1.
Jmol
–
Jmol is computer software for molecular modelling chemical structures in 3-dimensions. Jmol returns a 3D representation of a molecule that may be used as a teaching tool and it is written in the programming language Java, so it can run on the operating systems Windows, macOS, Linux, and Unix, if Java is installed. It is free and open-source software released under a GNU Lesser General Public License version 2.0, a standalone application and a software development kit exist that can be integrated into other Java applications, such as Bioclipse and Taverna. A popular feature is an applet that can be integrated into web pages to display molecules in a variety of ways, for example, molecules can be displayed as ball-and-stick models, space-filling models, ribbon diagrams, etc. Jmol supports a range of chemical file formats, including Protein Data Bank, Crystallographic Information File, MDL Molfile. There is also a JavaScript-only version, JSmol, that can be used on computers with no Java, the Jmol applet, among other abilities, offers an alternative to the Chime plug-in, which is no longer under active development. While Jmol has many features that Chime lacks, it does not claim to reproduce all Chime functions, most notably, Chime requires plug-in installation and Internet Explorer 6.0 or Firefox 2.0 on Microsoft Windows, or Netscape Communicator 4.8 on Mac OS9. Jmol requires Java installation and operates on a variety of platforms. For example, Jmol is fully functional in Mozilla Firefox, Internet Explorer, Opera, Google Chrome, fast and Scriptable Molecular Graphics in Web Browsers without Java3D
2.
ChEMBL
–
ChEMBL or ChEMBLdb is a manually curated chemical database of bioactive molecules with drug-like properties. It is maintained by the European Bioinformatics Institute, of the European Molecular Biology Laboratory, based at the Wellcome Trust Genome Campus, Hinxton, the database, originally known as StARlite, was developed by a biotechnology company called Inpharmatica Ltd. later acquired by Galapagos NV. The data was acquired for EMBL in 2008 with an award from The Wellcome Trust, resulting in the creation of the ChEMBL chemogenomics group at EMBL-EBI, the ChEMBL database contains compound bioactivity data against drug targets. Bioactivity is reported in Ki, Kd, IC50, and EC50, data can be filtered and analyzed to develop compound screening libraries for lead identification during drug discovery. ChEMBL version 2 was launched in January 2010, including 2.4 million bioassay measurements covering 622,824 compounds and this was obtained from curating over 34,000 publications across twelve medicinal chemistry journals. ChEMBLs coverage of available bioactivity data has grown to become the most comprehensive ever seen in a public database, in October 2010 ChEMBL version 8 was launched, with over 2.97 million bioassay measurements covering 636,269 compounds. ChEMBL_10 saw the addition of the PubChem confirmatory assays, in order to integrate data that is comparable to the type, ChEMBLdb can be accessed via a web interface or downloaded by File Transfer Protocol. It is formatted in a manner amenable to computerized data mining, ChEMBL is also integrated into other large-scale chemistry resources, including PubChem and the ChemSpider system of the Royal Society of Chemistry. In addition to the database, the ChEMBL group have developed tools and these include Kinase SARfari, an integrated chemogenomics workbench focussed on kinases. The system incorporates and links sequence, structure, compounds and screening data, the primary purpose of ChEMBL-NTD is to provide a freely accessible and permanent archive and distribution centre for deposited data. July 2012 saw the release of a new data service, sponsored by the Medicines for Malaria Venture. The data in this service includes compounds from the Malaria Box screening set, myChEMBL, the ChEMBL virtual machine, was released in October 2013 to allow users to access a complete and free, easy-to-install cheminformatics infrastructure. In December 2013, the operations of the SureChem patent informatics database were transferred to EMBL-EBI, in a portmanteau, SureChem was renamed SureChEMBL. 2014 saw the introduction of the new resource ADME SARfari - a tool for predicting and comparing cross-species ADME targets
3.
ChemSpider
–
ChemSpider is a database of chemicals. ChemSpider is owned by the Royal Society of Chemistry, the database contains information on more than 50 million molecules from over 500 data sources including, Each chemical is given a unique identifier, which forms part of a corresponding URL. This is an approach to develop an online chemistry database. The search can be used to widen or restrict already found results, structure searching on mobile devices can be done using free apps for iOS and for the Android. The ChemSpider database has been used in combination with text mining as the basis of document markup. The result is a system between chemistry documents and information look-up via ChemSpider into over 150 data sources. ChemSpider was acquired by the Royal Society of Chemistry in May,2009, prior to the acquisition by RSC, ChemSpider was controlled by a private corporation, ChemZoo Inc. The system was first launched in March 2007 in a release form. ChemSpider has expanded the generic support of a database to include support of the Wikipedia chemical structure collection via their WiChempedia implementation. A number of services are available online. SyntheticPages is an interactive database of synthetic chemistry procedures operated by the Royal Society of Chemistry. Users submit synthetic procedures which they have conducted themselves for publication on the site and these procedures may be original works, but they are more often based on literature reactions. Citations to the published procedure are made where appropriate. They are checked by an editor before posting. The pages do not undergo formal peer-review like a journal article. The comments are moderated by scientific editors. The intention is to collect practical experience of how to conduct useful chemical synthesis in the lab, while experimental methods published in an ordinary academic journal are listed formally and concisely, the procedures in ChemSpider SyntheticPages are given with more practical detail. Comments by submitters are included as well, other publications with comparable amounts of detail include Organic Syntheses and Inorganic Syntheses
4.
DrugBank
–
The DrugBank database is a comprehensive, freely accessible, online database containing information on drugs and drug targets. As both a bioinformatics and a resource, DrugBank combines detailed drug data with comprehensive drug target information. Because of its scope, comprehensive referencing and unusually detailed data descriptions. As a result, links to DrugBank are maintained for nearly all drugs listed in Wikipedia, DrugBank is widely used by the drug industry, medicinal chemists, pharmacists, physicians, students and the general public. Its extensive drug and drug-target data has enabled the discovery and repurposing of a number of existing drugs to treat rare, the latest release of the database contains 8227 drug entries including 2003 FDA-approved small molecule drugs,221 FDA-approved biotech drugs,93 nutraceuticals and over 6000 experimental drugs. Additionally,4270 non-redundant protein sequences are linked to these drug entries, each DrugCard entry contains more than 200 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data. Four additional databases, HMDB, T3DB, SMPDB and FooDB are also part of a suite of metabolomic/cheminformatic databases. The first version of DrugBank was released in 2006 and this early release contained relatively modest information about 841 FDA-approved small molecule drugs and 113 biotech drugs. It also included information on 2133 drug targets, the second version of DrugBank was released in 2009. This greatly expanded and improved version of the database included 1344 approved small molecule drugs and 123 biotech drugs as well as 3037 unique drug targets. Version 2.0 also included, for the first time, withdrawn drugs and illicit drugs, version 3.0 was released in 2011. This version contained 1424 approved small molecule drugs and 132 biotech drugs as well as >4000 unique drug targets, version 3.0 also included drug transporter data, drug pathway data, drug pricing, patent and manufacturing data as well as data on >5000 experimental drugs. Version 4.0 was released in 2014 and this version included 1558 FDA-approved small molecule drugs,155 biotech drugs and 4200 unique drug targets. Version 4.0 also incorporated information on drug metabolites, drug taxonomy, drug spectra, drug binding constants. Table 1 provides a complete statistical summary of the history of DrugBank’s development. All data in DrugBank is non-proprietary or is derived from a non-proprietary source and it is freely accessible and available to anyone. In addition, nearly every item is fully traceable and explicitly referenced to the original source. DrugBank data is available through a web interface and downloads
5.
European Chemicals Agency
–
ECHA is the driving force among regulatory authorities in implementing the EUs chemicals legislation. ECHA helps companies to comply with the legislation, advances the safe use of chemicals, provides information on chemicals and it is located in Helsinki, Finland. The Agency, headed by Executive Director Geert Dancet, started working on 1 June 2007, the REACH Regulation requires companies to provide information on the hazards, risks and safe use of chemical substances that they manufacture or import. Companies register this information with ECHA and it is freely available on their website. So far, thousands of the most hazardous and the most commonly used substances have been registered, the information is technical but gives detail on the impact of each chemical on people and the environment. This also gives European consumers the right to ask whether the goods they buy contain dangerous substances. The Classification, Labelling and Packaging Regulation introduces a globally harmonised system for classifying and labelling chemicals into the EU. This worldwide system makes it easier for workers and consumers to know the effects of chemicals, companies need to notify ECHA of the classification and labelling of their chemicals. So far, ECHA has received over 5 million notifications for more than 100000 substances, the information is freely available on their website. Consumers can check chemicals in the products they use, Biocidal products include, for example, insect repellents and disinfectants used in hospitals. The Biocidal Products Regulation ensures that there is information about these products so that consumers can use them safely. ECHA is responsible for implementing the regulation, the law on Prior Informed Consent sets guidelines for the export and import of hazardous chemicals. Through this mechanism, countries due to hazardous chemicals are informed in advance and have the possibility of rejecting their import. Substances that may have effects on human health and the environment are identified as Substances of Very High Concern 1. These are mainly substances which cause cancer, mutation or are toxic to reproduction as well as substances which persist in the body or the environment, other substances considered as SVHCs include, for example, endocrine disrupting chemicals. Companies manufacturing or importing articles containing these substances in a concentration above 0 and they are required to inform users about the presence of the substance and therefore how to use it safely. Consumers have the right to ask the retailer whether these substances are present in the products they buy, once a substance has been officially identified in the EU as being of very high concern, it will be added to a list. This list is available on ECHA’s website and shows consumers and industry which chemicals are identified as SVHCs, Substances placed on the Candidate List can then move to another list
6.
IUPHAR/BPS
–
The IUPHAR/BPS Guide to PHARMACOLOGY is an open-access website, acting as a portal to information on the biological targets of licensed drugs and other small molecules. The Guide to PHARMACOLOGY is developed as a joint venture between the International Union of Basic and Clinical Pharmacology and the British Pharmacological Society and this replaces and expands upon the original 2009 IUPHAR Database. The information featured includes pharmacological data, target and gene nomenclature, overviews and commentaries on each target family are included, with links to key references. The Guide to PHARMACOLOGY was initially made available online in December 2011 with additional material released in July 2012 and its network of over 700 specialist advisors contribute expertise and data. The current PI and Grant holder of the GtoPdb project is Prof. Jamie A. Davies, the development and release of the first version of the GtoPdb in 2012 was described in an editorial published in the British Journal of Pharmacology entitled Guide to Pharmacology. org- an update. The IUPHAR-DB is no longer being developed and all the contained within this site is now available through the Guide to PHARMACOLOGY. A complete list of all the approved drugs included on the website is available via the ligand list. The Guide to PHARMACOLOGY is being expanded to include information on targets and ligands. Search features on the website include quick and advanced search options, other features include Hot topic news items and a recent receptor-ligand pairing list. A hard copy summary of the database is published as The Concise Guide to Pharmacology 2015/2016 as a series of papers as a bi-annual supplement to the British Journal of Pharmacology. The Guide to PHARMACOLOGY includes links to other relevant resources via target, many of these resources maintain reciprocal links with the relevant Guide to PHARMACOLOGY pages. As of November 2015 the Wellcome Trust is supporting a new project to develop the Guide to Immumopharmacology, the latter continues to be supported by the British Pharmacological Society
7.
PubChem
–
PubChem is a database of chemical molecules and their activities against biological assays. The system is maintained by the National Center for Biotechnology Information, a component of the National Library of Medicine, PubChem can be accessed for free through a web user interface. Millions of compound structures and descriptive datasets can be downloaded via FTP. PubChem contains substance descriptions and small molecules with fewer than 1000 atoms and 1000 bonds, more than 80 database vendors contribute to the growing PubChem database. PubChem consists of three dynamically growing primary databases, as of 28 January 2016, Compounds,82.6 million entries, contains pure and characterized chemical compounds. Substances,198 million entries, contains also mixtures, extracts, complexes, bioAssay, bioactivity results from 1.1 million high-throughput screening programs with several million values. PubChem contains its own online molecule editor with SMILES/SMARTS and InChI support that allows the import and export of all common chemical file formats to search for structures and fragments. In the text search form the database fields can be searched by adding the name in square brackets to the search term. A numeric range is represented by two separated by a colon. The search terms and field names are case-insensitive, parentheses and the logical operators AND, OR, and NOT can be used. AND is assumed if no operator is used, example,0,5000,50,10 -5,5 PubChem was released in 2004. The American Chemical Society has raised concerns about the publicly supported PubChem database and they have a strong interest in the issue since the Chemical Abstracts Service generates a large percentage of the societys revenue. To advocate their position against the PubChem database, ACS has actively lobbied the US Congress, soon after PubChems creation, the American Chemical Society lobbied U. S. Congress to restrict the operation of PubChem, which they asserted competes with their Chemical Abstracts Service
8.
International Chemical Identifier
–
Initially developed by IUPAC and NIST from 2000 to 2005, the format and algorithms are non-proprietary. The continuing development of the standard has supported since 2010 by the not-for-profit InChI Trust. The current version is 1.04 and was released in September 2011, prior to 1.04, the software was freely available under the open source LGPL license, but it now uses a custom license called IUPAC-InChI Trust License. Not all layers have to be provided, for instance, the layer can be omitted if that type of information is not relevant to the particular application. InChIs can thus be seen as akin to a general and extremely formalized version of IUPAC names and they can express more information than the simpler SMILES notation and differ in that every structure has a unique InChI string, which is important in database applications. Information about the 3-dimensional coordinates of atoms is not represented in InChI, the InChI algorithm converts input structural information into a unique InChI identifier in a three-step process, normalization, canonicalization, and serialization. The InChIKey, sometimes referred to as a hashed InChI, is a fixed length condensed digital representation of the InChI that is not human-understandable. The InChIKey specification was released in September 2007 in order to facilitate web searches for chemical compounds and it should be noted that, unlike the InChI, the InChIKey is not unique, though collisions can be calculated to be very rare, they happen. In January 2009 the final 1.02 version of the InChI software was released and this provided a means to generate so called standard InChI, which does not allow for user selectable options in dealing with the stereochemistry and tautomeric layers of the InChI string. The standard InChIKey is then the hashed version of the standard InChI string, the standard InChI will simplify comparison of InChI strings and keys generated by different groups, and subsequently accessed via diverse sources such as databases and web resources. Every InChI starts with the string InChI= followed by the version number and this is followed by the letter S for standard InChIs. The remaining information is structured as a sequence of layers and sub-layers, the layers and sub-layers are separated by the delimiter / and start with a characteristic prefix letter. The six layers with important sublayers are, Main layer Chemical formula and this is the only sublayer that must occur in every InChI. The atoms in the formula are numbered in sequence, this sublayer describes which atoms are connected by bonds to which other ones. Describes how many hydrogen atoms are connected to each of the other atoms, the condensed,27 character standard InChIKey is a hashed version of the full standard InChI, designed to allow for easy web searches of chemical compounds. Most chemical structures on the Web up to 2007 have been represented as GIF files, the full InChI turned out to be too lengthy for easy searching, and therefore the InChIKey was developed. With all databases currently having below 50 million structures, such duplication appears unlikely at present, a recent study more extensively studies the collision rate finding that the experimental collision rate is in agreement with the theoretical expectations. Example, Morphine has the structure shown on the right, as the InChI cannot be reconstructed from the InChIKey, an InChIKey always needs to be linked to the original InChI to get back to the original structure
9.
Simplified molecular-input line-entry system
–
The simplified molecular-input line-entry system is a specification in form of a line notation for describing the structure of chemical species using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules, the original SMILES specification was initiated in the 1980s. It has since modified and extended. In 2007, a standard called OpenSMILES was developed in the open-source chemistry community. Other linear notations include the Wiswesser Line Notation, ROSDAL and SLN, the original SMILES specification was initiated by David Weininger at the USEPA Mid-Continent Ecology Division Laboratory in Duluth in the 1980s. The Environmental Protection Agency funded the project to develop SMILES. It has since modified and extended by others, most notably by Daylight Chemical Information Systems. In 2007, a standard called OpenSMILES was developed by the Blue Obelisk open-source chemistry community. Other linear notations include the Wiswesser Line Notation, ROSDAL and SLN, in July 2006, the IUPAC introduced the InChI as a standard for formula representation. SMILES is generally considered to have the advantage of being slightly more human-readable than InChI, the term SMILES refers to a line notation for encoding molecular structures and specific instances should strictly be called SMILES strings. However, the term SMILES is also used to refer to both a single SMILES string and a number of SMILES strings, the exact meaning is usually apparent from the context. The terms canonical and isomeric can lead to confusion when applied to SMILES. The terms describe different attributes of SMILES strings and are not mutually exclusive, typically, a number of equally valid SMILES strings can be written for a molecule. For example, CCO, OCC and CC all specify the structure of ethanol, algorithms have been developed to generate the same SMILES string for a given molecule, of the many possible strings, these algorithms choose only one of them. This SMILES is unique for each structure, although dependent on the algorithm used to generate it. These algorithms first convert the SMILES to a representation of the molecular structure. A common application of canonical SMILES is indexing and ensuring uniqueness of molecules in a database, there is currently no systematic comparison across commercial software to test if such flaws exist in those packages. SMILES notation allows the specification of configuration at tetrahedral centers, and these are structural features that cannot be specified by connectivity alone and SMILES which encode this information are termed isomeric SMILES
10.
Chemical formula
–
These are limited to a single typographic line of symbols, which may include subscripts and superscripts. A chemical formula is not a name, and it contains no words. Although a chemical formula may imply certain simple chemical structures, it is not the same as a full chemical structural formula. Chemical formulas can fully specify the structure of only the simplest of molecules and chemical substances, the simplest types of chemical formulas are called empirical formulas, which use letters and numbers indicating the numerical proportions of atoms of each type. Molecular formulas indicate the numbers of each type of atom in a molecule. For example, the formula for glucose is CH2O, while its molecular formula is C6H12O6. This is possible if the relevant bonding is easy to show in one dimension, an example is the condensed molecular/chemical formula for ethanol, which is CH3-CH2-OH or CH3CH2OH. For reasons of structural complexity, there is no condensed chemical formula that specifies glucose, chemical formulas may be used in chemical equations to describe chemical reactions and other chemical transformations, such as the dissolving of ionic compounds into solution. A chemical formula identifies each constituent element by its chemical symbol, in empirical formulas, these proportions begin with a key element and then assign numbers of atoms of the other elements in the compound, as ratios to the key element. For molecular compounds, these numbers can all be expressed as whole numbers. For example, the formula of ethanol may be written C2H6O because the molecules of ethanol all contain two carbon atoms, six hydrogen atoms, and one oxygen atom. Some types of compounds, however, cannot be written with entirely whole-number empirical formulas. An example is boron carbide, whose formula of CBn is a variable non-whole number ratio with n ranging from over 4 to more than 6.5. When the chemical compound of the consists of simple molecules. These types of formulas are known as molecular formulas and condensed formulas. A molecular formula enumerates the number of atoms to reflect those in the molecule, so that the formula for glucose is C6H12O6 rather than the glucose empirical formula. However, except for very simple substances, molecular chemical formulas lack needed structural information, for simple molecules, a condensed formula is a type of chemical formula that may fully imply a correct structural formula. For example, ethanol may be represented by the chemical formula CH3CH2OH
11.
Density
–
The density, or more precisely, the volumetric mass density, of a substance is its mass per unit volume. The symbol most often used for density is ρ, although the Latin letter D can also be used. Mathematically, density is defined as mass divided by volume, ρ = m V, where ρ is the density, m is the mass, and V is the volume. In some cases, density is defined as its weight per unit volume. For a pure substance the density has the numerical value as its mass concentration. Different materials usually have different densities, and density may be relevant to buoyancy, purity, osmium and iridium are the densest known elements at standard conditions for temperature and pressure but certain chemical compounds may be denser. Thus a relative density less than one means that the floats in water. The density of a material varies with temperature and pressure and this variation is typically small for solids and liquids but much greater for gases. Increasing the pressure on an object decreases the volume of the object, increasing the temperature of a substance decreases its density by increasing its volume. In most materials, heating the bottom of a results in convection of the heat from the bottom to the top. This causes it to rise relative to more dense unheated material, the reciprocal of the density of a substance is occasionally called its specific volume, a term sometimes used in thermodynamics. Density is a property in that increasing the amount of a substance does not increase its density. Archimedes knew that the irregularly shaped wreath could be crushed into a cube whose volume could be calculated easily and compared with the mass, upon this discovery, he leapt from his bath and ran naked through the streets shouting, Eureka. As a result, the term eureka entered common parlance and is used today to indicate a moment of enlightenment, the story first appeared in written form in Vitruvius books of architecture, two centuries after it supposedly took place. Some scholars have doubted the accuracy of this tale, saying among other things that the method would have required precise measurements that would have been difficult to make at the time, from the equation for density, mass density has units of mass divided by volume. As there are units of mass and volume covering many different magnitudes there are a large number of units for mass density in use. The SI unit of kilogram per metre and the cgs unit of gram per cubic centimetre are probably the most commonly used units for density.1,000 kg/m3 equals 1 g/cm3. In industry, other larger or smaller units of mass and or volume are often more practical, see below for a list of some of the most common units of density
12.
Boiling point
–
The boiling point of a substance is the temperature at which the vapor pressure of the liquid equals the pressure surrounding the liquid and the liquid changes into a vapor. The boiling point of a liquid varies depending upon the environmental pressure. A liquid in a vacuum has a lower boiling point than when that liquid is at atmospheric pressure. A liquid at high pressure has a boiling point than when that liquid is at atmospheric pressure. For a given pressure, different liquids boil at different temperatures, for example, water boils at 100 °C at sea level, but at 93.4 °C at 2,000 metres altitude. The normal boiling point of a liquid is the case in which the vapor pressure of the liquid equals the defined atmospheric pressure at sea level,1 atmosphere. At that temperature, the pressure of the liquid becomes sufficient to overcome atmospheric pressure. The standard boiling point has been defined by IUPAC since 1982 as the temperature at which boiling occurs under a pressure of 1 bar, the heat of vaporization is the energy required to transform a given quantity of a substance from a liquid into a gas at a given pressure. Liquids may change to a vapor at temperatures below their boiling points through the process of evaporation, evaporation is a surface phenomenon in which molecules located near the liquids edge, not contained by enough liquid pressure on that side, escape into the surroundings as vapor. On the other hand, boiling is a process in which molecules anywhere in the liquid escape, a saturated liquid contains as much thermal energy as it can without boiling. The saturation temperature is the temperature for a corresponding saturation pressure at which a liquid boils into its vapor phase, the liquid can be said to be saturated with thermal energy. Any addition of energy results in a phase transition. If the pressure in a system remains constant, a vapor at saturation temperature will begin to condense into its liquid phase as thermal energy is removed, similarly, a liquid at saturation temperature and pressure will boil into its vapor phase as additional thermal energy is applied. The boiling point corresponds to the temperature at which the pressure of the liquid equals the surrounding environmental pressure. Thus, the point is dependent on the pressure. Boiling points may be published with respect to the NIST, USA standard pressure of 101.325 kPa, at higher elevations, where the atmospheric pressure is much lower, the boiling point is also lower. The boiling point increases with increased pressure up to the critical point, the boiling point cannot be increased beyond the critical point. Likewise, the point decreases with decreasing pressure until the triple point is reached
13.
Aqueous solution
–
An aqueous solution is a solution in which the solvent is water. It is usually shown in chemical equations by appending to the relevant chemical formula, for example, a solution of table salt, or sodium chloride, in water would be represented as Na+ + Cl−. The word aqueous means pertaining to, related to, similar to, as water is an excellent solvent and is also naturally abundant, it is a ubiquitous solvent in chemistry. Substances that are hydrophobic often do not dissolve well in water, an example of a hydrophilic substance is sodium chloride. Acids and bases are aqueous solutions, as part of their Arrhenius definitions, the ability of a substance to dissolve in water is determined by whether the substance can match or exceed the strong attractive forces that water molecules generate between themselves. If the substance lacks the ability to dissolve in water the molecules form a precipitate, reactions in aqueous solutions are usually metathesis reactions. Metathesis reactions are another term for double-displacement, that is, when a cation displaces to form a bond with the other anion. The cation bonded with the latter anion will dissociate and bond with the other anion, aqueous solutions that conduct electric current efficiently contain strong electrolytes, while ones that conduct poorly are considered to have weak electrolytes. Those strong electrolytes are substances that are ionized in water. Nonelectrolytes are substances that dissolve in water yet maintain their molecular integrity, examples include sugar, urea, glycerol, and methylsulfonylmethane. When writing the equations of reactions, it is essential to determine the precipitate. To determine the precipitate, one must consult a chart of solubility, soluble compounds are aqueous, while insoluble compounds are the precipitate. Remember that there may not always be a precipitate, when performing calculations regarding the reacting of one or more aqueous solutions, in general one must know the concentration, or molarity, of the aqueous solutions. Solution concentration is given in terms of the form of the prior to it dissolving. Metal ions in aqueous solution Solubility Dissociation Acid-base reaction theories Properties of water Zumdahl S.1997, 4th ed. Boston, Houghton Mifflin Company
14.
Vitamin
–
A vitamin is an organic compound and a vital nutrient that an organism requires in limited amounts. For example, ascorbic acid is a vitamin for humans, supplementation is important for the treatment of certain health problems, but there is little evidence of nutritional benefit when used by otherwise healthy people. Thirteen vitamins are universally recognized at present, Vitamins are classified by their biological and chemical activity, not their structure. Thus, each vitamin refers to a number of compounds that all show the biological activity associated with a particular vitamin. Such a set of chemicals is grouped under an alphabetized vitamin generic descriptor title, such as vitamin A, which includes the compounds retinal, retinol, and four known carotenoids. Vitamers by definition are convertible to the form of the vitamin in the body. Some, such as vitamin D, have hormone-like functions as regulators of mineral metabolism, or regulators of cell and tissue growth and differentiation. The largest number of vitamins, the B complex vitamins, function as cofactors or the precursors for them. In this role, vitamins may be bound to enzymes as part of prosthetic groups, For example. They may also be less tightly bound to enzyme catalysts as coenzymes, for example, folic acid may carry methyl, formyl, and methylene groups in the cell. Although these roles in assisting enzyme-substrate reactions are vitamins best-known function, study of structural activity, function and their role in maintaining health is called vitaminology. Each vitamin is typically used in reactions, and therefore most have multiple functions. Vitamins are essential for the growth and development of a multicellular organism. Using the genetic blueprint inherited from its parents, a fetus begins to develop from the nutrients it absorbs and it requires certain vitamins and minerals to be present at certain times. These nutrients facilitate the chemical reactions that produce among other things, skin, bone, if there is serious deficiency in one or more of these nutrients, a child may develop a deficiency disease. Even minor deficiencies may cause permanent damage, for the most part, vitamins are obtained with food, but a few are obtained by other means. Humans can produce some vitamins from precursors they consume, examples include vitamin A, produced from beta carotene, and niacin, from the amino acid tryptophan. In those who are healthy, there is little evidence that supplements have any benefits with respect to cancer or heart disease
15.
Lecithin
–
Lecithins are usually phospholipids, composed of phosphoric acid with choline, glycerol or other fatty acids usually glycolipids or triglyceride. Glycerophospholipids in lecithin include phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol, phosphatidylserine, Lecithin was first isolated in 1845 by the French chemist and pharmacist Theodore Gobley. In 1850, he named the phosphatidylcholine lécithine, Lecithin can easily be extracted chemically using any non-polar solvent such as hexane, ethanol, acetone, petroleum ether, benzene, etc. or extraction can be done mechanically. It is usually available from such as soybeans, eggs, milk, marine sources, rapeseed, cottonseed. It has low solubility in water, but is an excellent emulsifier, in aqueous solution, its phospholipids can form either liposomes, bilayer sheets, micelles, or lamellar structures, depending on hydration and temperature. This results in a type of surfactant that usually is classified as amphipathic, Lecithin is sold as a food additive and dietary supplement. In cooking, it is used as an emulsifier and to prevent sticking. While lecithin is also a source of a variety of types of dietary fats. Lecithin is a source for methyl groups via its metabolite, trimethylglycine although this is consumed from plants. Phosphatidylcholine occurs in all organisms, being one of the major components of the phospholipid portion of the cell membrane. Commercial lecithin, as used by manufacturers, is a mixture of phospholipids in oil. The lecithin can be obtained by water degumming the extracted oil of seeds and it is a mixture of various phospholipids, and the composition depends on the origin of the lecithin. A major source of lecithin is soybean oil, the main phospholipids in lecithin from soya and sunflower are phosphatidyl choline, phosphatidyl inositol, phosphatidyl ethanolamine, and phosphatidic acid. They often are abbreviated to PC, PI, PE, and PA, purified phospholipids are produced by companies commercially. To modify the performance of lecithin to make it suitable for the product to which it is added, in hydrolysed lecithins, a portion of the phospholipids have one fatty acid removed by phospholipase. The most commonly used phospholipase is phospholipase A2, which removes the fatty acid at the C2 position of glycerol, lecithins may also be modified by a process called fractionation. During this process, lecithin is mixed with an alcohol, usually ethanol, some phospholipids, such as phosphatidylcholine, have good solubility in ethanol, whereas most other phospholipids do not dissolve well in ethanol. The ethanol is separated from the sludge, after which the ethanol is removed by evaporation to obtain a phosphatidylcholine-enriched lecithin fraction
16.
Quaternary ammonium cation
–
Quaternary ammonium cations, also known as quats, are positively charged polyatomic ions of the structure NR+4, R being an alkyl group or an aryl group. Unlike the ammonium ion and the primary, secondary, or tertiary ammonium cations, Quaternary ammonium salts or quaternary ammonium compounds are salts of quaternary ammonium cations. Quaternary ammonium compounds are prepared by the alkylation of amines with a halocarbon. In older literature this is called a Menshutkin reaction, however modern chemists usually refer to it simply as quaternization. The reaction can be used to produce a compound with unequal alkyl chain lengths and they also are stable toward most nucleophiles. The latter is indicated by the stability of the hydroxide salts such as tetramethylammonium hydroxide, because of their resilience, many unusual anions have been isolated as the quaternary ammonium salts. Examples include tetramethylammonium pentafluoroxenate, containing the highly reactive pentafluoroxenate ion, permanganate can be solubilized in organic solvents, when deployed as its NBu+4 salt. With exceptionally strong bases, quat cations degrade and they undergo Sommelet–Hauser rearrangement and Stevens rearrangement, as well as dealkylation under harsh conditions. Quaternary ammonium cations containing N–C–C–H units can also undergo the Hofmann elimination, Quaternary ammonium salts are used as disinfectants, surfactants, fabric softeners, and as antistatic agents. In liquid fabric softeners, the salts are often used. In dryer anticling strips, the salts are often used. Spermicidal jellies also contain quaternary ammonium salts, Quaternary ammonium compounds have also been shown to have antimicrobial activity. Certain quaternary ammonium compounds, especially those containing long alkyl chains, are used as antimicrobials, also good against fungi, amoebas, and enveloped viruses, quaternary ammonium compounds are believed to act by disrupting the cell membrane. Quaternary ammonium compounds are lethal to a variety of organisms except endospores, Mycobacterium tuberculosis. Quaternary ammonium compounds are cationic detergents, as well as disinfectants and they are very effective in combination with phenols. Quaternary ammonium compounds are deactivated by anionic detergents, also, they work best in soft waters. Effective levels are at 200 ppm and they are effective at temperatures up to 100 °C. Quaternary ammonium salts are used in the foodservice industry as sanitizing agents
17.
Ion
–
An ion is an atom or a molecule in which the total number of electrons is not equal to the total number of protons, giving the atom or molecule a net positive or negative electrical charge. Ions can be created, by chemical or physical means. In chemical terms, if an atom loses one or more electrons. If an atom gains electrons, it has a net charge and is known as an anion. Ions consisting of only a single atom are atomic or monatomic ions, because of their electric charges, cations and anions attract each other and readily form ionic compounds, such as salts. In the case of ionization of a medium, such as a gas, which are known as ion pairs are created by ion impact, and each pair consists of a free electron. The word ion comes from the Greek word ἰόν, ion, going and this term was introduced by English physicist and chemist Michael Faraday in 1834 for the then-unknown species that goes from one electrode to the other through an aqueous medium. Faraday also introduced the words anion for a charged ion. In Faradays nomenclature, cations were named because they were attracted to the cathode in a galvanic device, arrhenius explanation was that in forming a solution, the salt dissociates into Faradays ions. Arrhenius proposed that ions formed even in the absence of an electric current, ions in their gas-like state are highly reactive, and do not occur in large amounts on Earth, except in flames, lightning, electrical sparks, and other plasmas. These gas-like ions rapidly interact with ions of charge to give neutral molecules or ionic salts. These stabilized species are commonly found in the environment at low temperatures. A common example is the present in seawater, which are derived from the dissolved salts. Electrons, due to their mass and thus larger space-filling properties as matter waves, determine the size of atoms. Thus, anions are larger than the parent molecule or atom, as the excess electron repel each other, as such, in general, cations are smaller than the corresponding parent atom or molecule due to the smaller size of its electron cloud. One particular cation contains no electrons, and thus consists of a single proton - very much smaller than the parent hydrogen atom. Since the electric charge on a proton is equal in magnitude to the charge on an electron, an anion, from the Greek word ἄνω, meaning up, is an ion with more electrons than protons, giving it a net negative charge. A cation, from the Greek word κατά, meaning down, is an ion with fewer electrons than protons, there are additional names used for ions with multiple charges
18.
Counterion
–
A counterion is the ion that accompanies an ionic species in order to maintain electric neutrality. In table salt, the cation is the counterion for the chlorine anion. Counterions are the ions in ion exchange polymers and colloids. Ion exchange resins are polymers with a net negative or positive charge, cation exchange resins consist of an anionic polymer with countercations, typically Na+. The resin has an affinity for highly charged countercations, e. g. by Ca2+ in the case of water softening. Complementarily, anion exchange resins are typically provided in the form of chloride, counterions are used in phase-transfer catalysis. In a typical application lipophilic countercation such as benzalkonium solubilizes reagents in organic solvents, solubility of salts in organic solvents is a function of both the cation and the anion. The solubility of cations in organic solvents can be enhanced when the anion is lipophilic, similarly, the solubility of anions in organic solvents is enhanced with lipophilic cations. The most common lipophilic cations are quaternary ammonium cations, called quat salts, Lipophilic counteranions Lipophilic countercations Many cationic organometallic complexes are isolated with inert, noncoordinating counterions. Ferrocenium tetrafluoroborate is one such example, in order to achieve high ionic conductivity, electrochemical measurements are conducted in the presence of excess electrolyte. In water the electrolyte is often a salt such as potassium chloride. For measurements in nonaqueous solutions, salts composed of both lipophilic cations and anions are employed, e. g. tetrabutylammonium hexafluorophosphate, even in such cases potentials are influenced by ion-pairing, an effect that is accentuated in solvents of low dielectric constant. For many applications, the counterion simply provides charge and lipophilicity that allows manipulation of its partner ion, the counterion is expected to be chemically inert. For counteranions, inertness is expressed in terms of low Lewis basicity, the counterions are ideally rugged and unreactive. For quaternary ammonium and phosphonium countercations, inertness is related to their resistance of degradation by strong bases and strong nucleophiles
19.
Phosphatidylcholine
–
Phosphatidylcholines are a class of phospholipids that incorporate choline as a headgroup. They are also a member of the group of yellow-brownish fatty substances occurring in animal. Dipalmitoyl phosphatidylcholine is a component of pulmonary surfactant and is often used in the L/S ratio to calculate fetal lung maturity. While phosphatidylcholines are found in all plant and animal cells, they are absent in the membranes of most bacteria, gobley eventually completely described his lecithin from chemical structural point of view, in 1874. Phosphatidylcholines are such a component of lecithin that in some contexts the terms are sometimes used as synonyms. However, lecithin extracts consist of a mixture of phosphatidylcholine and other compounds and it is also used along with sodium taurocholate for simulating fed- and fasted-state biorelevant media in dissolution studies of highly lipophilic drugs. Phosphatidylcholine is a constituent of cell membranes and pulmonary surfactant. It is thought to be transported between membranes within the cell by phosphatidylcholine transfer protein, phosphatidylcholine also plays a role in membrane-mediated cell signaling and PCTP activation of other enzymes. This phospholipid is composed of a head group and glycerophosphoric acid. Usually, one is a fatty acid, and the other is an unsaturated fatty acid. However, there are examples of disaturated species. Animal lung phosphatidylcholine, for example, contains a proportion of Dipalmitoylphosphatidylcholine. Phospholipase D catalyzes the hydrolysis of phosphatidylcholine to form phosphatidic acid, phosphatidylcholine is a vital substance found in every cell of the human body. However, a review of clinical trials in humans found that there is not enough evidence to support lecithin or phosphatidylcholine supplementation for patients with dementia. The study does admit that a moderate benefit cannot be ruled out until further large studies are performed. Recent studies have examined potential benefits of phosphatidylcholine for liver repair, results are mixed in animal models, and no clinical evidence shows a health benefit in humans. One study shows the effect of phosphatidylcholine in mice with hepatitis A, hepatitis B. The administration of phosphatidylcholine for chronic, active hepatitis resulted in significant reduction of activity in mice
20.
Sphingomyelin
–
Sphingomyelin is a type of sphingolipid found in animal cell membranes, especially in the membranous myelin sheath that surrounds some nerve cell axons. It usually consists of phosphocholine and ceramide, or a head group, therefore. In humans, SPH represents ~85% of all sphingolipids, and typically make up 10-20 mol % of plasma membrane lipids, sphingomyelins contain phosphocholine or phosphoethanolamine as their polar head group and are therefore classified along with glycerophospholipids as phospholipids. Indeed, sphingomyelins resemble phosphatidylcholines in their properties and three-dimensional structure. Sphingomyelin was first isolated by German chemist Johann L. W, the structure of sphingomyelin was first reported in 1927 as N-acyl-sphingosine-1-phosphorylcholine. Sphingomyelin content in mammals ranges from 2 to 15% in most tissues, with higher concentrations found in tissues, red blood cells. Sphingomyelin has significant structural and functional roles in the cell and it is a plasma membrane component and participates in many signaling pathways. The metabolism of sphingomyelin creates many products that play significant roles in the cell, sphingomyelin consists of a phosphocholine head group, a sphingosine, and a fatty acid. It is one of the few membrane phospholipids not synthesized from glycerol, the sphingosine and fatty acid can collectively be categorized as a ceramide. This composition allows sphingomyelin to play significant roles in signaling pathways, sphingomyelin obtained from natural sources, such as eggs or bovine brain, contains fatty acids of various chain length. Sphingomyelin with set chain length, such as palmitoylsphingomyelin with a saturated 16 acyl chain, is available commercially, ideally, sphingomyelin molecules are shaped like a cylinder, however many molecules of sphingomyelin have a significant chain mismatch. The hydrophobic chains of sphingomyelin tend to be more saturated than other phospholipids. The main transition phase temperature of sphingomyelins is also compared to the phase transition temperature of similar phospholipids. This can introduce lateral heterogeneity in the membrane, generating domains in the membrane bilayer, sphingomyelin undergoes significant interactions with cholesterol. Cholesterol has the ability to eliminate the liquid to solid phase transition in phospholipids, due to sphingomyelin transition temperature being within physiological temperature ranges, cholesterol can play a significant role in the phase of sphingomyelin. Sphingomyelin are also prone to intermolecular hydrogen bonding than other phospholipids. Sphingomyelin is synthesized at the endoplasmic reticulum, where it can be found in low amounts and it is enriched at the plasma membrane with a greater concentration on the outer than the inner leaflet. The Golgi complex represents an intermediate between the ER and plasma membrane, with higher concentrations towards the trans side
21.
Phospholipid
–
Phospholipids are a class of lipids that are a major component of all cell membranes. They can form lipid bilayers because of their amphiphilic characteristic, the structure of the phospholipid molecule generally consists of two hydrophobic fatty acid tails and a hydrophilic head consisting of a phosphate group. The two components are joined together by a glycerol molecule, the phosphate groups can be modified with simple organic molecules such as choline. Biological membranes in eukaryotes also contain another class of lipid, sterol, interspersed among the phospholipids and together they provide membrane fluidity, purified phospholipids are produced commercially and have found applications in nanotechnology and materials science. An amphiphile is a term describing a chemical compound possessing both hydrophilic and lipophilic properties, the phospholipid head contains a negatively charged phosphate group and glycerol, it is hydrophilic. The phospholipid tails usually consists of 2 long fatty acid chains and these specific properties allow phospholipids to play an important role in the phospholipid bilayer. In biological systems, the phospholipids often occur with other molecules in a such as a cell membrane. Lipid bilayers occur when hydrophobic tails line up against one another, sterols contribute to membrane fluidity by hindering the packing together of phospholipids. However, this model has now superseded, as through the study of lipid polymorphism it is now known that the behaviour of lipids under physiological conditions is not simple. Liposomes are often composed of phosphatidylcholine-enriched phospholipids and may also contain mixed Phospholipid chains with surfactant properties, the ethosomal formulation of ketoconazole using phospholipids is a promising option for transdermal delivery in fungal infections. Computational simulations of phospholipids are often performed using molecular dynamics with force fields such as GROMOS, CHARMM, phospholipids are optically highly birefringent, i. e. their refractive index is different along their axis as opposed to perpendicular to it. There are no methods available for analysis of phospholipids since the close range of polarity between different phospholipid species makes detection difficult. Oil chemists often use spectroscopy to determine total Phosphorus abundance and then calculate approximate mass of phospholipids based on weight of expected fatty acid species. Modern lipid profiling employs more absolute methods of analysis, with magnetic resonance spectroscopy, particularly 31P-NMR. Phospholipid synthesis occurs in the adjacent to ER membrane that is studded with proteins that act in synthesis. Common sources of industrially produced phospholipids are soya, rapeseed, sunflower, chicken eggs, bovine milk, each source has a unique profile of individual phospholipid species and consequently differing applications in food, nutrition, pharmaceuticals, cosmetics and drug delivery. Some types of phospholipid can be split to produce products that function as second messengers in signal transduction, phospholipids also intervene in prostaglandin signal pathways as the raw material used by lipase enzymes to produce the prostaglandin precursors. In plants they serve as the raw material to produce Jasmonic acid, phospholipids can act as emulsifiers, enabling oils to form a colloid with water
22.
Cell membrane
–
The cell membrane is a biological membrane that separates the interior of all cells from the outside environment. The cell membrane is permeable to ions and organic molecules and controls the movement of substances in. The basic function of the membrane is to protect the cell from its surroundings. It consists of the bilayer with embedded proteins. Cell membranes can be artificially reassembled, Some authors that did not believe that there was a functional permeable boundary at the surface of the cell preferred to use the term plasmalemma to the extern region of the cell. The cell membrane surrounds the cytoplasm of living cells, physically separating the components from the extracellular environment. The cell membrane also plays a role in anchoring the cytoskeleton to provide shape to the cell, fungi, bacteria, most archaea, and plants also have a cell wall, which provides a mechanical support to the cell and precludes the passage of larger molecules. The cell membrane is permeable and able to regulate what enters and exits the cell. The movement of substances across the membrane can be passive, occurring without the input of cellular energy, or active. The membrane also maintains the cell potential, the cell membrane thus works as a selective filter that allows only certain things to come inside or go outside the cell. The cell employs a number of mechanisms that involve biological membranes,1. Passive osmosis and diffusion, Some substances such as carbon dioxide and oxygen, can move across the membrane by diffusion. Because the membrane acts as a barrier for certain molecules and ions, such a concentration gradient across a semipermeable membrane sets up an osmotic flow for the water. Transmembrane protein channels and transporters, Nutrients, such as sugars or amino acids, must enter the cell, such molecules diffuse passively through protein channels such as aquaporins in facilitated diffusion or are pumped across the membrane by transmembrane transporters. Protein channel proteins, also called permeases, are quite specific, recognizing and transporting only a limited food group of chemical substances. Endocytosis, Endocytosis is the process in which cells absorb molecules by engulfing them, the plasma membrane creates a small deformation inward, called an invagination, in which the substance to be transported is captured. The deformation then pinches off from the membrane on the inside of the cell, Endocytosis is a pathway for internalizing solid particles, small molecules and ions, and macromolecules. Endocytosis requires energy and is thus a form of active transport and this is the process of exocytosis
23.
Acetylcholine
–
Its name is derived from its chemical structure, it is an ester of acetic acid and choline. Parts in the body that use or are affected by acetylcholine are referred to as cholinergic, substances that interfere with acetylcholine activity are called anticholinergics. Acetylcholine is the used at the neuromuscular junction—in other words. This property means that drugs that affect cholinergic systems can have dangerous effects ranging from paralysis to convulsions. In the brain, acetylcholine functions as a neurotransmitter and as a neuromodulator, the brain contains a number of cholinergic areas, each with distinct functions. They play an important role in arousal, attention, memory, scopolamine, which acts mainly on muscarinic receptors in the brain, can cause delirium and amnesia. The addictive qualities of nicotine derive from its effects on nicotinic receptors in the brain. Acetylcholine has functions both in the nervous system and in the central nervous system. In the peripheral nervous system, acetylcholine activates muscles, and is a major neurotransmitter in the nervous system. In the CNS, cholinergic projections from the basal forebrain to the cerebral cortex, like many other biologically active substances, acetylcholine exerts its effects by binding to and activating receptors located on the surface of cells. There are two classes of acetylcholine receptor, nicotinic and muscarinic. Nicotinic acetylcholine receptors are ligand-gated ion channels permeable to sodium, potassium, in other words, they are ion channels embedded in cell membranes, capable of switching from a closed to open state when acetylcholine binds to them, in the open state they allow ions to pass through. Nicotinic receptors come in two types, known as muscle-type and neuronal-type. The muscle-type can be blocked by curare, the neuronal-type by hexamethonium. The main location of muscle-type receptors is on muscle cells, as described in detail below. Neuronal-type receptors are located in autonomic ganglia, and in the nervous system. Muscarinic acetylcholine receptors have a complex mechanism, and affect target cells over a longer time frame. In mammals, five subtypes of muscarinic receptors have been identified, labeled M1 through M5, all of them function as G protein-coupled receptors, meaning that they exert their effects via a second messenger system
24.
Adolph Strecker
–
Adolph Strecker was a German chemist who is remembered primarily for his work with amino acids. Strecker was born in Darmstadt, the son of Ludwig Strecker, Adolph Strecker attended school in Darmstadt until 1838 when he changed to the higher Gewerbeschule. After receiving his abitur in 1840, Strecker began studying science at the University of Gießen, in August 1842, Strecker received his PhD and began teaching at a realschule in Darmstadt. He refused one offer to work for Liebig, but in 1846 he accepted another, Strecker finished his habilitation in 1848 and became a lecturer at the university. Strecker investigated a variety of problems in both organic and inorganic chemistry during his time at Gießen. Examples include the masses of silver and carbon, the reactions of lactic acid, the decomposition of hippuric acid by nitric acid. While in Norway, Strecker focused on chemistry, covering a broad range of topics from organometallic chemistry to natural products. Also while in Norway, Strecker returned to Germany for several holidays, during one such visit to Darmstadt, he married on July 3,1852. His wife died on October 13,1853, he married a second time on September 29,1855, Strecker left Norway on Gmelins death in 1860 to accept the latters position at the University of Tübingen. There he conducted research on guanine, xanthine, caffeine, and theobromine, and on the very toxic thallium oxides and he moved to the University of Würzburg in 1870, but his first semester was interrupted by the Franco-Prussian War of 1870–1871. Strecker became an officer during the war and returned to the university after it, in the summer of 1871 he undertook a recreational holiday in Berchtesgaden, Bavaria, but his health began to deteriorate. Strecker died in Würzburg, where he is buried in the Hauptfriedhof, vieweg, Braunschweig 1851 Digital edition by the University and State Library Düsseldorf 2. 1877 The Strecker synthesis of amino acids involves the reaction of cyanide, ammonium chloride. The reaction can also be run with ammonia, hydrogen cyanide, because of the relative simplicity of the reactants, the Strecker synthesis has been invoked by those studying both the origin of life and meteoritic amino acids. Also named for Strecker are the Strecker degradation, which involves the conversion of acids into imines and then into ketones. Lepsius, Allgemeine Deutsche Biographie, volume 36, Leipzig, Duncker & Humblot – entry for Strecker Adolph Strecker – brief biography and two pictures at Tübingen University
25.
Bile
–
Bile or gall is a dark green to yellowish brown fluid, produced by the liver of most vertebrates, that aids the digestion of lipids in the small intestine. In humans, bile is produced continuously by the liver, after eating, this stored bile is discharged into the duodenum. The composition of gallbladder bile is 97% water,0. 7% bile salts,0. 2% bilirubin,0. 51% fats, and 200 meq/l inorganic salts. Bile was the yellow bile in the four humor system of medicine, about 400 to 800 ml of bile is produced per day in adult humans. Bile acts to some extent as a surfactant, helping to emulsify the lipids in food, the hydrophilic sides are negatively charged, and this charge prevents fat droplets coated with bile from re-aggregating into larger fat particles. Ordinarily, the micelles in the duodenum have a diameter around 14–33 μm, a triglyceride is broken down into two fatty acids and a monoglyceride, which are absorbed by the villi on the intestine walls. After being transferred across the membrane, the fatty acids reform into triglycerides. Without bile salts, most of the lipids in food would be excreted in faeces, since bile increases the absorption of fats, it is an important part of the absorption of the fat-soluble substances, such as the vitamins A, D, E, and K. Besides its digestive function, bile serves also as the route of excretion for bilirubin, bilirubin derives from hemoglobin by glucuronidation. Bile tends to be alkali on average, the pH of common duct bile is higher than that of the corresponding gallbladder bile. It becomes more acidic in the gallbladder the longer you go without eating, as an alkali, it also has the function of neutralizing any excess stomach acid before it enters the duodenum, the first section of the small intestine. Bile salts also act as bactericides, destroying many of the microbes that may be present in the food, in the absence of bile, fats become indigestible and are instead excreted in feces, a condition called steatorrhea. Feces lack their characteristic color and instead are white or gray. Steatorrhea can lead to deficiencies in essential fatty acids and fat-soluble vitamins, in addition, past the small intestine the gastrointestinal tract and gut flora are not adapted to processing fats, leading to problems in the large intestine. The cholesterol contained in bile will occasionally accrete into lumps in the gallbladder, cholesterol gallstones are generally treated through surgical removal of the gallbladder. However, they can sometimes be dissolved by increasing the concentration of naturally occurring bile acids, such as chenodeoxycholic acid. On an empty stomach – after repeated vomiting, for example – a persons vomit may be green or dark yellow, the bitter and greenish component may be bile or normal digestive juices originating in the stomach. The color of bile is often likened to fresh-cut grass, unlike components in the stomach that look greenish yellow or dark yellow
26.
Oscar Liebreich
–
Matthias Eugen Oscar Liebreich was a German pharmacologist. He was a native of Königsberg and he studied chemistry under Carl Remigius Fresenius in Wiesbaden, and studied medicine in Königsberg, Tübingen and Berlin, obtaining his degree in 1865. Beginning in 1867, he worked as an assistant in the department of the pathological institute under Rudolf Virchow. Later on, he became a professor of therapeutics and director of the institute in Berlin. In 1889 he was co-founder of the Balneologischen Gesellschaft in Berlin, in 1865, he gave the name protagon to a proximate principle discovered in the brain and in blood corpuscles. He also made valued contributions in his research of boracic acid. Liebreich edited the Therapeutische Monatshefte and the Encyklopädie der Therapie, and with Alexander Langgard, compendium der Arzneiverordnung, nach der Pharmakopoe für das deutsche Reich und den neuesten fremden Pharmakopoeen. 1896 Digital edition by the University and State Library Düsseldorf Effects of borax and boracic acid on the human system London and he was a younger brother of ophthalmologist Richard Liebreich. This article incorporates translated text from an equivalent article at the German Wikipedia, das Chloralhydrat, ein neues Hypnoticum und Anaestheticum und dessen Anwendung in der Medicin, eine Arzneimittel-Untersuchung. Thurston, H. T. Colby, F. M. eds
27.
National Academy of Medicine
–
The National Academy of Medicine, formerly called the Institute of Medicine, is an American nonprofit, non-governmental organization. The National Academy of Medicine provides national advice on issues relating to science, medicine, and health. Operating outside the framework of the U. S. federal government, it relies on a volunteer workforce of scientists and other experts, the institute was founded in 1970, under the congressional charter of the National Academy of Sciences as the Institute of Medicine. These changes took effect on July 1,2015, the National Academies attempt to obtain authoritative, objective, and scientifically balanced answers to difficult questions of national importance. The work is conducted by committees of volunteer scientists—leading national and international experts—who serve without compensation, committees are composed in an attempt to assure the requisite expertise and to avoid bias or conflict of interest. Victor Dzau is President and Chairman of the Council and his six-year term began on July 1,2014. The Interim Leonard D. Schaeffer Executive Officer is Clyde J. Behney, the majority of studies and other activities are requested and funded by the federal government. Private industry, foundations, and state and local governments also initiate studies, reports are made available online for free by the publishing arm of the United States National Academies, the National Academies Press, in multiple formats. The academy is both an honorific membership organization and a research organization. Election to active membership is both an honor and a commitment to serve in Institute affairs, the bylaws specify that no more than 80 new members shall be elected annually, including 10 from outside the United States. The announcement of newly elected members occurs at the Annual Meeting in October, as of October 20,2015, the number of regular members plus international and emeritus members is 2,012. The Food and Nutrition Board is body within the NAM set up to study the safety and it publishes principles and guidelines for good nutrition. It judges the relationship between nutrition, good health and disease prevention, the New York Times called the IOM the United States most esteemed and authoritative adviser on issues of health and medicine, and its reports can transform medical thinking around the world. It is accompanied by a medal and $20,000
28.
Cell signaling
–
Cell signaling is part of any communication process that governs basic activities of cells and coordinates all cell actions. The ability of cells to perceive and correctly respond to their microenvironment is the basis of development, tissue repair, errors in signaling interactions and cellular information processing are responsible for diseases such as cancer, autoimmunity, and diabetes. By understanding cell signaling, diseases may be treated effectively and, theoretically. Traditional work in biology has focused on studying individual parts of cell signaling pathways, systems biology research helps us to understand the underlying structure of cell signaling networks and how changes in these networks may affect the transmission and flow of information. Such networks are complex systems in their organization and may exhibit a number of emergent properties including bistability and ultrasensitivity, analysis of cell signaling networks requires a combination of experimental and theoretical approaches including the development and analysis of simulations and modeling. Long-range allostery is often a significant component of signaling events. Cell signaling has been most extensively studied in the context of human diseases, however, cell signaling may also occur between the cells of two different organisms. In many mammals, early embryo cells exchange signals with cells of the uterus, in the human gastrointestinal tract, bacteria exchange signals with each other and with human epithelial and immune system cells. For the yeast Saccharomyces cerevisiae during mating, some cells send a signal into their environment. The mating factor peptide may bind to a surface receptor on other yeast cells. Cell signaling can be classified to be mechanical and biochemical based on the type of the signal, mechanical signals are the forces exerted on the cell and the forces produced by the cell. These forces can both be sensed and responded by the cells, biochemical signals are the biochemical molecules such as proteins, lipids, ions and gases. These signals can be categorized based on the distance between signaling and responder cells, Signaling within, between, and amongst cells is subdivided into the following classifications, Intracrine signals are produced by the target cell that stay within the target cell. Autocrine signals are produced by the cell, are secreted. Sometimes autocrine cells can target cells close by if they are the type of cell as the emitting cell. An example of this are immune cells and these signals are transmitted along cell membranes via protein or lipid components integral to the membrane and are capable of affecting either the emitting cell or cells immediately adjacent. Paracrine signals target cells in the vicinity of the emitting cell, endocrine cells produce hormones that travel through the blood to reach all parts of the body. Cells communicate with each other via direct contact, over short distances, some cell–cell communication requires direct cell–cell contact
29.
Neurotransmission
–
Neurotransmission is essential for the process of communication between two neurons. In response to an action potential or graded electrical potential. The released neurotransmitter may then move across the synapse to be detected by, binding of neurotransmitters may influence the postsynaptic neuron in either an inhibitory or excitatory way. Neurons form elaborate networks through which nerve impulses travel, each neuron has as many as 15,000 connections with other neurons. Neurons do not touch each other, instead, neurons interact at close contact points called synapses, a neuron transports its information by way of an action potential. When the nerve impulse arrives at the synapse, it may cause the release of neurotransmitters, the postsynaptic neuron may receive inputs from many additional neurons, both excitatory and inhibitory. Excitatory inputs bring a neuron closer to threshold, while inhibitory inputs bring the neuron farther from threshold, an action potential is an all-or-none event, neurons whose membranes have not reached threshold will not fire, while those that do must fire. Once the action potential is initiated, it will propagate along the axon and this can take place in the cell body, in the axon, or in the axon terminal. Storage of the neurotransmitter in storage granules or vesicles in the axon terminal, calcium enters the axon terminal during an action potential, causing release of the neurotransmitter into the synaptic cleft. After its release, the transmitter binds to and activates a receptor in the postsynaptic membrane, the neurotransmitter is either destroyed enzymatically, or taken back into the terminal from which it came, where it can be reused, or degraded and removed. Neurotransmitters are spontaneously packed in vesicles and released in individual quanta-packets independently of presynaptic action potentials and this slow release is detectable and produces micro-inhibitory or micro-excitatory effects on the postsynaptic neuron. An action potential briefly amplifies this process, neurotransmitter containing vesicles cluster around active sites, and after they have been released may be recycled by one of three proposed mechanism. The first proposed mechanism involves partial opening and then re-closing of the vesicle, the second two involve the full fusion of the vesicle with the membrane, followed by recycling, or recycling into the endosome. The vesicle exocytosis is through to be driven by a complex called SNARE. Once released, a neurotransmitter enters the synapse and encounters receptors, neurotransmitters receptors can either be inotropic or g protein coupled. Inotropic receptors allow for ions to pass through when agonized by a ligand, the main model involves a receptor composed of multiple subunits that allow for coordination of ion preference. G protein coupled receptors, also called metabotropic receptors, when bound to by a ligand undergo conformational changes yielding in intracellular response, termination of neurotransmitter activity is usually done by a transporter, however enzymatic deactivation is also plausible. Each neuron connects with other neurons, receiving numerous impulses from them
30.
Protein biosynthesis
–
Protein synthesis is the process whereby biological cells generate new proteins, it is balanced by the loss of cellular proteins via degradation or export. Protein biosynthesis is regulated at multiple steps. They are principally during transcription and translation, the cistron DNA is transcribed into the first of a series of RNA intermediates. The last version is used as a template in synthesis of a polypeptide chain, Protein will often be synthesized directly from genes by translating mRNA. However, when a protein must be available on short notice or in large quantities, a proprotein is an inactive protein containing one or more inhibitory peptides that can be activated when the inhibitory sequence is removed by proteolysis during posttranslational modification. A preprotein is a form that contains a sequence that specifies its insertion into or through membranes. The signal peptide is cleaved off in the endoplasmic reticulum, preproproteins have both sequences still present. The amino acids are linked together to extend the growing protein chain. This whole complex of processes is carried out by the ribosome, the ribosome latches onto the end of an mRNA molecule and moves along it, capturing loaded tRNA molecules and joining together their amino acids to form a new protein chain. Protein biosynthesis, although similar, is different for prokaryotes and eukaryotes. In transcription an mRNA chain is generated, with one strand of the DNA double helix in the genome as a template and this strand is called the template strand. Transcription occurs in the nucleus, where the DNA is held. The DNA structure of the cell is made up of two made up of sugar and phosphate held together by hydrogen bonds between the bases of opposite strands. The sugar and the phosphate in each strand are joined together by stronger covalent bonds. The DNA is unzipped by the helicase, leaving the single nucleotide chain open to be copied. RNA polymerase reads the DNA strand from the 3-prime end to the 5-prime end, the general RNA structure is very similar to the DNA structure, but in RNA the nucleotide uracil takes the place that thymine occupies in DNA. The single strand of mRNA leaves the nucleus through nuclear pores, hnRNA then undergoes splicing of introns via spliceosomes to produce the final mRNA. The synthesis of proteins from RNA is known as translation, in eukaryotes, translation occurs in the cytoplasm, where the ribosomes are located
31.
Methyl group
–
A methyl group is an alkyl derived from methane, containing one carbon atom bonded to three hydrogen atoms — CH3. In formulas, the group is often abbreviated Me, such hydrocarbon groups occur in many organic compounds. It is a stable group in most molecules. While the methyl group is part of a larger molecule. The anion has eight electrons, the radical seven and the cation six. All three forms are highly reactive and rarely observed, the methylium cation exists in the gas phase, but is otherwise not encountered. Some compounds are considered to be sources of the CH3+ cation, the methanide anion exists only in rarefied gas phase or under exotic conditions. It can be produced by electrical discharge in ketene at low pressure, such reagents are generally prepared from the methyl halides, M + CH3X → MCH3 where M is an alkali metal. The methyl radical has the formula CH3 and it exists in dilute gases, but in more concentrated form it readily dimerizes to ethane. It can be produced by decomposition of only certain compounds. The reactivity of a methyl group depends on the adjacent substituents, methyl groups can be quite unreactive. For example, in compounds, the methyl group resists attack by even the strongest acids. The oxidation of a group occurs widely in nature and industry. The oxidation products derived from methyl are CH2OH, CHO, for example, permanganate often converts a methyl group to a carboxyl group, e. g. the conversion of toluene to benzoic acid. Ultimately oxidation of methyl groups gives protons and carbon dioxide, as seen in combustion, demethylation is a common process, and reagents that undergo this reaction are called methylating agents. Common methylating agents are dimethyl sulfate, methyl iodide, and methyl triflate, methanogenesis, the source of natural gas, arises via a demethylation reaction. Certain methyl groups can be deprotonated, for example, the acidity of the methyl groups in acetone is about 1020 more acidic than methane. The resulting carbanions are key intermediates in many reactions in organic synthesis and biosynthesis, fatty acids are produced in this way
32.
Betaine
–
A betaine thus may be a specific type of zwitterion. Historically the term was reserved for TMG only, biologically, betaine is involved in methylation reactions and detoxification of homocysteine. The pronunciation of the compound reflects its origin and first isolation from sugar beets, however, it is often pronounced beta-INE or even BEE-tayn. Intracellular accumulation of betaines, non-perturbing to enzyme function, protein structure and membrane integrity, permits water retention in cells and it is also a methyl donor of increasingly recognised significance in biology. The original betaine, N, N, N-trimethylglycine, was named after its discovery in sugar beet in the 19th century and it is a small N-trimethylated amino acid, existing in zwitterionic form at neutral pH. This substance is now often called glycine betaine to distinguish it from other betaines that are distributed in microorganisms, plants. Phosphonium betaines are intermediates in the Wittig reaction, the addition of betaine to polymerase chain reactions improves the amplification of DNA by reducing the formation of secondary structure in GC-rich regions. The addition of betaine has been reported to enhance the specificity of the chain reaction by eliminating the base pair composition dependence of DNA melting. Mesoionic Mesomeric betaine Ylide Cocamidopropyl betaine Osmoprotectants IUPAC, Compendium of Chemical Terminology, 2nd ed. Online corrected version, betaines
33.
European Food Safety Authority
–
The European Food Safety Authority is the agency of the European Union that provides independent scientific advice and communicates on existing and emerging risks associated with the food chain. EFSA was established in February 2002, is based in Parma, Italy, the work of EFSA covers all matters with a direct or indirect impact on food and feed safety, including animal health and welfare, plant protection and plant health and nutrition. EFSA also communicates to the public in an open and transparent way on all matters within its remit and they are appointed by the Management Board. The Advisory Forum advises the Executive Director, in particular in drafting a proposal for the EFSAs work programmes and it is composed of representatives of national bodies responsible for risk assessment in the Member States, with observers from Norway, Iceland, Switzerland and the European Commission. The Scientific Committee and its Scientific Panels provide scientific opinions and advice, each within their own sphere of competence, the number and names of the Scientific Panels are adapted in the light of technical and scientific development by the European Commission at EFSAs request. The independent scientific experts are appointed by the Management Board upon a proposal from the Executive Director for three-year terms, the scientific output of the European Food Safety Authority is published in the EFSA Journal, an open-access, online scientific journal. This concerns risk assessment in relation to food and feed and includes nutrition, animal health and welfare, plant health, EFSA has been criticised for their alleged overregulation, as well as allegations of frequent conflicts of interest. EFSA has also criticised by the NGO CHEM Trust for misrepresenting the results of their expert committees report on Bisphenol A in January 2015. EFSA claimed in the abstract, press release and briefing that Bisphenol A posed no risk to health, EFSA later modified the abstract to correct this error, though the press release remains unchanged. EFSA have argued that use of no concern in their press release and Bisphenol A briefing is to ensure these materials are accessible
34.
Liver (food)
–
The liver of mammals, fowl, and fish is commonly eaten as food by humans. Domestic pig, ox, lamb, calf, chicken, goose, animal livers are rich in iron, copper and preformed vitamin A.100 g cod liver contains 5 mg of vitamin A and 100 µg of vitamin D. Liver can be baked, boiled, broiled, fried, stir-fried, in many preparations, pieces of liver are combined with pieces of meat or kidneys, like in the various forms of Middle Eastern mixed grill. Liver is often made into spreads, well-known examples include liver pâté, foie gras, chopped liver, and leverpostej. Liver sausages such as Braunschweiger and liverwurst are also a valued meal, liver sausages may also be used as spreads. A traditional South African delicacy, namely Skilpadjies, is made of minced lambs liver wrapped in netvet, some fish livers are valued as food, especially the stingray liver. It is used to prepare delicacies, such as poached skate liver on toast in England, cod liver is a popular spread for bread or toast in several European countries. In Russia, it is served with potatoes, cod liver oil is commonly used as a dietary supplement. Very high doses of vitamin A have the potential to be toxic and can cause hypervitaminosis A, a dangerous disorder. There have been anecdotal reports and a few scientific studies of vitamin A poisoning due to the consumption of the livers of polar bears, walruses, bearded seals, moose. The livers of animals can contain very high levels of vitamin A. The Inuit will not eat the liver of polar bears or bearded seals and it has been estimated that consumption of 500 grams of polar bear liver would result in a toxic dose for a human. Russian sailor Alexander Konrad, who accompanied explorer Valerian Albanov in a tragic ordeal over the Arctic ice in 1912, vitamin A poisoning is less likely from consuming oil-based vitamin A products and liver than from consuming water-based and solid preparations. In 2012 the Government of Nunavut warned pregnant women to avoid eating ringed seal liver due to elevated levels of mercury, unrelated to its vitamin content, the liver of the pufferfish contains the highest concentration of the neurotoxin tetrodotoxin, which characterizes the species. As a result, it is not eaten, and its consumption is tightly regulated by Japanese law. Pig liver is a food in Hawaii. It used to be eaten on New Years Eve
35.
Cauliflower
–
Cauliflower is one of several vegetables in the species Brassica oleracea in the genus Brassica, which is in the family Brassicaceae. It is a plant that reproduces by seed. Typically, only the head is eaten – the edible white flesh sometimes called curd, the cauliflower head is composed of a white inflorescence meristem. Cauliflower heads resemble those in broccoli, which differs in having flower buds as the edible portion, Brassica oleracea also includes broccoli, brussels sprouts, cabbage, collard greens, and kale, collectively called cole crops, though they are of different cultivar groups. In the 1st century AD, Pliny included what he called cyma among his descriptions of cultivated plants in Natural History, plinys descriptions likely refer to the flowering heads of an earlier cultivated variety of Brassica oleracea, but comes close to describing modern cauliflower. In the 12th century, three varieties were described in Spain as introductions from Syria, where it had doubtless been grown for more than a thousand years. It is found in the writings of the Arab botanists Ibn al-Awwam and Ibn al-Baitar, françois Pierre La Varenne employed chouxfleurs in Le cuisinier françois. It was introduced in India in 1822 from England by the British, the origin of the name is from the Latin word caulis and flower. Cauliflower is relatively difficult to grow compared to cabbage, with problems such as an underdeveloped head. The earliest maturity possible for cauliflower is 7 to 12 weeks from transplanting, in the northern hemisphere, fall season plantings in July may enable harvesting before autumn frost. Long periods of sun exposure in summer hot weather may cause cauliflower heads to discolor with a red-purple hue, transplantable cauliflowers can be produced in containers as flats, hotbeds, or in the field. In soil that is loose, well-drained and fertile, field seedlings are shallow-planted 0.5 inches, ideal growing temperatures are about 65 °F when seedlings are 25 to 35 days old. Applications of fertilizer to developing seedlings begins when leaves appear, usually with a starter solution weekly, transplanting to the field normally begins late spring and may continue until mid-summer. Row spacing is about 15–18 inches, rapid vegetative growth after transplanting may benefit from such procedures as avoiding spring frosts, using starter solutions high in phosphorus, irrigating weekly, and applying fertilizer. The most important disorders affecting cauliflower quality are a stem, stunted head growth or buttoning, ricing, browning. Among major pests affecting cauliflower are aphids, root maggots, cutworms, moths, the plant is susceptible to black rot, black leg, club root, black leaf spot, and downy mildew. When cauliflower is mature, heads appear as white, compact, and 6–8 inches in diameter. Forced air cooling to remove heat from the field during hot weather may be needed for optimal preservation, short-term storage is possible using cool, high-humidity storage conditions
verify (what is 
?)
. PMID 19906248.
