Excretion is a process by which metabolic waste is eliminated from an organism. In vertebrates this is carried out by the lungs and skin; this is in contrast with secretion, where the substance may have specific tasks after leaving the cell. Excretion is an essential process in all forms of life. For example, in mammals urine is expelled through the urethra, part of the excretory system. In unicellular organisms, waste products are discharged directly through the surface of the cell. During life activities such as cellular respiration, several chemical reactions take place in the body; these are known as metabolism. These chemical reactions produce waste products such as carbon dioxide, salts and uric acid. Accumulation of these wastes beyond a level inside the body is harmful to the body; the excretory organs remove these wastes. This process of removal of metabolic waste from the body is known as excretion. Green plants produce carbon water as respiratory products. In green plants, the carbon dioxide released during respiration gets utilized during photosynthesis.
Oxygen is a by product generated during photosynthesis, exits through stomata, root cell walls, other routes. Plants can get rid of excess water by guttation, it has been shown that the leaf acts as an'excretophore' and, in addition to being a primary organ of photosynthesis, is used as a method of excreting toxic wastes via diffusion. Other waste materials that are exuded by some plants — resin, latex, etc. are forced from the interior of the plant by hydrostatic pressures inside the plant and by absorptive forces of plant cells. These latter processes do not need added energy, they act passively. However, during the pre-abscission phase, the metabolic levels of a leaf are high. Plants excrete some waste substances into the soil around them. In animals, the main excretory products are carbon dioxide, urea, uric acid and creatine; the liver and kidneys clear many substances from the blood, the cleared substances are excreted from the body in the urine and feces. Aquatic animals excrete ammonia directly into the external environment, as this compound has high solubility and there is ample water available for dilution.
In terrestrial animals ammonia-like compounds are converted into other nitrogenous materials as there is less water in the environment and ammonia itself is toxic. Birds excrete their nitrogenous wastes as uric acid in the form of a paste. Although this process is metabolically more expensive, it allows more efficient water retention and it can be stored more in the egg. Many avian species seabirds, can excrete salt via specialized nasal salt glands, the saline solution leaving through nostrils in the beak. In insects, a system involving Malpighian tubules is utilized to excrete metabolic waste. Metabolic waste diffuses or is transported into the tubule, which transports the wastes to the intestines; the metabolic waste is released from the body along with fecal matter. The excreted material may be called ejecta. In pathology the word ejecta is more used. UAlberta.ca, Animation of excretion Brian J Ford on leaf fall in Nature
Tar is a dark brown or black viscous liquid of hydrocarbons and free carbon, obtained from a wide variety of organic materials through destructive distillation. Tar can be produced from coal, petroleum, or peat. Production and trade in pine-derived tar was a major contributor in the economies of Northern Europe and Colonial America, its main use was in preserving wooden sailing vessels against rot. The largest user was the Royal Navy of the United Kingdom. Demand for tar declined with the advent of steel ships. Tar-like products can be produced from other forms of organic matter, such as peat. Mineral products resembling tar can be produced from fossil hydrocarbons, such as petroleum. Coal tar is produced from coal as a byproduct of coke production. "Tar" and "pitch" can be used interchangeably. There is a tendency to use "tar" for "pitch" for more solid substances. Both "tar" and "pitch" are applied to viscous forms of asphalt, such as the asphalt found in occurring tar pits. "Rangoon tar" known as "Burmese oil" or "Burmese naphtha", is a form of petroleum.
Oil sands exclusively produced in Alberta, are colloquially referred to as "tar sands" but are in fact composed of bitumen. Note, similar heavy crude grades from Venezuela are not referred to as "tar sands" by Wikipedia or the environmental community. In Northern Europe, the word "tar" refers to a substance, derived from the wood and roots of pine. In earlier times it was used as a water repellent coating for boats and roofs, it is still used as an additive in the flavoring of candy and other foods. Wood tar is microbicidal. Producing tar from wood was known in ancient Greece and has been used in Scandinavia since the Iron Age. For centuries, dating back at least to the 14th century, tar was among Sweden's most important exports. Sweden exported 13,000 barrels of tar in 1615 and 227,000 barrels in the peak year of 1863. Production nearly stopped in the early 20th century, when other chemicals replaced tar, wooden ships were replaced by steel ships. Traditional wooden boats are still sometimes tarred.
The heating of pine wood causes pitch to drip away from the wood and leave behind charcoal. Birch bark is used to make fine tar, known as "Russian oil", suitable for leather protection; the by-products of wood tar are charcoal. When deciduous tree woods are subjected to destructive distillation, the products are methanol and charcoal. Tar kilns are dry distillation ovens used in Scandinavia for producing tar from wood, they were built close from limestone or from more primitive holes in the ground. The bottom is sloped into an outlet hole to allow the tar to pour out; the wood is split into dimensions of a finger, stacked densely, covered tight with dirt and moss. If oxygen can enter, the wood might catch fire, the production would be ruined. On top of this, a fire lit. After a few hours, the tar continues to do so for a few days. Tar was used as tar paper and to seal the hulls of ships and boats. For millennia, wood tar was used to waterproof sails and boats, but today, sails made from inherently waterproof synthetic substances have reduced the demand for tar.
Wood tar is still used to seal traditional wooden boats and the roofs of historical shingle-roofed churches, as well as painting exterior walls of log buildings. Tar is a general disinfectant. Pine tar oil, or wood tar oil, is used for the surface treatment of wooden shingle roofs, boats and tubs and in the medicine and rubber industries. Pine tar has good penetration on the rough wood. An old wood tar oil recipe for the treatment of wood is one-third each genuine wood tar, balsam turpentine, boiled or raw linseed oil or Chinese tung oil. In Finland, wood tar was once considered a panacea reputed to heal "even those cut in twain through their midriff". A Finnish proverb states that "if sauna and tar won't help, the disease is fatal." Wood tar is used in traditional Finnish medicine because of its microbicidal properties. Wood tar is available diluted as tar water, which has numerous uses: As a flavoring for candies and alcohol; as a spice for food, like meat. As a scent for saunas. Tar water is mixed into water, turned into steam in the sauna.
As an anti-dandruff agent in shampoo. As a component of cosmetics. Mixing tar with linseed oil varnish produces tar paint. Tar paint has a translucent brownish hue and can be used to saturate and tone wood and protect it from weather. Tar paint can be toned with various pigments, producing translucent colors and preserving the wood texture. In English and French, "tar" is a substance derived from coal, it was one of the products of gasworks. Tar made from coal or petroleum is considered toxic and carcinogenic because of its high benzene content, though coal tar in low concentrations is used as a topical medicine. Coal and petroleum tar has a pungent odour. Coal tar is listed at number 1999 in the United Nations list of dangerous goods. Bitumen Creosote Pitch Pitch drop experiment Resin Rollins Tars Tarring and feathering Tar Heels Tar pit Tarmac Tar tar ^ "Geotimes – February 2005 – Mummy tar in ancient Egypt". Retrieved January 9, 2006. Details history and uses of "Rangoon Tar"
Regulation of therapeutic goods
The regulation of therapeutic goods, drugs and therapeutic devices, varies by jurisdiction. In some countries, such as the United States, they are regulated at the national level by a single agency. In other jurisdictions they are regulated at the state level, or at both state and national levels by various bodies, as is the case in Australia; the role of therapeutic goods regulation is designed to protect the health and safety of the population. Regulation is aimed at ensuring the safety and efficacy of the therapeutic goods which are covered under the scope of the regulation. In most jurisdictions, therapeutic goods must be registered. There is some degree of restriction of the availability of certain therapeutic goods depending on their risk to consumers. Modern drug regulation has historical roots in the response to the proliferation of universal antidotes which appeared in the wake of Mithridates' death. Mithridates had brought together physicians and shamans to concoct a potion that would make him immune to poisons.
Following his death, the Romans became keen on further developing the Mithridates potion's recipe. Mithridatium re-entered western society through multiple means; the first was through the Leechbook of the Bald, written somewhere between 900 and 950, which contained a formula for various remedies, including for a theriac. Additionally, theriac became a commercial good traded throughout Europe based on the works of Greek and Roman physicians; the resulting proliferation of various recipes needed to be curtailed in order to ensure that people were not passing off fake antidotes, which led to the development of government involvement and regulation. Additionally, the creation of these concoctions took on ritualistic form and were created in public and the process was observed and recorded, it was believed that if the concoction proved unsuccessful, it was due to the apothecaries’ process of making them and they could be held accountable because of the public nature of the creation. In the 9th century, many Muslim countries established an office of the hisba, which in addition to regulating compliance to Islamic principles and values took on the role of regulating other aspects of social and economic life, including the regulation of medicines.
Inspectors were appointed to employ oversight on those who were involved in the process of medicine creation and were given a lot of leigh weigh to ensure compliance and punishments were stringent. The first official'act', the'Apothecary Wares and Stuffs' Act was passed in 1540 by Henry VIII and set the foundation for others. Through this act, he encouraged physicians in his College of Physicians to appoint four people dedicated to inspecting what was being sold in apothecary shops. In conjunction with this first piece of legislation, there was an emergence of standard formulas for the creation of certain ‘drugs’ and ‘antidotes’ through Pharmacopoeias which first appeared in the form of a decree from Frederick II of Sicily in 1240 to use consistent and standard formulas; the first modern pharmacopoeias were the Florence Pharmacopoeia published in 1498, the Spanish Pharmacopoeia published in 1581 and the London Pharmacopoeia published in 1618. In the United States, regulation of drugs was a state right, as opposed to federal right.
But with the increase in fraudulent practices due to private incentives to maximize profits and poor enforcement of state laws, increased the need for stronger federal regulation. President Roosevelt signed the Federal Food and Drug Act in 1906 which established stricter standards. A 1911 Supreme Court decision, United States vs. Johnson, established that misleading statements were not covered under the FFDA; this directly led to Congress passing the Sherley Amendment which established a clearer definition of ‘misbranded’. Another key catalyst for advances in drug regulation were certain catastrophes that served as calls to the government to step in and impose regulations that would prevent repeats of those instances. One such instance occurred in 1937 when more than a hundred people died from using sulfanilamide elixir which had not gone through any safety testing; this directly led to the passing of the Federal, Food and Cosmetic Act in 1938. One other major catastrophe occurred in the late 1950s when Thalidomide, sold in Germany and sold around the world, led to 100,000 babies being born with various deformities.
The UK's Chief Medical Officer had established a group to look into safety of drugs on the market in 1959 prior to the crisis and was moving in the direction of address the problem of unregulated drugs entering the market. The crisis created a greater sense of emergency to establish safety and efficacy standards around the world; the UK started a temporary Committee on Safety of Drugs while they attempted to pass more comprehensive legislation. Though compliance and submission of drugs to the Committee on Safety of Drugs was not mandatory after, the pharmaceutical industry larger complied due to the thalidomide situation; the European Economic Commission passed a directive in 1965 in order to impose greater efficacy standards before marketing a drug. The United States congress passed the Drug Amendments Act of 1962 The Drug Amendments Act required the FDA to ensure that new drugs being introduced to the market had passed certain tests and standards. Both the EU and US acts introduced the requirements to ensure efficacy.
Of note, increased regulations and standards for testing led to greater innovation in pharm
The Jmol applet, among other abilities, offers an alternative to the Chime plug-in, no longer under active development. While Jmol has many features that Chime lacks, it does not claim to reproduce all Chime functions, most notably, the Sculpt mode. Chime requires plug-in installation and Internet Explorer 6.0 or Firefox 2.0 on Microsoft Windows, or Netscape Communicator 4.8 on Mac OS 9. Jmol operates on a wide variety of platforms. For example, Jmol is functional in Mozilla Firefox, Internet Explorer, Google Chrome, Safari. Chemistry Development Kit Comparison of software for molecular mechanics modeling Jmol extension for MediaWiki List of molecular graphics systems Molecular graphics Molecule editor Proteopedia PyMOL SAMSON Official website Wiki with listings of websites and moodles Willighagen, Egon. "Fast and Scriptable Molecular Graphics in Web Browsers without Java3D". Doi:10.1038/npre.2007.50.1
In chemistry, a radical is an atom, molecule, or ion that has an unpaired valence electron. With some exceptions, these unpaired electrons make radicals chemically reactive. Many radicals spontaneously dimerize. Most organic radicals have short lifetimes. A notable example of a radical is the hydroxyl radical, a molecule that has one unpaired electron on the oxygen atom. Two other examples are triplet triplet carbene which have two unpaired electrons. Radicals may be generated in a number of ways. Ionizing radiation, electrical discharges, electrolysis are known to produce radicals. Radicals are intermediates in many chemical reactions, more so than is apparent from the balanced equations. Radicals are important in combustion, atmospheric chemistry, plasma chemistry and many other chemical processes. A large fraction of natural products is generated by radical-generating enzymes. In living organisms, the radicals superoxide and nitric oxide and their reaction products regulate many processes, such as control of vascular tone and thus blood pressure.
They play a key role in the intermediary metabolism of various biological compounds. Such radicals can be messengers in a process dubbed redox signaling. A radical may be otherwise bound. In chemical equations, radicals are denoted by a dot placed to the right of the atomic symbol or molecular formula as follows: C l 2 → U V 2 C l ⋅ Radical reaction mechanisms use single-headed arrows to depict the movement of single electrons: The homolytic cleavage of the breaking bond is drawn with a'fish-hook' arrow to distinguish from the usual movement of two electrons depicted by a standard curly arrow; the second electron of the breaking bond moves to pair up with the attacking radical electron. Radicals take part in radical addition and radical substitution as reactive intermediates. Chain reactions involving radicals can be divided into three distinct processes; these are initiation and termination. Initiation reactions are those, they may involve the formation of radicals from stable species as in Reaction 1 above or they may involve reactions of radicals with stable species to form more radicals.
Propagation reactions are those reactions involving radicals in which the total number of radicals remains the same. Termination reactions are those reactions resulting in a net decrease in the number of radicals. Two radicals combine to form a more stable species, for example: 2Cl·→ Cl2 Radicals can form by breaking of covalent bonds by homolysis; the homolytic bond dissociation energies abbreviated as "ΔH °" are a measure of bond strength. Splitting H2 into 2H•, for example, requires a ΔH ° of +435 kJ·mol-1, while splitting Cl2 into 2Cl• requires a ΔH ° of +243 kJ·mol-1. For weak bonds, homolysis can be induced thermally. Strong bonds require high energy photons or flames to induce homolysis. Radicals or charged species add to non-radicals to give new radicals; this process is the basis of the radical chain reaction. Being prevalent and a diradical, O2 reacts with many organic compounds to generate radicals together with the hydroperoxide radical; this process is related to rancidification of unsaturated fats.
Radicals may be formed by single-electron oxidation or reduction of an atom or molecule. These redox reactions occur in electrochemical cells and in ionization chambers of mass spectrometers. Although radicals are short-lived due to their reactivity, there are long-lived radicals; these are categorized as follows: The prime example of a stable radical is molecular dioxygen. Another common example is nitric oxide. Organic radicals can be long lived if they occur in a conjugated π system, such as the radical derived from α-tocopherol. There are hundreds of examples of thiazyl radicals, which show low reactivity and remarkable thermodynamic stability with only a limited extent of π resonance stabilization. Persistent radical compounds are those whose longevity is due to steric crowding around the radical center, which makes it physically difficult for the radical to react with another molecule. Examples of these include Gomberg's triphenylmethyl radical, Fremy's salt, such as TEMPO, TEMPOL, nitronyl nitroxides, azephenylenyls and radicals derived from PTM and TTM.
Persistent radicals are generated in great quantity during combustion, "may be responsible for the oxidative stress resulting in cardiopulmonary disease and cancer, attributed to exposure to airborne fine particles". Gomberg's free radical can be generated by following reaction in lab - 3C-Cl + Ag === 3C• + AgCl The reason for persistivity of free radicals is either the delocalisation of unpaired electron or the unavailability of unpaired electron to other species due to the screening of neighbouring atoms/groups. Diradicals are molecules containing two radical centers. Multiple radical centers can exist in a molecule. Atmospheric oxygen exists as a diradical in its ground state as triplet oxygen; the low reactivity of atmospheric oxygen is due to its diradical state. Non-radical states of dioxygen are less stable tha
Drug metabolism is the metabolic breakdown of drugs by living organisms through specialized enzymatic systems. More xenobiotic metabolism is the set of metabolic pathways that modify the chemical structure of xenobiotics, which are compounds foreign to an organism's normal biochemistry, such as any drug or poison; these pathways are a form of biotransformation present in all major groups of organisms, are considered to be of ancient origin. These reactions act to detoxify poisonous compounds; the study of drug metabolism is called pharmacokinetics. The metabolism of pharmaceutical drugs is an important aspect of medicine. For example, the rate of metabolism determines the duration and intensity of a drug's pharmacologic action. Drug metabolism affects multidrug resistance in infectious diseases and in chemotherapy for cancer, the actions of some drugs as substrates or inhibitors of enzymes involved in xenobiotic metabolism are a common reason for hazardous drug interactions; these pathways are important in environmental science, with the xenobiotic metabolism of microorganisms determining whether a pollutant will be broken down during bioremediation, or persist in the environment.
The enzymes of xenobiotic metabolism the glutathione S-transferases are important in agriculture, since they may produce resistance to pesticides and herbicides. Drug metabolism is divided into three phases. In phase I, enzymes such as cytochrome P450 oxidases introduce reactive or polar groups into xenobiotics; these modified compounds are conjugated to polar compounds in phase II reactions. These reactions are catalysed by transferase enzymes such as glutathione S-transferases. In phase III, the conjugated xenobiotics may be further processed, before being recognised by efflux transporters and pumped out of cells. Drug metabolism converts lipophilic compounds into hydrophilic products that are more excreted; the exact compounds an organism is exposed to will be unpredictable, may differ over time. The major challenge faced by xenobiotic detoxification systems is that they must be able to remove the almost-limitless number of xenobiotic compounds from the complex mixture of chemicals involved in normal metabolism.
The solution that has evolved to address this problem is an elegant combination of physical barriers and low-specificity enzymatic systems. All organisms use cell membranes as hydrophobic permeability barriers to control access to their internal environment. Polar compounds cannot diffuse across these cell membranes, the uptake of useful molecules is mediated through transport proteins that select substrates from the extracellular mixture; this selective uptake means that most hydrophilic molecules cannot enter cells, since they are not recognised by any specific transporters. In contrast, the diffusion of hydrophobic compounds across these barriers cannot be controlled, organisms, cannot exclude lipid-soluble xenobiotics using membrane barriers. However, the existence of a permeability barrier means that organisms were able to evolve detoxification systems that exploit the hydrophobicity common to membrane-permeable xenobiotics; these systems therefore solve the specificity problem by possessing such broad substrate specificities that they metabolise any non-polar compound.
Useful metabolites are excluded since they are polar, in general contain one or more charged groups. The detoxification of the reactive by-products of normal metabolism cannot be achieved by the systems outlined above, because these species are derived from normal cellular constituents and share their polar characteristics. However, since these compounds are few in number, specific enzymes can remove them. Examples of these specific detoxification systems are the glyoxalase system, which removes the reactive aldehyde methylglyoxal, the various antioxidant systems that eliminate reactive oxygen species; the metabolism of xenobiotics is divided into three phases:- modification and excretion. These reactions act in concert to remove them from cells. In phase I, a variety of enzymes act to introduce polar groups into their substrates. One of the most common modifications is hydroxylation catalysed by the cytochrome P-450-dependent mixed-function oxidase system; these enzyme complexes act to incorporate an atom of oxygen into nonactivated hydrocarbons, which can result in either the introduction of hydroxyl groups or N-, O- and S-dealkylation of substrates.
The reaction mechanism of the P-450 oxidases proceeds through the reduction of cytochrome-bound oxygen and the generation of a highly-reactive oxyferryl species, according to the following scheme: O2 + NADPH + H+ + RH → NADP+ + H2O + ROHPhase I reactions may occur by oxidation, hydrolysis, cyclization and addition of oxygen or removal of hydrogen, carried out by mixed function oxidases in the liver. These oxidative reactions involve a cytochrome P450 monooxygenase, NADPH and oxygen; the classes of pharmaceutical drugs that utilize this method for their metabolism include phenothiazines and steroids. If the metabolites of phase I reactions are sufficiently polar, they may be excreted at this point. However, many phase I products are not eliminated and undergo a subsequent reaction in which an endogenous substrate combines with the newly incorporated functional group to
Simplified molecular-input line-entry system
The simplified molecular-input line-entry system is a specification in the 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 been extended. In 2007, an open standard called. Other linear notations include the Wiswesser line notation, ROSDAL, SYBYL Line Notation; the original SMILES specification was initiated by David Weininger at the USEPA Mid-Continent Ecology Division Laboratory in Duluth in the 1980s. Acknowledged for their parts in the early development were "Gilman Veith and Rose Russo and Albert Leo and Corwin Hansch for supporting the work, Arthur Weininger and Jeremy Scofield for assistance in programming the system." The Environmental Protection Agency funded the initial project to develop SMILES. It has since been modified and extended by others, most notably by Daylight Chemical Information Systems.
In 2007, an open 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 considered to have the advantage of being more human-readable than InChI; the term SMILES refers to a line notation for encoding molecular structures and specific instances should be called SMILES strings. However, the term SMILES is commonly used to refer to both a single SMILES string and a number of SMILES strings; the terms "canonical" and "isomeric" can lead to some confusion when applied to SMILES. The terms are not mutually exclusive. A number of 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; this SMILES is unique for each structure, although dependent on the canonicalization algorithm used to generate it, is termed the canonical SMILES.
These algorithms first convert the SMILES to an internal representation of the molecular structure. Various algorithms for generating canonical SMILES have been developed and include those by Daylight Chemical Information Systems, OpenEye Scientific Software, MEDIT, Chemical Computing Group, MolSoft LLC, the Chemistry Development Kit. A common application of canonical SMILES is indexing and ensuring uniqueness of molecules in a database; the original paper that described the CANGEN algorithm claimed to generate unique SMILES strings for graphs representing molecules, but the algorithm fails for a number of simple cases and cannot be considered a correct method for representing a graph canonically. There is 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, double bond geometry; these are structural features that cannot be specified by connectivity alone and SMILES which encode this information are termed isomeric SMILES.
A notable feature of these rules is. The term isomeric SMILES is applied to SMILES in which isotopes are specified. In terms of a graph-based computational procedure, SMILES is a string obtained by printing the symbol nodes encountered in a depth-first tree traversal of a chemical graph; the chemical graph is first trimmed to remove hydrogen atoms and cycles are broken to turn it into a spanning tree. Where cycles have been broken, numeric suffix labels are included to indicate the connected nodes. Parentheses are used to indicate points of branching on the tree; the resultant SMILES form depends on the choices: of the bonds chosen to break cycles, of the starting atom used for the depth-first traversal, of the order in which branches are listed when encountered. Atoms are represented by the standard abbreviation of the chemical elements, in square brackets, such as for gold. Brackets may be omitted in the common case of atoms which: are in the "organic subset" of B, C, N, O, P, S, F, Cl, Br, or I, have no formal charge, have the number of hydrogens attached implied by the SMILES valence model, are the normal isotopes, are not chiral centers.
All other elements must be enclosed in brackets, have charges and hydrogens shown explicitly. For instance, the SMILES for water may be written as either O or. Hydrogen may be written as a separate atom; when brackets are used, the symbol H is added if the atom in brackets is bonded to one or more hydrogen, followed by the number of hydrogen atoms if greater than 1 by the sign + for a positive charge or by - for a negative charge. For example, for ammonium. If there is more than one charge, it is written as digit.