1.
BRENDA
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BRENDA is an information system representing one of the most comprehensive enzyme repositories. It is a resource that comprises molecular and biochemical information on enzymes that have been classified by the IUBMB. Every classified enzyme is characterized with respect to its catalyzed biochemical reaction, kinetic properties of the corresponding reactants are described in detail. BRENDA contains enzyme-specific data manually extracted from scientific literature and additional data derived from automatic information retrieval methods such as text mining. It provides a user interface that allows a convenient and sophisticated access to the data. BRENDA was founded in 1987 at the former German National Research Centre for Biotechnology in Braunschweig and was published as a series of books. Its name was originally an acronym for the Braunschweig Enzyme Database, from 1996 to 2007, BRENDA was located at the University of Cologne. There, BRENDA developed into a publicly accessible enzyme information system, in 2007, BRENDA returned to Braunschweig. Currently, BRENDA is maintained and further developed at the Department of Bioinformatics, a major update of the data in BRENDA is performed twice a year. Besides the upgrade of its content, improvements of the interface are also incorporated into the BRENDA database. The latest update was performed in January 2015, Database, The database contains more than 40 data fields with enzyme-specific information on more than 7000 EC numbers that are classified according to the IUBMB. Currently, BRENDA contains manually annotated data from over 140,000 different scientific articles, each enzyme entry is clearly linked to at least one literature reference, to its source organism, and, where available, to the protein sequence of the enzyme. An important part of BRENDA represent the more than 110,000 enzyme ligands, the term ligand is used in this context to all low molecular weight compounds which interact with enzymes. These include not only metabolites of primary metabolism, co-substrates or cofactors, the origin of these molecules ranges from naturally occurring antibiotics to synthetic compounds that have been synthesized for the development of drugs or pesticides. Furthermore, cross-references to external resources such as sequence and 3D-structure databases. Extensions, Since 2006, the data in BRENDA is supplemented with information extracted from the literature by a co-occurrence based text mining approach. For this purpose, four text-mining repositories FRENDA, AMENDA, DRENDA and KENDA were introduced and these text-mining results were derived from the titles and abstracts of all articles in the literature database PubMed. Data access, There are several tools to access to the data in BRENDA
2.
MetaCyc
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The MetaCyc database contains extensive information on metabolic pathways and enzymes from many organisms. MetaCyc is also used in engineering and metabolomics research. MetaCyc contains extensive data on individual enzymes, describing their subunit structure, cofactors, activators and inhibitors, substrate specificity, MetaCyc data on reactions includes predicted atom mappings that describe the correspondence between atoms in the reactant compounds and the product compounds. It also provides enzyme mini-reviews and literature references, MetaCyc data on metabolites includes chemical structures, predicted Gibbs free energies of formation, and links to external databases
3.
Protein Data Bank
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The Protein Data Bank is a crystallographic database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The PDB is overseen by a called the Worldwide Protein Data Bank. The PDB is a key resource in areas of structural biology, most major scientific journals, and some funding agencies, now require scientists to submit their structure data to the PDB. Many other databases use protein structures deposited in the PDB, for example, SCOP and CATH classify protein structures, while PDBsum provides a graphic overview of PDB entries using information from other sources, such as Gene ontology. By 1971, one of Meyers programs, SEARCH, enabled researchers to access information from the database to study protein structures offline. SEARCH was instrumental in enabling networking, thus marking the beginning of the PDB. Upon Hamiltons death in 1973, Tom Koeztle took over direction of the PDB for the subsequent 20 years, in January 1994, Joel Sussman of Israels Weizmann Institute of Science was appointed head of the PDB. In October 1998, the PDB was transferred to the Research Collaboratory for Structural Bioinformatics, the new director was Helen M. Berman of Rutgers University. In 2003, with the formation of the wwPDB, the PDB became an international organization, the founding members are PDBe, RCSB, and PDBj. Each of the four members of wwPDB can act as deposition, data processing, the data processing refers to the fact that wwPDB staff review and annotate each submitted entry. The data are automatically checked for plausibility. The PDB database is updated weekly, likewise, the PDB holdings list is also updated weekly. As of 14 March 2017, the breakdown of current holdings is as follows,103,514 structures in the PDB have a structure factor file,9,057 structures have an NMR restraint file. 2,826 structures in the PDB have a chemical shifts file, therefore, the final conformation of the protein is obtained, in the latter case, by solving a distance geometry problem. A few proteins are determined by cryo-electron microscopy, the significance of the structure factor files, mentioned above, is that, for PDB structures determined by X-ray diffraction that have a structure file, the electron density map may be viewed. The data of such structures is stored on the electron density server, however, since 2007, the rate of accumulation of new protein structures appears to have plateaued. The file format used by the PDB was called the PDB file format. This original format was restricted by the width of computer punch cards to 80 characters per line, around 1996, the macromolecular Crystallographic Information file format, mmCIF, which is an extension of the CIF format started to be phased in
4.
PubMed
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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
5.
National Center for Biotechnology Information
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The National Center for Biotechnology Information is part of the United States National Library of Medicine, a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper, the NCBI houses a series of databases relevant to biotechnology and biomedicine and is an important resource for bioinformatics tools and services. Major databases include GenBank for DNA sequences and PubMed, a database for the biomedical literature. Other databases include the NCBI Epigenomics database, all these databases are available online through the Entrez search engine. NCBI is directed by David Lipman, one of the authors of the BLAST sequence alignment program. He also leads a research program, including groups led by Stephen Altschul, David Landsman, Eugene Koonin, John Wilbur, Teresa Przytycka. NCBI is listed in the Registry of Research Data Repositories re3data. org, NCBI has had responsibility for making available the GenBank DNA sequence database since 1992. GenBank coordinates with individual laboratories and other databases such as those of the European Molecular Biology Laboratory. Since 1992, NCBI has grown to other databases in addition to GenBank. The NCBI assigns a unique identifier to each species of organism, the NCBI has software tools that are available by WWW browsing or by FTP. For example, BLAST is a sequence similarity searching program, BLAST can do sequence comparisons against the GenBank DNA database in less than 15 seconds. RAG2/IL2RG The NCBI Bookshelf is a collection of freely accessible, downloadable, some of the books are online versions of previously published books, while others, such as Coffee Break, are written and edited by NCBI staff. BLAST is a used for calculating sequence similarity between biological sequences such as nucleotide sequences of DNA and amino acid sequences of proteins. BLAST is a tool for finding sequences similar to the query sequence within the same organism or in different organisms. It searches the query sequence on NCBI databases and servers and post the results back to the browser in chosen format. Input sequences to the BLAST are mostly in FASTA or Genbank format while output could be delivered in variety of such as HTML, XML formatting. HTML is the output format for NCBIs web-page. Entrez is both indexing and retrieval system having data from sources for biomedical research
6.
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
7.
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
8.
Chemical reaction
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A chemical reaction is a process that leads to the transformation of one set of chemical substances to another. Nuclear chemistry is a sub-discipline of chemistry that involves the reactions of unstable. The substance initially involved in a reaction are called reactants or reagents. Chemical reactions are characterized by a chemical change, and they yield one or more products. Reactions often consist of a sequence of individual sub-steps, the elementary reactions. Chemical reactions are described with chemical equations, which present the starting materials, end products. Chemical reactions happen at a characteristic reaction rate at a given temperature, typically, reaction rates increase with increasing temperature because there is more thermal energy available to reach the activation energy necessary for breaking bonds between atoms. Reactions may proceed in the forward or reverse direction until they go to completion or reach equilibrium, Reactions that proceed in the forward direction to approach equilibrium are often described as spontaneous, requiring no input of free energy to go forward. Non-spontaneous reactions require input of energy to go forward. Different chemical reactions are used in combinations during chemical synthesis in order to obtain a desired product, in biochemistry, a consecutive series of chemical reactions form metabolic pathways. These reactions are catalyzed by protein enzymes. Chemical reactions such as combustion in fire, fermentation and the reduction of ores to metals were known since antiquity, in the Middle Ages, chemical transformations were studied by Alchemists. They attempted, in particular, to lead into gold, for which purpose they used reactions of lead. The process involved heating of sulfate and nitrate minerals such as sulfate, alum. In the 17th century, Johann Rudolph Glauber produced hydrochloric acid and sodium sulfate by reacting sulfuric acid, further optimization of sulfuric acid technology resulted in the contact process in the 1880s, and the Haber process was developed in 1909–1910 for ammonia synthesis. From the 16th century, researchers including Jan Baptist van Helmont, Robert Boyle, the phlogiston theory was proposed in 1667 by Johann Joachim Becher. It postulated the existence of an element called phlogiston, which was contained within combustible bodies. This proved to be false in 1785 by Antoine Lavoisier who found the explanation of the combustion as reaction with oxygen from the air
9.
Aliphatic compound
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In organic chemistry, hydrocarbons are divided into two classes, aromatic compounds and aliphatic compounds also known as non-aromatic compounds. Aliphatics can be cyclic, but only aromatic compounds contain an especially stable ring of atoms, aliphatic compounds can be saturated, like Hexane, or unsaturated, like Hexene and Hexyne. Open-chain compounds contain no rings of any type, and are thus aliphatic, aliphatic compounds can be saturated, joined by single bonds, or unsaturated, with double bonds or triple bonds. Besides hydrogen, other elements can be bound to the chain, the most common being oxygen, nitrogen, sulfur. The least complex aliphatic compound is methane, most aliphatic compounds are flammable, allowing the use of hydrocarbons as fuel, such as methane in Bunsen burners and as liquefied natural gas, and acetylene in welding. The most important aliphatic compounds are, n-, iso- and cyclo-alkanes n-, iso- and cyclo-alkenes and -alkynes
10.
Cyanide
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A cyanide is any chemical compound that contains monovalent combining group CN. This group, known as the group, consists of a carbon atom triple-bonded to a nitrogen atom. The cyanide ion is isoelectronic with carbon monoxide and with molecular nitrogen, organic cyanides are usually called nitriles, in these, the CN group is linked by a covalent bond to a carbon-containing group, such as methyl in methyl cyanide. Because they do not release cyanide ions, nitriles are generally toxic, or in the case of insoluble polymers such as acrylic fiber. Hydrocyanic acid, also known as hydrogen cyanide, or HCN, is a volatile liquid used to prepare acrylonitrile, which is used in the production of acrylic fibers, synthetic rubber. Cyanides are employed in a number of processes, including fumigation, case hardening of iron and steel, electroplating. In nature, substances yielding cyanide are present in seeds, such as the pit of the cherry. In IUPAC nomenclature, organic compounds that have a functional group are called nitriles. An example of a nitrile is CH3CN, acetonitrile, also known as methyl cyanide, nitriles usually do not release cyanide ions. A functional group with a hydroxyl and cyanide bonded to the carbon is called cyanohydrin. Unlike nitriles, cyanohydridins do release hydrogen cyanide, in inorganic chemistry, salts containing the C≡N− ion are referred to as cyanides. The word is derived from the Greek kyanos, meaning dark blue, cyanides are produced by certain bacteria, fungi, and algae and are found in a number of plants. Cyanides are found in substantial amounts in certain seeds and fruit stones, e. g. those of apricots, apples, in plants, cyanides are usually bound to sugar molecules in the form of cyanogenic glycosides and defend the plant against herbivores. Cassava roots, an important potato-like food grown in tropical countries, the Madagascar bamboo Cathariostachys madagascariensis produces cyanide as a deterrent to grazing. In response, the bamboo lemur, which eats the bamboo, has developed a high tolerance to cyanide. The cyanide radical CN· has been identified in interstellar space, the cyanide radical is used to measure the temperature of interstellar gas clouds. Hydrogen cyanide is produced by the combustion or pyrolysis of certain materials under oxygen-deficient conditions, for example, it can be detected in the exhaust of internal combustion engines and tobacco smoke. Certain plastics, especially derived from acrylonitrile, release hydrogen cyanide when heated or burnt
11.
Aldehyde
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The group—without R—is the aldehyde group, also known as the formyl group. Aldehydes are common in organic chemistry, Aldehydes feature an sp2-hybridized, planar carbon center that is connected by a double bond to oxygen and a single bond to hydrogen. The C–H bond is not ordinarily acidic, because of resonance stabilization of the conjugate base, an α-hydrogen in an aldehyde is far more acidic, with a pKa near 15, compared to the acidity of a typical alkane. This acidification is attributed to the quality of the formyl center and the fact that the conjugate base. Related to, the group is somewhat polar. Aldehydes can exist in either the keto or the enol tautomer, keto-enol tautomerism is catalyzed by either acid or base. Usually the enol is the minority tautomer, but it is more reactive, the common names for aldehydes do not strictly follow official guidelines, such as those recommended by IUPAC, but these rules are useful. IUPAC prescribes the following nomenclature for aldehydes, Acyclic aliphatic aldehydes are named as derivatives of the longest carbon chain containing the aldehyde group, thus, HCHO is named as a derivative of methane, and CH3CH2CH2CHO is named as a derivative of butane. The name is formed by changing the suffix -e of the parent alkane to -al, so that HCHO is named methanal, in other cases, such as when a -CHO group is attached to a ring, the suffix -carbaldehyde may be used. Thus, C6H11CHO is known as cyclohexanecarbaldehyde, if the presence of another functional group demands the use of a suffix, the aldehyde group is named with the prefix formyl-. This prefix is preferred to methanoyl-, the word aldehyde was coined by Justus von Liebig as a contraction of the Latin alcohol dehydrogenatus. In the past, aldehydes were sometimes named after the corresponding alcohols, for example, the term formyl group is derived from the Latin word formica ant. This word can be recognized in the simplest aldehyde, formaldehyde, Aldehydes have properties that are diverse and that depend on the remainder of the molecule. Smaller aldehydes are more soluble in water, formaldehyde and acetaldehyde completely so, the volatile aldehydes have pungent odors. Aldehydes degrade in air via the process of autoxidation, the two aldehydes of greatest importance in industry, formaldehyde and acetaldehyde, have complicated behavior because of their tendency to oligomerize or polymerize. They also tend to hydrate, forming the geminal diol, the oligomers/polymers and the hydrates exist in equilibrium with the parent aldehyde. Aldehydes are readily identified by spectroscopic methods, using IR spectroscopy, they display a strong νCO band near 1700 cm−1. In their 1H NMR spectra, the formyl hydrogen center absorbs near δH =9 and this signal shows the characteristic coupling to any protons on the alpha carbon
12.
Ketone
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In chemistry, a ketone /ˈkiːtoʊn/ is an organic compound with the structure RCR, where R and R can be a variety of carbon-containing substituents. Ketones and aldehydes are simple compounds that contain a carbonyl group and they are considered simple because they do not have reactive groups like −OH or −Cl attached directly to the carbon atom in the carbonyl group, as in carboxylic acids containing −COOH. Many ketones are known and many are of importance in industry. Examples include many sugars and the industrial solvent acetone, which is the smallest ketone, the word ketone is derived from Aketon, an old German word for acetone. According to the rules of IUPAC nomenclature, ketones are named by changing the suffix -ane of the parent alkane to -anone, the position of the carbonyl group is usually denoted by a number. For the most important ketones, however, traditional names are still generally used. The common names of ketones are obtained by writing separately the names of the two alkyl groups attached to the group, followed by ketone as a separate word. The names of the groups are written alphabetically. When the two groups are the same, the prefix di- is added before the name of alkyl group. The positions of other groups are indicated by Greek letters, the α-carbon being the adjacent to carbonyl group. If both alkyl groups in a ketone are the same then the ketone is said to be symmetrical, although used infrequently, oxo is the IUPAC nomenclature for a ketone functional group. Other prefixes, however, are also used, for some common chemicals, keto or oxo refer to the ketone functional group. The term oxo is used widely through chemistry, for example, it also refers to an oxygen atom bonded to a transition metal. The ketone carbon is often described as sp2 hybridized, a description that includes both their electronic and molecular structure, ketones are trigonal planar around the ketonic carbon, with C−C−O and C−C−C bond angles of approximately 120°. Ketones differ from aldehydes in that the group is bonded to two carbons within a carbon skeleton. In aldehydes, the carbonyl is bonded to one carbon and one hydrogen and are located at the ends of carbon chains, ketones are also distinct from other carbonyl-containing functional groups, such as carboxylic acids, esters and amides. The carbonyl group is polar because the electronegativity of the oxygen is greater than that for carbon, thus, ketones are nucleophilic at oxygen and electrophilic at carbon. Because the carbonyl group interacts with water by bonding, ketones are typically more soluble in water than the related methylene compounds
13.
Aromatic
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Aromatic molecules are very stable, and do not break apart easily to react with other substances. Organic compounds that are not aromatic are classified as aliphatic compounds—they might be cyclic, since the most common aromatic compounds are derivatives of benzene, the word “aromatic” occasionally refers informally to benzene derivatives, and so it was first defined. Nevertheless, many aromatic compounds exist. In living organisms, for example, the most common aromatic rings are the bases in RNA and DNA. An aromatic functional group or other substituent is called an aryl group, the earliest use of the term aromatic was in an article by August Wilhelm Hofmann in 1855. Hofmann used the term for a class of compounds, many of which have odors. In terms of the nature of the molecule, aromaticity describes a conjugated system often made of alternating single and double bonds in a ring. This configuration allows for the electrons in the pi system to be delocalized around the ring, increasing the molecules stability. The molecule cannot be represented by one structure, but rather a hybrid of different structures. These molecules cannot be found in one of these representations, with the longer single bonds in one location. Rather, the molecule exhibits bond lengths in between those of single and double bonds and this commonly seen model of aromatic rings, namely the idea that benzene was formed from a six-membered carbon ring with alternating single and double bonds, was developed by August Kekulé. The model for benzene consists of two forms, which corresponds to the double and single bonds superimposing to produce six one-and-a-half bonds. Benzene is a stable molecule than would be expected without accounting for charge delocalization. As is standard for resonance diagrams, the use of an arrow indicates that two structures are not distinct entities but merely hypothetical possibilities. Neither is a representation of the actual compound, which is best represented by a hybrid of these structures. A C=C bond is shorter than a C−C bond, but benzene is perfectly hexagonal—all six carbon–carbon bonds have the same length, intermediate between that of a single and that of a double bond. In a cyclic molecule with three alternating double bonds, cyclohexatriene, the length of the single bond would be 1.54 Å. However, in a molecule of benzene, the length of each of the bonds is 1.40 Å, a better representation is that of the circular π-bond, in which the electron density is evenly distributed through a π-bond above and below the ring
14.
Herbivore
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A herbivore is an animal anatomically and physiologically adapted to eating plant material, for example foliage, for the main component of its diet. As a result of their plant diet, herbivorous animals typically have mouthparts adapted to rasping or grinding, horses and other herbivores have wide flat teeth that are adapted to grinding grass, tree bark, and other tough plant material. A large percentage of herbivores have mutualistic gut flora that help them digest plant matter and this gut flora is made up of cellulose-digesting protozoans or bacteria living in the herbivores intestines. Herbivore is the form of a modern Latin coinage, herbivora. Richard Owen employed the term in an 1854 work on fossil teeth. Herbivora is derived from the Latin herba meaning a small plant or herb, Herbivory is a form of consumption in which an organism principally eats autotrophs such as plants, algae and photosynthesizing bacteria. More generally, organisms feed on autotrophs in general are known as primary consumers. Herbivory usually refers to eating plants, fungi, bacteria and protists that feed on living plants are usually termed plant pathogens. Flowering plants that obtain nutrition from other living plants are usually termed parasitic plants, there is however no single exclusive and definitive ecological classification of consumption patterns, each textbook has its own variations on the theme. Insects fed on the spores of early Devonian plants, and the Rhynie chert also provides evidence that organisms fed on plants using a pierce, during the next 75 million years, plants evolved a range of more complex organs, such as roots and seeds. There is no evidence of any organism being fed upon until the middle-late Mississippian,330.9 million years ago, further than their arthropod status, the identity of these early herbivores is uncertain. Hole feeding and skeletonisation are recorded in the early Permian, with surface fluid feeding evolving by the end of that period, Herbivory among four-limbed terrestrial vertebrates, the tetrapods developed in the Late Carboniferous. Early tetrapods were large amphibious piscivores, while amphibians continued to feed on fish and insects, some reptiles began exploring two new food types, tetrapods and plants. The entire dinosaur order ornithischia was composed with herbivores dinosaurs, carnivory was a natural transition from insectivory for medium and large tetrapods, requiring minimal adaptation. In contrast, a set of adaptations was necessary for feeding on highly fibrous plant materials. Arthropods evolved herbivory in four phases, changing their approach to it in response to changing plant communities, tetrapod herbivores made their first appearance in the fossil record of their jaws near the Permio-Carboniferous boundary, approximately 300 million years ago. The earliest evidence of their herbivory has been attributed to dental occlusion, the evolution of dental occlusion led to a drastic increase in plant food processing and provides evidence about feeding strategies based on tooth wear patterns. Examination of phylogenetic frameworks of tooth and jaw morphologes has revealed that dental occlusion developed independently in several lineages tetrapod herbivores and this suggests that evolution and spread occurred simultaneously within various lineages
15.
Plant
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Plants are mainly multicellular, predominantly photosynthetic eukaryotes of the kingdom Plantae. The term is generally limited to the green plants, which form an unranked clade Viridiplantae. This includes the plants, conifers and other gymnosperms, ferns, clubmosses, hornworts, liverworts, mosses and the green algae. Green plants have cell walls containing cellulose and obtain most of their energy from sunlight via photosynthesis by primary chloroplasts and their chloroplasts contain chlorophylls a and b, which gives them their green color. Some plants are parasitic and have lost the ability to produce amounts of chlorophyll or to photosynthesize. Plants are characterized by sexual reproduction and alternation of generations, although reproduction is also common. There are about 300–315 thousand species of plants, of which the great majority, green plants provide most of the worlds molecular oxygen and are the basis of most of Earths ecologies, especially on land. Plants that produce grains, fruits and vegetables form humankinds basic foodstuffs, Plants play many roles in culture. They are used as ornaments and, until recently and in variety, they have served as the source of most medicines. The scientific study of plants is known as botany, a branch of biology, Plants are one of the two groups into which all living things were traditionally divided, the other is animals. The division goes back at least as far as Aristotle, who distinguished between plants, which generally do not move, and animals, which often are mobile to catch their food. Much later, when Linnaeus created the basis of the system of scientific classification. Since then, it has become clear that the plant kingdom as originally defined included several unrelated groups, however, these organisms are still often considered plants, particularly in popular contexts. When the name Plantae or plant is applied to a group of organisms or taxon. The evolutionary history of plants is not yet settled. Those which have been called plants are in bold, the way in which the groups of green algae are combined and named varies considerably between authors. Algae comprise several different groups of organisms which produce energy through photosynthesis, most conspicuous among the algae are the seaweeds, multicellular algae that may roughly resemble land plants, but are classified among the brown, red and green algae. Each of these groups also includes various microscopic and single-celled organisms
16.
Alpha/beta hydrolase superfamily
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The alpha/beta hydrolase superfamily is superfamily of hydrolytic enzymes of widely differing phylogenetic origin and catalytic function that share a common fold. The core of each enzyme is an alpha/beta-sheet, containing 8 beta strands connected by 6 alpha helices, the enzymes are believed to have diverged from a common ancestor, retaining little obvious sequence similarity, but preserving the arrangement of the catalytic residues. All have a triad, the elements of which are borne on loops. The alpha/beta hydrolase fold includes proteases, lipases, peroxidases, esterases, the ESTHER database provides a large collection of information about this superfamily of proteins
17.
Catalytic triad
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A catalytic triad refers to the three amino acid residues that function together at the centre of the active site of some hydrolase and transferase enzymes. An Acid-Base-Nucleophile triad is a motif for generating a nucleophilic residue for covalent catalysis. The nucleophile is most commonly a serine or cysteine amino acid, as well as divergent evolution of function, catalytic triads show some of the best examples of convergent evolution. Chemical constraints on catalysis have led to the same solution independently evolving in at least 23 separate superfamilies. Their mechanism of action is one of the best studied in biochemistry. The enzymes trypsin and chymotrypsin were first purified in the 1930s, a serine in each of trypsin and chymotrypsin was identified as the catalytic nucleophile in the 1950s. The structure of chymotrypsin was solved by X-ray crystallography in the 1960s, other proteases were sequenced and aligned to reveal a family of related proteases, now called the S1 family. Simultaneously, the structures of the evolutionarily unrelated papain and subtilisin proteases were found to contain analogous triads, the charge-relay mechanism for the activation of the nucleophile by the other triad members was proposed in the late 1960s. As more protease structures were solved by X-ray crystallography in the 1970s and 80s, understanding how chemical constraints on evolution led to the convergence of so many enzyme families on the same triad geometries has developed in the 2010s. The massive body of work on the charge-relay, covalent catalysis used by catalytic triads has led to the mechanism being the best characterised in all of biochemistry. Enzymes that contain an catalytic triad use it for one of two types, either to split a substrate or to transfer one portion of a substrate over to a second substrate. Triads are an inter-dependent set of residues in the site of an enzyme. These triad residues act together to make the nucleophile member highly reactive, catalytic triads perform covalent catalysis using a residue as a nucleophile. The reactivity of the residue is increased by the functional groups of the other triad members. The nucleophile is polarised and oriented by the base, which is itself bound, catalysis is performed in two stages. First, the nucleophile attacks the carbonyl carbon and forces the carbonyl oxygen to accept an electron. The build-up of negative charge on this intermediate is stabilized by an oxanion hole within the active site. The intermediate then collapses back to a carbonyl, ejecting the first half of the substrate, the ejection of this first leaving group is often aided by donation of a proton by the base
18.
Nucleophile
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A nucleophile is a chemical species that donates an electron pair to an electrophile to form a chemical bond in relation to a reaction. All molecules or ions with a pair of electrons or at least one pi bond can act as nucleophiles. Because nucleophiles donate electrons, they are by definition Lewis bases, Nucleophilic describes the affinity of a nucleophile to the nuclei. Nucleophilicity, sometimes referred to as strength, refers to a substances nucleophilic character and is often used to compare the affinity of atoms. Neutral nucleophilic reactions with solvents such as alcohols and water are named solvolysis, nucleophiles may take part in nucleophilic substitution, whereby a nucleophile becomes attracted to a full or partial positive charge. The terms nucleophile and electrophile were introduced by Christopher Kelk Ingold in 1933, the word nucleophile is derived from nucleus and the Greek word φιλος, philos for love. In general, in a row across the table, the more basic the ion the more reactive it is as a nucleophile. g. The iodide ion is more nucleophilic than the fluoride ion, many schemes attempting to quantify relative nucleophilic strength have been devised. The following empirical data have been obtained by measuring reaction rates for a number of reactions involving a large number of nucleophiles and electrophiles. Nucleophiles displaying the so-called alpha effect are usually omitted in this type of treatment. This treatment results in the values for typical nucleophilic anions, acetate 2.7, chloride 3.0, azide 4.0, hydroxide 4.2, aniline 4.5, iodide 5.0. Typical substrate constants are 0.66 for ethyl tosylate,0.77 for β-propiolactone,1.00 for 2, 3-epoxypropanol,0.87 for benzyl chloride, and 1.43 for benzoyl chloride. The equation predicts that, in a nucleophilic displacement on benzyl chloride, the Ritchie equation, derived in 1972, is another free-energy relationship, log 10 = N + where N+ is the nucleophile dependent parameter and k0 the reaction rate constant for water. In this equation, a substrate-dependent parameter like s in the Swain–Scott equation is absent, the equation states that two nucleophiles react with the same relative reactivity regardless of the nature of the electrophile, which is in violation of the Reactivity–selectivity principle. For this reason this equation is called the constant selectivity relationship. Many other reaction types have since been described. Typical Ritchie N+ values are,0.5 for methanol,5.9 for the anion,7.5 for the methoxide anion,8.5 for the azide anion. The values for the relative cation reactivities are -0.4 for the malachite green cation, +2.6 for the benzenediazonium cation, the constant s is defined as 1 with 2-methyl-1-pentene as the nucleophile
19.
Histidine
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Histidine is an α-amino acid that is used in the biosynthesis of proteins. It contains a group, a carboxylic acid group. Initially thought essential only for infants, longer-term studies have shown it is essential for adults also, Histidine was first isolated by German physician Albrecht Kossel and Sven Hedin in 1896. It is also a precursor to histamine, an inflammatory agent in immune responses. The conjugate acid of the side chain in histidine has a pKa of approximately 6.0. This means that, at physiologically relevant pH values, relatively small shifts in pH will change its average charge, below a pH of 6, the imidazole ring is mostly protonated as described by the Henderson–Hasselbalch equation. When protonated, the ring bears two NH bonds and has a positive charge. The positive charge is distributed between both nitrogens and can be represented with two equally important resonance structures. As the pH increases past approximately 6, one of the protons is lost, the remaining proton of the now-neutral imidazole ring can reside on either nitrogen, giving rise to what are known as the N1-H or N3-H tautomers. When both imidazole ring nitrogens are protonated, their 15N chemical shifts are similar, NMR shows that the chemical shift of N1-H drops slightly, whereas the chemical shift of N3-H drops considerably. This indicates that the N1-H tautomer is preferred, it is presumed due to hydrogen bonding to the neighboring ammonium, as the pH rises above 9, the chemical shifts of N1 and N3 become approximately 185 and 170 ppm. An entirely deprotonated form of the ring, the imidazolate ion, would be formed only above a pH of 14. This change in chemical shifts can be explained by the presumably decreased hydrogen bonding of an amine over an ammonium ion, and this should act to decrease the N1-H tautomer preference. The imidazole ring of histidine is aromatic at all pH values and it contains six pi electrons, four from two double bonds and two from a nitrogen lone pair. It can form pi stacking interactions, but is complicated by the positive charge and it does not absorb at 280 nm in either state, but does in the lower UV range more than some amino acids. The imidazole sidechain of histidine is a coordinating ligand in metalloproteins and is a part of catalytic sites in certain enzymes. It has the ability to switch between protonated and unprotonated states, which allows histidine to participate in acid-base catalysis, in catalytic triads, the basic nitrogen of histidine is used to abstract a proton from serine, threonine, or cysteine to activate it as a nucleophile. In a histidine proton shuttle, histidine is used to quickly shuttle protons and it can do this by abstracting a proton with its basic nitrogen to make a positively charged intermediate and then use another molecule, a buffer, to extract the proton from its acidic nitrogen
20.
Aspartic acid
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Aspartic acid, also known as aspartate, is an α-amino acid that is used in the biosynthesis of proteins. Similar to all other amino acids it contains an amino group and its α-amino group is in the protonated –NH+3 form under physiological conditions, while its α-carboxylic acid group is deprotonated −COO− under physiological conditions. Aspartic acid has a side chain which reacts with other amino acids, enzymes. Under physiological conditions in proteins the side chain usually occurs as the negatively charged aspartate form and it is a non-essential amino acid in humans, meaning the body can synthesize it as needed. D-Aspartate is one of two D-amino acids commonly found in mammals, in proteins aspartate sidechains are often hydrogen bonded, often as asx turns or asx motifs, which often occur at the N-termini of alpha helices. Asps L-isomer is one of the 22 proteinogenic amino acids, i. e. the building blocks of proteins. Asp is classified as acidic, with a pKa of 3.9, however in a peptide this is dependent on the local environment. Aspartic acid was first discovered in 1827 by Auguste-Arthur Plisson and Étienne Ossian Henry by hydrolysis of asparagine and their original method used lead hydroxide, but various other acids or bases are more commonly used instead. There are two forms or enantiomers of aspartic acid, the name aspartic acid can refer to either enantiomer or a mixture of two. Of these two forms, only one, L-aspartic acid, is incorporated into proteins. The biological roles of its counterpart, D-aspartic acid are more limited, where enzymatic synthesis will produce one or the other, most chemical syntheses will produce both forms, DL-aspartic acid, known as a racemic mixture. Because Aspartate can be synthesized by the body it is classified as an amino acid. In the human body, aspartate is most frequently synthesized through the transamination of oxaloacetate, the biosynthesis of aspartate is facilitated by an aminotransferase enzyme, the transfer of an amine group from another molecule such as alanine or glutamine yields aspartate and an alpha-keto acid. Aspartate is also a byproduct of the urea cycle, racemic aspartic acid can be synthesized from diethyl sodium phthalimidomalonate. The major disadvantage of the technique is that equimolar amounts of each enantiomer are made. Using biotechnology it is now possible to use immobilised enzymes to create just one type of enantiomer owing to their stereospecificity. In plants and microorganisms, aspartate is the precursor to several amino acids, including four that are essential for humans, methionine, threonine, isoleucine, the conversion of aspartate to these other amino acids begins with reduction of aspartate to its semialdehyde, O2CCHCH2CHO. Asparagine is derived from aspartate via transamidation, -O2CCHCH2CO2- + GCNH3+ O2CCHCH2CONH3+ + GCO In the urea cycle, aspartate, Aspartate has many other biochemical roles
21.
Serine
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Serine encoded by the codons UCU, UCC, UCA, UCG, AGU and AGC is an ɑ-amino acid that is used in the biosynthesis of proteins. It contains a group, a carboxyl group, and a side chain consisting of a hydroxymethyl group. It can be synthesized in the body under normal physiological circumstances. This compound is one of the naturally occurring amino acids. Only the L-stereoisomer appears naturally in proteins and it is not essential to the human diet, since it is synthesized in the body from other metabolites, including glycine. Serine was first obtained from silk protein, a rich source. Its name is derived from the Latin for silk, sericum, serines structure was established in 1902. The biosynthesis of serine starts with the oxidation of 3-phosphoglycerate to 3-phosphohydroxypyruvate, reductive amination of this ketone by phosphoserine transaminase yields 3-phosphoserine which is hydrolyzed to serine by phosphoserine phosphatase. In bacteria such as E. coli these enzymes are encoded by the genes serA, serC, glycine biosynthesis, Serine hydroxymethyltransferase also catalyzes the reversible conversions of L-serine to glycine and 5,6,7, 8-tetrahydrofolate to 5, 10-methylenetetrahydrofolate. SHMT is a pyridoxal phosphate dependent enzyme, glycine can also be formed from CO2, NH4+, and mTHF in a reaction catalyzed by glycine synthase. Industrially, L-serine is produced by fermentation, with an estimated 100-1000 tonnes per year produced, in the laboratory, racemic serine can be prepared from methyl acrylate via several steps, Serine is important in metabolism in that it participates in the biosynthesis of purines and pyrimidines. It is the precursor to several amino acids including glycine and cysteine and it is also the precursor to numerous other metabolites, including sphingolipids and folate, which is the principal donor of one-carbon fragments in biosynthesis. Serine plays an important role in the function of many enzymes. It has been shown to occur in the sites of chymotrypsin, trypsin. Serine sidechains are often bonded, the commonest small motifs formed are ST turns, ST motifs. As a constituent of proteins, its side chain can undergo O-linked glycosylation and it is one of three amino acid residues that are commonly phosphorylated by kinases during cell signaling in eukaryotes. Phosphorylated serine residues are often referred to as phosphoserine, Serine proteases are a common type of protease. D-Serine, synthesized in the brain by serine racemase from L-serine, serves as a neuromodulator by coactivating NMDA receptors, D-serine is a potent agonist at the glycine site of the NMDA-type glutamate receptor
22.
Serine protease
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Serine proteases are enzymes that cleave peptide bonds in proteins, in which serine serves as the nucleophilic amino acid at the active site. They are found ubiquitously in both eukaryotes and prokaryotes, Serine proteases fall into two broad categories based on their structure, chymotrypsin-like or subtilisin-like. In humans, they are responsible for coordinating various physiological functions, including digestion, immune response, the MEROPS protease classification system counts 16 superfamilies each containing many families. Each superfamily uses the catalytic triad or dyad in a different protein fold, the majority belong to the S1 family of the PA clan of proteases. For superfamilies, P = superfamily containing a mixture of nucleophile class families, within each superfamily, families are designated by their catalytic nucleophile. Families of Serine proteases Serine proteases are characterised by a distinctive structure and these enzymes can be further categorised based on their substrate specificity as either trypsin-like, chymotrypsin-like or elastase-like. Trypsin-like proteases cleave peptide bonds following a positively charged amino acid and this specificity is driven by the residue which lies at the base of the enzymes S1 pocket. The S1 pocket of chymotrypsin-like enzymes is more hydrophobic than in trypsin-like proteases and this results in a specificity for medium to large sized hydrophobic residues, such as tyrosine, phenylalanine and tryptophan. These include thrombin, tissue activating plasminogen and plasmin and they have been found to have roles in coagulation and digestion as well as in the pathophysiology of neurodegenerative disorders such as Alzheimers and Parkinsons induced dementia. Elastase-like proteases have a much smaller S1 cleft than either trypsin- or chymotrypsin-like proteases, consequently, residues such as alanine, glycine and valine tend to be preferred. Subtilisin is a protease in prokaryotes. Subtilisin is evolutionarily unrelated to the chymotrypsin-clan, but shares the same catalytic mechanism utilising a catalytic triad and this is the classic example used to illustrate convergent evolution, since the same mechanism evolved twice independently during evolution. The main player in the mechanism in the serine proteases is the catalytic triad. The triad is located in the site of the enzyme, where catalysis occurs. The triad is a structure consisting of three amino acids, His 57, Ser 195 and Asp 102. These three key amino acids play an essential role in the cleaving ability of the proteases. While the amino acid members of the triad are located far from one another on the sequence of the protein, due to folding, in the event of catalysis, an ordered mechanism occurs in which several intermediates are generated. The catalysis of the cleavage can be seen as a ping-pong catalysis, in which a substrate binds, a product is released, another substrate binds
23.
Lipase
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A lipase is any enzyme that catalyzes the hydrolysis of fats. Lipases are a subclass of the esterases, lipases perform essential roles in the digestion, transport and processing of dietary lipids in most, if not all, living organisms. Genes encoding lipases are present in certain viruses. Most lipases act at a position on the glycerol backbone of a lipid substrate. Several other types of lipase activities exist in nature, such as phospholipases and sphingomyelinases, some lipases are expressed and secreted by pathogenic organisms during an infection. Lipases are involved in biological processes which range from routine metabolism of dietary triglycerides to cell signaling. Thus, some activities are confined to specific compartments within cells while others work in extracellular spaces. In the example of lysosomal lipase, the enzyme is confined within an organelle called the lysosome, fungi and bacteria may secrete lipases to facilitate nutrient absorption from the external medium. Certain wasp and bee venoms contain phospholipases that enhance the effects of injury, as biological membranes are integral to living cells and are largely composed of phospholipids, lipases play important roles in cell biology. Malassezia globosa, a fungus that is thought to be the cause of dandruff, uses lipase to break down sebum into oleic acid and increase skin cell production. The main lipases of the digestive system are pancreatic lipase and pancreatic lipase related protein 2. Humans also have several other related enzymes, including hepatic lipase, endothelial lipase, not all of these lipases function in the gut. Other lipases include LIPH, LIPI, LIPJ, LIPK, LIPM, LIPN, MGLL, DAGLA, DAGLB, there also are a diverse array of phospholipases, but these are not always classified with the other lipases. Lipases serve important roles in human practices as ancient as yogurt, however, lipases are also being exploited as cheap and versatile catalysts to degrade lipids in more modern applications. Industrial application of lipases requires process intensification for continuous processing using tools like continuous flow microreactors at small scale, lipases are generally animal sourced, but can also be sourced microbially. Blood tests for lipase may be used to investigate and diagnose acute pancreatitis. Measured serum lipase values may vary depending on the method of analysis, lipase can also assist in the breakdown of fats into lipids in those undergoing pancreatic enzyme replacement therapy. It is a key component in Sollpura, alpha toxin Lysosomal acid lipase deficiency Peripheral membrane proteins Phospholipase A Phospholipase C Triglyceride lipase 25
24.
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
25.
Lysine
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Lysine, encoded by the codons AAA and AAG, is an α-amino acid that is used in the biosynthesis of proteins. It contains a group, an α-carboxylic acid group. It is essential in humans, meaning the body cannot synthesize it, lysine is a base, as are arginine and histidine. The ε-amino group often participates in hydrogen bonding and as a base in catalysis. The ε-amino group is attached to the carbon from the α-carbon. O-Glycosylation of hydroxylysine residues in the endoplasmic reticulum or Golgi apparatus is used to mark certain proteins for secretion from the cell, deficiencies may cause blindness, as well as many other problems due to its ubiquitous presence in proteins. As an essential amino acid, lysine is not synthesized in animals, in plants and most bacteria, it is synthesized from aspartic acid, L-aspartate is first converted to L-aspartyl-4-phosphate by aspartokinase. ATP is needed as a source for this step. β-Aspartate semialdehyde dehydrogenase converts this into β-aspartyl-4-semialdehyde, energy from NADPH is used in this conversion. 4-hydroxy-tetrahydrodipicolinate synthase adds a pyruvate group to the β-aspartyl-4-semialdehyde, and a molecule is removed. This causes cyclization and gives rise to -4-hydroxy-2,3,4 and this product is reduced to 2,3,4, 5-tetrahydrodipicolinate by 4-hydroxy-tetrahydrodipicolinate reductase. This reaction consumes an NADPH molecule and releases a water molecule. Tetrahydrodipicolinate N-acetyltransferase opens this ring and gives rise to N-succinyl-L-2-amino-6-oxoheptanedionate, two water molecules and one acyl-CoA enzyme are used in this reaction. This reaction is catalyzed by the enzyme succinyl diaminopimelate aminotransferase, a glutamic acid molecule is used in this reaction and an oxoacid is produced as a byproduct. N-succinyl-LL-2, 6-diaminoheptanedionate is converted into LL-2, 6-diaminoheptanedionate by succinyl diaminopimelate desuccinylase, a water molecule is consumed in this reaction and a succinate is produced a byproduct. LL-2, 6-diaminoheptanedionate is converted by diaminopimelate epimerase into meso-2, 6-diamino-heptanedionate, finally, meso-2, 6-diamino-heptanedionate is converted into L-lysine by diaminopimelate decarboxylase. It is worth noting, however, that in fungi, euglenoids, lysine is metabolised in mammals to give acetyl-CoA, via an initial transamination with α-ketoglutarate. The bacterial degradation of lysine yields cadaverine by decarboxylation, allysine is a derivative of lysine, used in the production of elastin and collagen
26.
Threonine
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Threonine encoded by the codons ACU, ACC, ACA, and ACG is an α-amino acid that is used in the biosynthesis of proteins. It contains a group, an α-carboxylic acid group. It is essential in humans, meaning the body cannot synthesize it, threonine is synthesized from aspartate in bacteria such as E. coli. Threonine sidechains are often bonded, the commonest small motifs formed are ST turns, ST motifs. The threonine residue is susceptible to numerous posttranslational modifications, the hydroxyl side-chain can undergo O-linked glycosylation. In addition, threonine residues undergo phosphorylation through the action of a threonine kinase, in its phosphorylated form, it can be referred to as phosphothreonine. It is a precursor of glycine, and can be used as a prodrug to reliably elevate brain glycine levels, threonine was discovered as the last of the 20 common proteinogenic amino acids in 1935s by William Cumming Rose, collaborating with Curtis Meyer and William Rose. Threonine can exist in four possible stereoisomers with the following configurations, however, the name L-threonine is used for one single diastereomer, -2-amino-3-hydroxybutanoic acid. The second stereoisomer, which is present in nature, is called L-allo-threonine. The two stereoisomers - and -2-amino-3-hydroxybutanoic acid are only of minor importance, as an essential amino acid, threonine is not synthesized in humans, hence we must ingest threonine in the form of threonine-containing proteins. In plants and microorganisms, threonine is synthesized from aspartic acid via α-aspartyl-semialdehyde, homoserine undergoes O-phosphorylation, this phosphate ester undergoes hydrolysis concomitant with relocation of the OH group. Enzymes involved in a typical biosynthesis of threonine include, aspartokinase β-aspartate semialdehyde dehydrogenase homoserine dehydrogenase homoserine kinase threonine synthase, threonine is metabolized in two ways, It is converted to pyruvate via threonine dehydrogenase. An intermediate in this pathway can undergo thiolysis with CoA to produce acetyl-CoA, in humans, it is converted to α-ketobutyrate. This is the pathway for threonine degradation. The mechanism of the first step is analogous to that catalyzed by serine dehydratase, foods high in threonine include cottage cheese, poultry, fish, meat, lentils, Black turtle bean and Sesame seeds. Racemic threonine can be prepared from crotonic acid by using mercury acetate. Threonine biosynthesis CID205 CID6288
27.
Oxyanion hole
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An oxyanion hole is a pocket in the active site of an enzyme that stabilizes transition state negative charge on a deprotonated oxygen or alkoxide. The pocket typically consists of backbone amides or positively charged residues, stabilising the transition state lowers the activation energy necessary for the reaction, and so promotes catalysis. Additionally, it may allow for insertion or positioning of a substrate, enzymes that catalyse multi-step reactions can have multiple oxyanion holes that stabilise different transition states in the reaction. Enzyme catalysis Active site Transition state Serine proteases#Catalytic mechanism Albert Lehninger, et al
28.
Cassava
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Manihot esculenta is a woody shrub native to South America of the spurge family, Euphorbiaceae. It is extensively cultivated as a crop in tropical and subtropical regions for its edible starchy tuberous root. Though it is often called yuca in Spanish and in the United States, it differs from the yucca, Cassava, when dried to a powdery extract, is called tapioca, its fermented, flaky version is named garri. Cassava is the third-largest source of carbohydrates in the tropics, after rice. Cassava is a staple food in the developing world, providing a basic diet for over half a billion people. It is one of the most drought-tolerant crops, capable of growing on marginal soils, Nigeria is the worlds largest producer of cassava, while Thailand is the largest exporter of dried cassava. Cassava is classified as sweet or bitter. Like other roots and tubers, both bitter and sweet varieties of cassava contain antinutritional factors and toxins, with the bitter varieties containing much larger amounts, the more toxic varieties of cassava are a fall-back resource in times of famine or food insecurity in some places. Farmers often prefer the bitter varieties because they deter pests, animals, the cassava root is long and tapered, with a firm, homogeneous flesh encased in a detachable rind, about 1 mm thick, rough and brown on the outside. Commercial cultivars can be 5 to 10 cm in diameter at the top, a woody vascular bundle runs along the roots axis. The flesh can be chalk-white or yellowish, Cassava roots are very rich in starch and contain small amounts of calcium, phosphorus, and vitamin C. However, they are poor in protein and other nutrients, in contrast, cassava leaves are a good source of protein, but deficient in the amino acid methionine and possibly tryptophan. Forms of the domesticated species can also be found growing in the wild in the south of Brazil. By 4,600 BC, manioc pollen appears in the Gulf of Mexico lowlands, the oldest direct evidence of cassava cultivation comes from a 1, 400-year-old Maya site, Joya de Cerén, in El Salvador. With its high potential, it had become a staple food of the native populations of northern South America, southern Mesoamerica. Cassava was a food of pre-Columbian peoples in the Americas and is often portrayed in indigenous art. The Moche people often depicted yuca in their ceramics, spaniards in their early occupation of Caribbean islands did not want to eat cassava or maize, which they considered insubstantial, dangerous, and not nutritious. They much preferred foods from Spain, specifically wheat bread, olive oil, red wine, and meat, for these Christians in the New World, cassava was not suitable for communion since it could not undergo transubstantiation and become the body of Christ
29.
Hevea brasiliensis
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Hevea brasiliensis, the Pará rubber tree, sharinga tree, seringueira, or, most commonly, the rubber tree or rubber plant, is a tree belonging to the family Euphorbiaceae. It is the most economically important member of the genus Hevea because the milky latex extracted from the tree is the source of natural rubber. H. brasiliensis is a deciduous tree growing to a height of up to 40 m in the wild. The trunk is cylindrical and may have a swollen, bottle-shaped base, the bark is some shade of brown, and the inner bark oozes latex when damaged. The leaves have three leaflets and are spirally arranged, the inflorescence include separate male and female flowers. The flowers are pungent, creamy-yellow and have no petals, the fruit is a capsule that contains three large seeds, it opens explosively when ripe. In the wild, the tree can reach a height of up to 100 feet, the white or yellow latex occurs in latex vessels in the bark, mostly outside the phloem. These vessels spiral up the tree in a helix which forms an angle of about 30 degrees with the horizontal. The tree requires a tropical or subtropical climate with a minimum of about 1,200 mm per year of rainfall, if frost does occur, the results can be disastrous for production. One frost can cause the rubber from a plantation to become brittle. Harvesters make incisions across the vessels, just deep enough to tap the vessels without harming the trees growth. This process is known as rubber tapping, latex production is highly variable from tree to tree and across clone types. As latex production declines with age, rubber trees are generally felled when they reach the age of 25 to 30 years, the earlier practice was to burn the trees, but in recent decades, the wood has been harvested for furniture making. The Pará rubber tree initially grew only in the Amazon rainforest, increasing demand and the discovery of the vulcanization procedure in 1839 led to the rubber boom in that region, enriching the cities of Belém and Manaus. The name of the tree derives from Pará, the second-largest Brazilian state and these trees were used to obtain rubber by the natives who inhabited its geographical distribution. The Olmec people of Mesoamerica extracted and produced similar forms of primitive rubber from analogous latex-producing trees such as Castilla elastica as early as 3,600 years ago, the rubber was used, among other things, to make the balls used in the Mesoamerican ballgame. Early attempts were made in 1873 to grow H. brasilensis outside Brazil, after some effort,12 seedlings were germinated at the Royal Botanic Gardens, Kew. These were sent to India for cultivation, but died, a second attempt was then made, some 70,000 seeds being smuggled to Kew in 1875, by Henry Wickham, in the service of the British Empire
30.
Arabidopsis thaliana
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Arabidopsis thaliana is a small flowering plant native to Eurasia. A. thaliana is considered a weed, it is found by roadsides, a winter annual with a relatively short life cycle, A. thaliana is a popular model organism in plant biology and genetics. For a complex multicellular eukaryote, A. thaliana has a small genome of approximately 135 megabase pairs. It was the first plant to have its genome sequenced, and is a tool for understanding the molecular biology of many plant traits, including flower development. Arabidopsis thaliana is a plant, usually growing to 20–25 cm tall. The leaves form a rosette at the base of the plant, leaves are covered with small, unicellular hairs. The flowers are 3 mm in diameter, arranged in a corymb, the fruit is a siliqua 5–20 mm long, containing 20–30 seeds. Roots are simple in structure, with a primary root that grows vertically downward. These roots form interactions with rhizosphere bacteria such as Bacillus megaterium, a. thaliana can complete its entire lifecycle in six weeks. The central stem produces flowers grows after about three weeks, and the flowers naturally self-pollinate. In the lab, A. thaliana may be grown in Petri plates, pots, or hydroponics, the plant was first described in 1577 in the Harz Mountains by Johannes Thal, a physician from Nordhausen, Thüringen, Germany, who called it Pilosella siliquosa. In 1753, Carl Linnaeus renamed the plant Arabis thaliana in honor of Thal, in 1842, the German botanist Gustav Heynhold erected the new genus Arabidopsis and placed the plant in that genus. The genus name, Arabidopsis, comes from Greek, meaning resembling Arabis, thousands of natural inbred accessions of A. thaliana have been collected from throughout its natural and introduced range. These accessions exhibit considerable genetic and phenotypic variation which can be used to study the adaptation of species to different environments. A. thaliana is native to Europe, Asia, and northwestern Africa and it also appears to be native in tropical afroalpine ecosystems. It has been introduced and naturalized worldwide, a. thaliana readily grows and often pioneers rocky, sandy and calcareous soils. It is generally considered a weed, due to its distribution in agricultural fields, roadside, railway lines, waste ground. Like most Brassicaceae species, A. thaliana is edible by humans as a salad or cooked, the first mutant in A. thaliana was documented in 1873 by Alexander Braun, describing a double flower phenotype
31.
Almond
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The almond is a species of tree native to the Middle East, the Indian subcontinent and North Africa. Almond is also the name of the edible and widely cultivated seed of this tree, within the genus Prunus, it is classified with the peach in the subgenus Amygdalus, distinguished from the other subgenera by corrugations on the shell surrounding the seed. The fruit of the almond is a drupe, consisting of a hull and a hard shell with the seed. Shelling almonds refers to removing the shell to reveal the seed, almonds are sold shelled or unshelled. Blanched almonds are shelled almonds that have been treated with hot water to soften the seedcoat, the almond is a deciduous tree, growing 4–10 m in height, with a trunk of up to 30 cm in diameter. The young twigs are green at first, becoming purplish where exposed to sunlight, the leaves are 3–5 inches long, with a serrated margin and a 2.5 cm petiole. The flowers are white to pink, 3–5 cm diameter with five petals, produced singly or in pairs. Almond grows best in Mediterranean climates with warm, dry summers and mild, the optimal temperature for their growth is between 15 and 30 °C and the tree buds have a chilling requirement of 300 to 600 hours below 7.2 °C to break dormancy. Almonds begin bearing an economic crop in the year after planting. Trees reach full bearing five to six years after planting, the fruit matures in the autumn, 7–8 months after flowering. The almond fruit measures 3. 5–6 cm long, in botanical terms, it is not a nut but a drupe. The outer covering or exocarp, fleshy in other members of Prunus such as the plum and cherry, is instead a thick, leathery, grey-green coat, inside the hull is a reticulated, hard, woody shell called the endocarp. Inside the shell is the seed, commonly called a nut. Generally, one seed is present, but occasionally two occur, the almond is native to the Mediterranean climate region of the Middle East, eastward as far as the Yamuna River in India. The wild form of domesticated almond grows in parts of the Levant, the fruit of the wild forms contains the glycoside amygdalin, which becomes transformed into deadly prussic acid after crushing, chewing, or any other injury to the seed. Selection of the type from the many bitter types in the wild marked the beginning of almond domestication. It is unclear as to which wild ancestor of the created the domesticated species. Zohary and Hopf believe that almonds were one of the earliest domesticated fruit trees due to the ability of the grower to raise attractive almonds from seed
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Cofactor (biochemistry)
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A cofactor is a non-protein chemical compound or metallic ion that is required for a proteins biological activity to happen. These proteins are enzymes, and cofactors can be considered helper molecules that assist in biochemical transformations. A coenzyme that is tightly or even covalently bound is termed a prosthetic group, the two subcategories under coenzyme are cosubstrates and prosthetic groups. Cosubstrates are transiently bound to the protein and will be released at some point, the prosthetic groups, on the other hand, are bound permanently to the protein. Both of them have the function, which is to facilitate the reaction of enzymes. Additionally, some sources also limit the use of the cofactor to inorganic substances. An inactive enzyme without the cofactor is called an apoenzyme, while the enzyme with cofactor is called a holoenzyme. Some enzymes or enzyme complexes require several cofactors, organic cofactors are often vitamins or made from vitamins. Many contain the nucleotide adenosine monophosphate as part of their structures, such as ATP, coenzyme A, FAD and this common structure may reflect a common evolutionary origin as part of ribozymes in an ancient RNA world. It has been suggested that the AMP part of the molecule can be considered to be a kind of handle by which the enzyme can grasp the coenzyme to switch it between different catalytic centers. Cofactors can be divided into two groups, organic cofactors, such as flavin or heme, and inorganic cofactors, such as the metal ions Mg2+, Cu+, Mn2+. Organic cofactors are sometimes divided into coenzymes and prosthetic groups. The term coenzyme refers specifically to enzymes and, as such, on the other hand, prosthetic group emphasizes the nature of the binding of a cofactor to a protein and, thus, refers to a structural property. Different sources give different definitions of coenzymes, cofactors. It should be noted that terms are often used loosely. However, the author could not arrive at a single all-encompassing definition of a coenzyme, the study of these cofactors falls under the area of bioinorganic chemistry. In nutrition, the list of essential trace elements reflects their role as cofactors, in humans this list commonly includes iron, magnesium, manganese, cobalt, copper, zinc, and molybdenum. Although chromium deficiency causes impaired glucose tolerance, no human enzyme that uses this metal as a cofactor has been identified, iodine is also an essential trace element, but this element is used as part of the structure of thyroid hormones rather than as an enzyme cofactor
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Cyanogenesis
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A cyanide is any chemical compound that contains monovalent combining group CN. This group, known as the group, consists of a carbon atom triple-bonded to a nitrogen atom. The cyanide ion is isoelectronic with carbon monoxide and with molecular nitrogen, organic cyanides are usually called nitriles, in these, the CN group is linked by a covalent bond to a carbon-containing group, such as methyl in methyl cyanide. Because they do not release cyanide ions, nitriles are generally toxic, or in the case of insoluble polymers such as acrylic fiber. Hydrocyanic acid, also known as hydrogen cyanide, or HCN, is a volatile liquid used to prepare acrylonitrile, which is used in the production of acrylic fibers, synthetic rubber. Cyanides are employed in a number of processes, including fumigation, case hardening of iron and steel, electroplating. In nature, substances yielding cyanide are present in seeds, such as the pit of the cherry. In IUPAC nomenclature, organic compounds that have a functional group are called nitriles. An example of a nitrile is CH3CN, acetonitrile, also known as methyl cyanide, nitriles usually do not release cyanide ions. A functional group with a hydroxyl and cyanide bonded to the carbon is called cyanohydrin. Unlike nitriles, cyanohydridins do release hydrogen cyanide, in inorganic chemistry, salts containing the C≡N− ion are referred to as cyanides. The word is derived from the Greek kyanos, meaning dark blue, cyanides are produced by certain bacteria, fungi, and algae and are found in a number of plants. Cyanides are found in substantial amounts in certain seeds and fruit stones, e. g. those of apricots, apples, in plants, cyanides are usually bound to sugar molecules in the form of cyanogenic glycosides and defend the plant against herbivores. Cassava roots, an important potato-like food grown in tropical countries, the Madagascar bamboo Cathariostachys madagascariensis produces cyanide as a deterrent to grazing. In response, the bamboo lemur, which eats the bamboo, has developed a high tolerance to cyanide. The cyanide radical CN· has been identified in interstellar space, the cyanide radical is used to measure the temperature of interstellar gas clouds. Hydrogen cyanide is produced by the combustion or pyrolysis of certain materials under oxygen-deficient conditions, for example, it can be detected in the exhaust of internal combustion engines and tobacco smoke. Certain plastics, especially derived from acrylonitrile, release hydrogen cyanide when heated or burnt
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Mandelonitrile
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Mandelonitrile is a chemical compound of the cyanohydrin class. Small amounts of mandelonitrile occur in the pits of some fruits, mandelonitrile is the aglycone part of the cyanogenic glycosides prunasin and amygdalin. The naturally occurring - enantiomer finds use as an intermediate in the preparation of optically active α-hydroxy carboxylic acids, α-hydroxy aldehydes, α-hydroxy ketones, mandelonitrile is broken down into cyanide and benzaldehyde by the enzyme mandelonitrile lyase. Racemic mandelonitrile may be prepared similar to many other cyanohydrins, in a one pot reaction, benzaldehyde is reacted with sodium bisulfite to give the corresponding adduct, which further reacts with aqueous sodium cyanide to give the racemic product
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Benzaldehyde
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Benzaldehyde is an organic compound consisting of a benzene ring with a formyl substituent. It is the simplest aromatic aldehyde and one of the most industrially useful and this colorless liquid has a characteristic almond-like odor. Benzaldehyde is the component of bitter almond oil and can be extracted from a number of other natural sources. Synthetic benzaldehyde is the agent in imitation almond extract, which is used to flavor cakes. Benzaldehyde was first extracted from bitter almonds in 1803 by the French pharmacist Martrès, in 1832 German chemists Friedrich Wöhler and Justus von Liebig first synthesized benzaldehyde. Benzaldehyde can be obtained by many processes, in the 1980s, an estimated 18 million kilograms were produced annually in Japan, Europe, and North America, a level that can be assumed to continue. Currently liquid phase chlorination and oxidation of toluene are the main routes, numerous other methods have been developed, such as the partial oxidation of benzyl alcohol, alkali hydrolysis of benzal chloride, and the carbonylation of benzene. Site-specific nuclear magnetic resonance spectroscopy, which evaluates 1H/2H isotope ratios, has used to differentiate between naturally occurring and synthetic benzaldehyde. Benzaldehyde and similar chemicals occur naturally in many foods, most of the benzaldehyde that people eat is from natural, traditional foods, such as almonds. Almonds, apricots, apples and cherry kernels, contain significant amounts of amygdalin and this glycoside breaks up under enzyme catalysis into benzaldehyde, hydrogen cyanide and two molecules of glucose. Benzaldehyde contributes to the scent of oyster mushrooms, on oxidation, benzaldehyde is converted into the odorless benzoic acid, which is a common impurity in laboratory samples. Benzyl alcohol can be formed from benzaldehyde by means of hydrogenation, benzaldehyde is commonly employed to confer almond flavor to foods and scented products. It is sometimes used in cosmetics products, in industrial settings, benzaldehyde is used chiefly as a precursor to other organic compounds, ranging from pharmaceuticals to plastic additives. The aniline dye malachite green is prepared from benzaldehyde and dimethylaniline and it is a precursor to certain acridine dyes as well. Via aldol condensations, benzaldehyde is converted into derivatives of cinnamaldehyde, the synthesis of mandelic acid starts from benzaldehyde, First hydrocyanic acid is added to benzaldehyde, and the resulting nitrile is subsequently hydrolysed to mandelic acid. It is used as a bee repellant, a small amount of benzaldehyde-containing solution is placed on a fume board near the honey combs. The bees promptly move away from the combs to get away from the fumes. Benzaldehyde allows the beekeeper to remove the honey frames from the bee hive with greater safety to both bees and the beekeeper, for a 70-kg human, the lethal dose is estimated at 50 mL
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Amaretto
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Amaretto is a sweet, almond-flavoured, Italian liqueur associated with Saronno, Italy. Various commercial brands are made from a base of apricot pits, almonds, Amaretto serves a variety of culinary uses, can be drunk by itself, and is added to other beverages to create several popular mixed drinks, as well as to coffee. The name amaretto originated as a diminutive of the Italian word amaro, meaning bitter, however, the bitterness is not unpalatable, and sweeteners—and sometimes sweet almonds—enhance the flavour in the final products. Thus one can interpret the name as a description of the taste as a little bitter. Conflation of amaro and amore has led to associations with romance, one should not confuse amaretto with amaro, a different family of Italian liqueurs that, while also sweetened, have a stronger bitter flavour deriving from herbs. Despite the known history on the introduction and acceptance of almonds into Italian cuisine, newer takes on the meanings, as the church was dedicated to the Virgin Mary, Luini needed to depict the Madonna, but was in need of a model. He found his inspiration in a young widowed innkeeper, who became his model, out of gratitude and affection, the woman wished to give him a gift. Her simple means did not permit much, so she steeped apricot kernels in brandy, Disaronno Originale has a characteristic bittersweet almond taste and is known for its distinctive appearance. Disaronno has been in production since about 1900. It claims its originale amarettos secret formula is unchanged from 1525 and its production remains in Saronno, but the product is sold worldwide. The company describes its amaretto as an infusion of apricot kernel oil with absolute alcohol, burnt sugar, the amber liqueur is presented in a rectangular glass decanter designed by a craftsman from Murano. The product was originally named Amaretto di Saronno Originale and it subsequently changed to Amaretto Disaronno, transforming the origin of the product into a more distinctive brand name. Finally, it changed once more to Disaronno Originale, it has not marketed itself as an amaretto since 2001, according to the Disaronno website, their amaretto contains no almonds, and is nut-free. Therefore, it is safe for people with nut or related allergies, Lazzaroni Amaretto, produced by Paolo Lazzaroni & Figli S. p. A. also presents itself as the first such liqueur. It is based on an infusion of Amaretti di Saronno, a process which imparts a delicate almond/apricot flavour. Lazzaroni claim the tale of the young couple blessed by the bishop as the origin of their family recipe, dating it to 1718. Many distillers produce their own brand of amaretto, among them are Bols, DeKuyper, Hiram Walker, Luxardo, Mr. Boston, Paramount, and Phillips. Amaretto serves a variety of culinary uses, Amaretto is added to desserts, including ice cream, which enhances the flavour of the dessert with almonds and complements chocolate
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Cyanohydrin
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A cyanohydrin is a functional group found in organic compounds in which a cyano and a hydroxy group are attached to the same carbon atom. The general formula is R2CCN, where R is H, alkyl, Cyanohydrins are industrially important precursors to carboxylic acids and some amino acids. Cyanohydrins are also prepared by displacement of sulfite by cyanide salts, acetone cyanohydrin, 2CCN is the cyanohydrin of acetone. It is generated as an intermediate in the production of methyl methacrylate. In the laboratory, this serves as a source of HCN. Thus, acetone cyanohydrin can be used for the preparation of other cyanohydrins, for the transformation of HCN to Michael acceptors, and for the formylation of arenes. Treatment of this cyanohydrin with lithium hydride affords anhydrous lithium cyanide, Mandelonitrile, with the formula C6H5CHCN, related cyanogenic glycosides are known, such as amygdalin. Glycolonitrile, also called hydroxyacetonitrile or formaldehyde cyanohydrin, is the compound with the formula HOCH2CN. It is the simplest cyanohydrin, being derived from formaldehyde, halohydrin IUPACs Gold Book definition of cyanohydrins
. PMID 16667728.
