1.
Covalent bond
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A covalent bond, also called a molecular bond, is a chemical bond that involves the sharing of electron pairs between atoms. These electron pairs are known as shared pairs or bonding pairs, for many molecules, the sharing of electrons allows each atom to attain the equivalent of a full outer shell, corresponding to a stable electronic configuration. Covalent bonding includes many kinds of interactions, including σ-bonding, π-bonding, metal-to-metal bonding, agostic interactions, bent bonds, the term covalent bond dates from 1939. In the molecule H2, the atoms share the two electrons via covalent bonding. Covalency is greatest between atoms of similar electronegativities, thus, covalent bonding does not necessarily require that the two atoms be of the same elements, only that they be of comparable electronegativity. Covalent bonding that entails sharing of electrons more than two atoms is said to be delocalized. The term covalence in regard to bonding was first used in 1919 by Irving Langmuir in a Journal of the American Chemical Society article entitled The Arrangement of Electrons in Atoms and Molecules. Langmuir wrote that we shall denote by the term covalence the number of pairs of electrons that an atom shares with its neighbors. The idea of covalent bonding can be traced several years before 1919 to Gilbert N. Lewis and he introduced the Lewis notation or electron dot notation or Lewis dot structure, in which valence electrons are represented as dots around the atomic symbols. Pairs of electrons located between atoms represent covalent bonds, multiple pairs represent multiple bonds, such as double bonds and triple bonds. An alternative form of representation, not shown here, has bond-forming electron pairs represented as solid lines, Lewis proposed that an atom forms enough covalent bonds to form a full outer electron shell. In the diagram of methane shown here, the atom has a valence of four and is, therefore, surrounded by eight electrons, four from the carbon itself. Each hydrogen has a valence of one and is surrounded by two electrons – its own one electron plus one from the carbon, walter Heitler and Fritz London are credited with the first successful quantum mechanical explanation of a chemical bond in 1927. Their work was based on the valence bond model, which assumes that a bond is formed when there is good overlap between the atomic orbitals of participating atoms. Atomic orbitals have specific directional properties leading to different types of covalent bonds, sigma bonds are the strongest covalent bonds and are due to head-on overlapping of orbitals on two different atoms. A single bond is usually a σ bond, pi bonds are weaker and are due to lateral overlap between p orbitals. A double bond between two given atoms consists of one σ and one π bond, and a bond is one σ. Covalent bonds are also affected by the electronegativity of the atoms which determines the chemical polarity of the bond
2.
Chemical bond
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A chemical bond is a lasting attraction between atoms that enables the formation of chemical compounds. The bond may result from the force of attraction between atoms with opposite charges, or through the sharing of electrons as in the covalent bonds. Since opposite charges attract via an electromagnetic force, the negatively charged electrons that are orbiting the nucleus. An electron positioned between two nuclei will be attracted to both of them, and the nuclei will be attracted toward electrons in this position and this attraction constitutes the chemical bond. This phenomenon limits the distance between nuclei and atoms in a bond, in general, strong chemical bonding is associated with the sharing or transfer of electrons between the participating atoms. All bonds can be explained by quantum theory, but, in practice, simplification rules allow chemists to predict the strength, directionality, the octet rule and VSEPR theory are two examples. Electrostatics are used to describe bond polarities and the effects they have on chemical substances, a chemical bond is an attraction between atoms. This attraction may be seen as the result of different behaviors of the outermost or valence electrons of atoms and these behaviors merge into each other seamlessly in various circumstances, so that there is no clear line to be drawn between them. However it remains useful and customary to differentiate different types of bond, which result in different properties of condensed matter. In the simplest view of a covalent bond, one or more electrons are drawn into the space between the two atomic nuclei, energy is released by bond formation. This is not as a reduction in energy, because the attraction of the two electrons to the two protons is offset by the electron-electron and proton-proton repulsions. In a polar covalent bond, one or more electrons are shared between two nuclei. Such weak intermolecular bonds give organic molecular substances, such as waxes and oils, their soft bulk character, also, the melting points of such covalent polymers and networks increase greatly. In a simplified view of a bond, the bonding electron is not shared at all. In this type of bond, the atomic orbital of one atom has a vacancy which allows the addition of one or more electrons. These newly added electrons potentially occupy a lower energy-state than they experience in a different atom, thus, one nucleus offers a more tightly bound position to an electron than does another nucleus, with the result that one atom may transfer an electron to the other. This transfer causes one atom to assume a net charge. The bond then results from electrostatic attraction between atoms and the atoms become positive or negatively charged ions, ionic bonds may be seen as extreme examples of polarization in covalent bonds
3.
Amino acid
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Amino acids are organic compounds containing amine and carboxyl functional groups, along with a side chain specific to each amino acid. The key elements of an acid are carbon, hydrogen, oxygen. About 500 amino acids are known and can be classified in many ways, in the form of proteins, amino acids comprise the second-largest component of human muscles, cells and other tissues. Outside proteins, amino acids perform critical roles in such as neurotransmitter transport. In biochemistry, amino acids having both the amine and the acid groups attached to the first carbon atom have particular importance. They are known as 2-, alpha-, or α-amino acids and they include the 22 proteinogenic amino acids, which combine into peptide chains to form the building-blocks of a vast array of proteins. These are all L-stereoisomers, although a few D-amino acids occur in bacterial envelopes, as a neuromodulator, twenty of the proteinogenic amino acids are encoded directly by triplet codons in the genetic code and are known as standard amino acids. The other two are selenocysteine, and pyrrolysine, pyrrolysine and selenocysteine are encoded via variant codons, for example, selenocysteine is encoded by stop codon and SECIS element. N-formylmethionine is generally considered as a form of methionine rather than as a separate proteinogenic amino acid, codon–tRNA combinations not found in nature can also be used to expand the genetic code and create novel proteins known as alloproteins incorporating non-proteinogenic amino acids. Many important proteinogenic and non-proteinogenic amino acids also play critical roles within the body. Nine proteinogenic amino acids are called essential for humans because they cannot be created from other compounds by the human body, others may be conditionally essential for certain ages or medical conditions. Essential amino acids may also differ between species, because of their biological significance, amino acids are important in nutrition and are commonly used in nutritional supplements, fertilizers, and food technology. Industrial uses include the production of drugs, biodegradable plastics, the first few amino acids were discovered in the early 19th century. In 1806, French chemists Louis-Nicolas Vauquelin and Pierre Jean Robiquet isolated a compound in asparagus that was subsequently named asparagine, cystine was discovered in 1810, although its monomer, cysteine, remained undiscovered until 1884. Glycine and leucine were discovered in 1820, usage of the term amino acid in the English language is from 1898. Proteins were found to yield amino acids after enzymatic digestion or acid hydrolysis, in the structure shown at the top of the page, R represents a side chain specific to each amino acid. The carbon atom next to the group is called the α–carbon. Amino acids containing an amino group bonded directly to the alpha carbon are referred to as amino acids
4.
Peptide
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Peptides are biologically occurring short chains of amino acid monomers linked by peptide bonds. The covalent chemical bonds are formed when the group of one amino acid reacts with the amine group of another. The shortest peptides are dipeptides, consisting of 2 amino acids joined by a peptide bond, followed by tripeptides, tetrapeptides. A polypeptide is a long, continuous, and unbranched peptide chain, hence, peptides fall under the broad chemical classes of biological oligomers and polymers, alongside nucleic acids, oligosaccharides and polysaccharides, etc. Peptides are distinguished from proteins on the basis of size, all peptides except cyclic peptides have an N-terminal and C-terminal residue at the end of the peptide. Ribosomal peptides Ribosomal peptides are synthesized by translation of mRNA and they are often subjected to proteolysis to generate the mature form. These function, typically in higher organisms, as hormones and signaling molecules, some organisms produce peptides as antibiotics, such as microcins. Since they are translated, the amino acid residues involved are restricted to those utilized by the ribosome, however, these peptides frequently have posttranslational modifications such as phosphorylation, hydroxylation, sulfonation, palmitoylation, glycosylation and disulfide formation. In general, they are linear, although lariat structures have been observed, more exotic manipulations do occur, such as racemization of L-amino acids to D-amino acids in platypus venom. Nonribosomal peptides Nonribosomal peptides are assembled by enzymes that are specific to each peptide, the most common non-ribosomal peptide is glutathione, which is a component of the antioxidant defenses of most aerobic organisms. Other nonribosomal peptides are most common in organisms, plants. These complexes are often out in a similar fashion. These peptides are often cyclic and can have highly complex cyclic structures, since the system is closely related to the machinery for building fatty acids and polyketides, hybrid compounds are often found. The presence of oxazoles or thiazoles often indicates that the compound was synthesized in this fashion, Peptones See also Tryptone Peptones are derived from animal milk or meat digested by proteolysis. In addition to containing small peptides, the material includes fats, metals, salts, vitamins. Peptones are used in nutrient media for growing bacteria and fungi, Peptide fragments Peptide fragments refer to fragments of proteins that are used to identify or quantify the source protein. Peptides received prominence in molecular biology for several reasons, the first is that peptides allow the creation of peptide antibodies in animals without the need of purifying the protein of interest. This involves synthesizing antigenic peptides of sections of the protein of interest and these will then be used to make antibodies in a rabbit or mouse against the protein
5.
Dipeptide
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In this usage, X dipeptide must be understood as di-X peptide. This nomenclature is continued by tripeptide, tetrapeptide, and so on, longer chains are called oligopeptide, polypeptide, dipeptides are produced from polypeptides by the action of the hydrolase enzyme dipeptidyl peptidase. Dietary proteins are digested to dipeptides and amino acids, and the dipeptides are absorbed more rapidly than the amino acids, dipeptides activate G-cells found in the stomach to secrete gastrin. The Bergmann azlactone peptide synthesis is an organic synthesis for the preparation of dipeptides. Carnosine is highly concentrated in muscle and brain tissues, anserine is found in the skeletal muscle and brain of mammals. Homoanserine is another dipeptide identified in the brain and muscles of mammals, kyotorphin is a neuroactive dipeptide which plays a role in pain regulation in the brain. Balenine has been identified in the muscles of several species of mammal, glorin is a chemotactic dipeptide for the slime mold Polysphondylium violaceum. Barettin is a dipeptide from the marine sponge Geodia barretti. For instance, alanine dipeptide is CH3CONHCHCONHCH3, an introduction to dipeptides at PeptideGuide
6.
Condensation reaction
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A condensation reaction is a chemical reaction in which two molecules or moieties, often functional groups, combine to form a larger molecule, together with the loss of a small molecule. Possible small molecules that are lost include water, acetic acid, hydrogen chloride, or methanol, condensations producing water as a byproduct are the opposite reaction of transformations involving hydrolysis, which split a reactant into two new species through addition of a water molecule. Condensation can be intermolecular or intramolecular, a simple example of an intermolecular condensation is the joining of two amino acids in the peptide bond, as is characteristic of all proteins. The condensation reaction-speed can be catalyzed, by adding a concentrated acid to the reaction. It effects it by acidifying the environment whereas the reaction takes place the acid thereby binds with the water molecules, condensation reactions can follow a variety of different reaction mechanisms, depending on the groups reacting and the conditions employed to perform the reaction. Many artificial, man-made chemical reactions, and many biological transformations are condensation reactions, condensation polymerization produces many important polymers, for example, nylon, polyester, and other condensation polymers and various epoxies. It is also the basis for the formation of silicates and polyphosphates. In condensation polymerization or step-growth polymerization, multiple reactions take place, joining monomers. It occurs for example in the synthesis of polyesters or nylons and it can be homopolymerization of a single monomer A-B with two different end groups that condense, or copolymerization of two co-monomers A-A and B-B. Condensation polymerization releases multiple small molecules, in contrast to polyaddition reactions, in general, condensation polymers form more slowly than addition polymers, often requiring heat. They are generally lower in molecular weight, monomers are consumed early in the reaction, the terminal functional groups remain active throughout, and short chains combine to form longer chains. A high conversion rate is required to achieve high molecular weights, anabolism Hydrolysis, the opposite of a condensation reaction Condensed tannins
7.
Carboxylic acid
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A carboxylic acid /ˌkɑːrbɒkˈsɪlɪk/ is an organic compound that contains a carboxyl group. The general formula of an acid is R–COOH, with R referring to the rest of the molecule. Carboxylic acids occur widely and include the amino acids and acetic acid, salts and esters of carboxylic acids are called carboxylates. When a carboxyl group is deprotonated, its conjugate base forms a carboxylate anion, carboxylate ions are resonance-stabilized, and this increased stability makes carboxylic acids more acidic than alcohols. Carboxylic acids can be seen as reduced or alkylated forms of the Lewis acid carbon dioxide, carboxylic acids are commonly identified using their trivial names, and usually have the suffix -ic acid. IUPAC-recommended names also exist, in system, carboxylic acids have an -oic acid suffix. For example, butyric acid is butanoic acid by IUPAC guidelines, the -oic acid nomenclature detail is based on the name of the previously-known chemical benzoic acid. Alternately, it can be named as a carboxy or carboxylic acid substituent on another parent structure, for example, 2-carboxyfuran. The carboxylate anion of an acid is usually named with the suffix -ate, in keeping with the general pattern of -ic acid and -ate for a conjugate acid and its conjugate base. For example, the base of acetic acid is acetate. The radical •COOH has only a fleeting existence. The acid dissociation constant of •COOH has been measured using electron paramagnetic resonance spectroscopy, the carboxyl group tends to dimerise to form oxalic acid. Because they are both hydrogen-bond acceptors and hydrogen-bond donors, they participate in hydrogen bonding. Together the hydroxyl and carbonyl group forms the functional group carboxyl, carboxylic acids usually exist as dimeric pairs in nonpolar media due to their tendency to self-associate. Smaller carboxylic acids are soluble in water, whereas higher carboxylic acids are less due to the increasing hydrophobic nature of the alkyl chain. These longer chain acids tend to be soluble in less-polar solvents such as ethers. Carboxylic acids tend to have higher boiling points than water, not only because of their surface area. Carboxylic acids tend to evaporate or boil as these dimers, for boiling to occur, either the dimer bonds must be broken or the entire dimer arrangement must be vaporised, both of which increase the enthalpy of vaporization requirements significantly
8.
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
9.
Amine
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In organic chemistry, amines are compounds and functional groups that contain a basic nitrogen atom with a lone pair. Amines are formally derivatives of ammonia, wherein one or more hydrogen atoms have been replaced by a substituent such as an alkyl or aryl group, important amines include amino acids, biogenic amines, trimethylamine, and aniline, see Category, Amines for a list of amines. Inorganic derivatives of ammonia are also called amines, such as chloramine, see Category, compounds with a nitrogen atom attached to a carbonyl group, thus having the structure R–CO–NR′R″, are called amides and have different chemical properties from amines. An aliphatic amine has no aromatic ring attached directly to the nitrogen atom, aromatic amines have the nitrogen atom connected to an aromatic ring as in the various anilines. The aromatic ring decreases the alkalinity of the amine, depending on its substituents, the presence of an amine group strongly increases the reactivity of the aromatic ring, due to an electron-donating effect. Amines are organized into four subcategories, Primary amines — Primary amines arise when one of three atoms in ammonia is replaced by an alkyl or aromatic. Important primary alkyl amines include, methylamine, most amino acids, Secondary amines — Secondary amines have two organic substituents bound to the nitrogen together with one hydrogen. Important representatives include dimethylamine, while an example of an aromatic amine would be diphenylamine, tertiary amines — In tertiary amines, nitrogen has three organic substituents. Examples include trimethylamine, which has a fishy smell. Cyclic amines — Cyclic amines are either secondary or tertiary amines, examples of cyclic amines include the 3-membered ring aziridine and the six-membered ring piperidine. N-methylpiperidine and N-phenylpiperidine are examples of tertiary amines. It is also possible to have four organic substituents on the nitrogen and these species are not amines but are quaternary ammonium cations and have a charged nitrogen center. Quaternary ammonium salts exist with many kinds of anions, Amines are named in several ways. Typically, the compound is given the prefix amino- or the suffix, the prefix N- shows substitution on the nitrogen atom. An organic compound with multiple amino groups is called a diamine, triamine, tetraamine, systematic names for some common amines, Hydrogen bonding significantly influences the properties of primary and secondary amines. Thus the melting point and boiling point of amines is higher than those of the corresponding phosphines, for example, methyl and ethyl amines are gases under standard conditions, whereas the corresponding methyl and ethyl alcohols are liquids. Amines possess a characteristic smell, liquid amines have a distinctive fishy smell. The nitrogen atom features a lone pair that can bind H+ to form an ammonium ion R3NH+
10.
Amino group
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In organic chemistry, amines are compounds and functional groups that contain a basic nitrogen atom with a lone pair. Amines are formally derivatives of ammonia, wherein one or more hydrogen atoms have been replaced by a substituent such as an alkyl or aryl group, important amines include amino acids, biogenic amines, trimethylamine, and aniline, see Category, Amines for a list of amines. Inorganic derivatives of ammonia are also called amines, such as chloramine, see Category, compounds with a nitrogen atom attached to a carbonyl group, thus having the structure R–CO–NR′R″, are called amides and have different chemical properties from amines. An aliphatic amine has no aromatic ring attached directly to the nitrogen atom, aromatic amines have the nitrogen atom connected to an aromatic ring as in the various anilines. The aromatic ring decreases the alkalinity of the amine, depending on its substituents, the presence of an amine group strongly increases the reactivity of the aromatic ring, due to an electron-donating effect. Amines are organized into four subcategories, Primary amines — Primary amines arise when one of three atoms in ammonia is replaced by an alkyl or aromatic. Important primary alkyl amines include, methylamine, most amino acids, Secondary amines — Secondary amines have two organic substituents bound to the nitrogen together with one hydrogen. Important representatives include dimethylamine, while an example of an aromatic amine would be diphenylamine, tertiary amines — In tertiary amines, nitrogen has three organic substituents. Examples include trimethylamine, which has a fishy smell. Cyclic amines — Cyclic amines are either secondary or tertiary amines, examples of cyclic amines include the 3-membered ring aziridine and the six-membered ring piperidine. N-methylpiperidine and N-phenylpiperidine are examples of tertiary amines. It is also possible to have four organic substituents on the nitrogen and these species are not amines but are quaternary ammonium cations and have a charged nitrogen center. Quaternary ammonium salts exist with many kinds of anions, Amines are named in several ways. Typically, the compound is given the prefix amino- or the suffix, the prefix N- shows substitution on the nitrogen atom. An organic compound with multiple amino groups is called a diamine, triamine, tetraamine, systematic names for some common amines, Hydrogen bonding significantly influences the properties of primary and secondary amines. Thus the melting point and boiling point of amines is higher than those of the corresponding phosphines, for example, methyl and ethyl amines are gases under standard conditions, whereas the corresponding methyl and ethyl alcohols are liquids. Amines possess a characteristic smell, liquid amines have a distinctive fishy smell. The nitrogen atom features a lone pair that can bind H+ to form an ammonium ion R3NH+
11.
Water
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Water is a transparent and nearly colorless chemical substance that is the main constituent of Earths streams, lakes, and oceans, and the fluids of most living organisms. Its chemical formula is H2O, meaning that its molecule contains one oxygen, Water strictly refers to the liquid state of that substance, that prevails at standard ambient temperature and pressure, but it often refers also to its solid state or its gaseous state. It also occurs in nature as snow, glaciers, ice packs and icebergs, clouds, fog, dew, aquifers, Water covers 71% of the Earths surface. It is vital for all forms of life. Only 2. 5% of this water is freshwater, and 98. 8% of that water is in ice and groundwater. Less than 0. 3% of all freshwater is in rivers, lakes, and the atmosphere, a greater quantity of water is found in the earths interior. Water on Earth moves continually through the cycle of evaporation and transpiration, condensation, precipitation. Evaporation and transpiration contribute to the precipitation over land, large amounts of water are also chemically combined or adsorbed in hydrated minerals. Safe drinking water is essential to humans and other even though it provides no calories or organic nutrients. There is a correlation between access to safe water and gross domestic product per capita. However, some observers have estimated that by 2025 more than half of the population will be facing water-based vulnerability. A report, issued in November 2009, suggests that by 2030, in developing regions of the world. Water plays an important role in the world economy, approximately 70% of the freshwater used by humans goes to agriculture. Fishing in salt and fresh water bodies is a source of food for many parts of the world. Much of long-distance trade of commodities and manufactured products is transported by boats through seas, rivers, lakes, large quantities of water, ice, and steam are used for cooling and heating, in industry and homes. Water is an excellent solvent for a variety of chemical substances, as such it is widely used in industrial processes. Water is also central to many sports and other forms of entertainment, such as swimming, pleasure boating, boat racing, surfing, sport fishing, Water is a liquid at the temperatures and pressures that are most adequate for life. Specifically, at atmospheric pressure of 1 bar, water is a liquid between the temperatures of 273.15 K and 373.15 K
12.
Dehydration reaction
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In chemistry and the biological sciences, a dehydration reaction is usually defined as a chemical reaction that involves the loss of a water molecule from the reacting molecule. Dehydration reactions are a subset of condensation reactions, because the hydroxyl group is a poor leaving group, having a Brønsted acid catalyst often helps by protonating the hydroxyl group to give the better leaving group, –OH2+. The reverse of a reaction is a hydration reaction. Common dehydrating agents used in organic synthesis include concentrated sulfuric acid, concentrated phosphoric acid, hot aluminium oxide, dehydration reactions and dehydration synthesis have the same meaning, and are often used interchangeably. Two monosaccharides, such as glucose and fructose, can be joined together using dehydration synthesis, the new molecule, consisting of two monosaccharides, is called a disaccharide. The process of hydrolysis is the reaction, meaning that the water is recombined with the two hydroxyl groups and the disaccharide reverts to being monosaccharides. In the related condensation reaction water is released two different reactants. In organic synthesis, there are examples of dehydration reaction
13.
Adenosine triphosphate
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Adenosine triphosphate is a nucleotide, also called a nucleoside triphosphate, is a small molecule used in cells as a coenzyme. It is often referred to as the unit of currency of intracellular energy transfer. ATP transports chemical energy within cells for metabolism, most cellular functions need energy in order to be carried out, synthesis of proteins, synthesis of membranes, movement of the cell, cellular division, transport of various solutes etc. The ATP is the molecule that carries energy to the place where the energy is needed, when ATP breaks into ADP and Pi, the breakdown of the last covalent link of phosphate liberates energy that is used in reactions where it is needed. Substrate-level phosphorylation, oxidative phosphorylation in cellular respiration, and photophosphorylation in photosynthesis are three mechanisms of ATP biosynthesis. Metabolic processes that use ATP as an energy source convert it back into its precursors, ATP is therefore continuously recycled in organisms, the human body, which on average contains only 250 grams of ATP, turns over its own body weight equivalent in ATP each day. ATP is used as a substrate in signal transduction pathways by kinases that phosphorylate proteins and it is also used by adenylate cyclase, which uses ATP to produce the second messenger molecule cyclic AMP. The ratio between ATP and AMP is used as a way for a cell to sense how much energy is available and control the metabolic pathways that produce and consume ATP. Apart from its roles in signaling and energy metabolism, ATP is also incorporated into nucleic acids by polymerases in the process of transcription, ATP is the neurotransmitter believed to signal the sense of taste. The structure of this consists of a purine base attached by the 9′ nitrogen atom to the 1′ carbon atom of a pentose sugar. Three phosphate groups are attached at the 5′ carbon atom of the pentose sugar and it is the addition and removal of these phosphate groups that inter-convert ATP, ADP and AMP. When ATP is used in DNA synthesis, the sugar is first converted to deoxyribose by ribonucleotide reductase. ATP was discovered in 1929 by Karl Lohmann, and independently by Cyrus Fiske and Yellapragada Subbarow of Harvard Medical School and it was proposed to be the intermediary molecule between energy-yielding and energy-requiring reactions in cells by Fritz Albert Lipmann in 1941. It was first artificially synthesized by Alexander Todd in 1948, ATP consists of adenosine – composed of an adenine ring and a ribose sugar – and three phosphate groups. The phosphoryl groups, starting with the group closest to the ribose, are referred to as the alpha, beta, consequently, it is closely related to the adenosine nucleotide, a monomer of RNA. ATP is highly soluble in water and is stable in solutions between pH6.8 and 7.4, but is rapidly hydrolysed at extreme pH. Consequently, ATP is best stored as an anhydrous salt, ATP is an unstable molecule in unbuffered water, in which it hydrolyses to ADP and phosphate. This is because the strength of the bonds between the groups in ATP is less than the strength of the hydrogen bonds, between its products, and water
14.
Protein
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Proteins are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, a linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide, short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides, or sometimes oligopeptides. The individual amino acid residues are bonded together by peptide bonds, the sequence of amino acid residues in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In general, the code specifies 20 standard amino acids, however. Sometimes proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors, proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes. Once formed, proteins only exist for a period of time and are then degraded and recycled by the cells machinery through the process of protein turnover. A proteins lifespan is measured in terms of its half-life and covers a wide range and they can exist for minutes or years with an average lifespan of 1–2 days in mammalian cells. Abnormal and or misfolded proteins are degraded more rapidly due to being targeted for destruction or due to being unstable. Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms, many proteins are enzymes that catalyse biochemical reactions and are vital to metabolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle. In animals, proteins are needed in the diet to provide the essential amino acids that cannot be synthesized, digestion breaks the proteins down for use in the metabolism. Methods commonly used to study structure and function include immunohistochemistry, site-directed mutagenesis, X-ray crystallography, nuclear magnetic resonance. Most proteins consist of linear polymers built from series of up to 20 different L-α-amino acids, all proteinogenic amino acids possess common structural features, including an α-carbon to which an amino group, a carboxyl group, and a variable side chain are bonded. Only proline differs from this structure as it contains an unusual ring to the N-end amine group. The amino acids in a chain are linked by peptide bonds. Once linked in the chain, an individual amino acid is called a residue, and the linked series of carbon, nitrogen. The peptide bond has two forms that contribute some double-bond character and inhibit rotation around its axis, so that the alpha carbons are roughly coplanar
15.
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
16.
Ribosome
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The ribosome is a complex molecular machine, found within all living cells, that serves as the site of biological protein synthesis. Ribosomes link amino acids together in the order specified by messenger RNA molecules, ribosomes consist of two major components, the small ribosomal subunit, which reads the RNA, and the large subunit, which joins amino acids to form a polypeptide chain. Each subunit is composed of one or more ribosomal RNA molecules, the ribosomes and associated molecules are also known as the translational apparatus. The sequence of DNA, which encodes the sequence of the acids in a protein, is copied into a messenger RNA chain. It may be copied many times into RNA chains, ribosomes can bind to a messenger RNA chain and use its sequence for determining the correct sequence of amino acids. Amino acids are selected, collected, and carried to the ribosome by transfer RNA molecules and it is during this binding that the correct translation of nucleic acid sequence to amino acid sequence occurs. For each coding triplet in the messenger RNA there is a distinct transfer RNA that matches, the attached amino acids are then linked together by another part of the ribosome. Once the protein is produced, it can then fold to produce a specific functional three-dimensional structure although during synthesis some proteins start folding into their correct form, a ribosome is made from complexes of RNAs and proteins and is therefore a ribonucleoprotein. When a ribosome finishes reading an mRNA molecule, these two subunits split apart, ribosomes are ribozymes, because the catalytic peptidyl transferase activity that links amino acids together is performed by the ribosomal RNA. Ribosomes are often associated with the membranes that make up the rough endoplasmic reticulum. Ribosomes from bacteria, archaea and eukaryotes in the system, resemble each other to a remarkable degree. They differ in their size, sequence, structure, and the ratio of protein to RNA, the differences in structure allow some antibiotics to kill bacteria by inhibiting their ribosomes, while leaving human ribosomes unaffected. In bacteria and archaea, more than one ribosome may move along a single mRNA chain at one time, each reading its sequence, ribosomes were first observed in the mid-1950s by Romanian cell biologist George Emil Palade, using an electron microscope, as dense particles or granules. The Nobel Prize in Chemistry 2009 was awarded to Venkatraman Ramakrishnan, Thomas A. Steitz and Ada E. Yonath for determining the detailed structure, the ribosome is a highly complex cellular machine. It is largely made up of specialized RNA known as ribosomal RNA as well as dozens of distinct proteins, the ribosomal proteins and rRNAs are arranged into two distinct ribosomal pieces of different size, known generally as the large and small subunit of the ribosome. Ribosomes consist of two subunits that fit together and work as one to translate the mRNA into a polypeptide chain during protein synthesis, because they are formed from two subunits of non-equal size, they are slightly longer in the axis than in diameter. Prokaryotic ribosomes are around 20 nm in diameter and are composed of 65% rRNA, eukaryotic ribosomes are between 25 and 30 nm in diameter with an rRNA-to-protein ratio that is close to 1. Bacterial ribosomes are composed of one or two rRNA strands, eukaryotic ribosomes contain one or three very large rRNA molecules and multiple smaller protein molecules
17.
Glutathione synthetase
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Glutathione synthetase is the second enzyme in the glutathione biosynthesis pathway. It catalyses the condensation of gamma-glutamylcysteine and glycine, to form glutathione, Glutathione synthetase is also a potent antioxidant. It is found in a number of species including bacteria, yeast, mammals. Deficiencies in GSS can cause a spectrum of symptoms in plants. In eukaryotes, this is a homodimeric enzyme, the substrate-binding domain has a 3-layer alpha/beta/alpha structure. This enzyme utilizes and stabilizes an acylphosphate intermediate to later perform a nucleophilic attack of glycine. Human and yeast glutathione synthetases are homodimers, meaning they are composed of two subunits of itself non-covalently bound to each other. On the other hand, E. coli glutathione synthetase is a homotetramer, nevertheless, they are part of the ATP-grasp superfamily, which consists of 21 enzymes that contain an ATP-grasp fold. Each subunit interacts with other through alpha helix and beta sheet hydrogen bonding interactions and contains two domains. One domain facilitates the ATP-grasp mechanism and the other is the active site for γ-glutamylcysteine. The ATP-grasp fold is conserved within the ATP-grasp superfamily and is characterized by two helices and beta sheets that hold onto the ATP molecule between them. The domain containing the active site exhibits interesting properties of specificity, crystalline structures have shown glutathione synthetase bound to GSH, ADP, two magnesium ions, and a sulfate ion. Two magnesium ions function to stabilize the intermediate, facilitate binding of ATP. Sulfate ion serves as a replacement for inorganic phosphate once the acylphosphate intermediate is formed inside the active site, the biosynthetic mechanisms for synthetases use energy from nucleoside triphosphates, whereas synthases do not. Glutathione synthetase stays true to this rule, in that it uses the energy generated by ATP, initially, the carboxylate group on γ-glutamylcysteine is converted into an acyl phosphate by the transfer of an inorganic phosphate group of ATP to generate an acyl phosphate intermediate. Then the amino group of glycine participates in an attack, displacing the phosphate group. After the final GSH product is made, it can be used by glutathione peroxidase to neutralize reactive oxygen species such as H2O2 or Glutathione S-transferases in the detoxification of xenobiotics, Glutathione synthetase is important for a variety of biological functions in multiple organisms. In Arabidopsis thaliana, low levels of glutathione synthetase have resulted in increased vulnerability to stressors such as metals, toxic organic chemicals
18.
Hydrolysis
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Hydrolysis usually means the cleavage of chemical bonds by the addition of water. When a carbohydrate is broken into its component sugar molecules by hydrolysis, generally, hydrolysis or saccharification is a step in the degradation of a substance. Hydrolysis can be the reverse of a reaction in which two molecules join together into a larger one and eject a water molecule. Thus hydrolysis adds water to break down, whereas condensation builds up by removing water, usually hydrolysis is a chemical process in which a molecule of water is added to a substance. Sometimes this addition causes both substance and water molecule to split into two parts, in such reactions, one fragment of the target molecule gains a hydrogen ion. A common kind of hydrolysis occurs when a salt of an acid or weak base is dissolved in water. Water spontaneously ionizes into hydroxide anions and hydronium cations, the salt also dissociates into its constituent anions and cations. For example, sodium acetate dissociates in water into sodium and acetate ions, sodium ions react very little with the hydroxide ions whereas the acetate ions combine with hydronium ions to produce acetic acid. In this case the net result is an excess of hydroxide ions. For example, dissolving sulfuric acid in water is accompanied by hydrolysis to give hydronium and bisulfate, for a more technical discussion of what occurs during such a hydrolysis, see Brønsted–Lowry acid–base theory. Acid–base-catalysed hydrolyses are very common, one example is the hydrolysis of amides or esters and their hydrolysis occurs when the nucleophile attacks the carbon of the carbonyl group of the ester or amide. In an aqueous base, hydroxyl ions are better nucleophiles than polar molecules such as water, in acids, the carbonyl group becomes protonated, and this leads to a much easier nucleophilic attack. The products for both hydrolyses are compounds with carboxylic acid groups, perhaps the oldest commercially practiced example of ester hydrolysis is saponification. It is the hydrolysis of a triglyceride with a base such as sodium hydroxide. During the process, glycerol is formed, and the fatty acids react with the base and these salts are called soaps, commonly used in households. In addition, in living systems, most biochemical reactions take place during the catalysis of enzymes, the catalytic action of enzymes allows the hydrolysis of proteins, fats, oils, and carbohydrates. As an example, one may consider proteases and they catalyse the hydrolysis of interior peptide bonds in peptide chains, as opposed to exopeptidases. However, proteases do not catalyse the hydrolysis of all kinds of proteins and their action is stereo-selective, Only proteins with a certain tertiary structure are targeted as some kind of orienting force is needed to place the amide group in the proper position for catalysis
19.
Joule
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The joule, symbol J, is a derived unit of energy in the International System of Units. It is equal to the transferred to an object when a force of one newton acts on that object in the direction of its motion through a distance of one metre. It is also the energy dissipated as heat when a current of one ampere passes through a resistance of one ohm for one second. It is named after the English physicist James Prescott Joule, one joule can also be defined as, The work required to move an electric charge of one coulomb through an electrical potential difference of one volt, or one coulomb volt. This relationship can be used to define the volt, the work required to produce one watt of power for one second, or one watt second. This relationship can be used to define the watt and this SI unit is named after James Prescott Joule. As with every International System of Units unit named for a person, note that degree Celsius conforms to this rule because the d is lowercase. — Based on The International System of Units, section 5.2. The CGPM has given the unit of energy the name Joule, the use of newton metres for torque and joules for energy is helpful to avoid misunderstandings and miscommunications. The distinction may be also in the fact that energy is a scalar – the dot product of a vector force. By contrast, torque is a vector – the cross product of a distance vector, torque and energy are related to one another by the equation E = τ θ, where E is energy, τ is torque, and θ is the angle swept. Since radians are dimensionless, it follows that torque and energy have the same dimensions, one joule in everyday life represents approximately, The energy required to lift a medium-size tomato 1 m vertically from the surface of the Earth. The energy released when that same tomato falls back down to the ground, the energy required to accelerate a 1 kg mass at 1 m·s−2 through a 1 m distance in space. The heat required to raise the temperature of 1 g of water by 0.24 °C, the typical energy released as heat by a person at rest every 1/60 s. The kinetic energy of a 50 kg human moving very slowly, the kinetic energy of a 56 g tennis ball moving at 6 m/s. The kinetic energy of an object with mass 1 kg moving at √2 ≈1.4 m/s, the amount of electricity required to light a 1 W LED for 1 s. Since the joule is also a watt-second and the unit for electricity sales to homes is the kW·h. For additional examples, see, Orders of magnitude The zeptojoule is equal to one sextillionth of one joule,160 zeptojoules is equivalent to one electronvolt. The nanojoule is equal to one billionth of one joule, one nanojoule is about 1/160 of the kinetic energy of a flying mosquito
20.
Mole (unit)
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The mole is the unit of measurement in the International System of Units for amount of substance. This number is expressed by the Avogadro constant, which has a value of 6. 022140857×1023 mol−1, the mole is one of the base units of the SI, and has the unit symbol mol. The mole is used in chemistry as a convenient way to express amounts of reactants and products of chemical reactions. For example, the chemical equation 2 H2 + O2 →2 H2O implies that 2 moles of dihydrogen and 1 mole of dioxygen react to form 2 moles of water. The mole may also be used to express the number of atoms, ions, the concentration of a solution is commonly expressed by its molarity, defined as the number of moles of the dissolved substance per litre of solution. For example, the relative molecular mass of natural water is about 18.015, therefore. The term gram-molecule was formerly used for essentially the same concept, the term gram-atom has been used for a related but distinct concept, namely a quantity of a substance that contains Avogadros number of atoms, whether isolated or combined in molecules. Thus, for example,1 mole of MgBr2 is 1 gram-molecule of MgBr2 but 3 gram-atoms of MgBr2, in honor of the unit, some chemists celebrate October 23, which is a reference to the 1023 scale of the Avogadro constant, as Mole Day. Some also do the same for February 6 and June 2, thus, by definition, one mole of pure 12C has a mass of exactly 12 g. It also follows from the definition that X moles of any substance will contain the number of molecules as X moles of any other substance. The mass per mole of a substance is called its molar mass, the number of elementary entities in a sample of a substance is technically called its amount. Therefore, the mole is a convenient unit for that physical quantity, one can determine the chemical amount of a known substance, in moles, by dividing the samples mass by the substances molar mass. Other methods include the use of the volume or the measurement of electric charge. The mass of one mole of a substance depends not only on its molecular formula, since the definition of the gram is not mathematically tied to that of the atomic mass unit, the number NA of molecules in a mole must be determined experimentally. The value adopted by CODATA in 2010 is NA =6. 02214129×1023 ±0. 00000027×1023, in 2011 the measurement was refined to 6. 02214078×1023 ±0. 00000018×1023. The number of moles of a sample is the sample mass divided by the mass of the material. The history of the mole is intertwined with that of mass, atomic mass unit, Avogadros number. The first table of atomic mass was published by John Dalton in 1805
21.
Thermodynamic free energy
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The thermodynamic free energy is the amount of work that a thermodynamic system can perform. The concept is useful in the thermodynamics of chemical or thermal processes in engineering, the free energy is the internal energy of a system minus the amount of energy that cannot be used to perform work. This unusable energy is given by the entropy of a multiplied by the temperature of the system. Like the internal energy, the energy is a thermodynamic state function. Energy is a generalization of free energy, since energy is the ability to do work which is free energy, free energy is that portion of any first-law energy that is available to perform thermodynamic work, i. e. work mediated by thermal energy. Free energy is subject to loss in the course of such work. Since first-law energy is conserved, it is evident that free energy is an expendable. Several free energy functions may be formulated based on system criteria, free energy functions are Legendre transformations of the internal energy. The Helmholtz free energy has a theoretical importance since it is proportional to the logarithm of the partition function for the canonical ensemble in statistical mechanics. The historically earlier Helmholtz free energy is defined as A = U − TS, where U is the energy, T is the absolute temperature. Its change is equal to the amount of work done on, or obtainable from. Thus its appellation work content, and the designation A from Arbeit, the Gibbs free energy is given by G = H − TS, where H is the enthalpy. Historically, these terms have been used inconsistently. In physics, free energy most often refers to the Helmholtz free energy, denoted by A, while in chemistry, since both fields use both functions, a compromise has been suggested, using A to denote the Helmholtz function and G for the Gibbs function. While A is preferred by IUPAC, G is sometimes still in use, the use of the words “latent heat” implied a similarity to latent heat in the more usual sense, it was regarded as chemically bound to the molecules of the body. In the adiabatic compression of a gas, the heat remained constant. During the early 19th century, the concept of perceptible or free caloric began to be referred to as “free heat” or heat set free. In 1824, for example, the French physicist Sadi Carnot, in his famous “Reflections on the Motive Power of Fire”, an increasing number of books and journal articles do not include the attachment “free”, referring to G as simply Gibbs energy
22.
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
23.
Wavelength
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In physics, the wavelength of a sinusoidal wave is the spatial period of the wave—the distance over which the waves shape repeats, and thus the inverse of the spatial frequency. Wavelength is commonly designated by the Greek letter lambda, the concept can also be applied to periodic waves of non-sinusoidal shape. The term wavelength is also applied to modulated waves. Wavelength depends on the medium that a wave travels through, examples of wave-like phenomena are sound waves, light, water waves and periodic electrical signals in a conductor. A sound wave is a variation in air pressure, while in light and other electromagnetic radiation the strength of the electric, water waves are variations in the height of a body of water. In a crystal lattice vibration, atomic positions vary, wavelength is a measure of the distance between repetitions of a shape feature such as peaks, valleys, or zero-crossings, not a measure of how far any given particle moves. For example, in waves over deep water a particle near the waters surface moves in a circle of the same diameter as the wave height. The range of wavelengths or frequencies for wave phenomena is called a spectrum, the name originated with the visible light spectrum but now can be applied to the entire electromagnetic spectrum as well as to a sound spectrum or vibration spectrum. In linear media, any pattern can be described in terms of the independent propagation of sinusoidal components. The wavelength λ of a sinusoidal waveform traveling at constant speed v is given by λ = v f, in a dispersive medium, the phase speed itself depends upon the frequency of the wave, making the relationship between wavelength and frequency nonlinear. In the case of electromagnetic radiation—such as light—in free space, the speed is the speed of light. Thus the wavelength of a 100 MHz electromagnetic wave is about, the wavelength of visible light ranges from deep red, roughly 700 nm, to violet, roughly 400 nm. For sound waves in air, the speed of sound is 343 m/s, the wavelengths of sound frequencies audible to the human ear are thus between approximately 17 m and 17 mm, respectively. Note that the wavelengths in audible sound are much longer than those in visible light, a standing wave is an undulatory motion that stays in one place. A sinusoidal standing wave includes stationary points of no motion, called nodes, the upper figure shows three standing waves in a box. The walls of the box are considered to require the wave to have nodes at the walls of the box determining which wavelengths are allowed, the stationary wave can be viewed as the sum of two traveling sinusoidal waves of oppositely directed velocities. Consequently, wavelength, period, and wave velocity are related just as for a traveling wave, for example, the speed of light can be determined from observation of standing waves in a metal box containing an ideal vacuum. In that case, the k, the magnitude of k, is still in the same relationship with wavelength as shown above
24.
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
25.
Lone pair
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In chemistry, a lone pair refers to a pair of valence electrons that are not shared with another atom and is sometimes called a non-bonding pair. Lone pairs are found in the outermost electron shell of atoms and they can be identified by using a Lewis structure. Electron pairs are therefore considered lone pairs if two electrons are paired but are not used in chemical bonding, thus, the number of lone pair electrons plus the number of bonding electrons equals the total number of valence electrons around an atom. Lone pair is a used in VSEPR theory which explains the shapes of molecules. They are also referred to in the chemistry of Lewis acids, however, not all non-bonding pairs of electrons are considered by chemists to be lone pairs. Examples are the transition metals where the non-bonding pairs do not influence molecular geometry and are said to be stereochemically inactive, in VSEPR theory the electron pairs on the oxygen atom in water form the vertices of a tetrahedron with the lone pairs on two of the four vertices. The H–O–H bond angle is with 104. 5°, less than the 109° predicted for an angle. The pairs often exhibit a negative polar character with their charge density and are located closer to the atomic nucleus on average compared to the bonding pair of electrons. The presence of a lone pair decreases the angle between the bonding pair of electrons, due to their high electric charge which causes great repulsion between the electrons. They are also used in the formation of a dative bond, for example, the creation of the hydronium ion occurs when acids are dissolved in water and is due to the oxygen atom donating a lone pair to the hydrogen ion. This can be more clearly when looked at it in two more common molecules. For example, in carbon dioxide, the atoms are on opposite sides of the carbon. Due to the force of the oxygen atoms lone pairs. This is an illustration of the VSEPR theory, lone pairs can make a contribution to a molecules dipole moment. NH3 has a moment of 1.47 D. There is also an associated with the lone pair and this reinforces the contribution made by the polar covalent N-H bonds to ammonias dipole moment. In contrast to NH3, NF3 has a lower dipole moment of 0.24 D. A stereochemically active lone pair is expected for divalent lead
26.
Amide
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An amide, also known as an acid amide, is a compound with the functional group RnExNR′2. Most common are carboxamides, but many other important types of amides are known, the term amide refers both to classes of compounds and to the functional group within those compounds. Amide can also refer to the base of ammonia or of an organic amine. For discussion of these anionic amides, see Alkali metal amides, the remainder of this article is about the carbonyl–nitrogen sense of amide. The simplest amides are derivatives of ammonia wherein one hydrogen atom has replaced by an acyl group. The ensemble is represented as RCNH2 and is described as a primary amide. Closely related and even more numerous are secondary amides which can be derived from amines and have the formula RCNHR′. Tertiary amides are commonly derived from amines and have the general structure RCNR′R″. Amides are usually regarded as derivatives of carboxylic acids in which the group has been replaced by an amine or ammonia. The lone pair of electrons on the nitrogen is delocalized into the carbonyl, consequently, the nitrogen in amides is not pyramidal. It is estimated that acetamide is described by resonance structure A for 62%, in the usual nomenclature, one adds the term amide to the stem of the parent acids name. For instance, the derived from acetic acid is named acetamide. IUPAC recommends ethanamide, but this and related names are rarely encountered. When the amide is derived from a primary or secondary amine, thus, the amide formed from dimethylamine and acetic acid is N, N-dimethylacetamide. Usually even this name is simplified to dimethylacetamide, cyclic amides are called lactams, they are necessarily secondary or tertiary amides. Functional groups consisting of –PNR2 and –SO2NR2 are phosphonamides and sulfonamides, some chemists make a pronunciation distinction between the two, saying /əˈmiːd/ for the carbonyl–nitrogen compound and /ˈeɪmaɪd/ for the anion. Others replace one of these with /ˈæmᵻd/, while others pronounce both /ˈæmᵻd/, making them homonyms. Compared to amines, amides are very weak bases, while the conjugate acid of an amine has a pKa of about 9.5, the conjugate acid of an amide has a pKa around −0.5
27.
Plane (geometry)
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In mathematics, a plane is a flat, two-dimensional surface that extends infinitely far. A plane is the analogue of a point, a line. When working exclusively in two-dimensional Euclidean space, the article is used, so. Many fundamental tasks in mathematics, geometry, trigonometry, graph theory and graphing are performed in a space, or in other words. Euclid set forth the first great landmark of mathematical thought, a treatment of geometry. He selected a small core of undefined terms and postulates which he used to prove various geometrical statements. Although the plane in its sense is not directly given a definition anywhere in the Elements. In his work Euclid never makes use of numbers to measure length, angle, in this way the Euclidean plane is not quite the same as the Cartesian plane. This section is concerned with planes embedded in three dimensions, specifically, in R3. In a Euclidean space of any number of dimensions, a plane is determined by any of the following. A line and a point not on that line, a line is either parallel to a plane, intersects it at a single point, or is contained in the plane. Two distinct lines perpendicular to the plane must be parallel to each other. Two distinct planes perpendicular to the line must be parallel to each other. Specifically, let r0 be the vector of some point P0 =. The plane determined by the point P0 and the vector n consists of those points P, with position vector r, such that the vector drawn from P0 to P is perpendicular to n. Recalling that two vectors are perpendicular if and only if their dot product is zero, it follows that the plane can be described as the set of all points r such that n ⋅ =0. Expanded this becomes a + b + c =0, which is the form of the equation of a plane. This is just a linear equation a x + b y + c z + d =0 and this familiar equation for a plane is called the general form of the equation of the plane
28.
Dihedral angle
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A dihedral angle is the angle between two intersecting planes. In chemistry it is the angle between planes through two sets of three atoms, having two atoms in common, in solid geometry it is defined as the union of a line and two half-planes that have this line as a common edge. In higher dimension, a dihedral angle represents the angle between two hyperplanes, a dihedral angle is an angle between two intersecting planes on a third plane perpendicular to the line of intersection. A torsion angle is an example of a dihedral angle. In stereochemistry every set of three atoms of a molecule defines a plane, when two such planes intersect, the angle between them is a dihedral angle. Dihedral angles are used to specify the molecular conformation, stereochemical arrangements corresponding to angles between 0° and ±90° are called syn, those corresponding to angles between ±90° and 180° anti. Similarly, arrangements corresponding to angles between 30° and 150° or between −30° and −150° are called clinal and those between 0° and ±30° or ±150° and 180° are called periplanar. The synperiplanar conformation is also known as the syn- or cis-conformation, antiperiplanar as anti or trans, for example, with n-butane two planes can be specified in terms of the two central carbon atoms and either of the methyl carbon atoms. The syn-conformation shown above, with an angle of 60° is less stable than the anti-configuration with a dihedral angle of 180°. For macromolecular usage the symbols T, C, G+, G−, A+, a Ramachandran plot, originally developed in 1963 by G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, is a way to visualize energetically allowed regions for backbone dihedral angles ψ against φ of amino acid residues in protein structure, the figure at right illustrates the definition of the φ and ψ backbone dihedral angles. In a protein chain three dihedral angles are defined as φ, ψ and ω, as shown in the diagram, the planarity of the peptide bond usually restricts ω to be 180° or 0°. The distance between the Cα atoms in the trans and cis isomers is approximately 3.8 and 2.9 Å, the cis isomer is mainly observed in Xaa–Pro peptide bonds. The sidechain dihedral angles tend to cluster near 180°, 60°, and −60°, which are called the trans, gauche+, the stability of certain sidechain dihedral angles is affected by the values φ and ψ. For instance, there are steric interactions between the Cγ of the side chain in the gauche+ rotamer and the backbone nitrogen of the next residue when ψ is near -60°. An alternative method is to calculate the angle between the vectors, nA and nB, which are normal to the planes. Cos φ = − n A ⋅ n B | n A | | n B | where nA · nB is the dot product of the vectors and |nA| |nB| is the product of their lengths. Any plane can also be described by two non-collinear vectors lying in that plane, taking their cross product yields a vector to the plane
29.
Synperiplanar
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Alkane stereochemistry concerns the stereochemistry of alkanes. Alkane conformers are one of the subjects of alkane stereochemistry, alkane conformers arise from rotation around sp3 hybridised carbon carbon sigma bonds. The smallest alkane with such a bond, ethane, exists as an infinite number of conformations with respect to rotation around the C–C bond. Two of these are recognised as energy minimum and energy maximum forms, the existence of specific conformations is due to hindered rotation around sigma bonds, although a role for hyperconjugation is proposed by a competing theory. The importance of energy minimum and energy maximum is seen by extension of these concepts to more complex molecules for which stable conformations may be predicted as minimum energy forms. The staggered conformation is more stable by 12.5 kJ/mol than the eclipsed conformation, in the eclipsed conformation the torsional angle is minimised. In butane, the two staggered conformations are no longer equivalent and represent two distinct conformers, the anti-conformation and the gauche conformation. Both conformations are free of torsional strain, but, in the gauche conformation, the interaction between the two methyl groups is repulsive, and an energy barrier results. The eclipsed methyl groups exert a greater steric strain because of their electron density compared to lone hydrogen atoms. The question of whether steric hindrance is responsible for the energy maximum is a topic of debate to this day. One alternative to the steric hindrance explanation is based on hyperconjugation as analyzed within the Natural Bond Orbital framework, in the staggered conformation, one C-H sigma bonding orbital donates electron density to the antibonding orbital of the other C-H bond. The energetic stabilization of this effect is maximized when the two orbitals have maximal overlap, occurring in the staggered conformation, there is no overlap in the eclipsed conformation, leading to a disfavored energy maximum. On the other hand, an analysis within quantitative molecular orbital theory shows that 2-orbital-4-electron repulsions are dominant over hyperconjugation, a valence bond theory study also emphasizes the importance of steric effects. Torsional strain results from resistance to twisting about a bond, in n-pentane, the terminal methyl groups experience additional pentane interference. Evidence for the structure in the crystalline state is derived from X-ray crystallography and from NMR spectroscopy. More alkane conformations exist in cyclic alkanes, see cyclohexane conformations, more on the impact of gauche interactions, see Gauche effect
30.
Antiperiplanar
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Alkane stereochemistry concerns the stereochemistry of alkanes. Alkane conformers are one of the subjects of alkane stereochemistry, alkane conformers arise from rotation around sp3 hybridised carbon carbon sigma bonds. The smallest alkane with such a bond, ethane, exists as an infinite number of conformations with respect to rotation around the C–C bond. Two of these are recognised as energy minimum and energy maximum forms, the existence of specific conformations is due to hindered rotation around sigma bonds, although a role for hyperconjugation is proposed by a competing theory. The importance of energy minimum and energy maximum is seen by extension of these concepts to more complex molecules for which stable conformations may be predicted as minimum energy forms. The staggered conformation is more stable by 12.5 kJ/mol than the eclipsed conformation, in the eclipsed conformation the torsional angle is minimised. In butane, the two staggered conformations are no longer equivalent and represent two distinct conformers, the anti-conformation and the gauche conformation. Both conformations are free of torsional strain, but, in the gauche conformation, the interaction between the two methyl groups is repulsive, and an energy barrier results. The eclipsed methyl groups exert a greater steric strain because of their electron density compared to lone hydrogen atoms. The question of whether steric hindrance is responsible for the energy maximum is a topic of debate to this day. One alternative to the steric hindrance explanation is based on hyperconjugation as analyzed within the Natural Bond Orbital framework, in the staggered conformation, one C-H sigma bonding orbital donates electron density to the antibonding orbital of the other C-H bond. The energetic stabilization of this effect is maximized when the two orbitals have maximal overlap, occurring in the staggered conformation, there is no overlap in the eclipsed conformation, leading to a disfavored energy maximum. On the other hand, an analysis within quantitative molecular orbital theory shows that 2-orbital-4-electron repulsions are dominant over hyperconjugation, a valence bond theory study also emphasizes the importance of steric effects. Torsional strain results from resistance to twisting about a bond, in n-pentane, the terminal methyl groups experience additional pentane interference. Evidence for the structure in the crystalline state is derived from X-ray crystallography and from NMR spectroscopy. More alkane conformations exist in cyclic alkanes, see cyclohexane conformations, more on the impact of gauche interactions, see Gauche effect
31.
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
32.
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
33.
Protein folding
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It is the physical process by which a polypeptide folds into its characteristic and functional three-dimensional structure from random coil. Each protein exists as a polypeptide or random coil when translated from a sequence of mRNA to a linear chain of amino acids. This polypeptide lacks any stable three-dimensional structure, as the polypeptide chain is being synthesized by the ribosome, the linear chain begins to fold into its three dimensional structure. Folding begins to occur even during translation of the polypeptide chain, amino acids interact with each other to produce a well-defined three-dimensional structure, the folded protein, known as the native state. The resulting three-dimensional structure is determined by the amino acid sequence or primary structure, the energy landscape describes the folding pathways in which the unfolded protein is able to assume its native state. Experiments beginning in the 1980s indicate the codon for an acid can also influence protein structure. The correct three-dimensional structure is essential to function, although parts of functional proteins may remain unfolded. Failure to fold into native structure generally produces inactive proteins, several neurodegenerative and other diseases are believed to result from the accumulation of amyloid fibrils formed by misfolded proteins. Many allergies are caused by folding of some proteins, because the immune system does not produce antibodies for certain protein structures. The primary structure of a protein, its linear amino-acid sequence, the amino acid composition is not as important as the sequence. The essential fact of folding, however, remains that the amino acid sequence of protein contains the information that specifies both the native structure and the pathway to attain that state. This is not to say that nearly identical amino acid sequences always fold similarly, conformations differ based on environmental factors as well, similar proteins fold differently based on where they are found. Formation of a structure is the first step in the folding process that a protein takes to assume its native structure. Formation of intramolecular hydrogen bonds provides another important contribution to protein stability, alpha helices are formed by hydrogen bonding of the backbone to form a spiral shape. The beta pleated sheet is a structure forms with the backbone bending over itself to form the hydrogen bonds. The hydrogen bonds are between the hydrogen and carbonyl carbon of the peptide bond. The alpha helices and beta pleated sheets can be amphipathic in nature, or contain a hydrophilic portion, secondary structure hierarchically gives way to tertiary structure formation. Tertiary structure of a protein involves a single chain, however
34.
Ester
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In chemistry, esters are chemical compounds derived from an acid in which at least one –OH group is replaced by an –O–alkyl group. Usually, esters are derived from an acid and an alcohol. Glycerides, which are fatty acid esters of glycerol, are important esters in biology, being one of the classes of lipids. Esters with low weight are commonly used as fragrances and found in essential oils. Phosphoesters form the backbone of DNA molecules, nitrate esters, such as nitroglycerin, are known for their explosive properties, while polyesters are important plastics, with monomers linked by ester moieties. The word ester was coined in 1848 by German chemist Leopold Gmelin, probably as a contraction of the German Essigäther, ester names are derived from the parent alcohol and the parent acid, where the latter may be organic or inorganic. Esters derived from more complex carboxylic acids are, on the hand, more frequently named using the systematic IUPAC name. For example, the ester hexyl octanoate, also known under the trivial name hexyl caprylate, has the formula CH36CO25CH3, the chemical formulas of organic esters usually take the form RCO2R′, where R and R′ are the hydrocarbon parts of the carboxylic acid and the alcohol, respectively. For example, butyl acetate, derived from butanol and acetic acid would be written CH3CO2C4H9, alternative presentations are common including BuOAc and CH3COOC4H9. Cyclic esters are called lactones, regardless of whether they are derived from an organic or an inorganic acid, one example of a lactone is γ-valerolactone. An uncommon class of organic esters are the orthoesters, which have the formula RC3, triethylorthoformate is derived, in terms of its name from orthoformic acid and ethanol. Esters can also be derived from an acid and an alcohol. For example, triphenyl phosphate is the derived from phosphoric acid. Organic carbonates are derived from acid, for example, ethylene carbonate is derived from carbonic acid. So far an alcohol and inorganic acid are linked via oxygen atoms, in corollary, boron features borinic esters, boronic esters, and borates. As oxygen is a group 16 chemical element, sulfur atoms can replace some oxygen atoms in carbon–oxygen–central inorganic atom covalent bonds of an ester, esters contain a carbonyl center, which gives rise to 120 ° C–C–O and O–C–O angles. Unlike amides, esters are structurally flexible functional groups because rotation about the C–O–C bonds has a low barrier and their flexibility and low polarity is manifested in their physical properties, they tend to be less rigid and more volatile than the corresponding amides. The pKa of the alpha-hydrogens on esters is around 25, the preference for the Z conformation is influenced by the nature of the substituents and solvent, if present
35.
Electronegativity
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Electronegativity, symbol χ, is a chemical property that describes the tendency of an atom to attract electrons towards itself. An atoms electronegativity is affected by both its number and the distance at which its valence electrons reside from the charged nucleus. The higher the associated electronegativity number, the more an element or compound attracts electrons towards it, the term electronegativity was introduced by Jöns Jacob Berzelius in 1811, though the concept was known even before that and was studied by many chemists including Avogadro. It has been shown to correlate with a number of chemical properties. Electronegativity cannot be measured and must be calculated from other atomic or molecular properties. The most commonly used method of calculation is that proposed by Linus Pauling. This gives a quantity, commonly referred to as the Pauling scale. When other methods of calculation are used, it is conventional to quote the results on a scale that covers the range of numerical values. As it is calculated, electronegativity is not a property of an atom alone. Properties of a free atom include ionization energy and electron affinity, on the most basic level, electronegativity is determined by factors like the nuclear charge and the number/location of other electrons present in the atomic shells. The opposite of electronegativity is electropositivity, a measure of an ability to donate electrons. Caesium is the least electronegative element in the table, while fluorine is most electronegative. According to valence bond theory, of which Pauling was a notable proponent, hydrogen was chosen as the reference, as it forms covalent bonds with a large variety of elements, its electronegativity was fixed first at 2.1, later revised to 2.20. It is also necessary to decide which of the two elements is the more electronegative, to calculate Pauling electronegativity for an element, it is necessary to have data on the dissociation energies of at least two types of covalent bond formed by that element. A. L.32 e V This is an approximate equation, Pauling obtained it by noting that a bond can be approximately represented as a quantum mechanical superposition of a covalent bond and two ionic bond-states. e. The geometric mean is equal to the arithmetic mean - which is applied in the first formula above - when the energies are of the similar value. The square root of this energy, Pauling notes, is approximately additive. Thus, it is this semi-empirical formula for energy that underlies Pauling electronegativity concept
36.
Carbonyl group
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In organic chemistry, a carbonyl group is a functional group composed of a carbon atom double-bonded to an oxygen atom, C=O. It is common to several classes of compounds, as part of many larger functional groups. A compound containing a group is often referred to as a carbonyl compound. The term carbonyl can also refer to carbon monoxide as a ligand in an inorganic or organometallic complex, the remainder of this article concerns itself with the organic chemistry definition of carbonyl, where carbon and oxygen share a double bond. A carbonyl group characterizes the types of compounds, Note that the most specific labels are usually employed. For example, ROR structures are known as acid anhydride rather than the more generic ester, other organic carbonyls are urea and the carbamates, the derivatives of acyl chlorides chloroformates and phosgene, carbonate esters, thioesters, lactones, lactams, hydroxamates, and isocyanates. Examples of inorganic compounds are carbon dioxide and carbonyl sulfide. A special group of compounds are 1, 3-dicarbonyl compounds that have acidic protons in the central methylene unit. Examples are Meldrums acid, diethyl malonate and acetylacetone, because oxygen is more electronegative than carbon, carbonyl compounds often have resonance structures which affect their reactivity. This relative electronegativity draws electron density away from carbon, increasing the bonds polarity, carbon can then be attacked by nucleophiles or a negatively charged part of another molecule. During the reaction, the double bond is broken. This reaction is known as addition-elimination or condensation, the electronegative oxygen also can react with an electrophile, for example a proton in an acidic solution or with Lewis acids to form an oxocarbenium ion. The polarity of oxygen also makes the alpha hydrogens of carbonyl compounds much more acidic than typical sp3 C-H bonds, for example, the pKa values of acetaldehyde and acetone are 16.7 and 19 respectively, while the pKa value of methane is extrapolated to be approximately 50. This is because a carbonyl is in resonance with an enol. The deprotonation of the enol with a base produces an enolate. Amides are the most stable of the carbonyl couplings due to their high resonance stabilization between the nitrogen-carbon and carbon-oxygen bonds, carbonyl groups can be reduced by reaction with hydride reagents such as NaBH4 and LiAlH4, with bakers yeast, or by catalytic hydrogenation. Ketones give secondary alcohols while aldehydes, esters and carboxylic acids give primary alcohols, carbonyls can be alkylated in nucleophilic addition reactions using organometallic compounds such as organolithium reagents, Grignard reagents, or acetylides. Carbonyls also may be alkylated by enolates as in aldol reactions, carbonyls are also the prototypical groups with vinylogous reactivity
37.
Carbon
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Carbon is a chemical element with symbol C and atomic number 6. It is nonmetallic and tetravalent—making four electrons available to form covalent chemical bonds, three isotopes occur naturally, 12C and 13C being stable, while 14C is a radioactive isotope, decaying with a half-life of about 5,730 years. Carbon is one of the few elements known since antiquity, Carbon is the 15th most abundant element in the Earths crust, and the fourth most abundant element in the universe by mass after hydrogen, helium, and oxygen. It is the second most abundant element in the body by mass after oxygen. The atoms of carbon can bond together in different ways, termed allotropes of carbon, the best known are graphite, diamond, and amorphous carbon. The physical properties of carbon vary widely with the allotropic form, for example, graphite is opaque and black while diamond is highly transparent. Graphite is soft enough to form a streak on paper, while diamond is the hardest naturally occurring material known, graphite is a good electrical conductor while diamond has a low electrical conductivity. Under normal conditions, diamond, carbon nanotubes, and graphene have the highest thermal conductivities of all known materials, all carbon allotropes are solids under normal conditions, with graphite being the most thermodynamically stable form. They are chemically resistant and require high temperature to react even with oxygen, the most common oxidation state of carbon in inorganic compounds is +4, while +2 is found in carbon monoxide and transition metal carbonyl complexes. The largest sources of carbon are limestones, dolomites and carbon dioxide, but significant quantities occur in organic deposits of coal, peat, oil. For this reason, carbon has often referred to as the king of the elements. The allotropes of carbon graphite, one of the softest known substances, and diamond. It bonds readily with other small atoms including other carbon atoms, Carbon is known to form almost ten million different compounds, a large majority of all chemical compounds. Carbon also has the highest sublimation point of all elements, although thermodynamically prone to oxidation, carbon resists oxidation more effectively than elements such as iron and copper that are weaker reducing agents at room temperature. Carbon is the element, with a ground-state electron configuration of 1s22s22p2. Its first four ionisation energies,1086.5,2352.6,4620.5 and 6222.7 kJ/mol, are higher than those of the heavier group 14 elements. Carbons covalent radii are normally taken as 77.2 pm,66.7 pm and 60.3 pm, although these may vary depending on coordination number, in general, covalent radius decreases with lower coordination number and higher bond order. Carbon compounds form the basis of all life on Earth
38.
Proteolysis
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Proteolysis is the breakdown of proteins into smaller polypeptides or amino acids. Uncatalysed, the hydrolysis of peptide bonds is extremely slow, taking hundreds of years, proteolysis is typically catalysed by cellular enzymes called proteases, but may also occur by intra-molecular digestion. Low pH or high temperatures can also cause proteolysis non-enzymatically and it is also important in the regulation of some physiological and cellular processes, as well as preventing the accumulation of unwanted or abnormal proteins in cells. Consequently, dis-regulation of proteolysis can cause diseases and is used in some venoms to damage their prey, proteolysis is important as an analytical tool for studying proteins in the laboratory, as well as industrially, for example in food processing and stain removal. Limited proteolysis of a polypeptide during or after translation in protein synthesis often occurs for many proteins and this may involve removal of the N-terminal methionine, signal peptide, and/or the conversion of an inactive or non-functional protein to an active one. The precursor to the functional form of protein is termed proprotein. For example, albumin is first synthesized as preproalbumin and contains a signal peptide. This forms the proalbumin after the signal peptide is cleaved, the initiating methionine may be removed during translation of the nascent protein. For E. coli, fMet is efficiently removed if the second residue is small and uncharged, in both prokaryotes and eukaryotes, the exposed N-terminal residue may determine the half-life of the protein according to the N-end rule. Proteins that are to be targeted to a particular organelle or for secretion have an N-terminal signal peptide directs the protein to its final destination. This signal peptide is removed by proteolysis after their transport through a membrane, the polyprotein pro-opiomelanocortin contains many polypeptide hormones. The cleavage pattern of POMC, however, may vary between different tissues, yielding different sets of polypeptide hormones from the same polyprotein, many viruses also produce their proteins initially as a single polypeptide chain that were translated from a polycistronic mRNA. This polypeptide is subsequently cleaved into individual polypeptide chains, many proteins and hormones are synthesized in the form of their precursors - zymogens, proenzymes, and prehormones. These proteins are cleaved to form their final active structures, insulin, for example, is synthesized as preproinsulin, which yields proinsulin after the signal peptide has been cleaved. The proinsulin is then cleaved at two positions to yield two polypeptide chains linked by two disulfide bonds, removal of two C-terminal residues from the B-chain then yields the mature insulin. Proteases in particular are synthesized in the form so that they may be safely stored in cells. This is to ensure that the protease is activated only in the location or context. Proteolysis can, therefore, be a method of regulating biological processes by turning inactive proteins into active ones, a good example is the blood clotting cascade whereby an initial event triggers a cascade of sequential proteolytic activation of many specific proteases, resulting in blood coagulation
39.
Intein
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An intein is a segment of a protein that is able to excise itself and join the remaining portions with a peptide bond in a process termed protein splicing. Inteins have also been called protein introns, intein-mediated protein splicing occurs after the intein-containing mRNA has been translated into a protein. This precursor protein contains three segments—an N-extein followed by the intein followed by a C-extein, after splicing has taken place, the resulting protein contains the N-extein linked to the C-extein, this splicing product is also termed an extein. In 1990 Hirata et al. demonstrated that the sequence in the yeast gene was transcribed into mRNA. Since then, inteins have been found in all three domains of life and in viruses, most reported inteins also contain an endonuclease domain that plays a role in intein propagation. In fact, many genes have unrelated intein-coding segments inserted at different positions, for these and other reasons, inteins are sometimes called selfish genetic elements, but it may be more accurate to call them parasitic. According to Dawkins gene centered view of evolution, all genes are selfish, within the database of all known inteins,113 known inteins are present in eukaryotes with minimum length of 138 amino acids and maximum length of 844 amino acids. The first intein was found encoded within the VMA gene of Saccharomyces cerevisiae and they were later found in fungi and in diverse proteins as well. A protein distantly related to known inteins containing protein, but closely related to metazoan hedgehog proteins, has described to have the intein sequence from Glomeromycota. Many of the newly described inteins contain homing endonucleases and some of these are apparently active, the abundance of intein in fungi indicates lateral transfer of intein-containing genes. While in eubacteria and archea, there are 289 and 182 known inteins until this literature review was written, not surprisingly, most intein in eubacteria and archea are found to be inserted into nucleic acid metabolic protein, like fungi. A transesterification occurs when the chain of the first residue of the C-extein attacks the newly formed ester to free the N-terminal end of the intein. This forms an intermediate in which the N-extein and C-extein are attached. Finally, the amino group of the C-extein now attacks the ester linking the N-. An O-N or S-N shift produces a peptide bond and the functional, inteins are very efficient at protein splicing, and they have accordingly found an important role in biotechnology. There are more than 200 inteins identified to date, sizes range from 100–800 AAs, inteins have been engineered for particular applications such as protein semisynthesis and the selective labeling of protein segments, which is useful for NMR studies of large proteins. The hydrophobicity of proteins is an obstacle to their import into mitochondria. Therefore, the insertion of a non-hydrophobic intein may allow this import to proceed, excision of the intein after import would then restore the protein to wild-type
40.
Thiol
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In organic chemistry, a thiol is an organosulfur compound that contains a carbon-bonded sulfhydryl or sulphydryl group. Thiols are the analogue of alcohols, and the word is a portmanteau of thion + alcohol. The –SH functional group itself is referred to as either a group or a sulfhydryl group. Many thiols have strong odors resembling that of garlic or rotten eggs, thiols are used as odorants to assist in the detection of natural gas, and the smell of natural gas is due to the smell of the thiol used as the odorant. Thiols are sometimes referred to as mercaptans, thiols and alcohols have similar connectivity. Because sulfur is a larger element than oxygen, the C–S bond lengths, the C–S–H angles approach 90° whereas the angle for the C-O-H group are more open. In the solid or liquids, the hydrogen-bonding between individual groups is weak, the main cohesive force being van der Waals interactions between the highly polarizable divalent sulfur centers. Due to the lesser electronegativity difference between sulfur and hydrogen compared to oxygen and hydrogen, an S–H bond is less polar than the hydroxyl group, thiols have a lower dipole moment relative to the corresponding alcohol. There are several ways to name the alkylthiols, The suffix -thiol is added to the name of the alkane and this method is nearly identical to naming an alcohol and is used by the IUPAC. The word mercaptan replaces alcohol in the name of the equivalent alcohol compound, example, CH3SH would be methyl mercaptan, just as CH3OH is called methyl alcohol. The term sulfanyl or mercapto is used as a prefix, many thiols have strong odors resembling that of garlic. The odors of thiols, particularly those of low weight, are often strong. The spray of skunks consists mainly of low-molecular-weight thiols and derivatives and these compounds are detectable by the human nose at concentrations of only 10 parts per billion. Human sweat contains /-3-methyl-3-sulfanylhexan-1-ol, detectable at 2 parts per billion and having a fruity, methanethiol is a strong-smelling volatile thiol, also detectable at parts per billion levels, found in male mouse urine. Lawrence C. Katz and co-workers showed that MTMT functioned as a semiochemical, activating certain mouse olfactory sensory neurons, attracting female mice. Copper has been shown to be required by a specific mouse olfactory receptor, MOR244-3, thiols are also responsible for a class of wine faults caused by an unintended reaction between sulfur and yeast and the skunky odor of beer that has been exposed to ultraviolet light. Not all thiols have unpleasant odors, for example, furan-2-ylmethanethiol contributes to the aroma of roasted coffee, whereas grapefruit mercaptan, a monoterpenoid thiol, is responsible for the characteristic scent of grapefruit. The effect of the compound is present only at low concentrations
41.
Hydroxy group
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A hydroxy or hydroxyl group is the entity with the formula OH. It contains oxygen bonded to hydrogen, in organic chemistry, alcohol and carboxylic acids contain hydroxy groups. The anion, called hydroxide, consists of a hydroxy group, according to IUPAC rules, the term hydroxyl refers to the radical OH only, while the functional group −OH is called hydroxy group. Water, alcohols, carboxylic acids, and many other hydroxy-containing compounds can be deprotonated readily and this behavior is rationalized by the disparate electronegativities of oxygen and hydrogen. Hydroxy-containing compounds engage in hydrogen bonding, which causes them to stick together, organic compounds, which are often poorly soluble in water, become water soluble when they contain two or more hydroxy groups, as illustrated by sugars and amino acid. The hydroxy group is pervasive in chemistry and biochemistry, many inorganic compounds contain hydroxy groups, including sulfuric acid, the chemical compound produced on the largest scale industrially. Hydroxy groups participate in the reactions that link simple biological molecules into long chains. The joining of a fatty acid to glycerol to form a triacylglycerol removes the −OH from the end of the fatty acid. The joining of two aldehyde sugars to form a disaccharide removes the −OH from the group at the aldehyde end of one sugar. The creation of a bond to link two amino acids to make a protein removes the −OH from the carboxy group of one amino acid. Hydroxyl radicals are highly reactive and undergo chemical reactions that make them short-lived, when biological systems are exposed to hydroxyl radicals, they can cause damage to cells, including those in humans, where they react with DNA, lipids, and proteins. In 2009, Indias Chandrayaan-1 satellite, NASAs Cassini spacecraft and the Deep Impact probe have each detected the presence of water by evidence of hydroxyl fragments on the Moon. As reported by Richard Kerr, A spectrometer detected an infrared absorption at a wavelength of 3.0 micrometers that only water or hydroxyl—a hydrogen, NASA also reported in 2009 that the LCROSS probe revealed an ultraviolet emission spectrum consistent with hydroxyl presence. The Venus Express orbiter sent back Venus science data from April 2006 until December 2014, results from Venus Express include the detection of hydroxyl in the atmosphere. Hydronium Ion Oxide Reece, Jane, Urry, Lisa, Cain, Michael, Wasserman, Steven, Minorsky, Peter, Jackson, berge, Susan, Golden, Brandy, Triglia, Logan
42.
Cyclol
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The cyclol hypothesis is the first structural model of a folded, globular protein. It was developed by Dorothy Wrinch in the late 1930s, and was based on three assumptions, firstly, the hypothesis assumes that two peptide groups can be crosslinked by a cyclol reaction, these crosslinks are covalent analogs of non-covalent hydrogen bonds between peptide groups. These reactions have been observed in the ergopeptides and other compounds, secondly, it assumes that, under some conditions, amino acids will naturally make the maximum possible number of cyclol crosslinks, resulting in cyclol molecules and cyclol fabrics. These cyclol molecules and fabrics have never been observed, finally, the hypothesis assumes that globular proteins have a tertiary structure corresponding to Platonic solids and semiregular polyhedra formed of cyclol fabrics with no free edges. Such closed cyclol molecules have not been observed either, the proposal and testing of the cyclol model also provides an excellent illustration of empirical falsifiability acting as part of the scientific method. By the mid-1930s, analytical ultracentrifugation studies by Theodor Svedberg had shown that proteins had a chemical structure. The same studies appeared to show that the weight of proteins fell into a few well-defined classes related by integers, such as Mw = 2p3q Da. However, it was difficult to determine the molecular weight. Svedberg had also shown that a change in solution conditions could cause a protein to disassemble into small subunits, the chemical structure of proteins was still under debate at that time. The most accepted hypothesis was that proteins are linear polypeptides, i. e. unbranched polymers of amino acids linked by peptide bonds. However, a protein is remarkably long—hundreds of amino-acid residues—and several distinguished scientists were unsure whether such long. Further doubts about the nature of proteins arose because some enzymes were observed to cleave proteins but not peptides, whereas other enzymes cleave peptides. Attempts to synthesize proteins in the test tube were unsuccessful, mainly due to the chirality of amino acids, hence, alternative chemical models of proteins were considered, such as the diketopiperazine hypothesis of Emil Abderhalden. However, no alternative model had yet explained why proteins yield only amino acids, the process of protein denaturation had been discovered in 1910 by Harriette Chick and Charles Martin, but its nature was still mysterious. In 1929, Hsien Wu hypothesized correctly that denaturation corresponded to protein unfolding, wus hypothesis was also advanced independently in 1936 by Mirsky and Linus Pauling. X-ray crystallography had just begun as a discipline in 1911, and had advanced rapidly from simple salt crystals to crystals of complex molecules such as cholesterol. However, even the smallest proteins have over 1000 atoms, which makes determining their structure far more complex, since protein structure was so poorly understood in the 1930s, the physical interactions responsible for stabilizing that structure were likewise unknown. Astbury hypothesized that the structure of proteins was stabilized by hydrogen bonds in β-sheets
43.
The Proteolysis Map
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The Proteolysis MAP is an integrated web resource focused on proteases. PMAP is to aid the researchers in reasoning about proteolytic networks. PMAP was originally created at the Burnham Institute for Medical Research, La Jolla, in 2004 the National Institutes of Health selected a team led by Jeffrey W. Smith, to establish the Center on Proteolytic Pathways. As part of the NIH Roadmap for Biomedical research, the center develops technology to study the behavior of proteins, proteases are a class of enzymes that regulate much of what happens in the human body, both inside the cell and out, by cleaving peptide bonds in proteins. Simply stated, life could not exist without them, extensive on-line classification system for proteases is deposited in the MEROPS database. Proteolytic pathways, or proteolysis, are the series of events controlled by proteases that occur in response to specific stimuli, proteaseDB and SubstrateDB, are driven by an automated annotation pipeline that generates dynamic ‘Molecule Pages’, rich in molecular information. CutDB has information on more than 6,600 proteolytic events, pathwayDB, just begun accumulation of metabolic pathways whose function can be dynamically modeled in a rule-based manner. Hypothetical networks are inferred by semi-automated culling from the literature, additionally, protease software tools are available for the analysis of individual proteases and proteome-wide data sets. Popular destinations in PMAP are Protease Molecule Pages and Substrate Molecule Pages, Substrate Molecule Pages display protein domains and experimentally derived protease cut-sites for a given protein target of interest
44.
International Standard Book Number
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The International Standard Book Number is a unique numeric commercial book identifier. An ISBN is assigned to each edition and variation of a book, for example, an e-book, a paperback and a hardcover edition of the same book would each have a different ISBN. The ISBN is 13 digits long if assigned on or after 1 January 2007, the method of assigning an ISBN is nation-based and varies from country to country, often depending on how large the publishing industry is within a country. The initial ISBN configuration of recognition was generated in 1967 based upon the 9-digit Standard Book Numbering created in 1966, the 10-digit ISBN format was developed by the International Organization for Standardization and was published in 1970 as international standard ISO2108. Occasionally, a book may appear without a printed ISBN if it is printed privately or the author does not follow the usual ISBN procedure, however, this can be rectified later. Another identifier, the International Standard Serial Number, identifies periodical publications such as magazines, the ISBN configuration of recognition was generated in 1967 in the United Kingdom by David Whitaker and in 1968 in the US by Emery Koltay. The 10-digit ISBN format was developed by the International Organization for Standardization and was published in 1970 as international standard ISO2108, the United Kingdom continued to use the 9-digit SBN code until 1974. The ISO on-line facility only refers back to 1978, an SBN may be converted to an ISBN by prefixing the digit 0. For example, the edition of Mr. J. G. Reeder Returns, published by Hodder in 1965, has SBN340013818 -340 indicating the publisher,01381 their serial number. This can be converted to ISBN 0-340-01381-8, the check digit does not need to be re-calculated, since 1 January 2007, ISBNs have contained 13 digits, a format that is compatible with Bookland European Article Number EAN-13s. An ISBN is assigned to each edition and variation of a book, for example, an ebook, a paperback, and a hardcover edition of the same book would each have a different ISBN. The ISBN is 13 digits long if assigned on or after 1 January 2007, a 13-digit ISBN can be separated into its parts, and when this is done it is customary to separate the parts with hyphens or spaces. Separating the parts of a 10-digit ISBN is also done with either hyphens or spaces, figuring out how to correctly separate a given ISBN number is complicated, because most of the parts do not use a fixed number of digits. ISBN issuance is country-specific, in that ISBNs are issued by the ISBN registration agency that is responsible for country or territory regardless of the publication language. Some ISBN registration agencies are based in national libraries or within ministries of culture, in other cases, the ISBN registration service is provided by organisations such as bibliographic data providers that are not government funded. In Canada, ISBNs are issued at no cost with the purpose of encouraging Canadian culture. In the United Kingdom, United States, and some countries, where the service is provided by non-government-funded organisations. Australia, ISBNs are issued by the library services agency Thorpe-Bowker
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PubMed Identifier
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PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at the National Institutes of Health maintains the database as part of the Entrez system of information retrieval, from 1971 to 1997, MEDLINE online access to the MEDLARS Online computerized database primarily had been through institutional facilities, such as university libraries. PubMed, first released in January 1996, ushered in the era of private, free, home-, the PubMed system was offered free to the public in June 1997, when MEDLINE searches via the Web were demonstrated, in a ceremony, by Vice President Al Gore. Information about the journals indexed in MEDLINE, and available through PubMed, is found in the NLM Catalog. As of 5 January 2017, PubMed has more than 26.8 million records going back to 1966, selectively to the year 1865, and very selectively to 1809, about 500,000 new records are added each year. As of the date,13.1 million of PubMeds records are listed with their abstracts. In 2016, NLM changed the system so that publishers will be able to directly correct typos. Simple searches on PubMed can be carried out by entering key aspects of a subject into PubMeds search window, when a journal article is indexed, numerous article parameters are extracted and stored as structured information. Such parameters are, Article Type, Secondary identifiers, Language, publication type parameter enables many special features. As these clinical girish can generate small sets of robust studies with considerable precision, since July 2005, the MEDLINE article indexing process extracts important identifiers from the article abstract and puts those in a field called Secondary Identifier. The secondary identifier field is to store numbers to various databases of molecular sequence data, gene expression or chemical compounds. For clinical trials, PubMed extracts trial IDs for the two largest trial registries, ClinicalTrials. gov and the International Standard Randomized Controlled Trial Number Register, a reference which is judged particularly relevant can be marked and related articles can be identified. If relevant, several studies can be selected and related articles to all of them can be generated using the Find related data option, the related articles are then listed in order of relatedness. To create these lists of related articles, PubMed compares words from the title and abstract of each citation, as well as the MeSH headings assigned, using a powerful word-weighted algorithm. The related articles function has been judged to be so precise that some researchers suggest it can be used instead of a full search, a strong feature of PubMed is its ability to automatically link to MeSH terms and subheadings. Examples would be, bad breath links to halitosis, heart attack to myocardial infarction, where appropriate, these MeSH terms are automatically expanded, that is, include more specific terms. Terms like nursing are automatically linked to Nursing or Nursing and this important feature makes PubMed searches automatically more sensitive and avoids false-negative hits by compensating for the diversity of medical terminology. The My NCBI area can be accessed from any computer with web-access, an earlier version of My NCBI was called PubMed Cubby
