1.
Chemical reaction
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A chemical reaction is a process that leads to the transformation of one set of chemical substances to another. Nuclear chemistry is a sub-discipline of chemistry that involves the reactions of unstable. The substance initially involved in a reaction are called reactants or reagents. Chemical reactions are characterized by a chemical change, and they yield one or more products. Reactions often consist of a sequence of individual sub-steps, the elementary reactions. Chemical reactions are described with chemical equations, which present the starting materials, end products. Chemical reactions happen at a characteristic reaction rate at a given temperature, typically, reaction rates increase with increasing temperature because there is more thermal energy available to reach the activation energy necessary for breaking bonds between atoms. Reactions may proceed in the forward or reverse direction until they go to completion or reach equilibrium, Reactions that proceed in the forward direction to approach equilibrium are often described as spontaneous, requiring no input of free energy to go forward. Non-spontaneous reactions require input of energy to go forward. Different chemical reactions are used in combinations during chemical synthesis in order to obtain a desired product, in biochemistry, a consecutive series of chemical reactions form metabolic pathways. These reactions are catalyzed by protein enzymes. Chemical reactions such as combustion in fire, fermentation and the reduction of ores to metals were known since antiquity, in the Middle Ages, chemical transformations were studied by Alchemists. They attempted, in particular, to lead into gold, for which purpose they used reactions of lead. The process involved heating of sulfate and nitrate minerals such as sulfate, alum. In the 17th century, Johann Rudolph Glauber produced hydrochloric acid and sodium sulfate by reacting sulfuric acid, further optimization of sulfuric acid technology resulted in the contact process in the 1880s, and the Haber process was developed in 1909–1910 for ammonia synthesis. From the 16th century, researchers including Jan Baptist van Helmont, Robert Boyle, the phlogiston theory was proposed in 1667 by Johann Joachim Becher. It postulated the existence of an element called phlogiston, which was contained within combustible bodies. This proved to be false in 1785 by Antoine Lavoisier who found the explanation of the combustion as reaction with oxygen from the air
2.
Metal
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A metal is a material that is typically hard, opaque, shiny, and has good electrical and thermal conductivity. Metals are generally malleable—that is, they can be hammered or pressed permanently out of shape without breaking or cracking—as well as fusible and ductile, about 91 of the 118 elements in the periodic table are metals, the others are nonmetals or metalloids. Some elements appear in both metallic and non-metallic forms, astrophysicists use the term metal to collectively describe all elements other than hydrogen and helium, the simplest two, in a star. The star fuses smaller atoms, mostly hydrogen and helium, to larger ones over its lifetime. In that sense, the metallicity of an object is the proportion of its matter made up of all chemical elements. Many elements and compounds that are not normally classified as metals become metallic under high pressures, the atoms of metallic substances are typically arranged in one of three common crystal structures, namely body-centered cubic, face-centered cubic, and hexagonal close-packed. In bcc, each atom is positioned at the center of a cube of eight others, in fcc and hcp, each atom is surrounded by twelve others, but the stacking of the layers differs. Some metals adopt different structures depending on the temperature, atoms of metals readily lose their outer shell electrons, resulting in a free flowing cloud of electrons within their otherwise solid arrangement. This provides the ability of metallic substances to easily transmit heat, while this flow of electrons occurs, the solid characteristic of the metal is produced by electrostatic interactions between each atom and the electron cloud. This type of bond is called a metallic bond, Metals are usually inclined to form cations through electron loss, reacting with oxygen in the air to form oxides over various timescales. Examples,4 Na + O2 →2 Na2O2 Ca + O2 →2 CaO4 Al +3 O2 →2 Al2O3, the transition metals are slower to oxidize because they form a passivating layer of oxide that protects the interior. Others, like palladium, platinum and gold, do not react with the atmosphere at all, some metals form a barrier layer of oxide on their surface which cannot be penetrated by further oxygen molecules and thus retain their shiny appearance and good conductivity for many decades. The oxides of metals are generally basic, as opposed to those of nonmetals, exceptions are largely oxides with very high oxidation states such as CrO3, Mn2O7, and OsO4, which have strictly acidic reactions. Painting, anodizing or plating metals are good ways to prevent their corrosion, however, a more reactive metal in the electrochemical series must be chosen for coating, especially when chipping of the coating is expected. Water and the two form an electrochemical cell, and if the coating is less reactive than the coatee. Metals in general have high conductivity, high thermal conductivity. Typically they are malleable and ductile, deforming under stress without cleaving, in terms of optical properties, metals are shiny and lustrous. Sheets of metal beyond a few micrometres in thickness appear opaque, although most metals have higher densities than most nonmetals, there is wide variation in their densities, lithium being the least dense solid element and osmium the densest
3.
Ribonucleotide reductase
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Ribonucleotide reductase, also known as ribonucleoside diphosphate reductase, is an enzyme that catalyzes the formation of deoxyribonucleotides from ribonucleotides. Deoxyribonucleotides in turn are used in the synthesis of DNA, the reaction catalyzed by RNR is strictly conserved in all living organisms. Furthermore, RNR plays a role in regulating the total rate of DNA synthesis so that DNA to cell mass is maintained at a constant ratio during cell division. A somewhat unusual feature of the RNR enzyme is that it catalyzes a reaction proceeds via a free radical mechanism of action. The substrates for RNR are ADP, GDP, CDP and UDP. dTDP is synthesized by another enzyme from dTMP, the iron-dependent enzyme, ribonucleotide reductase, is essential for DNA synthesis. Class I RNR enzymes are constructed from large RNR1 and small RNR2 subunits which associate to form a heterodimeric tetramer. Since the enzyme catalyses the de novo synthesis of deoxyribonucleotides, precursors to DNA synthesis, in Pfam, the second domain has been interpreted as two separate domains, a shorter all-alpha N-terminal domain, and a longer barrel C-terminal domain. RNR2 contains an iron center and a stable tyrosyl radical. In E. coli, the radical is located at position 122 providing the stable radical for the Class I RNR2 subunits. In A. aegypti, this radical is located at position 184. The tyrosyl radical is deeply buried inside the protein in a hydrophobic environment, the structure of two μ-oxo-linked irons is dominated by ligands that serve as iron binding sites, four carboxylates and two histidines. Association occurs between the C-terminus of RNR2 and the C-terminus of RNR1, enzymatic activity is dependent on association of the RNR1 and RNR2 subunits. The active site consists of the active groups from the RNR1 as well as the diferric center. Other residues of RNR2, such as aspartate, tryptophan, and these residues help in the transfer of the radical electron from tyrosine of RNR2 to cysteine of RNR1. The electron transfer begins on RNR2 tyrosine and continues in RNR2 to tryptophan, electron transfer from RNR2 to RNR1 occurs via tyrosine and continues on through tyrosine to cysteine in the active site. Site-directed mutations of the RNR primary structure indicate that all residues cited above participate in the long distance transfer of the radical to the active site. The enzyme ribonucleotide reductase catalyzes the de novo synthesis of dNDPs, catalysis of ribonucleoside 5’-diphosphates involves a reduction at the 2’-carbon of ribose 5-phosphate to form the 2’-deoxy derivative-reduced 2’-deoxyribonucleoside 5’-diphosphates. This reduction is initiated with the generation of a free radical, following a single reduction, RNR requires electrons donated from the dithiol groups of the protein thioredoxin
4.
Arsenic
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Arsenic is a chemical element with symbol As and atomic number 33. Arsenic occurs in minerals, usually in combination with sulfur and metals. It has various allotropes, but only the form is important to industry. The primary use of arsenic is in alloys of lead. Arsenic is a common dopant in semiconductor electronic devices. Arsenic and its compounds, especially the trioxide, are used in the production of pesticides, treated wood products, herbicides, a few species of bacteria are able to use arsenic compounds as respiratory metabolites. Trace quantities of arsenic are a dietary element in rats, hamsters, goats, chickens. However, arsenic poisoning occurs in multicellular life if quantities are larger than needed, Arsenic contamination of groundwater is a problem that affects millions of people across the world. The three most common allotropes are metallic gray, yellow, and black arsenic, with gray being the most common. Gray arsenic adopts a structure consisting of many interlocked, ruffled, six-membered rings. Because of weak bonding between the layers, gray arsenic is brittle and has a relatively low Mohs hardness of 3.5. Nearest and next-nearest neighbors form an octahedral complex, with the three atoms in the same double-layer being slightly closer than the three atoms in the next. This relatively close packing leads to a density of 5.73 g/cm3. Gray arsenic is a semimetal, but becomes a semiconductor with a bandgap of 1. 2–1.4 eV if amorphized, gray arsenic is also the most stable form. Yellow arsenic is soft and waxy, and somewhat similar to tetraphosphorus, both have four atoms arranged in a tetrahedral structure in which each atom is bound to each of the other three atoms by a single bond. This unstable allotrope, being molecular, is the most volatile, least dense, solid yellow arsenic is produced by rapid cooling of arsenic vapor, As 4. It is rapidly transformed into gray arsenic by light, the yellow form has a density of 1.97 g/cm3. Black arsenic is similar in structure to red phosphorus, black arsenic can also be formed by cooling vapor at around 100–220 °C
5.
Catalysis
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Catalysis is the increase in the rate of a chemical reaction due to the participation of an additional substance called a catalyst. In most cases, reactions occur faster with a catalyst because they require less activation energy, furthermore, since they are not consumed in the catalyzed reaction, catalysts can continue to act repeatedly. Often only tiny amounts are required in principle, in the presence of a catalyst, less free energy is required to reach the transition state, but the total free energy from reactants to products does not change. A catalyst may participate in multiple chemical transformations, the effect of a catalyst may vary due to the presence of other substances known as inhibitors or poisons or promoters. Catalyzed reactions have an activation energy than the corresponding uncatalyzed reaction, resulting in a higher reaction rate at the same temperature. However, the mechanics of catalysis is complex. Usually, the catalyst participates in this slowest step, and rates are limited by amount of catalyst, in heterogeneous catalysis, the diffusion of reagents to the surface and diffusion of products from the surface can be rate determining. A nanomaterial-based catalyst is an example of a heterogeneous catalyst, analogous events associated with substrate binding and product dissociation apply to homogeneous catalysts. Although catalysts are not consumed by the reaction itself, they may be inhibited, deactivated, in heterogeneous catalysis, typical secondary processes include coking where the catalyst becomes covered by polymeric side products. Additionally, heterogeneous catalysts can dissolve into the solution in a system or sublimate in a solid–gas system. The production of most industrially important chemicals involves catalysis, similarly, most biochemically significant processes are catalysed. Research into catalysis is a field in applied science and involves many areas of chemistry, notably organometallic chemistry. Catalysis is relevant to aspects of environmental science, e. g. the catalytic converter in automobiles. Many transition metals and transition metal complexes are used in catalysis as well, Catalysts called enzymes are important in biology. A catalyst works by providing a reaction pathway to the reaction product. The rate of the reaction is increased as this route has a lower activation energy than the reaction route not mediated by the catalyst. The disproportionation of hydrogen peroxide creates water and oxygen, as shown below,2 H2O2 →2 H2O + O2 This reaction is preferable in the sense that the reaction products are more stable than the starting material, though the uncatalysed reaction is slow. In fact, the decomposition of hydrogen peroxide is so slow that hydrogen peroxide solutions are commercially available and this reaction is strongly affected by catalysts such as manganese dioxide, or the enzyme peroxidase in organisms
6.
Nitrogenase
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Nitrogenases are enzymes that are produced by certain bacteria, such as cyanobacteria. These enzymes are responsible for the reduction of nitrogen to ammonia, nitrogenases are the only family of enzymes known to catalyze this reaction, which is a key step in the process of nitrogen fixation. Nitrogen fixation is required for all forms of life, with nitrogen being essential for the biosynthesis of molecules that create plants, animals, the equilibrium formation of ammonia from molecular hydrogen and nitrogen has an overall negative enthalpy of reaction, the activation energy is very high. Nitrogenase acts as a catalyst, reducing this energy barrier such that the reaction can take place at ambient temperatures, the nitrogenase complex consists of two proteins, The homodimeric Fe protein, a reductase which has a high reducing power and is responsible for the supply of electrons. The heterotetrameric MoFe protein, a nitrogenase which uses the electrons provided to reduce N2 to NH3, the Fe protein is a dimer of identical subunits which contains one cluster and weighs approximately 60-64kDa. The function of the Fe protein is to transfer electrons from a reducing agent, the transfer of electrons requires an input of chemical energy which comes from the binding and hydrolysis of ATP. The hydrolysis of ATP also causes a change within the nitrogenase complex, bringing the Fe protein. The MoFe protein is a heterotetramer consisting of two α subunits and two β subunits, weighing approximately 240-250kDa. The MoFe protein also contains two clusters, known as P-clusters, located at the interface between the α and β subunits and two FeMo cofactors, within the α subunits. The core of the P-cluster takes the form of two linked by a central sulfur atom. Each P-cluster is covalently linked to the MoFe protein by six cysteine residues, each FeMo cofactor consists of two non-identical clusters, and, which are linked by three sulfide ions. Each FeMo cofactor is covalently linked to the α subunit of the protein by one cysteine residue, electrons from the Fe protein enter the MoFe protein at the P-clusters, which then transfer the electrons to the FeMo cofactors. Each FeMo cofactor then acts as a site for nitrogen fixation, nitrogenase is an enzyme responsible for catalyzing nitrogen fixation, which is the reduction of nitrogen to ammonia and a process vital to sustaining life on Earth. There are three types of nitrogenase found in various nitrogen-fixing bacteria, molybdenum nitrogenase, vanadium nitrogenase, molybdenum nitrogenase, which can be found in diazotrophs and legumes, is the nitrogenase that has been studied the most extensively and thus is the most well characterized. Figures 1-2 display the structure and key catalytic components of molybdenum nitrogenase extracted from Azotobacter vinelandii. Vanadium nitrogenase and iron-only nitrogenase can both be found in species of Azotobacter as an alternative nitrogenase. Equations 1 and 2 show the reactions of nitrogen fixation in molybdenum nitrogenase. Component I is a MoFe protein in molybdenum nitrogenase, a VFe protein in vanadium nitrogenase, Component II is a Fe protein that contains the Fe-S cluster, which transfers electrons to Component I
7.
Isopenicillin N synthase
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Isopenicillin N synthase is a non-heme iron-dependent enzyme belonging to the oxidoreductase family. This enzyme catalyzes the formation of isopenicillin N from δ--L-cysteinyl-D-valine, N--L-cysteinyl-D-valine + O2 ⇌ isopenicillin N +2 H2O This reaction is a key step in the biosynthesis of penicillin and cephalosporin antibiotics. The active sites of most isopenicillin N synthases contain an iron ion and this enzyme is also called isopenicillin N synthetase. Just two histidine residues and one aspartic acid residue are entirely conserved, therefore, it is highly significant that these two histidine residues, His214 and His270, and one aspartic acid residue, Asp216, are precisely the ones essential for activity. When ACV binds the active site, Gln330 and one water molecule are replaced by the ACV thiolate, the linear tripeptide δ--L-cysteinyl-D-valine must first be assembled from its component amino acids by N--L-cysteinyl-D-valine synthase. This allows for the binding of the substrate ACV to the thiol group of the cysteine residue. This ligation of the thiolate to the iron center anchors the ACV within the active site, the ligation of ACV results in a reduction of the FeI/FeII redox potential. This allows dioxygen to bind, which changes the oxidation state, an intramolecular hydrogen transfer takes place from C-3 of the cysteine residue, taking the iron back to the +II state. A thioaldehyde and a ligand are produced in this process. The hydroperoxy ligand deprotonates the amide which then closes the ring by a nucleophilic attack at the thioaldehyde carbon. This causes the hydrogen atom at the C-3 of the residue to come closer to the iron oxo ligand which is highly electrophilic. A second hydrogen transfer occurs, most likely producing an isopropyl radical which closes the ring by attacking the thiolate sulfur atom. This shows how IPNS occupies an early and key role in the pathway of all of the penicillins and cephalosporins. This class of antibiotics is the most widely used and they act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls, which is especially important in Gram-positive organisms. They will not work for infections caused by viruses, such as colds or the flu
8.
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
9.
Xanthine oxidase
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Xanthine oxidase is a form of xanthine oxidoreductase, a type of enzyme that generates reactive oxygen species. These enzymes catalyze the oxidation of hypoxanthine to xanthine and can catalyze the oxidation of xanthine to uric acid. These enzymes play an important role in the catabolism of purines in some species, Xanthine oxidase is defined as an enzyme activity. The same protein, which in humans has the HGNC approved gene symbol XDH, for example, it efficiently converts 1-methylxanthine to 1-methyluric acid, but has little activity on 3-methylxanthine. Under some circumstances it can produce superoxide ion RH + H2O +2 O2 ⇌ ROH +2 O2− +2 H+. Because XO is an enzyme, with general low specificity, it can be combined with other compounds and enzymes and create reactive oxidants. XO has also found to produce the strong one-electron oxidant carbonate radical anion from oxidation with acetaldehyde in the presence of catalase. It was suggested that the radical was likely produced in one of the enzymes redox centers with a peroxymonocarbonate intermediate. Here is a diagram highlighting the pathways catalyzed by xanthine oxidase, the protein is large, having a molecular weight of 270 kDa, and has 2 flavin molecules,2 molybdenum atoms, and 8 iron atoms bound per enzymatic unit. The molybdenum atoms are contained as molybdopterin cofactors and are the sites of the enzyme. The iron atoms are part of ferredoxin iron-sulfur clusters and participate in electron transfer reactions, the active site of XO is composed of a molybdopterin unit with the molybdenum atom also coordinated by terminal oxygen, sulfur atoms and a terminal hydroxide. In the reaction with xanthine to uric acid, an oxygen atom is transferred from molybdenum to xanthine. The reformation of the molybdenum center occurs by the addition of water. Like other known molybdenum-containing oxidoreductases, the oxygen atom introduced to the substrate by XO originates from water rather than from dioxygen, Xanthine oxidase is a superoxide-producing enzyme found normally in serum and the lungs, and its activity is increased during influenza A infection. During severe liver damage, xanthine oxidase is released into the blood, because xanthine oxidase is a metabolic pathway for uric acid formation, the xanthine oxidase inhibitor allopurinol is used in the treatment of gout. Since xanthine oxidase is involved in the metabolism of 6-mercaptopurine, caution should be taken before administering allopurinol and 6-mercaptopurine, or its prodrug azathioprine, in conjunction. Xanthinuria is a genetic disorder where the lack of xanthine oxidase leads to high concentration of xanthine in blood. There is no treatment, sufferers are advised by doctors to avoid foods high in purine
10.
Glutaredoxin
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Glutaredoxins are small redox enzymes of approximately one hundred amino-acid residues that use glutathione as a cofactor. Glutaredoxins are oxidized by substrates, and reduced non-enzymatically by glutathione, in contrast to thioredoxins, which are reduced by thioredoxin reductase, no oxidoreductase exists that specifically reduces glutaredoxins. Instead, glutaredoxins are reduced by the oxidation of glutathione, oxidized glutathione is then regenerated by glutathione reductase. Together these components compose the glutathione system, like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulfide bond. It exists in either a reduced or a form where the two cysteine residues are linked in an intramolecular disulfide bond. Glutaredoxins function as carriers in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Moreover, GRX act in antioxidant defence by reducing dehydroascorbate, peroxiredoxins, beside their function in antioxidant defence, bacterial and plant GRX were shown to bind iron-sulfur clusters and to deliver the cluster to enzymes on demand. Glutaredoxin has been sequenced in a variety of species, on the basis of extensive sequence similarity, it has been proposed that Vaccinia virus protein O2L is, it seems, a glutaredoxin. Bacteriophage T4 thioredoxin seems to be evolution-related, in position 5 of the pattern T4, thioredoxin has Val instead of Pro. Approximately 30 GRX isoforms are described in the model plant Arabidopsis thaliana and 48 in Oryza sativa L, according to their redox-active centre, they are subgrouped in six classes of the CSY-, CGFS-, CC-type and 3 groups with additional domain of unknown function. The CC-type GRXs are only found in higher plants, in Arabidopsis GRXs are involved in flower development and Salicylic acid signalling. Glutaredoxin subgroup InterPro, IPR014025 GLRX, GLRX2, GLRX3, GLRX5, PTGES2 Enzyme database entry Glutaredoxins at the US National Library of Medicine Medical Subject Headings
. PMID 11752431.
