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.
Density
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The density, or more precisely, the volumetric mass density, of a substance is its mass per unit volume. The symbol most often used for density is ρ, although the Latin letter D can also be used. Mathematically, density is defined as mass divided by volume, ρ = m V, where ρ is the density, m is the mass, and V is the volume. In some cases, density is defined as its weight per unit volume. For a pure substance the density has the numerical value as its mass concentration. Different materials usually have different densities, and density may be relevant to buoyancy, purity, osmium and iridium are the densest known elements at standard conditions for temperature and pressure but certain chemical compounds may be denser. Thus a relative density less than one means that the floats in water. The density of a material varies with temperature and pressure and this variation is typically small for solids and liquids but much greater for gases. Increasing the pressure on an object decreases the volume of the object, increasing the temperature of a substance decreases its density by increasing its volume. In most materials, heating the bottom of a results in convection of the heat from the bottom to the top. This causes it to rise relative to more dense unheated material, the reciprocal of the density of a substance is occasionally called its specific volume, a term sometimes used in thermodynamics. Density is a property in that increasing the amount of a substance does not increase its density. Archimedes knew that the irregularly shaped wreath could be crushed into a cube whose volume could be calculated easily and compared with the mass, upon this discovery, he leapt from his bath and ran naked through the streets shouting, Eureka. As a result, the term eureka entered common parlance and is used today to indicate a moment of enlightenment, the story first appeared in written form in Vitruvius books of architecture, two centuries after it supposedly took place. Some scholars have doubted the accuracy of this tale, saying among other things that the method would have required precise measurements that would have been difficult to make at the time, from the equation for density, mass density has units of mass divided by volume. As there are units of mass and volume covering many different magnitudes there are a large number of units for mass density in use. The SI unit of kilogram per metre and the cgs unit of gram per cubic centimetre are probably the most commonly used units for density.1,000 kg/m3 equals 1 g/cm3. In industry, other larger or smaller units of mass and or volume are often more practical, see below for a list of some of the most common units of density
12.
Partition coefficient
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In the physical sciences, a partition-coefficient or distribution-coefficient is the ratio of concentrations of a compound in a mixture of two immiscible phases at equilibrium. This ratio is therefore a measure of the difference in solubility of the compound in two phases. In the chemical and pharmaceutical sciences, both phases usually are solvents, most commonly, one of the solvents is water while the second is hydrophobic such as 1-octanol. Hence the partition coefficient measures how hydrophilic or hydrophobic a chemical substance is, partition coefficients are useful in estimating the distribution of drugs within the body. Hydrophobic drugs with high octanol/water partition coefficients are distributed to hydrophobic areas such as lipid bilayers of cells. Conversely hydrophilic drugs are primarily in aqueous regions such as blood serum. If one of the solvents is a gas and the other a liquid, for example, the blood/gas partition coefficient of a general anesthetic measures how easily the anesthetic passes from gas to blood. Partition coefficients can also be defined one of the phases is solid, for instance, when one phase is a molten metal. The partitioning of a substance into a solid results in a solid solution, partition coefficients can be measured experimentally in various ways or estimated via calculation based on a variety of methods. Despite formal recommendation to the contrary, the partition coefficient remains the predominantly used term in the scientific literature. In contrast, the IUPAC recommends that the term no longer be used, rather. When one of the solvents is water and the other is a non-polar solvent, for measurements of distribution coefficients, the pH of the aqueous phase is buffered to a specific value such that the pH is not significantly perturbed by the introduction of the compound. In addition, since log D is pH-dependent, the pH at which the log D was measured must be specified. In areas such as drug discovery—areas involving partition phenomena in systems such as the human body—the log D at the physiologic pH,7.4, is of particular interest. It is often convenient to express the log D in terms of P I, defined above, the values in the following table are from the Dortmund Data Bank. They are sorted by the coefficient, smallest to largest. Values for other compounds may be found in a variety of available reviews, critical discussions of the challenges of measurement of log P, and related computation of its estimated values, appear in several reviews. Hence, the log P of a molecule is one used in decision-making by medicinal chemists in pre-clinical drug discovery, for example
13.
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
14.
Organic compound
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An organic compound is virtually any chemical compound that contains carbon, although a consensus definition remains elusive and likely arbitrary. Organic compounds are rare terrestrially, but of importance because all known life is based on organic compounds. The most basic petrochemicals are considered the building blocks of organic chemistry, for historical reasons discussed below, a few types of carbon-containing compounds, such as carbides, carbonates, simple oxides of carbon, and cyanides are considered inorganic. The distinction between organic and inorganic compounds, while useful in organizing the vast subject of chemistry. Organic chemistry is the science concerned with all aspects of organic compounds, Organic synthesis is the methodology of their preparation. The word organic is historical, dating to the 1st century, for many centuries, Western alchemists believed in vitalism. This is the theory that certain compounds could be synthesized only from their classical elements—earth, water, air, vitalism taught that these organic compounds were fundamentally different from the inorganic compounds that could be obtained from the elements by chemical manipulation. Vitalism survived for a while even after the rise of modern atomic theory and it first came under question in 1824, when Friedrich Wöhler synthesized oxalic acid, a compound known to occur only in living organisms, from cyanogen. A more decisive experiment was Wöhlers 1828 synthesis of urea from the inorganic salts potassium cyanate, urea had long been considered an organic compound, as it was known to occur only in the urine of living organisms. Wöhlers experiments were followed by others, in which increasingly complex organic substances were produced from inorganic ones without the involvement of any living organism. Even though vitalism has been discredited, scientific nomenclature retains the distinction between organic and inorganic compounds, still, even the broadest definition requires excluding alloys that contain carbon, including steel. The C-H definition excludes compounds that are considered organic, neither urea nor oxalic acid is organic by this definition, yet they were two key compounds in the vitalism debate. The IUPAC Blue Book on organic nomenclature specifically mentions urea and oxalic acid, other compounds lacking C-H bonds but traditionally considered organic include benzenehexol, mesoxalic acid, and carbon tetrachloride. Mellitic acid, which contains no C-H bonds, is considered an organic substance in Martian soil. The C-H bond-only rule also leads to somewhat arbitrary divisions in sets of carbon-fluorine compounds, for example, CF4 would be considered by this rule to be inorganic, whereas CF3H would be organic. Organic compounds may be classified in a variety of ways, one major distinction is between natural and synthetic compounds. Another distinction, based on the size of organic compounds, distinguishes between small molecules and polymers, natural compounds refer to those that are produced by plants or animals. Many of these are extracted from natural sources because they would be more expensive to produce artificially
15.
Metabolism
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Metabolism is the set of life-sustaining chemical transformations within the cells of living organisms. These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, usually, breaking down releases energy and building up consumes energy. The chemical reactions of metabolism are organized into metabolic pathways, in one chemical is transformed through a series of steps into another chemical. Enzymes act as catalysts that allow the reactions to proceed more rapidly, enzymes also allow the regulation of metabolic pathways in response to changes in the cells environment or to signals from other cells. The metabolic system of a particular organism determines which substances it will find nutritious, for example, some prokaryotes use hydrogen sulfide as a nutrient, yet this gas is poisonous to animals. The speed of metabolism, the rate, influences how much food an organism will require. A striking feature of metabolism is the similarity of the metabolic pathways. These striking similarities in metabolic pathways are likely due to their appearance in evolutionary history. Most of the structures that make up animals, plants and microbes are made from three classes of molecule, amino acids, carbohydrates and lipids. These biochemicals can be joined together to make such as DNA and proteins. Proteins are made of amino acids arranged in a linear chain joined together by peptide bonds, many proteins are enzymes that catalyze the chemical reactions in metabolism. Other proteins have structural or mechanical functions, such as those that form the cytoskeleton, Proteins are also important in cell signaling, immune responses, cell adhesion, active transport across membranes, and the cell cycle. Lipids are the most diverse group of biochemicals and their main structural uses are as part of biological membranes both internal and external, such as the cell membrane, or as a source of energy. Lipids are usually defined as hydrophobic or amphipathic biological molecules but will dissolve in organic solvents such as benzene or chloroform, the fats are a large group of compounds that contain fatty acids and glycerol, a glycerol molecule attached to three fatty acid esters is called a triacylglyceride. Several variations on this structure exist, including alternate backbones such as sphingosine in the sphingolipids. Steroids such as cholesterol are another class of lipids. Carbohydrates are aldehydes or ketones, with hydroxyl groups attached. Carbohydrates are the most abundant biological molecules, and fill numerous roles, such as the storage and transport of energy, the basic carbohydrate units are called monosaccharides and include galactose, fructose, and most importantly glucose
16.
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
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Sugar
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Sugar is the generic name for sweet, soluble carbohydrates, many of which are used in food. There are various types of derived from different sources. Simple sugars are called monosaccharides and include glucose, fructose, the table sugar or granulated sugar most customarily used as food is sucrose, a disaccharide of glucose and fructose. Sugar is used in prepared foods and it is added to some foods, in the body, sucrose is hydrolysed into the simple sugars fructose and glucose. Other disaccharides include maltose from malted grain, and lactose from milk, longer chains of sugars are called oligosaccharides or polysaccharides. Some other chemical substances, such as glycerol may also have a sweet taste, low-calorie food substitutes for sugar, described as artificial sweeteners, include aspartame and sucralose, a chlorinated derivative of sucrose. Sugars are found in the tissues of most plants and are present in sufficient concentrations for efficient commercial extraction in sugarcane, the world production of sugar in 2011 was about 168 million tonnes. The average person consumes about 24 kilograms of sugar each year, equivalent to over 260 food calories per person, since the latter part of the twentieth century, it has been questioned whether a diet high in sugars, especially refined sugars, is good for human health. Sugar has been linked to obesity, and suspected of, or fully implicated as a cause in the occurrence of diabetes, cardiovascular disease, dementia, macular degeneration, the etymology reflects the spread of the commodity. The English word sugar ultimately originates from the Sanskrit शर्करा, via Arabic سكر as granular or candied sugar, the contemporary Italian word is zucchero, whereas the Spanish and Portuguese words, azúcar and açúcar, respectively, have kept a trace of the Arabic definite article. The Old French word is zuchre and the contemporary French, sucre, the earliest Greek word attested is σάκχαρις. The English word jaggery, a brown sugar made from date palm sap or sugarcane juice, has a similar etymological origin – Portuguese jagara from the Sanskrit शर्करा. Sugar has been produced in the Indian subcontinent since ancient times and it was not plentiful or cheap in early times and honey was more often used for sweetening in most parts of the world. Originally, people chewed raw sugarcane to extract its sweetness, sugarcane was a native of tropical South Asia and Southeast Asia. Different species seem to have originated from different locations with Saccharum barberi originating in India and S. edule, one of the earliest historical references to sugarcane is in Chinese manuscripts dating back to 8th century BC that state that the use of sugarcane originated in India. Sugar was found in Europe by the 1st century AD, but only as an imported medicine and it is a kind of honey found in cane, white as gum, and it crunches between the teeth. It comes in lumps the size of a hazelnut, sugar is used only for medical purposes. Sugar remained relatively unimportant until the Indians discovered methods of turning sugarcane juice into granulated crystals that were easier to store, crystallized sugar was discovered by the time of the Imperial Guptas, around the 5th century AD
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Adenine
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It also has functions in protein synthesis and as a chemical component of DNA and RNA. The shape of adenine is complementary to either thymine in DNA or uracil in RNA, the image on the right shows pure adenine, as an independent molecule. When connected into DNA, a covalent bond is formed between deoxyribose sugar and the bottom left nitrogen, so removing the hydrogen, the remaining structure is called an adenine residue, as part of a larger molecule. Adenosine is adenine reacted with ribose as used in RNA and ATP, deoxyadenosine adenine attached to deoxyribose, adenine forms several tautomers, compounds that can be rapidly interconverted and are often considered equivalent. However, in isolated conditions, i. e. in an inert gas matrix and in the gas phase, purine metabolism involves the formation of adenine and guanine. Adenine is one of the two purine nucleobases used in forming nucleotides of the nucleic acids, in DNA, adenine binds to thymine via two hydrogen bonds to assist in stabilizing the nucleic acid structures. In RNA, which is used for synthesis, adenine binds to uracil. Adenine forms adenosine, a nucleoside, when attached to ribose and it forms adenosine triphosphate, a nucleoside triphosphate, when three phosphate groups are added to adenosine. Adenosine triphosphate is used in cellular metabolism as one of the methods of transferring chemical energy between chemical reactions. In older literature, adenine was sometimes called Vitamin B4 and it is no longer considered a true vitamin or part of the Vitamin B complex. However, two B vitamins, niacin and riboflavin, bind with adenine to form the essential cofactors nicotinamide adenine dinucleotide and flavin adenine dinucleotide, hermann Emil Fischer was one of the early scientists to study adenine. It was named in 1885 by Albrecht Kossel, in reference to the pancreas from which Kossels sample had been extracted. On August 8,2011, a report, based on NASA studies with meteorites found on Earth, was published suggesting building blocks of DNA and RNA may have been formed extraterrestrially in outer space
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Ribose
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Ribose is a carbohydrate with the formula C5H10O5, specifically, it is a pentose monosaccharide with linear form H−−4−H, which has all the hydroxyl groups on the same side in the Fischer projection. The term may refer to either of two enantiomers, the term usually indicates D-ribose, which occurs widely in nature and is discussed here. Its synthetic mirror image, L-ribose, is not found in nature, d-Ribose was first reported in 1891 by Emil Fischer. It is a C-2 carbon epimer of the sugar D-arabinose and ribose itself is named as a rearrangement of letters in the word arabinose. The ribose β-D-ribofuranose forms part of the backbone of RNA and it is related to deoxyribose, which is found in DNA. Phosphorylated derivatives of such as ATP and NADH play central roles in metabolism. CAMP and cGMP, formed from ATP and GTP, serve as messengers in some signalling pathways. Ribose is an aldopentose that, in its open form, has an aldehyde functional group at one end. In the conventional numbering scheme for monosaccharides, the atoms are numbered from C1 to C5. The deoxyribose derivative found in DNA differs from ribose by having a hydrogen atom in place of the group at C2. This hydroxyl group performs a function in RNA splicing, the beta-ribopyranose form predominates in aqueous solution. The “D-” in the name D-ribose refers to the stereochemistry of the carbon atom farthest away from the aldehyde group. In D-ribose, as in all D-sugars, this carbon atom has the configuration as in D-glyceraldehyde. Relative abundance of different forms of ribose in solution, β-D-ribopyranose, α-D-ribopyranose, β-D-ribofuranose, α-D-ribofuranose, in biology, D-ribose must be phosphorylated by the cell before it can be used. Ribokinase catalyzes this reaction by converting D-ribose to D-ribose 5-phosphate, once converted, D-ribose-5-phosphate is available for the manufacturing of the amino acids tryptophan and histidine, or for use in the pentose phosphate pathway. The absorption of D-ribose is 88–100% in the small intestines
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Adenosine triphosphate
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Adenosine triphosphate is a nucleotide, also called a nucleoside triphosphate, is a small molecule used in cells as a coenzyme. It is often referred to as the unit of currency of intracellular energy transfer. ATP transports chemical energy within cells for metabolism, most cellular functions need energy in order to be carried out, synthesis of proteins, synthesis of membranes, movement of the cell, cellular division, transport of various solutes etc. The ATP is the molecule that carries energy to the place where the energy is needed, when ATP breaks into ADP and Pi, the breakdown of the last covalent link of phosphate liberates energy that is used in reactions where it is needed. Substrate-level phosphorylation, oxidative phosphorylation in cellular respiration, and photophosphorylation in photosynthesis are three mechanisms of ATP biosynthesis. Metabolic processes that use ATP as an energy source convert it back into its precursors, ATP is therefore continuously recycled in organisms, the human body, which on average contains only 250 grams of ATP, turns over its own body weight equivalent in ATP each day. ATP is used as a substrate in signal transduction pathways by kinases that phosphorylate proteins and it is also used by adenylate cyclase, which uses ATP to produce the second messenger molecule cyclic AMP. The ratio between ATP and AMP is used as a way for a cell to sense how much energy is available and control the metabolic pathways that produce and consume ATP. Apart from its roles in signaling and energy metabolism, ATP is also incorporated into nucleic acids by polymerases in the process of transcription, ATP is the neurotransmitter believed to signal the sense of taste. The structure of this consists of a purine base attached by the 9′ nitrogen atom to the 1′ carbon atom of a pentose sugar. Three phosphate groups are attached at the 5′ carbon atom of the pentose sugar and it is the addition and removal of these phosphate groups that inter-convert ATP, ADP and AMP. When ATP is used in DNA synthesis, the sugar is first converted to deoxyribose by ribonucleotide reductase. ATP was discovered in 1929 by Karl Lohmann, and independently by Cyrus Fiske and Yellapragada Subbarow of Harvard Medical School and it was proposed to be the intermediary molecule between energy-yielding and energy-requiring reactions in cells by Fritz Albert Lipmann in 1941. It was first artificially synthesized by Alexander Todd in 1948, ATP consists of adenosine – composed of an adenine ring and a ribose sugar – and three phosphate groups. The phosphoryl groups, starting with the group closest to the ribose, are referred to as the alpha, beta, consequently, it is closely related to the adenosine nucleotide, a monomer of RNA. ATP is highly soluble in water and is stable in solutions between pH6.8 and 7.4, but is rapidly hydrolysed at extreme pH. Consequently, ATP is best stored as an anhydrous salt, ATP is an unstable molecule in unbuffered water, in which it hydrolyses to ADP and phosphate. This is because the strength of the bonds between the groups in ATP is less than the strength of the hydrogen bonds, between its products, and water
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Dephosphorylation
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Dephosphorylation is the removal of a phosphate group from an organic compound by hydrolysis. It is a reversible post-translational modification, dephosphorylation and its counterpart, phosphorylation, activate and deactivate enzymes by detaching or attaching phosphoric esters and anhydrides. A notable occurrence of dephosphorylation is the conversion of ATP to ADP, dephosphorylation employs a type of hydrolytic enzyme, or hydrolase, which cleave ester bonds. The prominent hydrolase subclass used in dephosphorylation is phosphatase, phosphatase removes phosphate groups by hydrolysing phosphoric acid monoesters into a phosphate ion and a molecule with a free hydroxyl group. The reversible phosphorylation-dephosphorylation reaction occurs in every physiological process, making proper function of protein phosphases necessary for organism viability, because protein dephosphorylation is a key process involved in cell signalling, protein phosphatases are implicated in conditions such as cardiac disease, diabetes, and Alzheimers disease. The discovery of dephosphorylation came from a series of experiments examining the enzyme phosphorylase isolated from rabbit skeletal muscle. In 1955, Edwin Krebs and Edmond Fischer used radiolabeled ATP to determine that phosphate is added to the residue of phosphorylase to convert it from its b to a form via phosphorylation. Subsequently, Krebs and Fischer showed that this phosphorylation is part of a kinase cascade, finally, after purifying the phosphorylated form of the enzyme, phosphorylase a, from rabbit liver, ion exchange chromatography was used to identify phosphoprotein phosphatase I and II. Edwin Krebs and Edmond Fischer won the 1992 Nobel Prize in Physiology or Medicine for the discovery of reversible protein phosphorylation, phosphorylation involves the covalent modification of the hydroxyl with a phosphate group through the nucleophilic attack of the alpha phosphate in ATP by the oxygen in the hydroxyl. Dephosphorylation involves removal of the group through a hydration reaction by addition of a molecule of water and release of the original phosphate group. Both processes are reversible and either mechanism can be used to activate or deactivate a protein, phosphorylation of a protein produces many biochemical effects, such as changing its conformation to alter its binding to a specific ligand to increase or reduce its activity. Phosphorylation and dephosphorylation can be used on all types of substrates, such as proteins, enzymes, membrane channels, signaling molecules. The sum of these processes is referred to as phosphoregulation, the deregulation of phosphorylation can lead to disease. During the synthesis of proteins, polypeptide chains, which are created by ribosomes translating mRNA, the dephosphorylation of proteins is a mechanism for modifying behavior of a protein, often by activating or inactivating an enzyme. Components of the protein synthetic apparatus also undergo phosphorylation and dephosphorylation, as part of postranslational modifications, phosphate groups may be removed from serine, threonine, or tyrosine. As such, pathways of signal transduction depend on sequential phosphorylation and dephosphorylation of a wide variety of proteins. ATP4− + H2O --> ADP3− + HPO42− + H+ Adenosine triphosphate, or ATP, in a spontaneous dephosphorylation reaction 30.5 kJ/mol is released, which is harnessed to drive cellular reactions. Overall, nonspontaneous reactions coupled to the dephosphorylation of ATP are spontaneous and this is important in driving oxidative phosphorylation
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ATPase
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ATPases are a class of enzymes that catalyze the decomposition of ATP into ADP and a free phosphate ion. This dephosphorylation reaction releases energy, which the enzyme harnesses to drive chemical reactions that would not otherwise occur. This process is used in all known forms of life. Some such enzymes are integral membrane proteins, and move solutes across the membrane, transmembrane ATPases import many of the metabolites necessary for cell metabolism and export toxins, wastes, and solutes that can hinder cellular processes. An important example is the sodium-potassium exchanger that maintains the membrane potential. And another example is the hydrogen potassium ATPase that acidifies the contents of the stomach, besides exchangers, other categories of transmembrane ATPase include co-transporters and pumps. Some of these, like the Na+/K+ATPase, cause a net flow of charge and these are called electrogenic and nonelectrogenic transporters, respectively. This process is considered active transport, for example, the blocking of the vesicular H+-ATPases would increase the pH inside vesicles and decrease the pH of the cytoplasm. This enzyme works when a proton moves down the concentration gradient and this unique spinning motion bonds ADP and P together to create ATP. ATP synthase can also function in reverse, that is, use energy released by ATP hydrolysis to pump protons against their electrochemical gradient, there are different types of ATPases, which can differ in function, structure and in the type of ions they transport. F-ATPases in mitochondria, chloroplasts and bacterial plasma membranes are the producers of ATP. V-ATPases are primarily found in vacuoles, catalysing ATP hydrolysis to transport solutes. E-ATPases are cell-surface enzymes that hydrolyze a range of NTPs, including extracellular ATP, P-ATPases are found in bacteria and also in eukaryotic plasma membranes and organelles. Its name is due to short time attachment of inorganic phosphate at the residues at the time of activation. Function of P-ATPase is to transport a variety of different compounds, like ions and phospholipids, there are many different classes of P-ATPases, which transports a specific type of ion. P-ATPases may be composed of one or two polypeptides, and can take two main conformations, E1 and E2
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Substrate-level phosphorylation
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Substrate-level phosphorylation is a metabolic reaction that results in the formation of ATP or GTP by the direct transfer of a phosphoryl group to ADP or GDP from another phosphorylated compound. This is the case in human erythrocytes, which have no mitochondria, substrate-level phosphorylation occurs in the cytoplasm of cells during glycolysis and in mitochondria during the Krebs cycle under both aerobic and anaerobic conditions. In the pay-off phase of glycolysis, a net of 2 ATP are produced by substrate-level phosphorylation, the first substrate-level phosphorylation occurs after the conversion of 3-phosphoglyceraldehyde and Pi and NAD+ to 1, 3-bisphosphoglycerate via glyceraldehyde 3-phosphate dehydrogenase. 1, 3-bisphosphoglycerate is then dephosphorylated via phosphoglycerate kinase, producing 3-phosphoglycerate, the second substrate-level phosphorylation occurs by dephosphorylating phosphoenolpyruvate, catalyzed by pyruvate kinase, producing pyruvate and ATP. During the preparatory phase, each 6-carbon glucose molecule is broken into two 3-carbon molecules, thus, in glycolysis dephosphorylation results in the production of 4 ATP. However, the preparatory phase consumes 2 ATP, so the net yield in glycolysis is 2 ATP. 2 molecules of NADH are also produced and can be used in oxidative phosphorylation to generate more ATP, ATP can be generated by substrate-level phosphorylation in mitochondria in a pathway that is independent from the proton motive force. In the matrix there are two reactions capable of substrate-level phosphorylation, utilizing either phosphoenolpyruvate carboxykinase or succinate-CoA ligase, mitochondrial phosphoenolpyruvate carboxykinase is thought to participate in the transfer of the phosphorylation potential from the matrix to the cytosol and vice versa. Succinate-CoA ligase is a composed of an invariant α-subunit and a substrate-specific ß-subunit. This combination results in either an ADP-forming succinate-CoA ligase or a GDP-forming succinate-CoA ligase, another form of substrate-level phosphorylation is also seen in working skeletal muscles and the brain. Phosphocreatine is stored as a readily available high-energy phosphate supply, then the ATP releases giving chemical energy. Substrate-level phosphorylation can also be observed in fermentation, an alternative method used to create ATP is through oxidative phosphorylation, which takes place during cellular respiration. This process utilizes the oxidation of NADH to NAD+, yielding 3 ATP, an electrochemical or chemiosmotic gradient of protons across the inner mitochondrial membrane is required to generate ATP from ADP and Pi, a key difference from substrate-level phosphorylation
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Oxidative phosphorylation
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Oxidative phosphorylation is the metabolic pathway in which cells use enzymes to oxidize nutrients, thereby releasing energy which is used to reform ATP. In most eukaryotes, this takes place inside mitochondria, almost all aerobic organisms carry out oxidative phosphorylation. This pathway is probably so pervasive because it is an efficient way of releasing energy. During oxidative phosphorylation, electrons are transferred from electron donors to electron acceptors such as oxygen and these redox reactions release energy, which is used to form ATP. These linked sets of proteins are called electron transport chains, in eukaryotes, five main protein complexes are involved, whereas in prokaryotes many different enzymes are present, using a variety of electron donors and acceptors. The energy released by electrons flowing through this electron transport chain is used to transport protons across the mitochondrial membrane. This generates potential energy in the form of a pH gradient and this store of energy is tapped by allowing protons to flow back across the membrane and down this gradient, through a large enzyme called ATP synthase, this process is known as chemiosmosis. This enzyme uses energy to generate ATP from adenosine diphosphate. This reaction is driven by the flow, which forces the rotation of a part of the enzyme. The enzymes carrying out this metabolic pathway are also the target of many drugs and this means one cannot occur without the other. These enzymes are like a battery, as they work to drive current through the circuit. The movement of protons creates an electrochemical gradient across the membrane and it has two components, a difference in proton concentration and a difference in electric potential, with the N-side having a negative charge. ATP synthase releases this energy by completing the circuit and allowing protons to flow down the electrochemical gradient. The electrochemical gradient drives the rotation of part of the enzymes structure, inversely, chloroplasts operate mainly on ΔpH. However, they require a small membrane potential for the kinetics of ATP synthesis. At least in the case of the fusobacterium P. modestum it drives the counter-rotation of subunits a and c of the FO motor of ATP synthase, the amount of energy released by oxidative phosphorylation is high, compared with the amount produced by anaerobic fermentation. These ATP yields are theoretical maximum values, in practice, some protons leak across the membrane, the electron transport chain carries both protons and electrons, passing electrons from donors to acceptors, and transporting protons across a membrane. These processes use both soluble and protein-bound transfer molecules, in mitochondria, electrons are transferred within the intermembrane space by the water-soluble electron transfer protein cytochrome c
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Photophosphorylation
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In the process of photosynthesis, the phosphorylation of ADP to form ATP using the energy of sunlight is called photophosphorylation. Only two sources of energy are available to living organisms, sunlight and reduction-oxidation reactions, all organisms produce ATP, which is the universal energy currency of life. Commonly in photosynthesis this involves photolysis of water and a continuous flow of electrons from water to PS||. In photophosphorylation, light energy is used to create an electron donor. Electrons then move spontaneously from donor to acceptor through a transport chain. ATP is made by an enzyme called ATP synthase, both the structure of this enzyme and its underlying gene are remarkably similar in all known forms of life. ATP synthase is powered by an electrochemical potential gradient, usually in the form of a proton gradient. The function of the transport chain is to produce this gradient. In all living organisms, a series of reactions is used to produce a transmembrane electrochemical potential gradient. Redox reactions are chemical reactions in which electrons are transferred from a molecule to an acceptor molecule. The underlying force driving these reactions is the Gibbs free energy of the reactants and products, the Gibbs free energy is the energy available to do work. Any reaction that decreases the overall Gibbs free energy of a system will proceed spontaneously, the transfer of electrons from a high-energy molecule to a lower-energy molecule can be spatially separated into a series of intermediate redox reactions. This is a transport chain. The fact that a reaction is thermodynamically possible does not mean that it will actually occur, a mixture of hydrogen gas and oxygen gas does not spontaneously ignite. It is necessary either to supply an activation energy or to lower the activation energy of the system. Living systems use complex macromolecular structures to lower the activation energies of biochemical reactions, electron transport chains produce energy in the form of a transmembrane electrochemical potential gradient. This energy is used to do useful work, the gradient can be used to transport molecules across membranes. It can be used to do work, such as rotating bacterial flagella
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Energy
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In physics, energy is the property that must be transferred to an object in order to perform work on – or to heat – the object, and can be converted in form, but not created or destroyed. The SI unit of energy is the joule, which is the transferred to an object by the mechanical work of moving it a distance of 1 metre against a force of 1 newton. Mass and energy are closely related, for example, with a sensitive enough scale, one could measure an increase in mass after heating an object. Living organisms require available energy to stay alive, such as the humans get from food. Civilisation gets the energy it needs from energy resources such as fuels, nuclear fuel. The processes of Earths climate and ecosystem are driven by the radiant energy Earth receives from the sun, the total energy of a system can be subdivided and classified in various ways. It may also be convenient to distinguish gravitational energy, thermal energy, several types of energy, electric energy. Many of these overlap, for instance, thermal energy usually consists partly of kinetic. Some types of energy are a mix of both potential and kinetic energy. An example is energy which is the sum of kinetic. Whenever physical scientists discover that a phenomenon appears to violate the law of energy conservation. Heat and work are special cases in that they are not properties of systems, in general we cannot measure how much heat or work are present in an object, but rather only how much energy is transferred among objects in certain ways during the occurrence of a given process. Heat and work are measured as positive or negative depending on which side of the transfer we view them from, the distinctions between different kinds of energy is not always clear-cut. In contrast to the definition, energeia was a qualitative philosophical concept, broad enough to include ideas such as happiness. The modern analog of this property, kinetic energy, differs from vis viva only by a factor of two, in 1807, Thomas Young was possibly the first to use the term energy instead of vis viva, in its modern sense. Gustave-Gaspard Coriolis described kinetic energy in 1829 in its modern sense, the law of conservation of energy was also first postulated in the early 19th century, and applies to any isolated system. It was argued for years whether heat was a physical substance, dubbed the caloric, or merely a physical quantity. In 1845 James Prescott Joule discovered the link between mechanical work and the generation of heat and these developments led to the theory of conservation of energy, formalized largely by William Thomson as the field of thermodynamics
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Thermodynamics
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Thermodynamics is a branch of science concerned with heat and temperature and their relation to energy and work. The behavior of these quantities is governed by the four laws of thermodynamics, the laws of thermodynamics are explained in terms of microscopic constituents by statistical mechanics. Thermodynamics applies to a variety of topics in science and engineering, especially physical chemistry, chemical engineering. The initial application of thermodynamics to mechanical heat engines was extended early on to the study of chemical compounds, Chemical thermodynamics studies the nature of the role of entropy in the process of chemical reactions and has provided the bulk of expansion and knowledge of the field. Other formulations of thermodynamics emerged in the following decades, statistical thermodynamics, or statistical mechanics, concerned itself with statistical predictions of the collective motion of particles from their microscopic behavior. In 1909, Constantin Carathéodory presented a mathematical approach to the field in his axiomatic formulation of thermodynamics. A description of any thermodynamic system employs the four laws of thermodynamics that form an axiomatic basis, the first law specifies that energy can be exchanged between physical systems as heat and work. In thermodynamics, interactions between large ensembles of objects are studied and categorized, central to this are the concepts of the thermodynamic system and its surroundings. A system is composed of particles, whose average motions define its properties, properties can be combined to express internal energy and thermodynamic potentials, which are useful for determining conditions for equilibrium and spontaneous processes. With these tools, thermodynamics can be used to describe how systems respond to changes in their environment and this can be applied to a wide variety of topics in science and engineering, such as engines, phase transitions, chemical reactions, transport phenomena, and even black holes. This article is focused mainly on classical thermodynamics which primarily studies systems in thermodynamic equilibrium, non-equilibrium thermodynamics is often treated as an extension of the classical treatment, but statistical mechanics has brought many advances to that field. Guericke was driven to make a vacuum in order to disprove Aristotles long-held supposition that nature abhors a vacuum. Shortly after Guericke, the English physicist and chemist Robert Boyle had learned of Guerickes designs and, in 1656, in coordination with English scientist Robert Hooke, using this pump, Boyle and Hooke noticed a correlation between pressure, temperature, and volume. In time, Boyles Law was formulated, which states that pressure, later designs implemented a steam release valve that kept the machine from exploding. By watching the valve rhythmically move up and down, Papin conceived of the idea of a piston and he did not, however, follow through with his design. Nevertheless, in 1697, based on Papins designs, engineer Thomas Savery built the first engine, although these early engines were crude and inefficient, they attracted the attention of the leading scientists of the time. Black and Watt performed experiments together, but it was Watt who conceived the idea of the condenser which resulted in a large increase in steam engine efficiency. Drawing on all the work led Sadi Carnot, the father of thermodynamics, to publish Reflections on the Motive Power of Fire
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Potential energy
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In physics, potential energy is energy possessed by a body by virtue of its position relative to others, stresses within itself, electric charge, and other factors. The unit for energy in the International System of Units is the joule, the term potential energy was introduced by the 19th century Scottish engineer and physicist William Rankine, although it has links to Greek philosopher Aristotles concept of potentiality. Potential energy is associated with forces that act on a body in a way that the work done by these forces on the body depends only on the initial and final positions of the body in space. These forces, that are called potential forces, can be represented at every point in space by vectors expressed as gradients of a scalar function called potential. Potential energy is the energy of an object. It is the energy by virtue of a position relative to other objects. Potential energy is associated with restoring forces such as a spring or the force of gravity. The action of stretching the spring or lifting the mass is performed by a force that works against the force field of the potential. This work is stored in the field, which is said to be stored as potential energy. If the external force is removed the field acts on the body to perform the work as it moves the body back to the initial position. Suppose a ball which mass is m, and it is in h position in height, if the acceleration of free fall is g, the weight of the ball is mg. There are various types of energy, each associated with a particular type of force. Chemical potential energy, such as the energy stored in fossil fuels, is the work of the Coulomb force during rearrangement of mutual positions of electrons and nuclei in atoms and molecules. Thermal energy usually has two components, the energy of random motions of particles and the potential energy of their mutual positions. Forces derivable from a potential are also called conservative forces, the work done by a conservative force is W = − Δ U where Δ U is the change in the potential energy associated with the force. The negative sign provides the convention that work done against a force field increases potential energy, common notations for potential energy are U, V, also Ep. Potential energy is closely linked with forces, in this case, the force can be defined as the negative of the vector gradient of the potential field. If the work for a force is independent of the path, then the work done by the force is evaluated at the start
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Kinetic energy
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In physics, the kinetic energy of an object is the energy that it possesses due to its motion. It is defined as the work needed to accelerate a body of a mass from rest to its stated velocity. Having gained this energy during its acceleration, the body maintains this kinetic energy unless its speed changes, the same amount of work is done by the body in decelerating from its current speed to a state of rest. In classical mechanics, the energy of a non-rotating object of mass m traveling at a speed v is 12 m v 2. In relativistic mechanics, this is an approximation only when v is much less than the speed of light. The standard unit of energy is the joule. The adjective kinetic has its roots in the Greek word κίνησις kinesis, the dichotomy between kinetic energy and potential energy can be traced back to Aristotles concepts of actuality and potentiality. The principle in classical mechanics that E ∝ mv2 was first developed by Gottfried Leibniz and Johann Bernoulli, Willem s Gravesande of the Netherlands provided experimental evidence of this relationship. By dropping weights from different heights into a block of clay, Émilie du Châtelet recognized the implications of the experiment and published an explanation. The terms kinetic energy and work in their present scientific meanings date back to the mid-19th century, early understandings of these ideas can be attributed to Gaspard-Gustave Coriolis, who in 1829 published the paper titled Du Calcul de lEffet des Machines outlining the mathematics of kinetic energy. William Thomson, later Lord Kelvin, is given the credit for coining the term kinetic energy c, energy occurs in many forms, including chemical energy, thermal energy, electromagnetic radiation, gravitational energy, electric energy, elastic energy, nuclear energy, and rest energy. These can be categorized in two classes, potential energy and kinetic energy. Kinetic energy is the movement energy of an object, Kinetic energy can be transferred between objects and transformed into other kinds of energy. Kinetic energy may be best understood by examples that demonstrate how it is transformed to, for example, a cyclist uses chemical energy provided by food to accelerate a bicycle to a chosen speed. On a level surface, this speed can be maintained without further work, except to overcome air resistance, the chemical energy has been converted into kinetic energy, the energy of motion, but the process is not completely efficient and produces heat within the cyclist. The kinetic energy in the moving cyclist and the bicycle can be converted to other forms, for example, the cyclist could encounter a hill just high enough to coast up, so that the bicycle comes to a complete halt at the top. The kinetic energy has now largely converted to gravitational potential energy that can be released by freewheeling down the other side of the hill. Since the bicycle lost some of its energy to friction, it never regains all of its speed without additional pedaling, the energy is not destroyed, it has only been converted to another form by friction
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Myosin
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Myosins comprise a superfamily of ATP-dependent motor proteins and are best known for their role in muscle contraction and their involvement in a wide range of other motility processes in eukaryotes. They are responsible for actin-based motility, the term was originally used to describe a group of similar ATPases found in the cells of both striated muscle tissue and smooth muscle tissue. Following the discovery by Pollard and Korn of enzymes with myosin-like function in Acanthamoeba castellanii, virtually all eukaryotic cells contain myosin isoforms. Some isoforms have specialized functions in cell types, while other isoforms are ubiquitous. The structure and function of myosin is strongly conserved across species, most myosin molecules are composed of a head, neck, and tail domain. The head domain binds the actin, and uses ATP hydrolysis to generate force. The neck domain acts as a linker and as an arm for transducing force generated by the catalytic motor domain. The neck domain can also serve as a site for myosin light chains which are distinct proteins that form part of a macromolecular complex. The tail domain generally mediates interaction with cargo molecules and/or other myosin subunits, in some cases, the tail domain may play a role in regulating motor activity. Multiple myosin II molecules generate force in skeletal muscle through a power stroke mechanism fuelled by the energy released from ATP hydrolysis, the power stroke occurs at the release of phosphate from the myosin molecule after the ATP hydrolysis while myosin is tightly bound to actin. The effect of release is a conformational change in the molecule that pulls against the actin. The release of the ADP molecule leads to the rigor state of myosin. The binding of a new ATP molecule will release myosin from actin, ATP hydrolysis within the myosin will cause it to bind to actin again to repeat the cycle. The combined effect of the power strokes causes the muscle to contract. The wide variety of genes found throughout the eukaryotic phyla were named according to different schemes as they were discovered. The nomenclature can therefore be somewhat confusing when attempting to compare the functions of proteins within. Skeletal muscle myosin, the most conspicuous of the myosin superfamily due to its abundance in muscle fibers, was the first to be discovered and this protein makes up part of the sarcomere and forms macromolecular filaments composed of multiple myosin subunits. Similar filament-forming myosin proteins were found in muscle, smooth muscle
31.
Actin
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Actin is a family of globular multi-functional proteins that form microfilaments. It is found in all eukaryotic cells, where it may be present at a concentration of over 100 μM. Many of these processes are mediated by extensive and intimate interactions of actin with cellular membranes, in vertebrates, three main groups of actin isoforms, alpha, beta, and gamma have been identified. The alpha actins, found in tissues, are a major constituent of the contractile apparatus. The beta and gamma actins coexist in most cell types as components of the cytoskeleton and it is believed that the diverse range of structures formed by actin enabling it to fulfill such a large range of functions is regulated through the binding of tropomyosin along the filaments. Other enzymes or organelles such as cilia can be anchored to this scaffolding in order to control the deformation of the cell membrane. It can also produce movement either by itself or with the help of molecular motors, Actin therefore contributes to processes such as the intracellular transport of vesicles and organelles as well as muscular contraction and cellular migration. It therefore plays an important role in embryogenesis, the healing of wounds, the evolutionary origin of actin can be traced to prokaryotic cells, which have equivalent proteins. Actin homologs from prokaryotes and archaea polymerize into different helical or linear filaments consisting of one or multiple strands, however the in-strand contacts and nucleotide binding sites are preserved in prokaryotes and in archaea. Lastly, actin plays an important role in the control of gene expression, a large number of illnesses and diseases are caused by mutations in alleles of the genes that regulate the production of actin or of its associated proteins. The production of actin is also key to the process of infection by some pathogenic microorganisms, mutations in the different genes that regulate actin production in humans can cause muscular diseases, variations in the size and function of the heart as well as deafness. The make-up of the cytoskeleton is also related to the pathogenicity of bacteria and viruses. Actin was first observed experimentally in 1887 by W. D. Halliburton, in 1942, Straub developed a novel technique for extracting muscle protein that allowed him to isolate substantial amounts of relatively pure actin. Straubs method is essentially the same as used in laboratories today. Adding ATP to a mixture of both proteins causes a decrease in viscosity, the hostilities of World War II meant Szent-Gyorgyi and Straub were unable to publish the work in Western scientific journals. Actin therefore only became known in the West in 1945. Straub suggested that the transformation of ATP-bound actin to ADP-bound actin played a role in muscular contraction, in fact, this is true only in smooth muscle, and was not supported through experimentation until 2001. The amino acid sequencing of actin was completed by M. Elzinga, the crystal structure of G-actin was solved in 1990 by Kabsch and colleagues
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Muscle contraction
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Muscle contraction is the activation of tension-generating sites within muscle fibers. The termination of muscle contraction is followed by muscle relaxation, which is a return of the fibers to their low tension-generating state. Muscle contractions can be described based on two variables, length and tension, a muscle contraction is described as isometric if the muscle tension changes but the muscle length remains the same. In contrast, a muscle contraction is isotonic if muscle length changes, if the muscle length shortens, the contraction is concentric, if the muscle length lengthens, the contraction is eccentric. In natural movements that underlie locomotor activity, muscle contractions are multifaceted as they are able to produce changes in length, therefore, neither length nor tension is likely to remain the same in muscles that contract during locomotor activity. In vertebrates, skeletal muscle contractions are neurogenic as they require synaptic input from neurons to produce muscle contractions. A single motor neuron is able to innervate multiple muscle fibers, once innervated, the protein filaments within each skeletal muscle fiber slide past each other to produce a contraction, which is explained by the sliding filament theory. The contraction produced can be described as a twitch, summation, or tetanus, in skeletal muscles, muscle tension is at its greatest when the muscle is stretched to an intermediate length as described by the length-tension relationship. Unlike skeletal muscle, the contractions of smooth and cardiac muscles are myogenic, the mechanisms of contraction in these muscle tissues are similar to those in skeletal muscle tissues. Muscle contractions can be described based on two variables, force and length, force itself can be differentiated as either tension or load. Muscle tension is the force exerted by the muscle on an object whereas a load is the force exerted by an object on the muscle, when muscle tension changes without any corresponding changes in muscle length, the muscle contraction is described as isometric. If the muscle length changes while muscle tension remains the same, in an isotonic contraction, the muscle length can either shorten to produce a concentric contraction or lengthen to produce an eccentric contraction. Furthermore, if the muscle length shortens, the contraction is concentric, but if the muscle length lengthens, then the contraction is eccentric. In natural movements that underlie locomotor activity, muscle contractions are multifaceted as they are able to produce changes in length, therefore, neither length nor tension is likely to remain constant when the muscle is active during locomotor activity. An isometric contraction of a muscle generates tension without changing length, an example can be found when the muscles of the hand and forearm grip an object, the joints of the hand do not move, but muscles generate sufficient force to prevent the object from being dropped. In isotonic contraction, the tension in the muscle remains constant despite a change in muscle length and this occurs when a muscles force of contraction matches the total load on the muscle. In concentric contraction, muscle tension is sufficient to overcome the load, and this occurs when the force generated by the muscle exceeds the load opposing its contraction. During a concentric contraction, a muscle is stimulated to contract according to the sliding filament theory and this occurs throughout the length of the muscle, generating a force at the origin and insertion, causing the muscle to shorten and changing the angle of the joint
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Kilojoule
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The joule, symbol J, is a derived unit of energy in the International System of Units. It is equal to the transferred to an object when a force of one newton acts on that object in the direction of its motion through a distance of one metre. It is also the energy dissipated as heat when a current of one ampere passes through a resistance of one ohm for one second. It is named after the English physicist James Prescott Joule, one joule can also be defined as, The work required to move an electric charge of one coulomb through an electrical potential difference of one volt, or one coulomb volt. This relationship can be used to define the volt, the work required to produce one watt of power for one second, or one watt second. This relationship can be used to define the watt and this SI unit is named after James Prescott Joule. As with every International System of Units unit named for a person, note that degree Celsius conforms to this rule because the d is lowercase. — Based on The International System of Units, section 5.2. The CGPM has given the unit of energy the name Joule, the use of newton metres for torque and joules for energy is helpful to avoid misunderstandings and miscommunications. The distinction may be also in the fact that energy is a scalar – the dot product of a vector force. By contrast, torque is a vector – the cross product of a distance vector, torque and energy are related to one another by the equation E = τ θ, where E is energy, τ is torque, and θ is the angle swept. Since radians are dimensionless, it follows that torque and energy have the same dimensions, one joule in everyday life represents approximately, The energy required to lift a medium-size tomato 1 m vertically from the surface of the Earth. The energy released when that same tomato falls back down to the ground, the energy required to accelerate a 1 kg mass at 1 m·s−2 through a 1 m distance in space. The heat required to raise the temperature of 1 g of water by 0.24 °C, the typical energy released as heat by a person at rest every 1/60 s. The kinetic energy of a 50 kg human moving very slowly, the kinetic energy of a 56 g tennis ball moving at 6 m/s. The kinetic energy of an object with mass 1 kg moving at √2 ≈1.4 m/s, the amount of electricity required to light a 1 W LED for 1 s. Since the joule is also a watt-second and the unit for electricity sales to homes is the kW·h. For additional examples, see, Orders of magnitude The zeptojoule is equal to one sextillionth of one joule,160 zeptojoules is equivalent to one electronvolt. The nanojoule is equal to one billionth of one joule, one nanojoule is about 1/160 of the kinetic energy of a flying mosquito
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Mole (unit)
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The mole is the unit of measurement in the International System of Units for amount of substance. This number is expressed by the Avogadro constant, which has a value of 6. 022140857×1023 mol−1, the mole is one of the base units of the SI, and has the unit symbol mol. The mole is used in chemistry as a convenient way to express amounts of reactants and products of chemical reactions. For example, the chemical equation 2 H2 + O2 →2 H2O implies that 2 moles of dihydrogen and 1 mole of dioxygen react to form 2 moles of water. The mole may also be used to express the number of atoms, ions, the concentration of a solution is commonly expressed by its molarity, defined as the number of moles of the dissolved substance per litre of solution. For example, the relative molecular mass of natural water is about 18.015, therefore. The term gram-molecule was formerly used for essentially the same concept, the term gram-atom has been used for a related but distinct concept, namely a quantity of a substance that contains Avogadros number of atoms, whether isolated or combined in molecules. Thus, for example,1 mole of MgBr2 is 1 gram-molecule of MgBr2 but 3 gram-atoms of MgBr2, in honor of the unit, some chemists celebrate October 23, which is a reference to the 1023 scale of the Avogadro constant, as Mole Day. Some also do the same for February 6 and June 2, thus, by definition, one mole of pure 12C has a mass of exactly 12 g. It also follows from the definition that X moles of any substance will contain the number of molecules as X moles of any other substance. The mass per mole of a substance is called its molar mass, the number of elementary entities in a sample of a substance is technically called its amount. Therefore, the mole is a convenient unit for that physical quantity, one can determine the chemical amount of a known substance, in moles, by dividing the samples mass by the substances molar mass. Other methods include the use of the volume or the measurement of electric charge. The mass of one mole of a substance depends not only on its molecular formula, since the definition of the gram is not mathematically tied to that of the atomic mass unit, the number NA of molecules in a mole must be determined experimentally. The value adopted by CODATA in 2010 is NA =6. 02214129×1023 ±0. 00000027×1023, in 2011 the measurement was refined to 6. 02214078×1023 ±0. 00000018×1023. The number of moles of a sample is the sample mass divided by the mass of the material. The history of the mole is intertwined with that of mass, atomic mass unit, Avogadros number. The first table of atomic mass was published by John Dalton in 1805
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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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Catabolic
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Catabolism is the set of metabolic pathways that breaks down molecules into smaller units that are either oxidized to release energy, or used in other anabolic reactions. Catabolism breaks down molecules into smaller units. Cells use the monomers released from breaking down polymers to construct new polymer molecules, or degrade the monomers further to simple waste products. Cellular wastes include lactic acid, acetic acid, carbon dioxide, ammonia and this molecule acts as a way for the cell to transfer the energy released by catabolism to the energy-requiring reactions that make up anabolism. Catabolism therefore provides the energy necessary for the maintenance and growth of cells. There are many signals that control catabolism, most of the known signals are hormones and the molecules involved in metabolism itself. Endocrinologists have traditionally classified many of the hormones as anabolic or catabolic, the so-called classic catabolic hormones known since the early 20th century are cortisol, glucagon, and adrenaline. In recent decades, many more hormones with at least some catabolic effects have been discovered, including cytokines, orexin, many of these catabolic hormones express an anti-catabolic effect in muscle tissue. One study found that the administration of epinephrine had an anti-proteolytic effect, another study found that catecholamines in general, greatly decreased the rate of muscle catabolism. Autophagy Dehydration synthesis Hydrolysis Nocturnal post absorptive catabolism Psilacetin § Pharmacology Sarcopenia Media related to Catabolism at Wikimedia Commons
37.
Glycolysis
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Glycolysis is the metabolic pathway that converts glucose C6H12O6, into pyruvate, CH3COCOO− + H+. The free energy released in this process is used to form the high-energy molecules ATP, glycolysis is a determined sequence of ten enzyme-catalyzed reactions. The intermediates provide entry points to glycolysis, for example, most monosaccharides, such as fructose and galactose, can be converted to one of these intermediates. The intermediates may also be directly useful, for example, the intermediate dihydroxyacetone phosphate is a source of the glycerol that combines with fatty acids to form fat. Glycolysis is an oxygen independent metabolic pathway, meaning that it not use molecular oxygen for any of its reactions. However the products of glycolysis are sometimes metabolized using atmospheric oxygen, when molecular oxygen is used for the metabolism of the products of glycolysis the process is usually referred to as aerobic, whereas if no oxygen is used the process is said to be anaerobic. Thus, glycolysis occurs, with variations, in all organisms. The wide occurrence of glycolysis indicates that it is one of the most ancient metabolic pathways, glycolysis could thus have originated from chemical constraints of the prebiotic world. Glycolysis occurs in most organisms in the cytosol of the cell, the most common type of glycolysis is the Embden–Meyerhof–Parnas, which was discovered by Gustav Embden, Otto Meyerhof, and Jakub Karol Parnas. Glycolysis also refers to other pathways, such as the Entner–Doudoroff pathway, however, the discussion here will be limited to the Embden–Meyerhof–Parnas pathway. The overall reaction of glycolysis is, The use of symbols in this equation makes it appear unbalanced with respect to oxygen atoms, hydrogen atoms, and charges. In the cellular environment, all three groups of ADP dissociate into −O− and H+, giving ADP3−, and this ion tends to exist in an ionic bond with Mg2+. ATP behaves identically except that it has four groups, giving ATPMg2−. When these differences along with the charges on the two phosphate groups are considered together, the net charges of −4 on each side are balanced. For simple fermentations, the metabolism of one molecule of glucose to two molecules of pyruvate has a net yield of two molecules of ATP, most cells will then carry out further reactions to repay the used NAD+ and produce a final product of ethanol or lactic acid. Many bacteria use inorganic compounds as hydrogen acceptors to regenerate the NAD+, cells performing aerobic respiration synthesize much more ATP, but not as part of glycolysis. These further aerobic reactions use pyruvate and NADH + H+ from glycolysis, the pathway of glycolysis as it is known today took almost 100 years to fully discover. The combined results of many experiments were required in order to understand the pathway as a whole
38.
Citric acid cycle
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Its central importance to many biochemical pathways suggests that it was one of the earliest established components of cellular metabolism and may have originated abiogenically. The name of this pathway is derived from citric acid that is consumed. In addition, the cycle consumes acetate and water, reduces NAD+ to NADH, the NADH generated by the TCA cycle is fed into the oxidative phosphorylation pathway. The net result of two closely linked pathways is the oxidation of nutrients to produce usable chemical energy in the form of ATP. In eukaryotic cells, the citric acid cycle occurs in the matrix of the mitochondrion, components of the TCA cycle were derived from anaerobic bacteria, and the TCA cycle itself may have evolved more than once. Theoretically there are alternatives to the TCA cycle, however. If several TCA alternatives had evolved independently, they all appear to have converged to the TCA cycle, the citric acid cycle is a key metabolic pathway that connects carbohydrate, fat, and protein metabolism. The reactions of the cycle are carried out by 8 enzymes that completely oxidize acetate, in the form of acetyl-CoA, through catabolism of sugars, fats, and proteins, the two-carbon organic product acetyl-CoA is produced which enters the citric acid cycle. The NADH and FADH2 generated by the citric acid cycle are in used by the oxidative phosphorylation pathway to generate energy-rich adenosine triphosphate. Acetyl-CoA may also be obtained from the oxidation of fatty acids, the citrate then goes through a series of chemical transformations, losing two carboxyl groups as CO2. The carbons lost as CO2 originate from what was oxaloacetate, not directly from acetyl-CoA, the carbons donated by acetyl-CoA become part of the oxaloacetate carbon backbone after the first turn of the citric acid cycle. Loss of the acetyl-CoA-donated carbons as CO2 requires several turns of the citric acid cycle. However, because of the role of the citric acid cycle in anabolism, they not be lost. Most of the energy available by the oxidative steps of the cycle is transferred as energy-rich electrons to NAD+. For each acetyl group that enters the citric cycle, three molecules of NADH are produced. Electrons are also transferred to the electron acceptor Q, forming QH2, at the end of each cycle, the four-carbon oxaloacetate has been regenerated, and the cycle continues. Two carbon atoms are oxidized to CO2, the energy from these reactions is transferred to other processes through GTP. The NADH generated in the TCA cycle may later be oxidized to drive ATP synthesis in a type of process called oxidative phosphorylation, FADH2 is covalently attached to succinate dehydrogenase, an enzyme which functions both in the CAC and the mitochondrial electron transport chain in oxidative phosphorylation
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. PMID 22199166.