1.
Jmol
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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
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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
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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
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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
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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
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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
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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
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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
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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
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These are limited to a single typographic line of symbols, which may include subscripts and superscripts. A chemical formula is not a name, and it contains no words. Although a chemical formula may imply certain simple chemical structures, it is not the same as a full chemical structural formula. Chemical formulas can fully specify the structure of only the simplest of molecules and chemical substances, the simplest types of chemical formulas are called empirical formulas, which use letters and numbers indicating the numerical proportions of atoms of each type. Molecular formulas indicate the numbers of each type of atom in a molecule. For example, the formula for glucose is CH2O, while its molecular formula is C6H12O6. This is possible if the relevant bonding is easy to show in one dimension, an example is the condensed molecular/chemical formula for ethanol, which is CH3-CH2-OH or CH3CH2OH. For reasons of structural complexity, there is no condensed chemical formula that specifies glucose, chemical formulas may be used in chemical equations to describe chemical reactions and other chemical transformations, such as the dissolving of ionic compounds into solution. A chemical formula identifies each constituent element by its chemical symbol, in empirical formulas, these proportions begin with a key element and then assign numbers of atoms of the other elements in the compound, as ratios to the key element. For molecular compounds, these numbers can all be expressed as whole numbers. For example, the formula of ethanol may be written C2H6O because the molecules of ethanol all contain two carbon atoms, six hydrogen atoms, and one oxygen atom. Some types of compounds, however, cannot be written with entirely whole-number empirical formulas. An example is boron carbide, whose formula of CBn is a variable non-whole number ratio with n ranging from over 4 to more than 6.5. When the chemical compound of the consists of simple molecules. These types of formulas are known as molecular formulas and condensed formulas. A molecular formula enumerates the number of atoms to reflect those in the molecule, so that the formula for glucose is C6H12O6 rather than the glucose empirical formula. However, except for very simple substances, molecular chemical formulas lack needed structural information, for simple molecules, a condensed formula is a type of chemical formula that may fully imply a correct structural formula. For example, ethanol may be represented by the chemical formula CH3CH2OH
11.
Aqueous solution
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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
12.
Safety data sheet
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A safety data sheet, material safety data sheet, or product safety data sheet is an important component of product stewardship, occupational safety and health, and spill-handling procedures. SDS formats can vary from source to source within a country depending on national requirements, SDSs are a widely used system for cataloging information on chemicals, chemical compounds, and chemical mixtures. SDS information may include instructions for the use and potential hazards associated with a particular material or product. The SDS should be available for reference in the area where the chemicals are being stored or in use, there is also a duty to properly label substances on the basis of physico-chemical, health and/or environmental risk. Labels can include hazard symbols such as the European Union standard symbols, a SDS for a substance is not primarily intended for use by the general consumer, focusing instead on the hazards of working with the material in an occupational setting. It is important to use an SDS specific to country and supplier, as the same product can have different formulations in different countries. The formulation and hazard of a product using a name may vary between manufacturers in the same country. Safety data sheets have made an integral part of the system of Regulation No 1907/2006. The SDS must be supplied in a language of the Member State where the substance or mixture is placed on the market. The 16 sections are, SECTION1, Identification of the substance/mixture, relevant identified uses of the substance or mixture and uses advised against 1.3. Details of the supplier of the safety data sheet 1.4, Emergency telephone number SECTION2, Hazards identification 2.1. Classification of the substance or mixture 2.2, Other hazards SECTION3, Composition/information on ingredients 3.1. Mixtures SECTION4, First aid measures 4.1, Description of first aid measures 4.2. Most important symptoms and effects, both acute and delayed 4.3, indication of any immediate medical attention and special treatment needed SECTION5, Firefighting measures 5.1. Special hazards arising from the substance or mixture 5.3, advice for firefighters SECTION6, Accidental release measure 6.1. Personal precautions, protective equipment and emergency procedures 6.2, methods and material for containment and cleaning up 6.4. Reference to other sections SECTION7, Handling and storage 7.1, conditions for safe storage, including any incompatibilities 7.3. Specific end use SECTION8, Exposure controls/personal protection 8.1, Exposure controls SECTION9, Physical and chemical properties 9.1
13.
Refractive index
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In optics, the refractive index or index of refraction n of a material is a dimensionless number that describes how light propagates through that medium. It is defined as n = c v, where c is the speed of light in vacuum, for example, the refractive index of water is 1.333, meaning that light travels 1.333 times faster in a vacuum than it does in water. The refractive index determines how light is bent, or refracted. The refractive indices also determine the amount of light that is reflected when reaching the interface, as well as the angle for total internal reflection. This implies that vacuum has a index of 1. The refractive index varies with the wavelength of light and this is called dispersion and causes the splitting of white light into its constituent colors in prisms and rainbows, and chromatic aberration in lenses. Light propagation in absorbing materials can be described using a refractive index. The imaginary part then handles the attenuation, while the real part accounts for refraction, the concept of refractive index is widely used within the full electromagnetic spectrum, from X-rays to radio waves. It can also be used with wave phenomena such as sound, in this case the speed of sound is used instead of that of light and a reference medium other than vacuum must be chosen. Thomas Young was presumably the person who first used, and invented, at the same time he changed this value of refractive power into a single number, instead of the traditional ratio of two numbers. The ratio had the disadvantage of different appearances, newton, who called it the proportion of the sines of incidence and refraction, wrote it as a ratio of two numbers, like 529 to 396. Hauksbee, who called it the ratio of refraction, wrote it as a ratio with a fixed numerator, hutton wrote it as a ratio with a fixed denominator, like 1.3358 to 1. Young did not use a symbol for the index of refraction, in the next years, others started using different symbols, n, m, and µ. For visible light most transparent media have refractive indices between 1 and 2, a few examples are given in the adjacent table. These values are measured at the yellow doublet D-line of sodium, with a wavelength of 589 nanometers, gases at atmospheric pressure have refractive indices close to 1 because of their low density. Almost all solids and liquids have refractive indices above 1.3, aerogel is a very low density solid that can be produced with refractive index in the range from 1.002 to 1.265. Moissanite lies at the end of the range with a refractive index as high as 2.65. Most plastics have refractive indices in the range from 1.3 to 1.7, for infrared light refractive indices can be considerably higher
14.
Relative permittivity
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The relative permittivity of a material is its permittivity expressed as a ratio relative to the permittivity of vacuum. Permittivity is a property that affects the Coulomb force between two point charges in the material. Relative permittivity is the factor by which the field between the charges is decreased relative to vacuum. Likewise, relative permittivity is the ratio of the capacitance of a capacitor using that material as a dielectric, relative permittivity is also commonly known as dielectric constant, a term deprecated in physics and engineering as well as in chemistry. Relative permittivity is typically denoted as εr and is defined as ε r = ε ε0, where ε is the complex frequency-dependent absolute permittivity of the material, and ε0 is the vacuum permittivity. Relative permittivity is a number that is in general complex-valued, its real and imaginary parts are denoted as. The relative permittivity of a medium is related to its electric susceptibility, χe, in anisotropic media the relative permittivity is a second rank tensor. The relative permittivity of a material for a frequency of zero is known as its relative permittivity. The historical term for the relative permittivity is dielectric constant and it is still commonly used, but has been deprecated by standards organizations, because of its ambiguity, as some older authors used it for the absolute permittivity ε. The permittivity may be quoted either as a property or as a frequency-dependent variant. It has also used to refer to only the real component εr of the complex-valued relative permittivity. In the causal theory of waves, permittivity is a complex quantity, the imaginary part corresponds to a phase shift of the polarization P relative to E and leads to the attenuation of electromagnetic waves passing through the medium. By definition, the relative permittivity of vacuum is equal to 1. The relative static permittivity, εr, can be measured for static electric fields as follows, first the capacitance of a test capacitor, then, using the same capacitor and distance between its plates, the capacitance Cx with a dielectric between the plates is measured. The relative dielectric constant can be calculated as ε r = C x C0. For time-variant electromagnetic fields, this quantity becomes frequency-dependent, an indirect technique to calculate εr is conversion of radio frequency S-parameter measurement results. A description of frequently used S-parameter conversions for determination of the frequency-dependent εr of dielectrics can be found in this bibliographic source, alternatively, resonance based effects may be employed at fixed frequencies. The relative permittivity is a piece of information when designing capacitors
15.
Infrared spectroscopy
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Infrared spectroscopy involves the interaction of infrared radiation with matter. It covers a range of techniques, mostly based on absorption spectroscopy, as with all spectroscopic techniques, it can be used to identify and study chemicals. Sample may be solid, liquid, or gas, the method or technique of infrared spectroscopy is conducted with an instrument called an infrared spectrometer to produce an infrared spectrum. An IR spectrum is essentially a graph of infrared light absorbance on the vertical axis vs. frequency or wavelength on the horizontal axis, typical units of frequency used in IR spectra are reciprocal centimeters, with the symbol cm−1. Units of IR wavelength are commonly given in micrometers, symbol μm, a common laboratory instrument that uses this technique is a Fourier transform infrared spectrometer. Two-dimensional IR is also possible as discussed below, the infrared portion of the electromagnetic spectrum is usually divided into three regions, the near-, mid- and far- infrared, named for their relation to the visible spectrum. The higher-energy near-IR, approximately 14000–4000 cm−1 can excite overtone or harmonic vibrations, the mid-infrared, approximately 4000–400 cm−1 may be used to study the fundamental vibrations and associated rotational-vibrational structure. The far-infrared, approximately 400–10 cm−1, lying adjacent to the region, has low energy. The names and classifications of these subregions are conventions, and are loosely based on the relative molecular or electromagnetic properties. Infrared spectroscopy exploits the fact that molecules absorb frequencies that are characteristic of their structure and these absorptions occur at resonant frequencies, i. e. the frequency of the absorbed radiation matches the vibrational frequency. The energies are affected by the shape of the potential energy surfaces, the masses of the atoms. In particular, in the Born–Oppenheimer and harmonic approximations, i. e, the resonant frequencies are also related to the strength of the bond and the mass of the atoms at either end of it. Thus, the frequency of the vibrations are associated with a normal mode of motion. In order for a mode in a sample to be IR active. A permanent dipole is not necessary, as the rule requires only a change in dipole moment, a molecule can vibrate in many ways, and each way is called a vibrational mode. For molecules with N number of atoms, linear molecules have 3N –5 degrees of vibrational modes, as an example H2O, a non-linear molecule, will have 3 ×3 –6 =3 degrees of vibrational freedom, or modes. Simple diatomic molecules have only one bond and only one vibrational band, if the molecule is symmetrical, e. g. N2, the band is not observed in the IR spectrum, but only in the Raman spectrum. Asymmetrical diatomic molecules, e. g. CO, absorb in the IR spectrum, more complex molecules have many bonds, and their vibrational spectra are correspondingly more complex, i. e. big molecules have many peaks in their IR spectra
16.
Nuclear magnetic resonance spectroscopy
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Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy, is a research technique that exploits the magnetic properties of certain atomic nuclei. This type of spectroscopy determines the physical and chemical properties of atoms or the molecules in which they are contained and it relies on the phenomenon of nuclear magnetic resonance and can provide detailed information about the structure, dynamics, reaction state, and chemical environment of molecules. Suitable samples range from small compounds analyzed with 1-dimensional proton or carbon-13 NMR spectroscopy to large proteins or nucleic acids using 3 or 4-dimensional techniques. The impact of NMR spectroscopy on the sciences has been substantial because of the range of information, NMR spectra are unique, well-resolved, analytically tractable and often highly predictable for small molecules. Thus, in organic chemistry practice, NMR analysis is used to confirm the identity of a substance, different functional groups are obviously distinguishable, and identical functional groups with differing neighboring substituents still give distinguishable signals. NMR has largely replaced traditional wet chemistry tests such as reagents or typical chromatography for identification. A disadvantage is that a large amount, 2–50 mg, of a purified substance is required. Preferably, the sample should be dissolved in a solvent, because NMR analysis of solids requires a dedicated MAS machine, the timescale of NMR is relatively long, and thus it is not suitable for observing fast phenomena, producing only an averaged spectrum. NMR spectrometers are relatively expensive, universities usually have them, modern NMR spectrometers have a very strong, large and expensive liquid helium-cooled superconducting magnet, because resolution directly depends on magnetic field strength. There are even benchtop NMR spectrometers, the Purcell group at Harvard University and the Bloch group at Stanford University independently developed NMR spectroscopy in the late 1940s and early 1950s. Edward Mills Purcell and Felix Bloch shared the 1952 Nobel Prize in Physics for their discoveries, when placed in a magnetic field, NMR active nuclei absorb electromagnetic radiation at a frequency characteristic of the isotope. The resonant frequency, energy of the absorption, and the intensity of the signal are proportional to the strength of the magnetic field, for example, in a 21 Tesla magnetic field, protons resonate at 900 MHz. It is common to refer to a 21 T magnet as a 900 MHz magnet, spinning the sample is necessary to average out diffusional motion. Whereas, measurements of diffusion constants are done the sample stationary and spinning off, the vast majority of nuclei in a solution would belong to the solvent, and most regular solvents are hydrocarbons and would contain NMR-reactive protons. The most used deuterated solvent is deuterochloroform, although deuterium oxide and deuterated DMSO are used for hydrophilic analytes, the chemical shifts are slightly different in different solvents, depending on electronic solvation effects. NMR spectra are often calibrated against the known solvent residual proton peak instead of added tetramethylsilane, to detect the very small frequency shifts due to nuclear magnetic resonance, the applied magnetic field must be constant throughout the sample volume. High resolution NMR spectrometers use shims to adjust the homogeneity of the field to parts per billion in a volume of a few cubic centimeters. In order to detect and compensate for inhomogeneity and drift in the magnetic field, in modern NMR spectrometers shimming is adjusted automatically, though in some cases the operator has to optimize the shim parameters manually to obtain the best possible resolution
17.
Mass spectrometry
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Mass spectrometry is an analytical technique that ionizes chemical species and sorts the ions based on their mass-to-charge ratio. In simpler terms, a mass spectrum measures the masses within a sample, mass spectrometry is used in many different fields and is applied to pure samples as well as complex mixtures. A mass spectrum is a plot of the ion signal as a function of the mass-to-charge ratio, in a typical MS procedure, a sample, which may be solid, liquid, or gas, is ionized, for example by bombarding it with electrons. This may cause some of the molecules to break into charged fragments. The ions are detected by a capable of detecting charged particles. Results are displayed as spectra of the abundance of detected ions as a function of the mass-to-charge ratio. The atoms or molecules in the sample can be identified by correlating known masses to the masses or through a characteristic fragmentation pattern. Goldstein called these positively charged anode rays Kanalstrahlen, the translation of this term into English is canal rays. Wien found that the charge-to-mass ratio depended on the nature of the gas in the discharge tube, thomson later improved on the work of Wien by reducing the pressure to create the mass spectrograph. The word spectrograph had become part of the international scientific vocabulary by 1884, a mass spectroscope is similar to a mass spectrograph except that the beam of ions is directed onto a phosphor screen. A mass spectroscope configuration was used in early instruments when it was desired that the effects of adjustments be quickly observed, once the instrument was properly adjusted, a photographic plate was inserted and exposed. The term mass spectroscope continued to be used though the direct illumination of a phosphor screen was replaced by indirect measurements with an oscilloscope. The use of the mass spectroscopy is now discouraged due to the possibility of confusion with light spectroscopy. Mass spectrometry is often abbreviated as mass-spec or simply as MS, modern techniques of mass spectrometry were devised by Arthur Jeffrey Dempster and F. W. Aston in 1918 and 1919 respectively. Sector mass spectrometers known as calutrons were used for separating the isotopes of uranium developed by Ernest O. Lawrence during the Manhattan Project, calutron mass spectrometers were used for uranium enrichment at the Oak Ridge, Tennessee Y-12 plant established during World War II. In 1989, half of the Nobel Prize in Physics was awarded to Hans Dehmelt, a mass spectrometer consists of three components, an ion source, a mass analyzer, and a detector. The ionizer converts a portion of the sample into ions, there is a wide variety of ionization techniques, depending on the phase of the sample and the efficiency of various ionization mechanisms for the unknown species. An extraction system removes ions from the sample, which are then targeted through the mass analyzer, the differences in masses of the fragments allows the mass analyzer to sort the ions by their mass-to-charge ratio
18.
Proteinogenic amino acid
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Proteinogenic amino acids are amino acids that are incorporated biosynthetically into proteins during translation. The word proteinogenic means protein creating, throughout known life, there are 22 genetically encoded amino acids,20 in the standard genetic code and an additional 2 that can be incorporated by special translation mechanisms. The latter often results from post-translational modification of proteins, some non-proteinogenic amino acids are incorporated into nonribosomal peptides which are synthesized by non-ribosomal peptide synthetases. In some methanogenic prokaryotes, the UAG codon can also be translated to pyrrolysine, in eukaryotes, there are only 21 proteinogenic amino acids, the 20 of the standard genetic code, plus selenocysteine. Humans can synthesize 12 of these from other or from other molecules of intermediary metabolism. The other nine must be consumed, and so they are called essential amino acids, the essential amino acids are histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. The proteinogenic amino acids have been found to be related to the set of amino acids that can be recognized by ribozyme autoaminoacylation systems, thus, non-proteinogenic amino acids would have been excluded by the contingent evolutionary success of nucleotide-based life forms. The following illustrates the structures and abbreviations of the 21 amino acids that are encoded for protein synthesis by the genetic code of eukaryotes. The structures given below are standard chemical structures, not the typical zwitterion forms that exist in aqueous solutions, the masses listed are based on weighted averages of the elemental isotopes at their natural abundances. Forming a peptide bond results in elimination of a molecule of water, general chemical properties §, Values for Asp, Cys, Glu, His, Lys & Tyr were determined using the amino acid residue placed centrally in an alanine pentapeptide. The value for Arg is from Pace et al, the value for Sec is from Byun & Kang. The pKa value of Pyrrolysine has not been reported, note, The pKa value of an amino-acid residue in a small peptide is typically slightly different when it is inside a protein. Protein pKa calculations are used to calculate the change in the pKa value of an amino-acid residue in this situation. In mass spectrometry of peptides and proteins, knowledge of the masses of the residues is useful, the mass of the peptide or protein is the sum of the residue masses plus the mass of water. The residue masses are calculated from the chemical formulas and atomic weights. In mass spectrometry, ions may also one or more protons. § Monoisotopic mass The table below lists the abundance of amino acids in E. coli cells, negative numbers indicate the metabolic processes are energy favorable and do not cost net ATP of the cell. The abundance of amino acids includes amino acids in free form, the proteinogenic set used by known life on Earth appears to be arbitrarily selected by evolution, according to current knowledge, from many hundreds of possible alpha-type amino acids
19.
Cell (biology)
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The cell is the basic structural, functional, and biological unit of all known living organisms. A cell is the smallest unit of life that can replicate independently, the study of cells is called cell biology. Cells consist of cytoplasm enclosed within a membrane, which contains many such as proteins. Organisms can be classified as unicellular or multicellular, while the number of cells in plants and animals varies from species to species, humans contain more than 10 trillion cells. Most plant and animal cells are only under a microscope. The cell was discovered by Robert Hooke in 1665, who named the unit for its resemblance to cells inhabited by Christian monks in a monastery. Cells emerged on Earth at least 3.5 billion years ago, Cells are of two types, eukaryotic, which contain a nucleus, and prokaryotic, which do not. Prokaryotes are single-celled organisms, while eukaryotes can be either single-celled or multicellular, prokaryotic cells were the first form of life on Earth, characterised by having vital biological processes including cell signaling and being self-sustaining. They are simpler and smaller than eukaryotic cells, and lack membrane-bound organelles such as the nucleus, prokaryotes include two of the domains of life, bacteria and archaea. The DNA of a prokaryotic cell consists of a chromosome that is in direct contact with the cytoplasm. The nuclear region in the cytoplasm is called the nucleoid, most prokaryotes are the smallest of all organisms ranging from 0.5 to 2.0 µm in diameter. Though most prokaryotes have both a cell membrane and a wall, there are exceptions such as Mycoplasma and Thermoplasma which only possess the cell membrane layer. The envelope gives rigidity to the cell and separates the interior of the cell from its environment, the cell wall consists of peptidoglycan in bacteria, and acts as an additional barrier against exterior forces. It also prevents the cell from expanding and bursting from osmotic pressure due to a hypotonic environment, some eukaryotic cells also have a cell wall. Inside the cell is the region that contains the genome, ribosomes. The genetic material is found in the cytoplasm. Prokaryotes can carry extrachromosomal DNA elements called plasmids, which are usually circular, linear bacterial plasmids have been identified in several species of spirochete bacteria, including members of the genus Borrelia notably Borrelia burgdorferi, which causes Lyme disease. Though not forming a nucleus, the DNA is condensed in a nucleoid, plasmids encode additional genes, such as antibiotic resistance genes
20.
Protein biosynthesis
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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
21.
Non-essential amino acid
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An essential amino acid, or indispensable amino acid, is an amino acid that cannot be synthesized de novo by the organism, and thus must be supplied in its diet. The nine amino acids humans cannot synthesize are phenylalanine, valine, threonine, tryptophan, methionine, leucine, isoleucine, lysine and these six are arginine, cysteine, glycine, glutamine, proline, and tyrosine. Five amino acids are dispensable in humans, meaning they can be synthesized in the body and these five are alanine, aspartic acid, asparagine, glutamic acid and serine. Pyrrolysine, sometimes considered the 22nd amino acid, is not used by humans, eukaryotes can synthesize some of the amino acids from other substrates. Consequently, only a subset of the amino acids used in protein synthesis are essential nutrients, estimating the daily requirement for the indispensable amino acids has proven to be difficult, these numbers have undergone considerable revision over the last 20 years. The following table lists the WHO recommended daily amounts currently in use for essential amino acids in adult humans, food sources are identified based on the USDA National Nutrient Database Release. The recommended daily intakes for children aged three years and older is 10% to 20% higher than adult levels and those for infants can be as much as 150% higher in the first year of life, cysteine, tyrosine, and arginine are always required by infants and growing children. Various attempts have been made to express the quality or value of various kinds of protein, measures include the biological value, net protein utilization, protein efficiency ratio, protein digestibility-corrected amino acid score and complete proteins concept. Thus, various feedstuffs may be fed in combination to increase net protein utilization, eating various plant foods in combination can provide a protein of higher biological value. Certain native combinations of foods, such as corn and beans, soybeans and rice, or red beans and rice, for example, while 100 g of raw broccoli only provides 28 kcal and 3 g of protein, it has over 100 mg of protein per kcal. An egg contains five times as many calories but only four times as much protein, however, a carrot has only 23 mg protein per kcal or twice the minimum recommendation, a banana meets the minimum, and an apple is below recommendation. It is recommended that adult humans obtain 10–35% of their calories as protein, the US FDA daily reference value of 50 g protein per 2000 kcal is 25 mg/kcal per day. This led William Cumming Rose to the discovery of the amino acid threonine. Roses later work showed that eight amino acids are essential for human beings. Longer term studies established histidine as also essential for adult humans, the distinction between essential and non-essential amino acids is somewhat unclear, as some amino acids can be produced from others. The sulfur-containing amino acids, methionine and homocysteine, can be converted into each other but neither can be synthesized de novo in humans, likewise, cysteine can be made from homocysteine but cannot be synthesized on its own. So, for convenience, sulfur-containing amino acids are considered a single pool of nutritionally equivalent amino acids as are the aromatic amino acid pair. Likewise arginine, ornithine, and citrulline, which are interconvertible by the cycle, are considered a single group
22.
Greek language
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Greek is an independent branch of the Indo-European family of languages, native to Greece and other parts of the Eastern Mediterranean. It has the longest documented history of any living language, spanning 34 centuries of written records and its writing system has been the Greek alphabet for the major part of its history, other systems, such as Linear B and the Cypriot syllabary, were used previously. The alphabet arose from the Phoenician script and was in turn the basis of the Latin, Cyrillic, Armenian, Coptic, Gothic and many other writing systems. Together with the Latin texts and traditions of the Roman world, during antiquity, Greek was a widely spoken lingua franca in the Mediterranean world and many places beyond. It would eventually become the official parlance of the Byzantine Empire, the language is spoken by at least 13.2 million people today in Greece, Cyprus, Italy, Albania, Turkey, and the Greek diaspora. Greek roots are used to coin new words for other languages, Greek. Greek has been spoken in the Balkan peninsula since around the 3rd millennium BC, the earliest written evidence is a Linear B clay tablet found in Messenia that dates to between 1450 and 1350 BC, making Greek the worlds oldest recorded living language. Among the Indo-European languages, its date of earliest written attestation is matched only by the now extinct Anatolian languages, the Greek language is conventionally divided into the following periods, Proto-Greek, the unrecorded but assumed last ancestor of all known varieties of Greek. The unity of Proto-Greek would have ended as Hellenic migrants entered the Greek peninsula sometime in the Neolithic era or the Bronze Age, Mycenaean Greek, the language of the Mycenaean civilisation. It is recorded in the Linear B script on tablets dating from the 15th century BC onwards, Ancient Greek, in its various dialects, the language of the Archaic and Classical periods of the ancient Greek civilisation. It was widely known throughout the Roman Empire, after the Roman conquest of Greece, an unofficial bilingualism of Greek and Latin was established in the city of Rome and Koine Greek became a first or second language in the Roman Empire. The origin of Christianity can also be traced through Koine Greek, Medieval Greek, also known as Byzantine Greek, the continuation of Koine Greek in Byzantine Greece, up to the demise of the Byzantine Empire in the 15th century. Much of the written Greek that was used as the language of the Byzantine Empire was an eclectic middle-ground variety based on the tradition of written Koine. Modern Greek, Stemming from Medieval Greek, Modern Greek usages can be traced in the Byzantine period and it is the language used by the modern Greeks, and, apart from Standard Modern Greek, there are several dialects of it. In the modern era, the Greek language entered a state of diglossia, the historical unity and continuing identity between the various stages of the Greek language is often emphasised. Greek speakers today still tend to regard literary works of ancient Greek as part of their own rather than a foreign language and it is also often stated that the historical changes have been relatively slight compared with some other languages. According to one estimation, Homeric Greek is probably closer to demotic than 12-century Middle English is to modern spoken English, Greek is spoken by about 13 million people, mainly in Greece, Albania and Cyprus, but also worldwide by the large Greek diaspora. Greek is the language of Greece, where it is spoken by almost the entire population
23.
Cheese
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Cheese is a food derived from milk that is produced in a wide range of flavors, textures, and forms by coagulation of the milk protein casein. It comprises proteins and fat from milk, usually the milk of cows, buffalo, goats, during production, the milk is usually acidified, and adding the enzyme rennet causes coagulation. The solids are separated and pressed into final form, Some cheeses have molds on the rind, the outer layer, or throughout. Most cheeses melt at cooking temperature, hundreds of types of cheese from various countries are produced. Their styles, textures and flavors depend on the origin of the milk, whether they have been pasteurized, the content, the bacteria and mold, the processing. Herbs, spices, or wood smoke may be used as flavoring agents, the yellow to red color of many cheeses, such as Red Leicester, is produced by adding annatto. Other ingredients may be added to some cheeses, such as pepper, garlic. For a few cheeses, the milk is curdled by adding acids such as vinegar or lemon juice, most cheeses are acidified to a lesser degree by bacteria, which turn milk sugars into lactic acid, then the addition of rennet completes the curdling. Vegetarian alternatives to rennet are available, most are produced by fermentation of the fungus Mucor miehei, cheesemakers near a dairy region may benefit from fresher, lower-priced milk, and lower shipping costs. Cheese is valued for its portability, long life, and high content of fat, protein, calcium, generally speaking, hard cheeses, such as parmesan last longer than soft cheeses, such as Brie or goats milk cheese. The long storage life of some cheeses, especially when encased in a protective rind, There is some debate as to the best way to store cheese, but some experts say that wrapping it in cheese paper provides optimal results. Cheese paper is coated in a plastic on the inside. A specialist seller of cheese is known as a cheesemonger. Becoming an expert in this field requires some formal education and years of tasting and hands-on experience, the cheesemonger is responsible for all aspects of the cheese inventory, selecting the cheese menu, purchasing, receiving, storage, and ripening. The word cheese comes from Latin caseus, from which the modern word casein is also derived, the earliest source is from the proto-Indo-European root *kwat-, which means to ferment, become sour. The word cheese comes from chese and cīese or cēse, the Online Etymological Dictionary states that cheese comes from Old English cyse, cese. from West Germanic *kasjus, from Latin caseus cheese. The Online Etymological Dictionary states that the word is of. unknown origin, perhaps from a PIE root *kwat- to ferment, Old Norse ostr, Danish ost, Swedish ost are related to Latin ius broth, sauce, juice. When the Romans began to make hard cheeses for their legionaries supplies and it is from this word that the French fromage, proper Italian formaggio, Catalan formatge, Breton fourmaj, and Provençal furmo are derived
24.
Justus von Liebig
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Justus Freiherr von Liebig was a German chemist who made major contributions to agricultural and biological chemistry, and was considered the founder of organic chemistry. As a professor at the University of Giessen, he devised the modern laboratory-oriented teaching method and he also developed a manufacturing process for beef extracts, and founded a company, Liebig Extract of Meat Company, that later trademarked the Oxo brand beef bouillon cube. Justus von Liebig was born in Darmstadt into the family of Johann Georg Liebig. His father was a drysalter and hardware merchant who compounded and sold paints, varnishes and pigments, from childhood Justus was fascinated with chemistry. At the age of 13, Liebig lived through the year without a summer, Germany was among the hardest-hit in the global famine that ensued, and the experience is said to have shaped Liebigs later work. Thanks in part to Liebigs innovations in fertilizers and agriculture, the 1816 famine became known as the last great subsistence crisis in the Western world, Liebig attended grammar school at the Ludwig-Georgs-Gymnasium in Darmstadt, from the age of 8 to 14. He worked with his father for the two years, then attended the University of Bonn, studying under Karl Wilhelm Gottlob Kastner. When Kastner moved to the University of Erlangen, Liebig followed him, Liebig left Erlangen in March 1822, in part because of his involvement with the radical Korps Rhenania but also because of his hopes for more advanced chemical studies. The circumstances are clouded by possible scandal, in late 1822 Liebig went to study in Paris on a grant obtained for him by Kastner from the Hessian government. He worked in the laboratory of Joseph Louis Gay-Lussac, and was also befriended by Alexander von Humboldt. Liebigs doctorate from Erlangen was conferred on 23 June 1823, a time after he left. Kastner pleaded that the requirement of a dissertation be waived, Liebig left Paris to return to Darmstadt in April 1824. On 26 May 1824, at the age of 21 and with Humboldts recommendation, Liebigs appointment was part of an attempt to modernize the University of Giessen and attract more students. He received a stipend, without laboratory funding or access to facilities. Vogt was happy to support a reorganization in which pharmacy was taught by Liebig and became the responsibility of the faculty of arts, Zimmermann found himself competing unsuccessfully with Liebig for students and their lecture fees. He refused to allow Liebig to use existing space and equipment, the deaths of Zimmermann and a Professor Blumhof who taught technology and mining opened the way for Liebig to apply for a full professorship. Liebig was appointed to the chair in chemistry on 7 December 1825, receiving a considerably increased salary. Liebig married Henriette Jettchen Moldenhauer, the daughter of a state official and they had five children, Georg, Agnes, Hermann, Johanna and Marie
25.
Casein
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Casein is the name for a family of related phosphoproteins. These proteins are found in mammalian milk, making up 80% of the proteins in cows milk. Casein has a variety of uses, from being a major component of cheese, to use as a food additive. As a food source, casein supplies amino acids, carbohydrates, casein contains a high number of proline residues, which do not interact. There are also no disulfide bridges, as a result, it has relatively little tertiary structure. It is relatively hydrophobic, making it soluble in water. However, in sharp contrast to surfactant micelles, the interior of a micelle is highly hydrated. The caseins in the micelles are held together by calcium ions, any of several molecular models could account for the special conformation of casein in the micelles. One of them proposes the micellar nucleus is formed by several submicelles, another model suggests the nucleus is formed by casein-interlinked fibrils. Finally, the most recent model proposes a link among the caseins for gelling to take place. All three models consider micelles as colloidal particles formed by casein aggregates wrapped up in soluble κ-casein molecules, the isoelectric point of casein is 4.6. Since milks pH is 6.6, casein has a charge in milk. While it is insoluble in neutral salt solutions, it is readily dispersible in dilute alkalis and in salt solutions such as aqueous sodium oxalate. The enzyme trypsin can hydrolyze a phosphate-containing peptone and it is used to form a type of organic adhesive. Casein paint is a fast-drying, water-soluble medium used by artists and it is still widely used by scene painters, although acrylic has made inroads in that field as well. Casein-based glues, formulated from casein, water, hydrated lime and sodium hydroxide were popular for woodworking, including for aircraft, casein glue is also used in transformer manufacturing due to its oil permeability. While largely replaced with synthetic resins, casein-based glues still have a use in niche applications, such as laminating fireproof doors. Cheese consists of proteins and fat from milk, usually the milk of cows, buffalo, goats and it is produced by coagulation of casein
26.
Functional group
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In organic chemistry, functional groups are specific groups of atoms or bonds within molecules that are responsible for the characteristic chemical reactions of those molecules. The same functional group will undergo the same or similar chemical reaction regardless of the size of the molecule it is a part of, however, its relative reactivity can be modified by other functional groups nearby. The atoms of functional groups are linked to other and to the rest of the molecule by covalent bonds. Any subgroup of atoms of a compound also may be called a radical, and if a covalent bond is broken homolytically, Functional groups can also be charged, e. g. in carboxylate salts, which turns the molecule into a polyatomic ion or a complex ion. Complexation and solvation is also caused by interactions of functional groups. In the common rule of thumb like dissolves like, it is the shared or mutually well-interacting functional groups give rise to solubility. For example, sugar dissolves in water because both share the functional group and hydroxyls interact strongly with each other. Combining the names of groups with the names of the parent alkanes generates what is termed a systematic nomenclature for naming organic compounds. In traditional nomenclature, the first carbon atom after the carbon that attaches to the group is called the alpha carbon, the second, beta carbon. IUPAC conventions call for numeric labeling of the position, e. g. 4-aminobutanoic acid, in traditional names various qualifiers are used to label isomers, for example isopropanol is an isomer is n-propanol. The following is a list of functional groups. In the formulas, the symbols R and R usually denote an attached hydrogen, or a side chain of any length. Functional groups, called hydrocarbyl, that only carbon and hydrogen. Each one differs in type of reactivity, there are also a large number of branched or ring alkanes that have specific names, e. g. tert-butyl, bornyl, cyclohexyl, etc. Hydrocarbons may form charged structures, positively charged carbocations or negative carbanions, examples are tropylium and triphenylmethyl cations and the cyclopentadienyl anion. Haloalkanes are a class of molecule that is defined by a carbon–halogen bond and this bond can be relatively weak or quite stable. In general, with the exception of fluorinated compounds, haloalkanes readily undergo nucleophilic substitution reactions or elimination reactions, the substitution on the carbon, the acidity of an adjacent proton, the solvent conditions, etc. all can influence the outcome of the reactivity. Compounds that contain nitrogen in this category may contain C-O bonds, compounds that contain sulfur exhibit unique chemistry due to their ability to form more bonds than oxygen, their lighter analogue on the periodic table
27.
Hydrophobe
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In chemistry, hydrophobicity is the physical property of a molecule that is seemingly repelled from a mass of water. In contrast, hydrophiles are attracted to water, Hydrophobic molecules tend to be nonpolar and, thus, prefer other neutral molecules and nonpolar solvents. Because water molecules are polar, hydrophobes do not dissolve well among them, Hydrophobic molecules in water often cluster together, forming micelles. Water on hydrophobic surfaces will exhibit a high contact angle, examples of hydrophobic molecules include the alkanes, oils, fats, and greasy substances in general. Hydrophobic materials are used for oil removal from water, the management of oil spills, Hydrophobic is often used interchangeably with lipophilic, fat-loving. However, the two terms are not synonymous, while hydrophobic substances are usually lipophilic, there are exceptions—such as the silicones and fluorocarbons. The term hydrophobe comes from the Ancient Greek ὑδρόφοβος, having a horror of water, constructed from ὕδωρ, water, thus, the two immiscible phases will change so that their corresponding interfacial area will be minimal. This effect can be visualized in the phenomenon called phase separation, Superhydrophobic surfaces, such as the leaves of the lotus plant, are those that are extremely difficult to wet. The contact angles of a water droplet exceeds 150° and the angle is less than 10°. This is referred to as the Lotus effect, and is primarily a physical property related to interfacial tension, in 1805, Thomas Young defined the contact angle θ by analyzing the forces acting on a fluid droplet resting on a solid surface surrounded by a gas. Wenzels equation shows that microstructuring a surface amplifies the natural tendency of the surface, a hydrophobic surface becomes more hydrophobic when microstructured – its new contact angle becomes greater than the original. However, a hydrophilic surface becomes more hydrophilic when microstructured – its new contact angle less than the original. Liquid in the Cassie–Baxter state is more mobile than in the Wenzel state and we can predict whether the Wenzel or Cassie–Baxter state should exist by calculating the new contact angle with both equations. By a minimization of free energy argument, the relation that predicted the new contact angle is the state most likely to exist. Stated in mathematical terms, for the Cassie–Baxter state to exist, a new criterion for the switch between Wenzel and Cassie-Baxter states has been developed recently based on surface roughness and surface energy. Contact angle is a measure of static hydrophobicity, and contact angle hysteresis, contact angle hysteresis is a phenomenon that characterizes surface heterogeneity. When a pipette injects a liquid onto a solid, the liquid will form some contact angle, as the pipette injects more liquid, the droplet will increase in volume, the contact angle will increase, but its three-phase boundary will remain stationary until it suddenly advances outward. The contact angle the droplet had immediately before advancing outward is termed the advancing contact angle, the receding contact angle is now measured by pumping the liquid back out of the droplet
28.
Phenylalanine
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Phenylalanine is an α-amino acid with the formula C 9H 11NO2. It can be viewed as a benzyl group substituted for the group of alanine. This essential amino acid is classified as neutral, and nonpolar because of the inert, the L-isomer is used to biochemically form proteins, coded for by DNA. The codons for L-phenylalanine are UUU and UUC, Phenylalanine is a precursor for tyrosine, the monoamine neurotransmitters dopamine, norepinephrine, and epinephrine, and the skin pigment melanin. Phenylalanine is found naturally in the breast milk of mammals and it is used in the manufacture of food and drink products and sold as a nutritional supplement for its reputed analgesic and antidepressant effects. It is a precursor to the neuromodulator phenethylamine, a commonly used dietary supplement. The first description of phenylalanine was made in 1879, when Schulze and Barbieri identified a compound with the formula, C9H11NO2. In 1882, Erlenmeyer and Lipp first synthesized phenylalanine from phenylacetaldehyde, hydrogen cyanide, the genetic codon for phenylalanine was first discovered by J. Heinrich Matthaei and Marshall W. Nirenberg in 1961. This discovery helped to establish the nature of the relationship that links information stored in genomic nucleic acid with protein expression in the living cell. As an essential amino acid, phenylalanine is not synthesized de novo in humans and other animals, good sources of phenylalanine are eggs, chicken, liver, beef, milk, and soybeans. L-Phenylalanine is biologically converted into L-tyrosine, another one of the DNA-encoded amino acids, L-tyrosine in turn is converted into L-DOPA, which is further converted into dopamine, norepinephrine, and epinephrine. The latter three are known as the catecholamines, Phenylalanine uses the same active transport channel as tryptophan to cross the blood–brain barrier. The corresponding enzymes in for those compounds are the amino acid hydroxylase family. Phenylalanine is the compound used in the synthesis of flavonoids. Lignan is derived from phenylalanine and from tyrosine, Phenylalanine is converted to cinnamic acid by the enzyme phenylalanine ammonia-lyase. The genetic disorder phenylketonuria is the inability to metabolize phenylalanine because of a lack of the enzyme phenylalanine hydroxylase, individuals with this disorder are known as phenylketonurics and must regulate their intake of phenylalanine. A variant form of phenylketonuria called hyperphenylalaninemia is caused by the inability to synthesize a cofactor called tetrahydrobiopterin, pregnant women with hyperphenylalaninemia may show similar symptoms of the disorder but these indicators will usually disappear at the end of gestation. Pregnant women with PKU must control their blood phenylalanine levels even if the fetus is heterozygus for the defective gene because the fetus could be affected due to hepatic immaturity
29.
Genetic code
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The genetic code is the set of rules by which information encoded within genetic material is translated into proteins by living cells. Translation is accomplished by the ribosome, which links amino acids in an order specified by mRNA, using transfer RNA molecules to carry amino acids, the genetic code is highly similar among all organisms and can be expressed in a simple table with 64 entries. The code defines how sequences of nucleotide triplets, called codons, with some exceptions, a three-nucleotide codon in a nucleic acid sequence specifies a single amino acid. The vast majority of genes are encoded with a single scheme and that scheme is often referred to as the canonical or standard genetic code, or simply the genetic code, though variant codes exist. While the genetic code determines a proteins amino acid sequence, other genomic regions determine when, efforts to understand how proteins are encoded began after DNAs structure was discovered in 1953. George Gamow postulated that sets of three bases must be employed to encode the 20 standard amino acids used by living cells to build proteins, the Crick, Brenner et al. experiment first demonstrated that codons consist of three DNA bases. Marshall Nirenberg and Heinrich J. Matthaei were the first to reveal the nature of a codon in 1961 and they used a cell-free system to translate a poly-uracil RNA sequence and discovered that the polypeptide that they had synthesized consisted of only the amino acid phenylalanine. They thereby deduced that the codon UUU specified the amino acid phenylalanine, therefore, the codon AAA specified the amino acid lysine, and the codon CCC specified the amino acid proline. Using various copolymers most of the remaining codons were then determined, subsequent work by Har Gobind Khorana identified the rest of the genetic code. Shortly thereafter, Robert W. Holley determined the structure of transfer RNA and this work was based upon Ochoas earlier studies, yielding the latter the Nobel Prize in Physiology or Medicine in 1959 for work on the enzymology of RNA synthesis. Extending this work, Nirenberg and Philip Leder revealed the triplet nature. In these experiments, various combinations of mRNA were passed through a filter that contained ribosomes, unique triplets promoted the binding of specific tRNAs to the ribosome. Leder and Nirenberg were able to determine the sequences of 54 out of 64 codons in their experiments, Khorana, Holley and Nirenberg received the 1968 Nobel for their work. The three stop codons were named by discoverers Richard Epstein and Charles Steinberg, amber was named after their friend Harris Bernstein, whose last name means amber in German. The other two stop codons were named ochre and opal in order to keep the color names theme, H. Murakami and M. Sisido extended some codons to have four and five bases. Steven A. Benner constructed a functional 65th codon, in 2016 the first stable semisynthetic organism was created. It was a bacterium with two synthetic bases, in 2017 a mouse engineered with an extended genetic code that can produce proteins with unnatural amino acids was reported. A codon is defined by the initial nucleotide from which starts and sets the frame for a run of successive triplets
30.
Phenol
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Phenol, also known as carbolic acid, is an aromatic organic compound with the molecular formula C6H5OH. It is a crystalline solid that is volatile. The molecule consists of a phenyl group bonded to a hydroxyl group and it is mildly acidic and requires careful handling due to its propensity to cause chemical burns. Phenol was first extracted from tar, but today is produced on a large scale from petroleum. It is an important industrial commodity as a precursor to many materials and it is primarily used to synthesize plastics and related materials. Phenol and its derivatives are essential for production of polycarbonates, epoxies, Bakelite, nylon, detergents, herbicides such as phenoxy herbicides. Phenol is appreciably soluble in water, with about 84.2 g dissolving in 1000 mL, homogeneous mixtures of phenol and water at phenol to water mass ratios of ~2.6 and higher are possible. The sodium salt of phenol, sodium phenoxide, is far more water-soluble and it reacts completely with aqueous NaOH to lose H+, whereas most alcohols react only partially. One explanation for the increased acidity over alcohols is resonance stabilization of the anion by the aromatic ring. In this way, the charge on oxygen is delocalized on to the ortho. In another explanation, increased acidity is the result of orbital overlap between the lone pairs and the aromatic system. The pKa of the enol of acetone is 10.9, the acidities of phenol and acetone enol diverge in the gas phase owing to the effects of solvation. About 1⁄3 of the acidity of phenol is attributable to inductive effects. Phenolate esters are more stable toward hydrolysis than acid anhydrides and acyl halides but are sufficiently reactive under mild conditions to facilitate the formation of amide bonds, Phenol exhibits keto-enol tautomerism with its unstable keto tautomer cyclohexadienone, but only a tiny fraction of phenol exists as the keto form. The equilibrium constant for enolisation is approximately 10−13, meaning only one in every ten trillion molecules is in the keto form at any moment. The small amount of stabilisation gained by exchanging a C=C bond for a C=O bond is more than offset by the large destabilisation resulting from the loss of aromaticity, Phenol therefore exists essentially entirely in the enol form. Phenoxides are enolates stabilised by aromaticity, under normal circumstances, phenoxide is more reactive at the oxygen position, but the oxygen position is a hard nucleophile whereas the alpha-carbon positions tend to be soft. Phenol is highly reactive toward electrophilic aromatic substitution as the oxygen atoms pi electrons donate electron density into the ring, by this general approach, many groups can be appended to the ring, via halogenation, acylation, sulfonation, and other processes
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Signal transduction
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Proteins responsible for detecting stimuli are generally termed receptors, although in some cases the term sensor is used. The changes elicited by ligand binding in a receptor give rise to a cascade of events along a signalling pathway. When signalling pathways interact with one another they form networks, which allow cellular responses to be coordinated and these molecular events are the basic mechanisms controlling cell growth, proliferation, metabolism and many other processes. In multicellular organisms, signal transduction pathways have evolved to regulate cell communication in a variety of ways. Each component of a pathway is classified according to the role it plays with respect to the initial stimulus. Ligands are termed first messengers, while receptors are the signal transducers, such effectors are often linked to second messengers, which can activate secondary effectors, and so on. Depending on the efficiency of the nodes, a signal can be amplified, as with other signals, the transduction of biological signals is characterised by delay, noise and interference, which can range from negligible to pathological. With the advent of computational biology, the analysis of signalling pathways and networks has become a tool to understand cellular functions. The basis for signal transduction is the transformation of a certain stimulus into a biochemical signal, traditionally, signals that reach the central nervous system are classified as senses. These are transmitted from neuron to neuron in a process called synaptic transmission, many other intercellular signal relay mechanisms exist in multicellular organisms, such as those that govern embryonic development. The majority of signal transduction pathways involve the binding of signalling molecules, known as ligands, the combination of a signaling molecule with a receptor causes a change in the conformation of the receptor, known as receptor activation. Most ligands are soluble molecules from the medium which bind to cell surface receptors. These include growth factors, cytokines and neurotransmitters, components of the extracellular matrix such as fibronectin and hyaluronan can also bind to such receptors. In addition, some such as steroid hormones are lipid-soluble. In the case of hormone receptors, their stimulation leads to binding to the promoter region of steroid-responsive genes. Not all classifications of signalling molecules take into account the nature of each class member. For example, odorants belong to a range of molecular classes, as do neurotransmitters. Moreover, some molecules may fit more than one class, e. g. epinephrine is a neurotransmitter when secreted by the central nervous system
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Protein kinase
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A protein kinase is a kinase enzyme that modifies other proteins by chemically adding phosphate groups to them. Phosphorylation usually results in a change of the target protein by changing enzyme activity, cellular location. The human genome contains about 500 protein kinase genes and they constitute about 2% of all human genes, up to 30% of all human proteins may be modified by kinase activity, and kinases are known to regulate the majority of cellular pathways, especially those involved in signal transduction. The chemical activity of a kinase involves transferring a phosphate group from a nucleoside triphosphate, most kinases act on both serine and threonine, others act on tyrosine, and a number act on all three. There are also protein kinases that phosphorylate other amino acids, including histidine kinases that phosphorylate histidine residues, because protein kinases have profound effects on a cell, their activity is highly regulated. Kinases are turned on or off by phosphorylation, by binding of proteins or inhibitor proteins, or small molecules. The catalytic subunits of protein kinases are highly conserved. Eukaryotic protein kinases are enzymes that belong to an extensive family of proteins that share a conserved catalytic core. There are a number of conserved regions in the domain of protein kinases. In the N-terminal extremity of the catalytic domain there is a stretch of residues in the vicinity of a lysine amino acid. In the central part of the domain, there is a conserved aspartic acid. The human protein kinase family is divided into the groups, AGC kinases - containing PKA, PKC. CaM kinases - containing the calcium/calmodulin-dependent protein kinases, cK1 - containing the casein kinase 1 group. CMGC - containing CDK, MAPK, GSK3 and CLK kinases, STE - containing the homologs of yeast Sterile 7, Sterile 11, and Sterile 20 kinases. TK - containing the tyrosine kinases, TKL - containing the tyrosine-kinase like group of kinases. Serine/threonine protein kinases phosphorylate the OH group of serine or threonine, activity of these protein kinases can be regulated by specific events, as well as numerous chemical signals, including cAMP/cGMP, diacylglycerol, and Ca2+/calmodulin. One very important group of protein kinases are the MAP kinases, important subgroups are the kinases of the ERK subfamily, typically activated by mitogenic signals, and the stress-activated protein kinases JNK and p38. While MAP kinases are serine/threonine-specific, they are activated by combined phosphorylation on serine/threonine and tyrosine residues, tyrosine-specific protein kinases phosphorylate tyrosine amino acid residues, and like serine/threonine-specific kinases are used in signal transduction
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Photosynthesis
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Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that can later be released to fuel the organisms activities. In most cases, oxygen is released as a waste product. Most plants, most algae, and cyanobacteria perform photosynthesis, such organisms are called photoautotrophs, in plants, these proteins are held inside organelles called chloroplasts, which are most abundant in leaf cells, while in bacteria they are embedded in the plasma membrane. In these light-dependent reactions, some energy is used to strip electrons from suitable substances, such as water, in the Calvin cycle, atmospheric carbon dioxide is incorporated into already existing organic carbon compounds, such as ribulose bisphosphate. Using the ATP and NADPH produced by the light-dependent reactions, the compounds are then reduced and removed to form further carbohydrates. Cyanobacteria appeared later, the oxygen they produced contributed directly to the oxygenation of the Earth. Today, the rate of energy capture by photosynthesis globally is approximately 130 terawatts. Photosynthetic organisms also convert around 100–115 thousand million tonnes of carbon into biomass per year. Photosynthetic organisms are photoautotrophs, which means that they are able to synthesize food directly from carbon dioxide, however, not all organisms that use light as a source of energy carry out photosynthesis, photoheterotrophs use organic compounds, rather than carbon dioxide, as a source of carbon. In plants, algae, and cyanobacteria, photosynthesis releases oxygen and this is called oxygenic photosynthesis and is by far the most common type of photosynthesis used by living organisms. Although there are differences between oxygenic photosynthesis in plants, algae, and cyanobacteria, the overall process is quite similar in these organisms. There are also varieties of anoxygenic photosynthesis, used mostly by certain types of bacteria. Carbon dioxide is converted into sugars in a process called carbon fixation, photosynthesis provides the energy in the form of free electrons that are used to split carbon from carbon dioxide that is then used to fix that carbon once again as carbohydrate. Carbon fixation is a redox reaction, so photosynthesis supplies the energy that drives both process. In the first stage, light-dependent reactions or light reactions capture the energy of light and use it to make the energy-storage molecules ATP, during the second stage, the light-independent reactions use these products to capture and reduce carbon dioxide. Most organisms that utilize oxygenic photosynthesis use visible light for the light-dependent reactions, some organisms employ even more radical variants of photosynthesis. Some archea use a method that employs a pigment similar to those used for vision in animals. The bacteriorhodopsin changes its configuration in response to sunlight, acting as a proton pump and this produces a proton gradient more directly, which is then converted to chemical energy
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Chloroplast
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Chloroplasts /ˈklɔːrəˌplæsts, -plɑːsts/ are organelles, specialized subunits, in plant and algal cells. Their discovery inside plant cells is usually credited to Julius von Sachs and they then use the ATP and NADPH to make organic molecules from carbon dioxide in a process known as the Calvin cycle. Chloroplasts carry out a number of functions, including fatty acid synthesis, much amino acid synthesis. The number of chloroplasts per cell varies from one, in algae, up to 100 in plants like Arabidopsis. A chloroplast is a type of known as a plastid. Other plastid types, such as the leucoplast and the chromoplast, contain little chlorophyll, chloroplasts are highly dynamic—they circulate and are moved around within plant cells, and occasionally pinch in two to reproduce. Their behavior is influenced by environmental factors like light color. Chloroplasts, like mitochondria, contain their own DNA, which is thought to be inherited from their ancestor—a photosynthetic cyanobacterium that was engulfed by a eukaryotic cell. Chloroplasts cannot be made by the plant cell and must be inherited by each cell during cell division. With one exception, all chloroplasts can probably be traced back to a single endosymbiotic event, despite this, chloroplasts can be found in an extremely wide set of organisms, some not even directly related to each other—a consequence of many secondary and even tertiary endosymbiotic events. The word chloroplast is derived from the Greek words chloros, which means green, and plastes, the first definitive description of a chloroplast was given by Hugo von Mohl in 1837 as discrete bodies within the green plant cell. In 1883, A. F. W. Schimper would name these bodies as chloroplastids, in 1884, Eduard Strasburger adopted the term chloroplasts. Chloroplasts are one of many types of organelles in the plant cell and they are considered to have originated from cyanobacteria through endosymbiosis—when a eukaryotic cell engulfed a photosynthesizing cyanobacterium that became a permanent resident in the cell. Mitochondria are thought to have come from an event, where an aerobic prokaryote was engulfed. This origin of chloroplasts was first suggested by the Russian biologist Konstantin Mereschkowski in 1905 after Andreas Schimper observed in 1883 that chloroplasts closely resemble cyanobacteria, chloroplasts are only found in plants, algae, and the amoeboid Paulinella chromatophora. Cyanobacteria are considered the ancestors of chloroplasts and they are sometimes called blue-green algae even though they are prokaryotes. They are a phylum of bacteria capable of carrying out photosynthesis. Cyanobacteria also contain a cell wall, which is thicker than in other gram-negative bacteria
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Photosystem II
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Photosystem II is the first protein complex in the light-dependent reactions of oxygenic photosynthesis. It is located in the membrane of plants, algae. Within the photosystem, enzymes capture photons of light to electrons that are then transferred through a variety of coenzymes. The energized electrons are replaced by oxidizing water to hydrogen ions. By replenishing lost electrons with electrons from the splitting of water, the hydrogen ions generated by the oxidation of water help to create a proton gradient that is used by ATP synthase to generate ATP. The energized electrons transferred to plastoquinone are ultimately used to reduce NADP+ to NADPH or are used in cyclic photophosphorylation, the core of PSII consists of a pseudo-symmetric heterodimer of two homologous proteins D1 and D2. Because the positive charge is not shared across two molecules, the pigment is highly oxidizing and can take part in the splitting of water. Photosystem II is composed of around 20 subunits as well as other accessory, there are different crystal structures of photosystem II. The PDB accession codes for this protein are 3WU2, 3BZ1, 3BZ2, 2AXT, 1S5L, 1W5C, 1ILX, 1FE1, the oxygen-evolving complex is the site of water oxidation. It is a metallo-oxo cluster comprising four manganese ions and one divalent calcium ion, when it oxidizes water, producing oxygen gas and protons, it sequentially delivers the four electrons from water to a tyrosine sidechain and then to P680 itself. The structure of the complex is still contentious. However, crystallography in combination with a variety of other methods such as EXAFS. One possibility is the cubane-like structure, in 2011 the OEC of PSII was resolved to a level of 1. Photosynthetic water splitting is one of the most important reactions on the planet, moreover, artificial photosynthetic water-splitting may contribute to the effective use of sunlight as an alternative energy-source. The mechanism of oxidation is still not fully elucidated. The oxidation of water to molecular oxygen requires extraction of four electrons, the experimental evidence that oxygen is released through cyclic reaction of oxygen evolving complex within one PSII was provided by Pierre Joliot et al. In the absence of light, the OEC will relax to the S1 state, the S1 state is largely considered to consist of manganese ions with oxidation states of Mn3+, Mn3+, Mn4+, Mn4+. Finally, the intermediate S-states were proposed by Jablonsky and Lazar as a regulatory mechanism, oxygen evolution P680 Photosynthesis Photosystem Photosystem I Photosystem II light-harvesting protein Reaction Centre Photoinhibition
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Redox
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Redox is a chemical reaction in which the oxidation states of atoms are changed. Any such reaction involves both a process and a complementary oxidation process, two key concepts involved with electron transfer processes. Redox reactions include all chemical reactions in which atoms have their oxidation state changed, in general, the chemical species from which the electron is stripped is said to have been oxidized, while the chemical species to which the electron is added is said to have been reduced. It can be explained in terms, Oxidation is the loss of electrons or an increase in oxidation state by a molecule, atom. Reduction is the gain of electrons or a decrease in state by a molecule, atom. As an example, during the combustion of wood, oxygen from the air is reduced, the reaction can occur relatively slowly, as in the case of rust, or more quickly, as in the case of fire. Redox is a portmanteau of reduction and oxidation, the word oxidation originally implied reaction with oxygen to form an oxide, since dioxygen was historically the first recognized oxidizing agent. Later, the term was expanded to encompass oxygen-like substances that accomplished parallel chemical reactions, ultimately, the meaning was generalized to include all processes involving loss of electrons. The word reduction originally referred to the loss in weight upon heating a metallic ore such as an oxide to extract the metal. In other words, ore was reduced to metal, antoine Lavoisier showed that this loss of weight was due to the loss of oxygen as a gas. Later, scientists realized that the atom gains electrons in this process. The meaning of reduction then became generalized to all processes involving gain of electrons. Even though reduction seems counter-intuitive when speaking of the gain of electrons, it help to think of reduction as the loss of oxygen. Since electrons are charged, it is also helpful to think of this as reduction in electrical charge. The electrochemist John Bockris has used the words electronation and deelectronation to describe reduction and oxidation processes respectively when they occur at electrodes and these words are analogous to protonation and deprotonation, but they have not been widely adopted by chemists. The term hydrogenation could be used instead of reduction, since hydrogen is the agent in a large number of reactions. But, unlike oxidation, which has been generalized beyond its root element, the word redox was first used in 1928. The processes of oxidation and reduction occur simultaneously and cannot happen independently of one another, the oxidation alone and the reduction alone are each called a half-reaction, because two half-reactions always occur together to form a whole reaction
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Chlorophyll
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Chlorophyll is any of several closely related green pigments found in cyanobacteria and the chloroplasts of algae and plants. Its name is derived from the Greek words χλωρός, chloros and φύλλον, chlorophyll is essential in photosynthesis, allowing plants to absorb energy from light. Chlorophyll absorbs light most strongly in the portion of the electromagnetic spectrum. Conversely, it is a poor absorber of green and near-green portions of the spectrum, chlorophyll molecules are specifically arranged in and around photosystems that are embedded in the thylakoid membranes of chloroplasts. Two types of chlorophyll exist in the photosystems of green plants, chlorophyll was first isolated and named by Joseph Bienaimé Caventou and Pierre Joseph Pelletier in 1817. Chlorophyll is vital for photosynthesis, which plants to absorb energy from light. Chlorophyll molecules are arranged in and around photosystems that are embedded in the thylakoid membranes of chloroplasts. In these complexes, chlorophyll serves two primary functions, the two currently accepted photosystem units are photosystem II and photosystem I, which have their own distinct reaction centres, named P680 and P700, respectively. These centres are named after the wavelength of their red-peak absorption maximum, the identity, function and spectral properties of the types of chlorophyll in each photosystem are distinct and determined by each other and the protein structure surrounding them. Once extracted from the protein into a solvent, these chlorophyll pigments can be separated into chlorophyll a, the function of the reaction center of chlorophyll is to absorb light energy and transfer it to other parts of the photosystem. The absorbed energy of the photon is transferred to an electron in a process called charge separation, the removal of the electron from the chlorophyll is an oxidation reaction. The chlorophyll donates the high energy electron to a series of molecular intermediates called a transport chain. The charged reaction center of chlorophyll is reduced back to its ground state by accepting an electron stripped from water. The electron that reduces P680+ ultimately comes from the oxidation of water into O2 and this reaction is how photosynthetic organisms such as plants produce O2 gas, and is the source for practically all the O2 in Earths atmosphere. Electron transfer reactions in the membranes are complex, however. NADPH is an agent used to reduce CO2 into sugars as well as other biosynthetic reactions. Thus, the other chlorophylls in the photosystem and antenna pigment proteins all cooperatively absorb, besides chlorophyll a, there are other pigments, called accessory pigments, which occur in these pigment–protein antenna complexes. Chlorophyll is a pigment, which is structurally similar to
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Protein
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Proteins are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, a linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide, short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides, or sometimes oligopeptides. The individual amino acid residues are bonded together by peptide bonds, the sequence of amino acid residues in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In general, the code specifies 20 standard amino acids, however. Sometimes proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors, proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes. Once formed, proteins only exist for a period of time and are then degraded and recycled by the cells machinery through the process of protein turnover. A proteins lifespan is measured in terms of its half-life and covers a wide range and they can exist for minutes or years with an average lifespan of 1–2 days in mammalian cells. Abnormal and or misfolded proteins are degraded more rapidly due to being targeted for destruction or due to being unstable. Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms, many proteins are enzymes that catalyse biochemical reactions and are vital to metabolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle. In animals, proteins are needed in the diet to provide the essential amino acids that cannot be synthesized, digestion breaks the proteins down for use in the metabolism. Methods commonly used to study structure and function include immunohistochemistry, site-directed mutagenesis, X-ray crystallography, nuclear magnetic resonance. Most proteins consist of linear polymers built from series of up to 20 different L-α-amino acids, all proteinogenic amino acids possess common structural features, including an α-carbon to which an amino group, a carboxyl group, and a variable side chain are bonded. Only proline differs from this structure as it contains an unusual ring to the N-end amine group. The amino acids in a chain are linked by peptide bonds. Once linked in the chain, an individual amino acid is called a residue, and the linked series of carbon, nitrogen. The peptide bond has two forms that contribute some double-bond character and inhibit rotation around its axis, so that the alpha carbons are roughly coplanar
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Chicken as food
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Chicken is the most common type of poultry in the world. In developed countries, chickens are usually subject to intensive farming methods, the modern chicken is a descendant of red junglefowl hybrids along with the grey junglefowl first raised thousands of years ago in the northern parts of the Indian subcontinent. Chicken as a meat has been depicted in Babylonian carvings from around 600 BC, Chicken was one of the most common meats available in the Middle Ages. It was eaten over most of the Eastern hemisphere and a number of different kinds of such as capons, pullets. It was one of the ingredients in the so-called white dish. In the United States in the 1800s, chicken was more expensive than other meats, Chicken consumption in the United States increased during World War II due to a shortage of beef and pork. In Europe, consumption of chicken overtook that of beef and veal in 1996, modern varieties of chicken such as the Cornish Cross, are bred specifically for meat production, with an emphasis placed on the ratio of feed to meat produced by the animal. The most common breeds of chicken consumed in the US are Cornish, chickens raised specifically for food are called broilers. In the United States, broilers are typically butchered at a young age, modern Cornish Cross hybrids, for example, are butchered as early as 8 weeks for fryers and 12 weeks for roasting birds. Capons produce more and fattier meat, for this reason, they are considered a delicacy and were particularly popular in the Middle Ages. Main Breast, These are white meat and are relatively dry, leg, Comprises two segments, The drumstick, this is dark meat and is the lower part of the leg, the thigh, also dark meat, this is the upper part of the leg. Wing, Often served as a meal or bar food. Buffalo wings are a typical example, Comprises three segments, the drumette, shaped like a small drumstick, the middle flat segment, containing two bones, and the tip, sometimes discarded. Other Chicken feet, These contain relatively little meat, and are mainly for the skin. Although considered exotic in Western cuisine, the feet are common fare in other cuisines, especially in the Caribbean, giblets, organs such as the heart, gizzards, and liver may be included inside a butchered chicken or sold separately. Head, Considered a delicacy in China, the head is split down the middle, kidneys, Normally left in when a broiler carcass is processed, they are found in deep pockets on each side of the vertebral column. Neck, This is served in various Asian dishes and it is stuffed to make helzel among Ashkenazi Jews. Oysters, Located on the back, near the thigh, these small, pygostyle and testicles, These are commonly eaten in East Asia and some parts of South East Asia
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