrial production of yeast blocks was enhanced by the introduction of the press in 1867. In 1872, Baron Max de Springer developed a process to create granulated yeast. Yeasts are chemoorganotrophs, as they use organic compounds as a source of energy, carbon is obtained mostly from hexose sugars, such as glucose and fructose, or disaccharides such as sucrose and maltose. Some species can metabolize pentose sugars such as ribose, alcohols, Yeast species either require oxygen for aerobic cellular respiration or are anaerobic, but also have aerobic methods of energy production
5.
Jmol
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Jmol is computer software for molecular modelling chemical structures in 3-dimensions. Jmol returns a 3D representation of a molecule that may be used as a teaching tool and it is written in the programming language Java, so it can run on the operating systems Windows, macOS, Linux, and Unix, if Java is installed. It is free and open-source software released under a GNU Lesser General Public License version 2.0, a standalone application and a software development kit exist that can be integrated into other Java applications, such as Bioclipse and Taverna. A popular feature is an applet that can be integrated into web pages to display molecules in a variety of ways, for example, molecules can be displayed as ball-and-stick models, space-filling models, ribbon diagrams, etc. Jmol supports a range of chemical file formats, including Protein Data Bank, Crystallographic Information File, MDL Molfile. There is also a JavaScript-only version, JSmol, that can be used on computers with no Java, the Jmol applet, among other abilities, offers an alternative to the Chime plug-in, which is no longer under active development. While Jmol has many features that Chime lacks, it does not claim to reproduce all Chime functions, most notably, Chime requires plug-in installation and Internet Explorer 6.0 or Firefox 2.0 on Microsoft Windows, or Netscape Communicator 4.8 on Mac OS9. Jmol requires Java installation and operates on a variety of platforms. For example, Jmol is fully functional in Mozilla Firefox, Internet Explorer, Opera, Google Chrome, fast and Scriptable Molecular Graphics in Web Browsers without Java3D
6.
RNA
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Ribonucleic acid is a polymeric molecule essential in various biological roles in coding, decoding, regulation, and expression of genes. RNA and DNA are nucleic acids, and, along with proteins and carbohydrates, like DNA, RNA is assembled as a chain of nucleotides, but unlike DNA it is more often found in nature as a single-strand folded onto itself, rather than a paired double-strand. Cellular organisms use messenger RNA to convey information that directs synthesis of specific proteins. Many viruses encode their genetic information using an RNA genome, some RNA molecules play an active role within cells by catalyzing biological reactions, controlling gene expression, or sensing and communicating responses to cellular signals. One of these processes is protein synthesis, a universal function where RNA molecules direct the assembly of proteins on ribosomes. This process uses transfer RNA molecules to deliver amino acids to the ribosome, analysis of these RNAs has revealed that they are highly structured. Unlike DNA, their structures do not consist of long double helices, in this fashion, RNAs can achieve chemical catalysis. For instance, determination of the structure of the enzyme that catalyzes peptide bond formation—revealed that its active site is composed entirely of RNA. Each nucleotide in RNA contains a sugar, with carbons numbered 1 through 5. A base is attached to the 1 position, in general, adenine, cytosine, guanine, adenine and guanine are purines, cytosine and uracil are pyrimidines. A phosphate group is attached to the 3 position of one ribose, the phosphate groups have a negative charge each, making RNA a charged molecule. The bases form hydrogen bonds between cytosine and guanine, between adenine and uracil and between guanine and uracil, however, other interactions are possible, such as a group of adenine bases binding to each other in a bulge, or the GNRA tetraloop that has a guanine–adenine base-pair. An important structural feature of RNA that distinguishes it from DNA is the presence of a group at the 2 position of the ribose sugar. The A-form geometry results in a deep and narrow major groove. RNA is transcribed with only four bases, but these bases, pseudouridine, in which the linkage between uracil and ribose is changed from a C–N bond to a C–C bond, and ribothymidine are found in various places. Another notable modified base is hypoxanthine, a deaminated adenine base whose nucleoside is called inosine, inosine plays a key role in the wobble hypothesis of the genetic code. The specific roles of many of these modifications in RNA are not fully understood, the functional form of single-stranded RNA molecules, just like proteins, frequently requires a specific tertiary structure. The scaffold for this structure is provided by secondary structural elements that are hydrogen bonds within the molecule and this leads to several recognizable domains of secondary structure like hairpin loops, bulges, and internal loops
7.
ATP synthase
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ATP synthase is an important enzyme that creates the energy storage molecule adenosine triphosphate. ATP is the most commonly used energy currency of cells for most organisms and it is formed from adenosine diphosphate and inorganic phosphate, and needs energy for its formation. Located within the membrane and the inner mitochondrial membrane, ATP synthase consists of two regions the FO portion embedded within the membrane. The F1 portion of the ATP synthase is outside the membrane, the nomenclature of the enzyme has a long history. These functional regions consist of different protein subunits — refer to tables, the F1 particle is large and can be seen in the transmission electron microscope by negative staining. These are particles of 9 nm diameter that pepper the inner mitochondrial membrane and this ATPase activity was further associated with the creation of ATP by a long series of experiments in many laboratories. The FO region of ATP synthase is a pore that is embedded in the mitochondrial membrane. It consists of three main subunits A, B, and C, and six additional subunits, d, e, f, g, F6, and 8. The research group of John E. Walker, then at the MRC Laboratory of Molecular Biology in Cambridge, the structure, at the time the largest asymmetric protein structure known, indicated that Boyers rotary-catalysis model was, in essence, correct. For elucidating this, Boyer and Walker shared half of the 1997 Nobel Prize in Chemistry, the crystal structure of the F1 showed alternating alpha and beta subunits, arranged like segments of an orange around a rotating asymmetrical gamma subunit. A portion of the FO rotates as the pass through the membrane. The major F1 subunits are prevented from rotating in sympathy with the central stalk rotor by a stalk that joins the alpha3beta3 to the non-rotating portion of FO. The structure of the intact ATP synthase is currently known at low-resolution from electron cryo-microscopy studies of the complex, the cryo-EM model of ATP synthase suggests that the peripheral stalk is a flexible structure that wraps around the complex as it joins F1 to FO. Under the right conditions, the reaction can also be carried out in reverse. The binding change mechanism involves the active site of a β subunits cycling between three states, in the open state, ADP and phosphate enter the active site, in the adjacent diagram, this is shown in red. The protein then closes up around the molecules and binds them loosely — the loose state, finally, the active site cycles back to the open state, releasing ATP and binding more ADP and phosphate, ready for the next cycle of ATP production. Like other enzymes, the activity of F1FO ATP synthase is reversible, the overall process of creating energy in this fashion is termed oxidative phosphorylation. The same process takes place in the mitochondria, where ATP synthase is located in the mitochondrial membrane
8.
Enzyme inhibitor
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An enzyme inhibitor is a molecule that binds to an enzyme and decreases its activity. Since blocking an enzymes activity can kill a pathogen or correct a metabolic imbalance and they are also used in pesticides. The binding of an inhibitor can stop a substrate from entering the active site and/or hinder the enzyme from catalyzing its reaction. Inhibitor binding is reversible or irreversible. Irreversible inhibitors usually react with the enzyme and change it chemically and these inhibitors modify key amino acid residues needed for enzymatic activity. In contrast, reversible inhibitors bind non-covalently and different types of inhibition are produced depending on whether these inhibitors bind to the enzyme, many drug molecules are enzyme inhibitors, so their discovery and improvement is an active area of research in biochemistry and pharmacology. A medicinal enzyme inhibitor is often judged by its specificity and its potency, a high specificity and potency ensure that a drug will have few side effects and thus low toxicity. Enzyme inhibitors also occur naturally and are involved in the regulation of metabolism, for example, enzymes in a metabolic pathway can be inhibited by downstream products. This type of negative feedback slows the production line when products begin to build up and is an important way to maintain homeostasis in a cell, other cellular enzyme inhibitors are proteins that specifically bind to and inhibit an enzyme target. This can help control enzymes that may be damaging to a cell, a well-characterised example of this is the ribonuclease inhibitor, which binds to ribonucleases in one of the tightest known protein–protein interactions. Natural enzyme inhibitors can also be poisons and are used as defences against predators or as ways of killing prey, reversible inhibitors attach to enzymes with non-covalent interactions such as hydrogen bonds, hydrophobic interactions and ionic bonds. Multiple weak bonds between the inhibitor and the active site combine to produce strong and specific binding, in contrast to substrates and irreversible inhibitors, reversible inhibitors generally do not undergo chemical reactions when bound to the enzyme and can be easily removed by dilution or dialysis. There are four kinds of reversible enzyme inhibitors and they are classified according to the effect of varying the concentration of the enzymes substrate on the inhibitor. In competitive inhibition, the substrate and inhibitor cannot bind to the enzyme at the same time, as shown in the figure on the right. This usually results from the inhibitor having an affinity for the site of an enzyme where the substrate also binds. This type of inhibition can be overcome by high concentrations of substrate. However, the apparent Km will increase as it takes a higher concentration of the substrate to reach the Km point, competitive inhibitors are often similar in structure to the real substrate. In uncompetitive inhibition, the inhibitor binds only to the substrate-enzyme complex and this type of inhibition causes Vmax to decrease and Km to decrease
9.
European Chemicals Agency
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ECHA is the driving force among regulatory authorities in implementing the EUs chemicals legislation. ECHA helps companies to comply with the legislation, advances the safe use of chemicals, provides information on chemicals and it is located in Helsinki, Finland. The Agency, headed by Executive Director Geert Dancet, started working on 1 June 2007, the REACH Regulation requires companies to provide information on the hazards, risks and safe use of chemical substances that they manufacture or import. Companies register this information with ECHA and it is freely available on their website. So far, thousands of the most hazardous and the most commonly used substances have been registered, the information is technical but gives detail on the impact of each chemical on people and the environment. This also gives European consumers the right to ask whether the goods they buy contain dangerous substances. The Classification, Labelling and Packaging Regulation introduces a globally harmonised system for classifying and labelling chemicals into the EU. This worldwide system makes it easier for workers and consumers to know the effects of chemicals, companies need to notify ECHA of the classification and labelling of their chemicals. So far, ECHA has received over 5 million notifications for more than 100000 substances, the information is freely available on their website. Consumers can check chemicals in the products they use, Biocidal products include, for example, insect repellents and disinfectants used in hospitals. The Biocidal Products Regulation ensures that there is information about these products so that consumers can use them safely. ECHA is responsible for implementing the regulation, the law on Prior Informed Consent sets guidelines for the export and import of hazardous chemicals. Through this mechanism, countries due to hazardous chemicals are informed in advance and have the possibility of rejecting their import. Substances that may have effects on human health and the environment are identified as Substances of Very High Concern 1. These are mainly substances which cause cancer, mutation or are toxic to reproduction as well as substances which persist in the body or the environment, other substances considered as SVHCs include, for example, endocrine disrupting chemicals. Companies manufacturing or importing articles containing these substances in a concentration above 0 and they are required to inform users about the presence of the substance and therefore how to use it safely. Consumers have the right to ask the retailer whether these substances are present in the products they buy, once a substance has been officially identified in the EU as being of very high concern, it will be added to a list. This list is available on ECHA’s website and shows consumers and industry which chemicals are identified as SVHCs, Substances placed on the Candidate List can then move to another list
10.
Boiling point
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The boiling point of a substance is the temperature at which the vapor pressure of the liquid equals the pressure surrounding the liquid and the liquid changes into a vapor. The boiling point of a liquid varies depending upon the environmental pressure. A liquid in a vacuum has a lower boiling point than when that liquid is at atmospheric pressure. A liquid at high pressure has a boiling point than when that liquid is at atmospheric pressure. For a given pressure, different liquids boil at different temperatures, for example, water boils at 100 °C at sea level, but at 93.4 °C at 2,000 metres altitude. The normal boiling point of a liquid is the case in which the vapor pressure of the liquid equals the defined atmospheric pressure at sea level,1 atmosphere. At that temperature, the pressure of the liquid becomes sufficient to overcome atmospheric pressure. The standard boiling point has been defined by IUPAC since 1982 as the temperature at which boiling occurs under a pressure of 1 bar, the heat of vaporization is the energy required to transform a given quantity of a substance from a liquid into a gas at a given pressure. Liquids may change to a vapor at temperatures below their boiling points through the process of evaporation, evaporation is a surface phenomenon in which molecules located near the liquids edge, not contained by enough liquid pressure on that side, escape into the surroundings as vapor. On the other hand, boiling is a process in which molecules anywhere in the liquid escape, a saturated liquid contains as much thermal energy as it can without boiling. The saturation temperature is the temperature for a corresponding saturation pressure at which a liquid boils into its vapor phase, the liquid can be said to be saturated with thermal energy. Any addition of energy results in a phase transition. If the pressure in a system remains constant, a vapor at saturation temperature will begin to condense into its liquid phase as thermal energy is removed, similarly, a liquid at saturation temperature and pressure will boil into its vapor phase as additional thermal energy is applied. The boiling point corresponds to the temperature at which the pressure of the liquid equals the surrounding environmental pressure. Thus, the point is dependent on the pressure. Boiling points may be published with respect to the NIST, USA standard pressure of 101.325 kPa, at higher elevations, where the atmospheric pressure is much lower, the boiling point is also lower. The boiling point increases with increased pressure up to the critical point, the boiling point cannot be increased beyond the critical point. Likewise, the point decreases with decreasing pressure until the triple point is reached
11.
Phosphoric acid
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Phosphoric acid is a mineral acid having the chemical formula H3PO4. Orthophosphoric acid refers to acid, which is the IUPAC name for this compound. The prefix ortho is used to distinguish the acid from related phosphoric acids, orthophosphoric acid is a non-toxic acid, which, when pure, is a solid at room temperature and pressure. The conjugate base of phosphoric acid is the phosphate ion, H 2PO−4, which in turn has a conjugate base of hydrogen phosphate, HPO2−4. Phosphates are nutritious for all forms of life, Phosphoric acids and phosphates are also important in biology. The most common source of acid is an 85% aqueous solution, such solutions are colourless, odourless. The 85% solution is a liquid, but still pourable. Although phosphoric acid does not meet the definition of a strong acid. Because of the percentage of phosphoric acid in this reagent. For the sake of labeling and simplicity, the 85% represents H3PO4 as if it were all orthophosphoric acid, dilute aqueous solutions of phosphoric acid exist in the ortho- form. Orthophosphoric acid molecules can combine with themselves to form a variety of compounds which are referred to as phosphoric acids. Anhydrous phosphoric acid, a low melting solid, is obtained by dehydration of 85% phosphoric acid by heating under a vacuum. The anion after the second dissociation, HPO2−4, is the phosphate anion. The anion after the third dissociation, PO3−4, is the phosphate or orthophosphate anion, for each of the dissociation reactions shown above, there is a separate acid dissociation constant, called Ka1, Ka2, and Ka3 given at 25 °C. Associated with these three dissociation constants are corresponding pKa1=2.12, pKa2=7.21, and pKa3=12.67 values at 25 °C, similarly, the non-toxic, anion salts of triprotic organic citric acid are also often used to make buffers. Phosphates are found pervasively in biology, especially in the derived from phosphorylated sugars, such as DNA, RNA. There is an article on phosphate as an anion or its salts. Upon heating orthophosphoric acid, condensation of the units can be induced by driving off the water formed from condensation
12.
Nucleotide
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Nucleotides are organic molecules that serve as the monomer units for forming the nucleic acid polymers DNA and RNA, both of which are essential biomolecules in all life-forms on Earth. Nucleotides are the blocks of nucleic acids, they are composed of three subunit molecules, a nitrogenous base, a five-carbon sugar, and at least one phosphate group. They are also known as phosphate nucleotides, a nucleoside is a nitrogenuous base and a 5-carbon sugar. Thus a nucleoside plus a group yields a nucleotide. Nucleotides also play a role in life-form metabolism at the fundamental. In addition, nucleotides participate in signaling, and are incorporated into important cofactors of enzymatic reactions. In experimental biochemistry, nucleotides can be radiolabeled with radionuclides to yield radionucleotides, a nucleotide is composed of three distinctive chemical sub-units, a five-carbon sugar molecule, a nitrogenous base—which two together are called a nucleoside—and one phosphate group. With all three joined, a nucleotide is also termed a nucleoside monophosphate, thus, the terms nucleoside diphosphate or nucleoside triphosphate may also indicate nucleotides. Nucleotides contain either a purine or a pyrimidine base—i. e, the nitrogenous base molecule, also known as a nucleobase—and are termed ribonucleotides if the sugar is ribose, or deoxyribonucleotides if the sugar is deoxyribose. These chain-joins of sugar and phosphate molecules create a backbone strand for a single- or double helix, in any one strand, the chemical orientation of the chain-joins runs from the 5-end to the 3-end —referring to the five carbon sites on sugar molecules in adjacent nucleotides. Unlike in nucleic acid nucleotides, singular cyclic nucleotides are formed when the group is bound twice to the same sugar molecule. These individual nucleotides function in cell metabolism rather than the nucleic acid structures of long-chain molecules, nucleic acids then are polymeric macromolecules assembled from nucleotides, the monomer-units of nucleic acids. The purine bases adenine and guanine and pyrimidine base cytosine occur in both DNA and RNA, while the pyrimidine bases thymine and uracil in just one, adenine forms a base pair with thymine with two hydrogen bonds, while guanine pairs with cytosine with three hydrogen bonds. Nucleotides can be synthesized by a variety of both in vitro and in vivo. In vivo, nucleotides can be synthesized de novo or recycled through salvage pathways, the components used in de novo nucleotide synthesis are derived from biosynthetic precursors of carbohydrate and amino acid metabolism, and from ammonia and carbon dioxide. The liver is the organ of de novo synthesis of all four nucleotides. De novo synthesis of pyrimidines and purines follows two different pathways, purines, however, are first synthesized from the sugar template onto which the ring synthesis occurs. For reference, the syntheses of the purine and pyrimidine nucleotides are carried out by several enzymes in the cytoplasm of the cell, nucleotides undergo breakdown such that useful parts can be reused in synthesis reactions to create new nucleotides
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