1.
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
2.
Isomer
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An isomer is a molecule with the same molecular formula as another molecule, but with a different chemical structure. That is, isomers contain the number of atoms of each element. Isomers do not necessarily share similar properties, unless they also have the functional groups. There are two forms of isomerism, structural isomerism and stereoisomerism. In structural isomers, sometimes referred to as constitutional isomers, the atoms, Structural isomers have different IUPAC names and may or may not belong to the same functional group. For example, two position isomers would be 2-fluoropropane and 1-fluoropropane, illustrated on the side of the diagram above. In skeletal isomers the main chain is different between the two isomers. This type of isomerism is most identifiable in secondary and tertiary alcohol isomers, tautomers are structural isomers that spontaneously interconvert with each other, even when pure. They have different chemical properties and, as a consequence, distinct reactions characteristic to each form are observed, if the interconversion reaction is fast enough, tautomers cannot be isolated from each other. An example is when they differ by the position of a proton, such as in keto/enol tautomerism, there is, however, another isomer of C3H8O that has significantly different properties, methoxyethane. Unlike the isomers of propanol, methoxyethane has an oxygen connected to two carbons rather than to one carbon and one hydrogen. Methoxyethane is an ether, not an alcohol, because it lacks a hydroxyl group, propadiene and propyne are examples of isomers containing different bond types. Propadiene contains two double bonds, whereas propyne contains one triple bond, in stereoisomers the bond structure is the same, but the geometrical positioning of atoms and functional groups in space differs. This class includes enantiomers which are non-superposable mirror-images of each other, and diastereomers, enantiomers always contain chiral centers and diastereomers often do, but there are some diastereomers that neither are chiral nor contain chiral centers. Another type of isomer, conformational isomers, may be rotamers, diastereomers, for example, ortho- position-locked biphenyl systems have enantiomers. E/Z isomers, which have restricted rotation at a bond, are configurational isomers. They are classified as diastereomers, whether or not they contain any chiral centers, e/Z notation depicts absolute stereochemistry, which is an unambiguous descriptor based on CIP priorities. Cis–trans isomers are used to describe any molecules with restricted rotation in the molecule, for molecules with C=C double bonds, these descriptors describe relative stereochemistry only based on group bulkiness or principal carbon chain, and so can be ambiguous
3.
Chemical formula
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These are limited to a single typographic line of symbols, which may include subscripts and superscripts. A chemical formula is not a name, and it contains no words. Although a chemical formula may imply certain simple chemical structures, it is not the same as a full chemical structural formula. Chemical formulas can fully specify the structure of only the simplest of molecules and chemical substances, the simplest types of chemical formulas are called empirical formulas, which use letters and numbers indicating the numerical proportions of atoms of each type. Molecular formulas indicate the numbers of each type of atom in a molecule. For example, the formula for glucose is CH2O, while its molecular formula is C6H12O6. This is possible if the relevant bonding is easy to show in one dimension, an example is the condensed molecular/chemical formula for ethanol, which is CH3-CH2-OH or CH3CH2OH. For reasons of structural complexity, there is no condensed chemical formula that specifies glucose, chemical formulas may be used in chemical equations to describe chemical reactions and other chemical transformations, such as the dissolving of ionic compounds into solution. A chemical formula identifies each constituent element by its chemical symbol, in empirical formulas, these proportions begin with a key element and then assign numbers of atoms of the other elements in the compound, as ratios to the key element. For molecular compounds, these numbers can all be expressed as whole numbers. For example, the formula of ethanol may be written C2H6O because the molecules of ethanol all contain two carbon atoms, six hydrogen atoms, and one oxygen atom. Some types of compounds, however, cannot be written with entirely whole-number empirical formulas. An example is boron carbide, whose formula of CBn is a variable non-whole number ratio with n ranging from over 4 to more than 6.5. When the chemical compound of the consists of simple molecules. These types of formulas are known as molecular formulas and condensed formulas. A molecular formula enumerates the number of atoms to reflect those in the molecule, so that the formula for glucose is C6H12O6 rather than the glucose empirical formula. However, except for very simple substances, molecular chemical formulas lack needed structural information, for simple molecules, a condensed formula is a type of chemical formula that may fully imply a correct structural formula. For example, ethanol may be represented by the chemical formula CH3CH2OH
4.
Glycolysis
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Glycolysis is the metabolic pathway that converts glucose C6H12O6, into pyruvate, CH3COCOO− + H+. The free energy released in this process is used to form the high-energy molecules ATP, glycolysis is a determined sequence of ten enzyme-catalyzed reactions. The intermediates provide entry points to glycolysis, for example, most monosaccharides, such as fructose and galactose, can be converted to one of these intermediates. The intermediates may also be directly useful, for example, the intermediate dihydroxyacetone phosphate is a source of the glycerol that combines with fatty acids to form fat. Glycolysis is an oxygen independent metabolic pathway, meaning that it not use molecular oxygen for any of its reactions. However the products of glycolysis are sometimes metabolized using atmospheric oxygen, when molecular oxygen is used for the metabolism of the products of glycolysis the process is usually referred to as aerobic, whereas if no oxygen is used the process is said to be anaerobic. Thus, glycolysis occurs, with variations, in all organisms. The wide occurrence of glycolysis indicates that it is one of the most ancient metabolic pathways, glycolysis could thus have originated from chemical constraints of the prebiotic world. Glycolysis occurs in most organisms in the cytosol of the cell, the most common type of glycolysis is the Embden–Meyerhof–Parnas, which was discovered by Gustav Embden, Otto Meyerhof, and Jakub Karol Parnas. Glycolysis also refers to other pathways, such as the Entner–Doudoroff pathway, however, the discussion here will be limited to the Embden–Meyerhof–Parnas pathway. The overall reaction of glycolysis is, The use of symbols in this equation makes it appear unbalanced with respect to oxygen atoms, hydrogen atoms, and charges. In the cellular environment, all three groups of ADP dissociate into −O− and H+, giving ADP3−, and this ion tends to exist in an ionic bond with Mg2+. ATP behaves identically except that it has four groups, giving ATPMg2−. When these differences along with the charges on the two phosphate groups are considered together, the net charges of −4 on each side are balanced. For simple fermentations, the metabolism of one molecule of glucose to two molecules of pyruvate has a net yield of two molecules of ATP, most cells will then carry out further reactions to repay the used NAD+ and produce a final product of ethanol or lactic acid. Many bacteria use inorganic compounds as hydrogen acceptors to regenerate the NAD+, cells performing aerobic respiration synthesize much more ATP, but not as part of glycolysis. These further aerobic reactions use pyruvate and NADH + H+ from glycolysis, the pathway of glycolysis as it is known today took almost 100 years to fully discover. The combined results of many experiments were required in order to understand the pathway as a whole
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.
Structural isomer
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Structural isomerism, or constitutional isomerism, is a form of isomerism in which molecules with the same molecular formula have bonded together in different orders, as opposed to stereoisomerism. There are multiple synonyms for constitutional isomers, three categories of constitutional isomers are skeletal, positional, and functional isomers. Positional isomers are also called regioisomers, in chain isomerism, or skeletal isomerism, components of the skeleton are distinctly re-ordered to create different structures. Pentane exists as three isomers, n-pentane, isopentane and neopentane, in position isomerism a functional group or other substituent changes position on a parent structure. In the table below, the group can occupy three different positions on an n-pentane chain forming three different compounds. Many aromatic isomers exist because substituents can be positioned on different parts of the benzene ring, only one isomer of phenol or hydroxybenzene exists but cresol or methylphenol has three isomers where the additional methyl group can be placed on three different positions on the ring. Xylenol has one group and two methyl groups and a total of 6 isomers exist. Functional isomers are structural isomers that have the molecular formula. These groups of atoms are called groups, functionalities. Another way to say this is that two compounds with the molecular formula, but different functional groups, are functional isomers. For example, cyclohexane and 1-hexene both have the formula C6H12 and these two are considered functional group isomers because cyclohexane is a cycloalkane and hex-1-ene is an alkene. For two molecules to be functional isomers, they must contain key groups of atoms arranged in particular ways, some of the best examples come from organic chemistry. Depending on how the atoms are arranged, it can represent two different compounds dimethyl ether CH3-O-CH3 or ethanol CH3CH2-O-H, dimethyl ether and ethanol are functional isomers. The carbon chain-oxygen-carbon chain functionality is called an ether, the carbon chain-oxygen-hydrogen functionality is called an alcohol. If the functionalities stay the same, but their locations change, 1-Propanol and 2-propanol are structural isomers, but they are not functional isomers. The functional group is present in both of these compounds, but they are not the same, while some chemists use the terms structural isomer and functional isomer interchangeably, not all structural isomers are functional isomers. Functional isomers are most often identified in chemistry using infrared spectroscopy, infrared radiation corresponds to the energies associated primarily with molecular vibration. The alcohol functionality has a very distinct vibration called OH-stretch that is due to hydrogen bonding, all alcohols in liquid and solid form absorb infrared radiation at certain wavelengths
7.
Stereoisomerism
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Stereoisomers are isomeric molecules that have the same molecular formula and sequence of bonded atoms, but differ in the three-dimensional orientations of their atoms in space. This contrasts with structural isomers, which share the same molecular formula, by definition, molecules that are stereoisomers of each other represent the same structural isomer. Enantiomers, also known as optical isomers, are two stereoisomers that are related to other by a reflection, They are mirror images of each other that are non-superimposable. Human hands are an analog of stereoisomerism. Every stereogenic center in one has the configuration in the other. As a result, different enantiomers of a compound may have different biological effects. Pure enantiomers also exhibit the phenomenon of optical activity and can be separated only with the use of a chiral agent, in nature, only one enantiomer of most chiral biological compounds, such as amino acids, is present. Diastereomers are stereoisomers not related through a reflection operation and they are not mirror images of each other. These include meso compounds, cis–trans isomers, and non-enantiomeric optical isomers, diastereomers seldom have the same physical properties. In the example shown below, the form of tartaric acid forms a diastereomeric pair with both levo and dextro tartaric acids, which form an enantiomeric pair. Please refer to Chirality for more regarding the D- and L- labels. Stereoisomerism about double bonds arises because rotation about the bond is restricted. The simplest examples of cis-trans isomerism are the 1, 2-disubstituted ethenes, molecule I is cis-1, 2-dichloroethene and molecule II is trans-1, 2-dichloroethene. Due to occasional ambiguity, IUPAC adopted a rigorous system wherein the substituents at each end of the double bond are assigned priority based on their atomic number. If the high-priority substituents are on the side of the bond. If they are on sides, it is E. Since chlorine has an atomic number than hydrogen, it is the highest-priority group. Using this notation to name the above pictured molecules, molecule I is -1, 2-dichloroethene and molecule II is -1 and it is not the case that Z and cis or E and trans are always interchangeable
8.
2-Butene
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2-Butene is an acyclic alkene with four carbon atoms. It is the simplest alkene exhibiting cis/trans-isomerism, that is, it exists as two geometric isomers cis-2-butene and trans-2-butene and it is a petrochemical, produced by the catalytic cracking of crude oil or the dimerization of ethylene. Its main uses are in the production of gasoline and butadiene, the two isomers are extremely difficult to separate by distillation because of the proximity of their boiling points. However, separation is unnecessary in most industrial settings, as both isomers behave similarly in most of the desired reactions, a typical industrial 2-butene mixture is 70% -2-butene and 30% -2-butene. Butane and 1-butene are common impurities, present at 1% or more in industrial mixtures, SIDS Initial Assessment Report for 2-Butene from the Organisation for Economic Co-operation and Development
9.
Activation energy
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You may say activation energy may also be defined as the minimum energy required to start a chemical reaction. But this is incorrect, for the energy needed to start a reaction is 0. Activation energy of a reaction is denoted by Ea and given in units of kilojoules per mole or kilocalories per mole. Activation energy can be thought of as the height of the barrier separating two minima of potential energy. For a chemical reaction to proceed at a rate, there should exist an appreciable number of molecules with translational energy equal to or greater than the activation energy. The Arrhenius equation gives the basis of the relationship between the activation energy and the rate at which a reaction proceeds. Even without knowing A, Ea can be evaluated from the variation in reaction rate coefficients as a function of temperature, there are two objections to associating this activation energy with the threshold barrier for an elementary reaction. First, it is unclear as to whether or not reaction does proceed in one step. In some cases, rates of decrease with increasing temperature. When following an exponential relationship so the rate constant can still be fit to an Arrhenius expression. Elementary reactions exhibiting these negative activation energies are typically barrierless reactions, increasing the temperature leads to a reduced probability of the colliding molecules capturing one another, expressed as a reaction cross section that decreases with increasing temperature. Such a situation no longer leads itself to direct interpretations as the height of a potential spot, a substance that modifies the transition state to lower the activation energy is termed a catalyst, a biological catalyst is termed an enzyme. It is important to note that a catalyst increases the rate of reaction without being consumed by it, in addition, while the catalyst lowers the activation energy, it does not change the energies of the original reactants or products. Rather, the reactant energy and the product energy remain the same, in the Arrhenius equation, the term activation energy is used to describe the energy required to reach the transition state. Likewise, the Eyring equation is an equation that also describes the rate of a reaction. Instead of also using Ea, however, the Eyring equation uses the concept of Gibbs energy and this implies that the equation is similar but not identical to the Arrhenius one, because the Gibbs energy contains an entropic term in addition to the enthalpic one. Chemical kinetics Fire point Mean kinetic temperature Quantum tunnelling
10.
Ultraviolet
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Ultraviolet is an electromagnetic radiation with a wavelength from 10 nm to 400 nm, shorter than that of visible light but longer than X-rays. UV radiation constitutes about 10% of the light output of the Sun. It is also produced by electric arcs and specialized lights, such as lamps, tanning lamps. Consequently, the effects of UV are greater than simple heating effects. Suntan, freckling and sunburn are familiar effects of over-exposure, along with risk of skin cancer. Living things on dry land would be damaged by ultraviolet radiation from the Sun if most of it were not filtered out by the Earths atmosphere. More-energetic, shorter-wavelength extreme UV below 121 nm ionizes air so strongly that it is absorbed before it reaches the ground, Ultraviolet is also responsible for the formation of bone-strengthening vitamin D in most land vertebrates, including humans. The UV spectrum thus has both beneficial and harmful to human health. Ultraviolet rays are invisible to most humans, the lens in a human eye ordinarily filters out UVB frequencies or higher, and humans lack color receptor adaptations for ultraviolet rays. Under some conditions, children and young adults can see ultraviolet down to wavelengths of about 310 nm, near-UV radiation is visible to some insects, mammals, and birds. Small birds have a fourth color receptor for ultraviolet rays, this gives birds true UV vision, reindeer use near-UV radiation to see polar bears, who are poorly visible in regular light because they blend in with the snow. UV also allows mammals to see urine trails, which is helpful for animals to find food in the wild. The males and females of some species look identical to the human eye. Ultraviolet means beyond violet, violet being the color of the highest frequencies of visible light, Ultraviolet has a higher frequency than violet light. He called them oxidizing rays to emphasize chemical reactivity and to them from heat rays. The terms chemical and heat rays were eventually dropped in favour of ultraviolet and infrared radiation, in 1878 the effect of short-wavelength light on sterilizing bacteria was discovered. By 1903 it was known the most effective wavelengths were around 250 nm, in 1960, the effect of ultraviolet radiation on DNA was established. The discovery of the ultraviolet radiation below 200 nm, named vacuum ultraviolet because it is absorbed by air, was made in 1893 by the German physicist Victor Schumann
11.
Reaction rate
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The reaction rate or speed of reaction for a reactant or product in a particular reaction is intuitively defined as how quickly or slowly a reaction takes place. Chemical kinetics is the part of chemistry that studies reaction rates. The concepts of chemical kinetics are applied in many disciplines, such as engineering, enzymology. Consider a typical reaction, a A + b B → p P + q Q The lowercase letters represent stoichiometric coefficients, while the capital letters represent the reactants. Reaction rate usually has the units of mol L−1 s−1, the rate of a reaction is always positive. A negative sign is present to indicate that the reactant concentration is decreasing. )The IUPAC recommends that the unit of time should always be the second. The rate of reaction differs from the rate of increase of concentration of a product P by a constant factor and for a reactant A by minus the reciprocal of the stoichiometric number. The stoichiometric numbers are included so that the rate is independent of which reactant or product species is chosen for measurement. For example, if a =1 and b =3 then B is consumed three times more rapidly than A, but v = -d/dt = -d/dt is uniquely defined. The above definition is valid for a single reaction, in a closed system of constant volume. If water is added to a pot containing salty water, the concentration of salt decreases, although there is no chemical reaction. When applied to the system at constant volume considered previously, this equation reduces to, r = d d t. Here N0 is the Avogadro constant, for a single reaction in a closed system of varying volume the so-called rate of conversion can be used, in order to avoid handling concentrations. It is defined as the derivative of the extent of reaction with respect to time, also V is the volume of reaction and Ci is the concentration of substance i. When side products or reaction intermediates are formed, the IUPAC recommends the use of the rate of appearance and rate of disappearance for products and reactants. Reaction rates may also be defined on a basis that is not the volume of the reactor, when a catalyst is used the reaction rate may be stated on a catalyst weight or surface area basis. If the basis is a specific catalyst site that may be counted by a specified method. The nature of the reaction, Some reactions are faster than others
12.
Enzyme kinetics
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Enzyme kinetics is the study of the chemical reactions that are catalysed by enzymes. In enzyme kinetics, the rate is measured and the effects of varying the conditions of the reaction are investigated. Enzymes are usually protein molecules that manipulate other molecules — the enzymes substrates, kinetic studies on enzymes that only bind one substrate, such as triosephosphate isomerase, aim to measure the affinity with which the enzyme binds this substrate and the turnover rate. Some other examples of enzymes are phosphofructokinase and hexokinase, both of which are important for cellular respiration, when enzymes bind multiple substrates, such as dihydrofolate reductase, enzyme kinetics can also show the sequence in which these substrates bind and the sequence in which products are released. An example of enzymes that bind a single substrate and release multiple products are proteases, others join two substrates together, such as DNA polymerase linking a nucleotide to DNA. Although these mechanisms are often a series of steps, there is typically one rate-determining step that determines the overall kinetics. This rate-determining step may be a reaction or a conformational change of the enzyme or substrates. Knowledge of the structure is helpful in interpreting kinetic data. For example, the structure can suggest how substrates and products bind during catalysis, what changes occur during the reaction, not all biological catalysts are protein enzymes, RNA-based catalysts such as ribozymes and ribosomes are essential to many cellular functions, such as RNA splicing and translation. The main difference between ribozymes and enzymes is that RNA catalysts are composed of nucleotides, whereas enzymes are composed of amino acids, ribozymes also perform a more limited set of reactions, although their reaction mechanisms and kinetics can be analysed and classified by the same methods. The reaction catalysed by an enzyme uses exactly the same reactants, like other catalysts, enzymes do not alter the position of equilibrium between substrates and products. However, unlike uncatalysed chemical reactions, enzyme-catalysed reactions display saturation kinetics, the substrate concentration midway between these two limiting cases is denoted by KM. The two most important kinetic properties of an enzyme are how quickly the enzyme becomes saturated with a substrate. Knowing these properties suggests what an enzyme might do in the cell, Enzyme assays are laboratory procedures that measure the rate of enzyme reactions. Because enzymes are not consumed by the reactions they catalyse, enzyme assays usually follow changes in the concentration of substrates or products to measure the rate of reaction. There are many methods of measurement, spectrophotometric assays are most convenient since they allow the rate of the reaction to be measured continuously. Although radiometric assays require the removal and counting of samples they are extremely sensitive. An analogous approach is to use mass spectrometry to monitor the incorporation or release of stable isotopes as substrate is converted into product, the most sensitive enzyme assays use lasers focused through a microscope to observe changes in single enzyme molecules as they catalyse their reactions
13.
Reaction progress kinetic analysis
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While the concepts guiding reaction progress kinetic analysis are not new, the process was formalized by Professor Donna Blackmond in the late 1990s and has since seen increasingly widespread use. Furthermore, information obtained by observation of the reaction time may provide insight regarding unexpected behavior such as induction periods, catalyst deactivation. Reaction progress kinetic analysis relies on the ability to monitor the reaction conversion over time. This goal may be accomplished by a range of techniques, the most common of which are described below, while these techniques are sometimes categorized as differential or integral, simple mathematical manipulation allows interconversion of the data obtained by either of the two. Regardless of the technique implemented, it is advantageous to confirm the validity in the system of interest by monitoring with an additional independent method. From the concentration data, the rate of reaction time may be obtained by taking the derivative of a polynomial fit to the experimental curve. Reaction progress NMR may be classified as a technique as the primary data collected are proportional to concentration vs. time. Reaction progress NMR may, however, often be run at variable temperature, the rate of reactant consumption and/or product formation may be abstracted from the change of absorbance over time. In situ IR may be classified as a technique as the primary data collected are proportional to concentration vs. time. From these data, the material or product concentration over time may be obtained by simply taking the integral of a polynomial fit to the experimental curve. With increases in the availability of spectrometers with in situ monitoring capabilities, the rate of reactant consumption and/or product formation may be abstracted from the change of absorbance over time, again leading to classification as an integral technique. Calorimetry may be used to monitor the course of a reaction, since the heat flux of the reaction. Reaction calorimetry may be classified as a technique since the primary data collected are proportional to rate vs. time. From these data, the material or product concentration over time may be obtained by simply taking the integral of a polynomial fit to the experimental curve. While reaction calorimetry is less frequently employed than a number of other techniques, and SOMO-activation by organocatalysts Despite their shortcomings, these techniques may serve as excellent calibration methods. Reaction progress data may often most simply be presented as plot of substrate concentration vs. time or fraction conversion vs. time. Normalizing data to fractional conversion may be helpful as it allows multiple reactions run with different absolute amounts or concentrations to be compared on the same plot. Data may also commonly be presented as a plot of reaction rate vs. time, data from reaction progress kinetics experiments are also often presented via a rate vs. substrate concentration plot
14.
Irreversible process
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In science, a process that is not reversible is called irreversible. This concept arises frequently in thermodynamics, a system that undergoes an irreversible process may still be capable of returning to its initial state, however, the impossibility occurs in restoring the environment to its own initial conditions. An irreversible process increases the entropy of the universe, however, because entropy is a state function, the change in entropy of the system is the same whether the process is reversible or irreversible. The second law of thermodynamics can be used to determine whether a process is reversible or not, all complex natural processes are irreversible. A certain amount of energy will be used as the molecules of the working body do work on each other when they change from one state to another. Many biological processes that were thought to be reversible have been found to actually be a pairing of two irreversible processes. Thermodynamics defines the behaviour of large numbers of entities, whose exact behavior is given by more specific laws. The irreversibility of thermodynamics must be statistical in nature, that is, that it must be highly unlikely, but not impossible. The German physicist Rudolf Clausius, in the 1850s, was the first to quantify the discovery of irreversibility in nature through his introduction of the concept of entropy. For example, a cup of hot coffee placed in an area of temperature will transfer heat to its surroundings. However, that same initial cup of coffee will never absorb heat from its surroundings causing it to grow even hotter with the temperature of the room decreasing, therefore, the process of the coffee cooling down is irreversible unless extra energy is added to the system. However, a paradox arose when attempting to reconcile microanalysis of a system with observations of its macrostate, many processes are mathematically reversible in their microstate when analyzed using classical Newtonian mechanics. His formulas quantified the work done by William Thomson, 1st Baron Kelvin who had argued that, in 1890, he published his first explanation of nonlinear dynamics, also called chaos theory. Sensitivity to initial conditions relating to the system and its environment at the compounds into an exhibition of irreversible characteristics within the observable. In the physical realm, many processes are present to which the inability to achieve 100% efficiency in energy transfer can be attributed. The following is a list of events which contribute to the irreversibility of processes. The internal energy of the gas remains the same, while the volume increases, the original state cannot be recovered by simply compressing the gas to its original volume, since the internal energy will be increased by this compression. The original state can only be recovered by then cooling the re-compressed system, the diagram to the right applies only if the first expansion is free
15.
Isotopic labeling
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Isotopic labeling is a technique used to track the passage of an isotope through a reaction, metabolic pathway, or cell. The reactant is labeled by replacing specific atoms by their isotope, the reactant is then allowed to undergo the reaction. The position of the isotopes in the products is measured to determine the sequence the isotopic atom followed in the reaction or the metabolic pathway. The nuclides used in isotopic labeling may be stable nuclides or radionuclides, in the latter case, the labeling is called radiolabeling. In isotopic labeling, there are ways to detect the presence of labeling isotopes, through their mass, vibrational mode. Mass spectrometry detects the difference in a mass, while infrared spectroscopy detects the difference in the isotopes vibrational modes. Nuclear magnetic resonance detects atoms with different gyromagnetic ratios, the radioactive decay can be detected through an ionization chamber or autoradiographs of gels. An example of the use of isotopic labeling is the study of phenol in water by replacing common hydrogen with deuterium, only the hydroxyl group was affected, indicating that the other 5 hydrogen atoms did not participate in these exchange reactions. An isotopic tracer, is used in chemistry and biochemistry to help understand chemical reactions and interactions, in this technique, one or more of the atoms of the molecule of interest is substituted for an atom of the same chemical element, but of a different isotope. The difference in the number of neutrons, however, means that it can be detected separately from the atoms of the same element. Nuclear magnetic resonance and mass spectrometry are used to investigate the mechanisms of chemical reactions, NMR and MS detects isotopic differences, which allows information about the position of the labeled atoms in the products structure to be determined. With information on the positioning of the atoms in the products. Radioactive isotopes can be tested using the autoradiographs of gels in gel electrophoresis, the radiation emitted by compounds containing the radioactive isotopes darkens a piece of photographic film, recording the position of the labeled compounds relative to one another in the gel. Isotope tracers are used in the form of isotope ratios. Isotopic tracers are some of the most important tools in geology because they can be used to understand complex mixing processes in earth systems, further discussion of the application of isotopic tracers in geology is covered under the heading of isotope geochemistry. Isotopic tracers are usually subdivided into two categories, stable isotope tracers and radiogenic isotope tracers, stable isotope tracers involve only non-radiogenic isotopes and usually are mass-dependent. In theory, any element with two isotopes can be used as an isotopic tracer. However, the most commonly used stable isotope tracers involve relatively light isotopes, a radiogenic isotope tracer involves an isotope produced by radioactive decay, which is usually in a ratio with a non-radiogenic isotope
16.
Diffusion
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Diffusion is the net movement of molecules or atoms from a region of high concentration to a region of low concentration. This is also referred to as the movement of a substance down a concentration gradient, a gradient is the change in the value of a quantity with the change in another variable. The word diffusion derives from the Latin word, diffundere, which means to spread out, a distinguishing feature of diffusion is that it results in mixing or mass transport, without requiring bulk motion. Thus, diffusion should not be confused with convection, or advection, an example of a situation in which bulk flow and diffusion can be differentiated is the mechanism by which oxygen enters the body during external respiration. The lungs are located in the cavity, which expands as the first step in external respiration. This expansion leads to an increase in volume of the alveoli in the lungs and this creates a pressure gradient between the air outside the body and the alveoli. The air moves down the gradient through the airways of the lungs and into the alveoli until the pressure of the air. The air arriving in the alveoli has a concentration of oxygen than the “stale” air in the alveoli. The increase in oxygen concentration creates a concentration gradient for oxygen between the air in the alveoli and the blood in the capillaries that surround the alveoli, oxygen then moves by diffusion, down the concentration gradient, into the blood. The other consequence of the air arriving in alveoli is that the concentration of carbon dioxide in the alveoli decreases and this creates a concentration gradient for carbon dioxide to diffuse from the blood into the alveoli. The pumping action of the heart then transports the blood around the body, as the left ventricle of the heart contracts, the volume decreases, which increases the pressure in the ventricle. This creates a gradient between the heart and the capillaries, and blood moves through blood vessels by bulk flow. The concept of diffusion is widely used in, physics, chemistry, biology, sociology, economics, however, in each case, the object that is undergoing diffusion is “spreading out” from a point or location at which there is a higher concentration of that object. In the phenomenological approach, diffusion is the movement of a substance from a region of high concentration to a region of low concentration without bulk motion, according to Ficks laws, the diffusion flux is proportional to the negative gradient of concentrations. It goes from regions of higher concentration to regions of lower concentration, some time later, various generalizations of Ficks laws were developed in the frame of thermodynamics and non-equilibrium thermodynamics. From the atomistic point of view, diffusion is considered as a result of the walk of the diffusing particles. In molecular diffusion, the molecules are self-propelled by thermal energy. Random walk of small particles in suspension in a fluid was discovered in 1827 by Robert Brown, the theory of the Brownian motion and the atomistic backgrounds of diffusion were developed by Albert Einstein
17.
Chemical equilibrium
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In a chemical reaction, chemical equilibrium is the state in which both reactants and products are present in concentrations which have no further tendency to change with time. Usually, this results when the forward reaction proceeds at the same rate as the reverse reaction. The reaction rates of the forward and backward reactions are not zero. Thus, there are no net changes in the concentrations of the reactant, such a state is known as dynamic equilibrium. The concept of chemical equilibrium was developed after Berthollet found that chemical reactions are reversible. For any reaction mixture to exist at equilibrium, the rates of the forward and backward reactions are equal, conversely the equilibrium position is said to be far to the left if hardly any product is formed from the reactants. Since at equilibrium forward and backward rates are equal, k + α β = k − σ τ, K c = k + k − = σ τ α β By convention the products form the numerator. Equality of forward and backward reaction rates, however, is a condition for chemical equilibrium. Adding a catalyst will affect both the reaction and the reverse reaction in the same way and will not have an effect on the equilibrium constant. The catalyst will speed up both reactions thereby increasing the speed at which equilibrium is reached, although the macroscopic equilibrium concentrations are constant in time, reactions do occur at the molecular level. This is an example of dynamic equilibrium, equilibria, like the rest of thermodynamics, are statistical phenomena, averages of microscopic behavior. Le Châteliers principle gives an idea of the behavior of a system when changes to its reaction conditions occur. If a dynamic equilibrium is disturbed by changing the conditions, the position of equilibrium moves to partially reverse the change. For example, adding more S from the outside will cause an excess of products, and this can also be deduced from the equilibrium constant expression for the reaction, K = If increases must increase and CH 3CO−2 must decrease. The H2O is left out, as it is the solvent and its concentration remains high, a quantitative version is given by the reaction quotient. J. W. Gibbs suggested in 1873 that equilibrium is attained when the Gibbs free energy of the system is at its minimum value, what this means is that the derivative of the Gibbs energy with respect to reaction coordinate vanishes, signalling a stationary point. This derivative is called the reaction Gibbs energy and corresponds to the difference between the chemical potentials of reactants and products at the composition of the reaction mixture and this criterion is both necessary and sufficient. If a mixture is not at equilibrium, the liberation of the excess Gibbs energy is the force for the composition of the mixture to change until equilibrium is reached
18.
Reaction mechanism
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In chemistry, a reaction mechanism is the step by step sequence of elementary reactions by which overall chemical change occurs. A chemical mechanism is a conjecture that tries to describe in detail what takes place at each stage of an overall chemical reaction. The detailed steps of a reaction are not observable in most cases and it also describes each reactive intermediate, activated complex, and transition state, and which bonds are broken, and which bonds are formed. A complete mechanism must also explain the reason for the reactants and catalyst used, the stereochemistry observed in reactants and products, all products formed and the amount of each. The electron or arrow pushing method is used in illustrating a reaction mechanism, for example. A reaction mechanism must also account for the order in which molecules react, often what appears to be a single-step conversion is in fact a multistep reaction. Reaction intermediates are often free radicals or ions, the kinetics are explained in terms of the energy needed for the conversion of the reactants to the proposed transition states. Information about the mechanism of a reaction is provided by the use of chemical kinetics to determine the rate equation. Consider the following reaction for example, CO + NO2 → CO2 + NO In this case and this form suggests that the rate-determining step is a reaction between two molecules of NO2. The elementary steps should add up to the original reaction, when determining the overall rate law for a reaction, the slowest step is the step that determines the reaction rate. Because the first step is the slowest step, it is the rate-determining step, because it involves the collision of two NO2 molecules, it is a bimolecular reaction with a rate law of r = k 2. Other reactions may have mechanisms of several consecutive steps, in organic chemistry, one of the first reaction mechanisms proposed was that for the benzoin condensation, put forward in 1903 by A. J. Lapworth. There are also more complex such as chain reactions, in which the propagation steps of the chain form a closed cycle. A correct reaction mechanism is an important part of accurate predictive modeling, for many combustion and plasma systems, detailed mechanisms are not available or require development. Rate constants or thermochemical data are not available in the literature. Computational chemistry methods can also be used to calculate potential energy surfaces for reactions, molecularity in chemistry is the number of colliding molecular entities that are involved in a single reaction step. A reaction step involving one molecular entity is called unimolecular, a reaction step involving two molecular entities is called bimolecular. A reaction step involving three molecular entities is called termolecular
19.
Phosphoglucomutase
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Phosphoglucomutase is an enzyme that transfers a phosphate group on an α-D-glucose monomer from the 1 to the 6 position in the forward direction or the 6 to the 1 position in the reverse direction. More precisely, it facilitates the interconversion of glucose 1-phosphate and glucose 6-phosphate, after glycogen phosphorylase catalyzes the phosphorolytic cleavage of a glucosyl residue from the glycogen polymer, the freed glucose has a phosphate group on its 1-carbon. This glucose 1-phosphate molecule is not itself a useful metabolic intermediate, glucose 6-phosphate’s metabolic fate depends on the needs of the cell at the time it is generated. If the cell is low on energy, then glucose 6-phosphate will travel down the glycolytic pathway, eventually yielding two molecules of adenosine triphosphate. If this reaction is taking place in the liver, the enzyme glucose 6-phosphatase can also catalyze the conversion of glucose 6-phosphate to glucose, muscle cells, however, lack glucose 6-phosphatase, so they cannot share their glycogen stores with the rest of the body. Phosphoglucomutase also acts in the fashion when blood glucose levels are high. In this case, phosphoglucomutase catalyzes the conversion of glucose 6-phosphate to glucose 1-phosphate and this glucose-1-phosphate can then react with UTP to yield UDP-glucose in a reaction catalyzed by UDP-glucose-pyrophosphorylase. If activated by insulin, glycogen synthase will proceed to clip the glucose from the UDP-glucose complex onto a glycogen polymer, Phosphoglucomutase effects a phosphoryl group shift by exchanging a phosphoryl group with the substrate. Isotopic labeling experiments have confirmed that this reaction proceeds through a glucose 1, the enzyme then undergoes a rapid diffusional reorientation to position the 1-phosphate of the bisphosphate intermediate properly relative to the dephosphorylated enzyme. Later structural studies confirmed that the site in the enzyme that becomes phosphorylated and dephosphorylated is the oxygen of the active-site serine residue. A bivalent metal ion, usually magnesium or cadmium, is required for activity and has been shown to complex directly with the phosphoryl group esterified to the active-site serine. Each phosphoglucomutase monomer can be divided into four domains, I-IV. Each monomer comprises four distinct α/β structural units, each of which one of the four strands in each monomers β-sheet and is made up only of the residues in a given sequence domain. Human muscle contains two phosphoglucomutases with nearly identical properties, PGM I and PGM II. One or the other of forms is missing in some humans congenitally. PGM deficiency is a rare condition that does not have a set of well-characterized physiological symptoms. PGM1, PGM2, PGM3, PGM5 mutase Beta-phosphoglucomutase Phosphoglucomutase at the US National Library of Medicine Medical Subject Headings
20.
Transition state
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The transition state of a chemical reaction is a particular configuration along the reaction coordinate. It is defined as the corresponding to the highest potential energy along this reaction coordinate. At this point, assuming a perfectly irreversible reaction, colliding reactant molecules always go on to form products and it is often marked with the double dagger ‡ symbol. The concept of a state has been important in many theories of the rates at which chemical reactions occur. This started with the state theory, which was first developed around 1935 by Eyring, Evans and Polanyi. A collision between reactant molecules may or may not result in a successful reaction, the outcome depends on factors such as the relative kinetic energy, relative orientation and internal energy of the molecules. Even if the partners form an activated complex they are not bound to go on and form products. Because of the rules of quantum mechanics, the state cannot be captured or directly observed. This is sometimes expressed by stating that the state has a fleeting existence. However, cleverly manipulated spectroscopic techniques can get us as close as the timescale of the technique allows, femtochemical IR spectroscopy was developed for precisely that reason, and it is possible to probe molecular structure extremely close to the transition point. Often along the reaction coordinate reactive intermediates are present not much lower in energy from a transition state making it difficult to distinguish between the two, Transition state structures can be determined by searching for first-order saddle points on the potential energy surface of the chemical species of interest. A first-order saddle point is a point of index one, that is. This is further described in the geometry optimization. The Hammond–Leffler Postulate states that the structure of the state more closely resembles either the products or the starting material. A transition state resembles the reactants more than the products is said to be early. Thus, the Hammond–Leffler Postulate predicts a transition state for an endothermic reaction. A dimensionless reaction coordinate that quantifies the lateness of a state can be used to test the validity of the Hammond–Leffler Postulate for a particular reaction. One demonstration of principle is found in the two bicyclic compounds depicted below
21.
Acid
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An acid is a molecule or ion capable of donating a hydron, or, alternatively, capable of forming a covalent bond with an electron pair. The first category of acids is the donors or Brønsted acids. In the special case of solutions, proton donors form the hydronium ion H3O+ and are known as Arrhenius acids. Brønsted and Lowry generalized the Arrhenius theory to include non-aqueous solvents, acids form aqueous solutions with a sour taste, can turn blue litmus red, and react with bases and certain metals to form salts. The word acid is derived from the Latin acidus/acēre meaning sour, an aqueous solution of an acid has a pH less than 7 and is colloquially also referred to as acid, while the strict definition refers only to the solute. A lower pH means a higher acidity, and thus a higher concentration of hydrogen ions in the solution. Chemicals or substances having the property of an acid are said to be acidic, common aqueous acids include hydrochloric acid, acetic acid, sulfuric acid, and citric acid. As these examples show, acids can be solutions or pure substances, strong acids and some concentrated weak acids are corrosive, but there are exceptions such as carboranes and boric acid. The second category of acids are Lewis acids, which form a covalent bond with an electron pair, however, hydrogen chloride, acetic acid, and most other Brønsted-Lowry acids cannot form a covalent bond with an electron pair and are therefore not Lewis acids. Conversely, many Lewis acids are not Arrhenius or Brønsted-Lowry acids, in modern terminology, an acid is implicitly a Brønsted acid and not a Lewis acid, since chemists almost always refer to a Lewis acid explicitly as a Lewis acid. Modern definitions are concerned with the chemical reactions common to all acids. Most acids encountered in life are aqueous solutions, or can be dissolved in water, so the Arrhenius. The Brønsted-Lowry definition is the most widely used definition, unless otherwise specified, hydronium ions are acids according to all three definitions. Interestingly, although alcohols and amines can be Brønsted-Lowry acids, they can function as Lewis bases due to the lone pairs of electrons on their oxygen and nitrogen atoms. The Swedish chemist Svante Arrhenius attributed the properties of acidity to hydrogen ions or protons in 1884, an Arrhenius acid is a substance that, when added to water, increases the concentration of H+ ions in the water. Thus, an Arrhenius acid can also be described as a substance that increases the concentration of ions when added to water. Examples include molecular substances such as HCl and acetic acid, an Arrhenius base, on the other hand, is a substance which increases the concentration of hydroxide ions when dissolved in water. Thus, an Arrhenius acid could also be said to be one that decreases hydroxide concentration, in an acidic solution, the concentration of hydronium ions is greater than 10−7 moles per liter
22.
Functional group
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In organic chemistry, functional groups are specific groups of atoms or bonds within molecules that are responsible for the characteristic chemical reactions of those molecules. The same functional group will undergo the same or similar chemical reaction regardless of the size of the molecule it is a part of, however, its relative reactivity can be modified by other functional groups nearby. The atoms of functional groups are linked to other and to the rest of the molecule by covalent bonds. Any subgroup of atoms of a compound also may be called a radical, and if a covalent bond is broken homolytically, Functional groups can also be charged, e. g. in carboxylate salts, which turns the molecule into a polyatomic ion or a complex ion. Complexation and solvation is also caused by interactions of functional groups. In the common rule of thumb like dissolves like, it is the shared or mutually well-interacting functional groups give rise to solubility. For example, sugar dissolves in water because both share the functional group and hydroxyls interact strongly with each other. Combining the names of groups with the names of the parent alkanes generates what is termed a systematic nomenclature for naming organic compounds. In traditional nomenclature, the first carbon atom after the carbon that attaches to the group is called the alpha carbon, the second, beta carbon. IUPAC conventions call for numeric labeling of the position, e. g. 4-aminobutanoic acid, in traditional names various qualifiers are used to label isomers, for example isopropanol is an isomer is n-propanol. The following is a list of functional groups. In the formulas, the symbols R and R usually denote an attached hydrogen, or a side chain of any length. Functional groups, called hydrocarbyl, that only carbon and hydrogen. Each one differs in type of reactivity, there are also a large number of branched or ring alkanes that have specific names, e. g. tert-butyl, bornyl, cyclohexyl, etc. Hydrocarbons may form charged structures, positively charged carbocations or negative carbanions, examples are tropylium and triphenylmethyl cations and the cyclopentadienyl anion. Haloalkanes are a class of molecule that is defined by a carbon–halogen bond and this bond can be relatively weak or quite stable. In general, with the exception of fluorinated compounds, haloalkanes readily undergo nucleophilic substitution reactions or elimination reactions, the substitution on the carbon, the acidity of an adjacent proton, the solvent conditions, etc. all can influence the outcome of the reactivity. Compounds that contain nitrogen in this category may contain C-O bonds, compounds that contain sulfur exhibit unique chemistry due to their ability to form more bonds than oxygen, their lighter analogue on the periodic table
23.
Active site
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In biology, the active site is the region of an enzyme where substrate molecules bind and undergo a chemical reaction. The active site consists of residues that form bonds with the substrate. The active site is usually a groove or pocket of the enzyme which can be located in a tunnel within the enzyme. An active site can catalyse a reaction repeatedly as its residues are not altered at the end of the reaction, usually, an enzyme molecule has only one active site, and the active site fits with one specific type of substrate. An active site contains a site that binds the substrate. Residues in the site form hydrogen bonds, hydrophobic interactions. In order to function, the site needs to be in a specific conformation. A tighter fit between a site and the substrate molecule is believed to increase efficiency of a reaction. Most enzymes have deeply buried active sites, which can be accessed by a substrate via access channels, there are two proposed models of how enzymes fit to their specific substrate, the lock and key model and the induced fit model. Emil Fischers lock and key model assumes that the site is a perfect fit for a specific substrate. Daniel Koshlands theory of enzyme-substrate binding is that the active site, the induced fit model is a development of the lock-and-key model and assumes that an active site is flexible and it changes shape until the substrate is completely bound. The substrate is thought to induce a change in the shape of the active site, the hypothesis also predicts that the presence of certain residues in the active site will encourage the enzyme to locate the correct substrate. Conformational changes may occur as the substrate is bound. After the products of the move away from the enzyme. Once the substrate is bound and oriented in the active site, the residues of the catalytic site are typically very close to the binding site, and some residues can have dual-roles in both binding and catalysis. Catalytic residues of the site interact with the substrate to lower the energy of a reaction. They do this by a number of different mechanisms, firstly, they can act as donors or acceptors of protons or other groups on the substrate to facilitate the reaction. They can also form electrostatic interactions to stabilise charge buildup on the state or leaving group
24.
Enoyl CoA isomerase
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It plays a particularly important role in the metabolism of unsaturated fatty acids. It does so by shifting the position of the bonds in the acyl-CoA intermediates. The reaction mechanism is detailed in Figure 1, and the base that initiates the isomerization, the double bond serves as the target of oxidation and carbon-to-carbon bond cleavage, thereby shortening the fatty acid chain. There are two divisions among the mitochondrial enoyl Co-A isomerase, short-chain and long-chain, in an immunoblot, antibodies were run against all enoyl CoA isomerase. However, two of these isomerases had antibody attachment, the short chain isomerase and the multifunctional enzyme. There was one enzyme which did not have binding specificity to this antibody, long-chain isomerase was found when it eluted at a lower potassium phosphate concentration in the gradient. Thus, the discovery of three sub-classes of enoyl CoA isomerase was made, although all three classes of enzymes have the same function, there is little overlap among their amino acid sequences. For example, only 40 out of 302 amino acid sequences are the same between monofunctional peroxisomal and mitochondrial enzymes in humans, in fact, in mammals, the peroxisomal enzyme has an extra N-terminal domain that is not present in the mitochondrial counterpart. Also, it has found to be a subunit of the peroxisomal trifunctional enzyme. In that sense, for many organisms, the mitochondrial enzyme is essential for deriving maximum energy from lipids. Mitochondria of rat liver contain more than one enoyl Co-A isomerase, peroxisomes of plants and of rat liver are very different in the way they operate. Despite their primary structure similarities, there are differences among the different specimen, to begin with, the peroxisomes of rat liver are a multifunctional enzyme including enoyl-CoA isomerase, enoyl-CoA hydratase, and L--3-hydroxyacyl-CoA dehydrogenase. Three different enzymes reside on this entity allowing this enzyme to perform isomerization, hydration, isomerase activity on the multifunctional enzyme occurs at the amino-terminal catalytic half of the protein along with the hydratase activity. The dehydrogenase activity of enoyl-CoA occurs in the carboxyl-terminal and this removes the need for a substrate transferring enzyme. On the other hand, the cotyledons convert long-chain 3-trans-enoyl-CoA, long-chain 3-cis-enoyl-CoA, as previously mentioned, plant enoyl-CoA isomerase exclusively forms the 2-trans isomer as product. It does not act on 4-cis-enoyl-CoA species or 2-trans- 4-trans-dienoyl-CoA species, in comparing the products of the plant peroxisome and the multifunctional enzyme of rat liver, the plant has no hydratase activity. The Plant form did not form a 2-cis-isomer or D- or L-3 hydroxy derivative, the turnover rates of these the two sub divisions of peroxisomes are very different. The Kcat/Km ratio in cotyledons is 10^6 M-1s-1 which outperforms the ratio.07 * 10^6 M-1s-1, due to a high turnover rate, the plant peroxisomes contain a lesser amount of enoyl-CoA isomerase than their counterparts in the rat liver
25.
Stereochemistry
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Stereochemistry, a subdiscipline of chemistry, involves the study of the relative spatial arrangement of atoms that form the structure of molecules and their manipulation. An important branch of stereochemistry is the study of chiral molecules, stereochemistry is also known as 3D chemistry because the prefix stereo- means three-dimensionality. The study of stereochemistry focuses on stereoisomers and spans the spectrum of organic, inorganic, biological, physical. This property, the physical property in which the two types of tartrate salts differed, is due to optical isomerism. In 1874, Jacobus Henricus van t Hoff and Joseph Le Bel explained optical activity in terms of the arrangement of the atoms bound to carbon. Cahn–Ingold–Prelog priority rules are part of a system for describing a molecules stereochemistry and they rank the atoms around a stereocenter in a standard way, allowing the relative position of these atoms in the molecule to be described unambiguously. A Fischer projection is a way to depict the stereochemistry around a stereocenter. An often cited example of the importance of stereochemistry relates to the thalidomide disaster, thalidomide is a pharmaceutical drug, first prepared in 1957 in Germany, prescribed for treating morning sickness in pregnant women. The drug was discovered to be teratogenic, causing genetic damage to early embryonic growth and development. Some of the proposed mechanisms of teratogenecity involve a different biological function for the -. In the human body however, thalidomide undergoes racemization, even if one of the two enantiomers is administered as a drug, the other enantiomer is produced as a result of metabolism. Accordingly, it is incorrect to state one of the stereoisomer is safe while the other is teratogenic. Thalidomide is currently used for the treatment of diseases, notably cancer. Strict regulations and controls have been enabled to avoid its use by pregnant women and this disaster was a driving force behind requiring strict testing of drugs before making them available to the public. Torsional strain results from resistance to twisting about a bond
26.
Enantiomer
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A single chiral atom or similar structural feature in a compound causes that compound to have two possible structures which are non-superposable, each a mirror image of the other. Each member of the pair is termed an enantiomorph, the property is termed enantiomerism. The presence of multiple features in a given compound increases the number of geometric forms possible. Enantiopure compounds refer to samples having, within the limits of detection and they are sometimes called optical isomers for this reason. Enantiomer members often have different chemical reactions with other enantiomer substances, since many biological molecules are enantiomers, there is sometimes a marked difference in the effects of two enantiomers on biological organisms. Owing to this discovery, drugs composed of one enantiomer can be developed to enhance the pharmacological efficacy. An example is eszopiclone, which is enantiopure and therefore administered in doses that are exactly 1/2 of the older, in the case of eszopiclone, the S enantiomer is responsible for all the desired effects, while the other enantiomer seems to be inactive. A dose of 2 mg of zopiclone must be administered to produce the therapeutic effect as 1 mg of eszopiclone. In chemical synthesis of enantiomeric substances, non-enantiomeric precursors inevitably produce racemic mixtures, in the absence of an effective enantiomeric environment, separation of a racemic mixture into its enantiomeric components is impossible. The R/S system is an important nomenclature system for denoting distinct enantiomers, another system is based on prefix notation for optical activity, - and - or d- and l-. The Latin for left and right is laevus and dexter, respectively, left and right have always had moral connotations, and the Latin words for these are sinister and rectus. The English word right is a cognate of rectus and this is the origin of the D, L and S, R notations, and the employment of prefixes levo- and dextro- in common names. Most compounds that one or more asymmetric carbon atoms show enantiomerism. There are a few compounds that do have asymmetric carbon atoms. An example of such an enantiomer is the sedative thalidomide, which was sold in a number of countries across the world from 1957 until 1961 and it was withdrawn from the market when it was found to cause of birth defects. One enantiomer caused the desirable effects, while the other, unavoidably present in equal quantities. The herbicide mecoprop is a mixture, with the --enantiomer possessing the herbicidal activity. Another example is the antidepressant drugs escitalopram and citalopram, citalopram is a racemate, escitalopram is a pure enantiomer
27.
Serine
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Serine encoded by the codons UCU, UCC, UCA, UCG, AGU and AGC is an ɑ-amino acid that is used in the biosynthesis of proteins. It contains a group, a carboxyl group, and a side chain consisting of a hydroxymethyl group. It can be synthesized in the body under normal physiological circumstances. This compound is one of the naturally occurring amino acids. Only the L-stereoisomer appears naturally in proteins and it is not essential to the human diet, since it is synthesized in the body from other metabolites, including glycine. Serine was first obtained from silk protein, a rich source. Its name is derived from the Latin for silk, sericum, serines structure was established in 1902. The biosynthesis of serine starts with the oxidation of 3-phosphoglycerate to 3-phosphohydroxypyruvate, reductive amination of this ketone by phosphoserine transaminase yields 3-phosphoserine which is hydrolyzed to serine by phosphoserine phosphatase. In bacteria such as E. coli these enzymes are encoded by the genes serA, serC, glycine biosynthesis, Serine hydroxymethyltransferase also catalyzes the reversible conversions of L-serine to glycine and 5,6,7, 8-tetrahydrofolate to 5, 10-methylenetetrahydrofolate. SHMT is a pyridoxal phosphate dependent enzyme, glycine can also be formed from CO2, NH4+, and mTHF in a reaction catalyzed by glycine synthase. Industrially, L-serine is produced by fermentation, with an estimated 100-1000 tonnes per year produced, in the laboratory, racemic serine can be prepared from methyl acrylate via several steps, Serine is important in metabolism in that it participates in the biosynthesis of purines and pyrimidines. It is the precursor to several amino acids including glycine and cysteine and it is also the precursor to numerous other metabolites, including sphingolipids and folate, which is the principal donor of one-carbon fragments in biosynthesis. Serine plays an important role in the function of many enzymes. It has been shown to occur in the sites of chymotrypsin, trypsin. Serine sidechains are often bonded, the commonest small motifs formed are ST turns, ST motifs. As a constituent of proteins, its side chain can undergo O-linked glycosylation and it is one of three amino acid residues that are commonly phosphorylated by kinases during cell signaling in eukaryotes. Phosphorylated serine residues are often referred to as phosphoserine, Serine proteases are a common type of protease. D-Serine, synthesized in the brain by serine racemase from L-serine, serves as a neuromodulator by coactivating NMDA receptors, D-serine is a potent agonist at the glycine site of the NMDA-type glutamate receptor
28.
Absolute configuration
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Absolute configurations for a chiral molecule are most often obtained by X-ray crystallography. All enantiomerically pure chiral molecules crystallise in one of the 65 Sohncke groups, alternative techniques are Optical rotatory dispersion, vibrational circular dichroism and the use of chiral shift reagents in proton NMR and Coulomb Explosion Imaging. When the absolute configuration is obtained the assignment of R or S is based on the Cahn–Ingold–Prelog priority rules, absolute configurations are also relevant to characterization of crystals. Until 1951 it was not possible to obtain the absolute configuration of chiral compounds and it was at some time decided that -glyceraldehyde was the -enantiomer. The configuration of chiral compounds was then related to that of -glyceraldehyde by sequences of chemical reactions. For example, oxidation of -glyceraldehyde with mercury oxide gives -glyceric acid, thus the absolute configuration of -glyceric acid must be the same as that of -glyceraldehyde. Nitric acid oxidation of -isoserine gives -glyceric acid, establishing that -isoserine also has the absolute configuration. -Isoserine can be converted by a process of bromination and zinc reduction to give -lactic acid. If a reaction gave the enantiomer of a configuration, as indicated by the opposite sign of optical rotation. The compound investigated was -sodium rubidium tartrate and from its configuration it was deduced that the original guess for -glyceraldehyde was correct, the R / S system is an important nomenclature system for denoting enantiomers. is written in italics and parentheses. If there are multiple chiral carbons, e. g. a number specifies the location of the carbon preceding each configuration, the R / S system also has no fixed relation to the D/L system. For example, the one of serine contains a hydroxyl group. If a thiol group, -SH, were swapped in for it, but this substitution would invert the molecules R / S labeling, because the CIP priority of CH2OH is lower than that for CO2H but the CIP priority of CH2SH is higher than that for CO2H. In the D/L system, they are nearly all consistent—naturally occurring amino acids are all L, in the R / S system, they are mostly S, but there are some common exceptions. An enantiomer can be named by the direction in which it rotates the plane of polarized light, if it rotates the light clockwise, that enantiomer is labeled. The and isomers have also been termed d- and l-, respectively, naming with d- and l- is easy to confuse with D- and L- labeling and is therefore discouraged by IUPAC. An optical isomer can be named by the configuration of its atoms. The D/L system, not to be confused with the d- and l-system, see above, glyceraldehyde is chiral itself, and its two isomers are labeled D and L
. PMID 5726186.
