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Alloy The introduction of the blast furnace to Europe in the Middle Ages meant that people could produce pig iron in much higher volumes than wrought iron. Because pig iron could be melted, people began to develop processes to reduce carbon in liquid pig iron to create steel. Puddling had been used in China since the first century, and was introduced in Europe during the 1700s, where molten pig iron was stirred while exposed to the air, to remove the carbon by oxidation. In 1858, Henry Bessemer developed a process of steel-making by blowing hot air through liquid pig iron to reduce the carbon content. The Bessemer process led to the first large scale manufacture of steel. Steel is an alloy of iron and carbon, but the term "alloy steel" usually only refers to steels that contain other elements— like vanadium, molybdenum, or cobalt—in amounts sufficient to alter the properties of the base steel. Since ancient times, when steel was used primarily for tools and weapons, the methods of producing and working the metal were often closely guarded secrets. Even long after the Age of reason, the steel industry was very competitive and manufacturers went through great lengths to keep their processes confidential, resisting any attempts to scientifically analyze the material for fear it would reveal their methods. For example, the people of Sheffield, a center of steel production in England, were known to routinely bar visitors and tourists from entering town to deter industrial espionage | https://en.wikipedia.org/wiki?curid=1187 |
Alloy Thus, almost no metallurgical information existed about steel until 1860. Because of this lack of understanding, steel was not generally considered an alloy until the decades between 1930 and 1970 (primarily due to the work of scientists like William Chandler Roberts-Austen, Adolf Martens, and Edgar Bain), so "alloy steel" became the popular term for ternary and quaternary steel-alloys. After Benjamin Huntsman developed his crucible steel in 1740, he began experimenting with the addition of elements like manganese (in the form of a high-manganese pig-iron called "spiegeleisen"), which helped remove impurities such as phosphorus and oxygen; a process adopted by Bessemer and still used in modern steels (albeit in concentrations low enough to still be considered carbon steel). Afterward, many people began experimenting with various alloys of steel without much success. However, in 1882, Robert Hadfield, being a pioneer in steel metallurgy, took an interest and produced a steel alloy containing around 12% manganese. Called mangalloy, it exhibited extreme hardness and toughness, becoming the first commercially viable alloy-steel. Afterward, he created silicon steel, launching the search for other possible alloys of steel. Robert Forester Mushet found that by adding tungsten to steel it could produce a very hard edge that would resist losing its hardness at high temperatures. "R. Mushet's special steel" (RMS) became the first high-speed steel | https://en.wikipedia.org/wiki?curid=1187 |
Alloy Mushet's steel was quickly replaced by tungsten carbide steel, developed by Taylor and White in 1900, in which they doubled the tungsten content and added small amounts of chromium and vanadium, producing a superior steel for use is lathes and machining tools. In 1903 the Wright brothers used a chromium-nickel steel to make the crankshaft for their airplane engine, while in 1908 Henry Ford began using vanadium steels for parts like crankshafts and valves in his Model T Ford, due to their higher strength and resistance to high temperatures. In 1912, the Krupp Ironworks in Germany developed a rust-resistant steel by adding 21% chromium and 7% nickel, producing the first stainless steel. Nonferrous alloys contain no appreciable amounts of iron. The first alloys, bronze and brass, were used for thousands of years, along with lead alloys, pewter and others—but these were all made from metals that were fairly non-reactive and could be smelted over open flames. In the 18th century, Antoine Lavoisier helped to establish the oxygen theory of combustion, displacing the defunct phlogiston theory that had ruled since the late Middle Ages. The oxygen theory helped correctly explain the phenomenon of things like oxidation of metals (i.e., rust) and how rocky ores transform into metals when heated. Lavoisier predicted that many of the earths, salts, and alkalis—for example in alum, a salt used since antiquity—contained metallic bases that were too reactive to oxygen to smelt by the usual methods | https://en.wikipedia.org/wiki?curid=1187 |
Alloy His work eventually led to the periodic table of elements, which helped confirm the existence of these "missing metals." Due to their high reactivity, most metals were not discovered until the 19th century. A method for extracting aluminium from bauxite was proposed by Humphry Davy in 1807, using an electric arc. Although his attempts were unsuccessful, by 1855 the first sales of pure aluminium reached the market. However, as extractive metallurgy was still in its infancy, most aluminium extraction-processes produced unintended alloys contaminated with other elements found in the ore; the most abundant of which was copper. These aluminium-copper alloys (at the time termed "aluminum bronze") preceded pure aluminium, offering greater strength and hardness over the soft, pure metal, and to a slight degree were found to be heat treatable. However, due to their softness and limited hardenability these alloys found little practical use, and were more of a novelty, until the Wright brothers used an aluminium alloy to construct the first airplane engine in 1903. During the time between 1865 and 1910, processes for extracting many other metals were discovered, such as chromium, vanadium, tungsten, iridium, cobalt, and molybdenum, and various alloys were developed. Prior to 1910, research mainly consisted of private individuals tinkering in their own laboratories | https://en.wikipedia.org/wiki?curid=1187 |
Alloy However, as the aircraft and automotive industries began growing, research into alloys became an industrial effort in the years following 1910, as new magnesium alloys were developed for pistons and wheels in cars, and pot metal for levers and knobs, and aluminium alloys developed for airframes and aircraft skins were put into use. In 1906, precipitation hardening alloys were discovered by Alfred Wilm. Precipitation hardening alloys, such as certain alloys of aluminium, titanium, and copper, are heat-treatable alloys that soften when quenched (cooled quickly), and then harden over time. Wilm had been searching for a way to harden aluminium alloys for use in machine-gun cartridge cases. Knowing that aluminium-copper alloys were heat-treatable to some degree, Wilm tried quenching a ternary alloy of aluminium, copper, and the addition of magnesium, but was initially disappointed with the results. However, when Wilm retested it the next day he discovered that the alloy increased in hardness when left to age at room temperature, and far exceeded his expectations. Although an explanation for the phenomenon was not provided until 1919, duralumin was one of the first "age hardening" alloys used, becoming the primary building material for the first Zeppelins, and was soon followed by many others. Because they often exhibit a combination of high strength and low weight, these alloys became widely used in many forms of industry, including the construction of modern aircraft. | https://en.wikipedia.org/wiki?curid=1187 |
Allotropy or allotropism () is the property of some chemical elements to exist in two or more different forms, in the same physical state, known as allotropes of the elements. Allotropes are different structural modifications of an element; the atoms of the element are bonded together in a different manner. For example, the allotropes of carbon include diamond (the carbon atoms are bonded together in a tetrahedral lattice arrangement), graphite (the carbon atoms are bonded together in sheets of a hexagonal lattice), graphene (single sheets of graphite), and fullerenes (the carbon atoms are bonded together in spherical, tubular, or ellipsoidal formations). The term "allotropy" is used for elements only, not for compounds. The more general term, used for any crystalline material, is polymorphism. refers only to different forms of an element within the same phase (i.e.: solid, liquid or gas states); the differences between these states would not alone constitute examples of allotropy. For some elements, allotropes have different molecular formulae despite difference in phase; for example, two allotropes of oxygen (dioxygen, O, and ozone, O) can both exist in the solid, liquid and gaseous states. Other elements do not maintain distinct allotropes in different phases; for example, phosphorus has numerous solid allotropes, which all revert to the same P form when melted to the liquid state. The concept of allotropy was originally proposed in 1841 by the Swedish scientist Baron Jöns Jakob Berzelius (1779–1848) | https://en.wikipedia.org/wiki?curid=1839 |
Allotropy The term is derived . After the acceptance of Avogadro's hypothesis in 1860, it was understood that elements could exist as polyatomic molecules, and two allotropes of oxygen were recognized as O and O. In the early 20th century, it was recognized that other cases such as carbon were due to differences in crystal structure. By 1912, Ostwald noted that the allotropy of elements is just a special case of the phenomenon of polymorphism known for compounds, and proposed that the terms allotrope and allotropy be abandoned and replaced by polymorph and polymorphism. Although many other chemists have repeated this advice, IUPAC and most chemistry texts still favour the usage of allotrope and allotropy for elements only. Allotropes are different structural forms of the same element and can exhibit quite different physical properties and chemical behaviours. The change between allotropic forms is triggered by the same forces that affect other structures, i.e., pressure, light, and temperature. Therefore, the stability of the particular allotropes depends on particular conditions. For instance, iron changes from a body-centered cubic structure (ferrite) to a face-centered cubic structure (austenite) above 906 °C, and tin undergoes a modification known as tin pest from a metallic form to a semiconductor form below 13.2 °C (55.8 °F). As an example of allotropes having different chemical behaviour, ozone (O) is a much stronger oxidizing agent than dioxygen (O) | https://en.wikipedia.org/wiki?curid=1839 |
Allotropy Typically, elements capable of variable coordination number and/or oxidation states tend to exhibit greater numbers of allotropic forms. Another contributing factor is the ability of an element to catenate. Examples of allotropes include: Among the metallic elements that occur in nature in significant quantities (56 up to U, without Tc and Pm), almost half (27) are allotropic at ambient pressure: Li, Be, Na, Ca, Ti, Mn, Fe, Co, Sr, Y, Zr, Sn, La, Ce, Pr, Nd, Sm, Gd, Tb, Dy, Yb, Hf, Tl, Th, Pa and U. Some phase transitions between allotropic forms of technologically relevant metals are those of Ti at 882 °C, Fe at 912 °C and 1394 °C, Co at 422 °C, Zr at 863 °C, Sn at 13 °C and U at 668 °C and 776 °C. In 2017, the concept of nanoallotropy was proposed by Prof. Rafal Klajn of the Organic Chemistry Department of the Weizmann Institute of Science. Nanoallotropes, or allotropes of nanomaterials, are nanoporous materials that have the same chemical composition (e.g., Au), but differ in their architecture at the nanoscale (that is, on a scale 10 to 100 times the dimensions of individual atoms). Such nanoallotropes may help create ultra-small electronic devices and find other industrial applications. The different nanoscale architectures translate into different properties, as was demonstrated for surface-enhanced Raman scattering performed on several different nanoallotropes of gold. A two-step method for generating nanoallotropes was also created. | https://en.wikipedia.org/wiki?curid=1839 |
Acid–base reaction An acid–base reaction is a chemical reaction that occurs between an acid and a base. It can be used to determine pH. Several theoretical frameworks provide alternative conceptions of the reaction mechanisms and their application in solving related problems; these are called the acid–base theories, for example, Brønsted–Lowry acid–base theory. Their importance becomes apparent in analyzing acid–base reactions for gaseous or liquid species, or when acid or base character may be somewhat less apparent. The first of these concepts was provided by the French chemist Antoine Lavoisier, around 1776. It is important to think of the acid-base reaction models as theories that complement each other. For example, the current Lewis model has the broadest definition of what an acid and base are, with the Bronsted-Lowry theory being a subset of what acids and bases are, and the Arrhenius theory being the most restrictive. The first scientific concept of acids and bases was provided by Lavoisier in around 1776. Since Lavoisier's knowledge of strong acids was mainly restricted to oxoacids, such as (nitric acid) and (sulfuric acid), which tend to contain central atoms in high oxidation states surrounded by oxygen, and since he was not aware of the true composition of the hydrohalic acids (HF, HCl, HBr, and HI), he defined acids in terms of their containing "oxygen", which in fact he named from Greek words meaning "acid-former" (from the Greek οξυς ("oxys") meaning "acid" or "sharp" and γεινομαι ("geinomai") meaning "engender") | https://en.wikipedia.org/wiki?curid=3038 |
Acid–base reaction The Lavoisier definition held for over 30 years, until the 1810 article and subsequent lectures by Sir Humphry Davy in which he proved the lack of oxygen in , HTe, and the hydrohalic acids. However, Davy failed to develop a new theory, concluding that "acidity does not depend upon any particular elementary substance, but upon peculiar arrangement of various substances". One notable modification of oxygen theory was provided by Jöns Jacob Berzelius, who stated that acids are oxides of nonmetals while bases are oxides of metals. In 1838, Justus von Liebig proposed that an acid is a hydrogen-containing compound whose hydrogen can be replaced by a metal. This redefinition was based on his extensive work on the chemical composition of organic acids, finishing the doctrinal shift from oxygen-based acids to hydrogen-based acids started by Davy. Liebig's definition, while completely empirical, remained in use for almost 50 years until the adoption of the Arrhenius definition. The first modern definition of acids and bases in molecular terms was devised by Svante Arrhenius. A hydrogen theory of acids, it followed from his 1884 work with Friedrich Wilhelm Ostwald in establishing the presence of ions in aqueous solution and led to Arrhenius receiving the Nobel Prize in Chemistry in 1903. As defined by Arrhenius: This causes the protonation of water, or the creation of the hydronium (HO) ion | https://en.wikipedia.org/wiki?curid=3038 |
Acid–base reaction Thus, in modern times, the symbol H is interpreted as a shorthand for HO, because it is now known that a bare proton does not exist as a free species in aqueous solution. The Arrhenius definitions of acidity and alkalinity are restricted to aqueous solutions, and refer to the concentration of the solvent ions. Under this definition, pure HSO and HCl dissolved in toluene are not acidic, and molten NaOH and solutions of calcium amide in liquid ammonia are not alkaline. This led to the development of the Bronsted-Lowry theory and subsequent Lewis theory to account for these non-aqueous exceptions. Overall, to qualify as an Arrhenius acid, upon the introduction to water, the chemical must either cause, directly or otherwise: Conversely, to qualify as an Arrhenius base, upon the introduction to water, the chemical must either cause, directly or otherwise: The reaction of an acid with a base is called a neutralization reaction. The products of this reaction are a salt and water. In this traditional representation an acid–base neutralization reaction is formulated as a double-replacement reaction. For example, the reaction of hydrochloric acid, HCl, with sodium hydroxide, NaOH, solutions produces a solution of sodium chloride, NaCl, and some additional water molecules. The modifier (aq) in this equation was implied by Arrhenius, rather than included explicitly. It indicates that the substances are dissolved in water | https://en.wikipedia.org/wiki?curid=3038 |
Acid–base reaction Though all three substances, HCl, NaOH and NaCl are capable of existing as pure compounds, in aqueous solutions they are fully dissociated into the aquated ions H, Cl, Na and OH. The Brønsted–Lowry definition, formulated in 1923, independently by Johannes Nicolaus Brønsted in Denmark and Martin Lowry in England, is based upon the idea of protonation of bases through the deprotonation of acids – that is, the ability of acids to "donate" hydrogen ions (H)—otherwise known as protons—to bases, which "accept" them. An acid–base reaction is, thus, the removal of a hydrogen ion from the acid and its addition to the base. The removal of a hydrogen ion from an acid produces its "conjugate base", which is the acid with a hydrogen ion removed. The reception of a proton by a base produces its "conjugate acid", which is the base with a hydrogen ion added. Unlike the previous definitions, the Brønsted–Lowry definition does not refer to the formation of salt and solvent, but instead to the formation of "conjugate acids" and "conjugate bases", produced by the transfer of a proton from the acid to the base. In this approach, acids and bases are fundamentally different in behavior from salts, which are seen as electrolytes, subject to the theories of Debye, Onsager, and others. An acid and a base react not to produce a salt and a solvent, but to form a new acid and a new base. The concept of neutralization is thus absent | https://en.wikipedia.org/wiki?curid=3038 |
Acid–base reaction Brønsted–Lowry acid–base behavior is formally independent of any solvent, making it more all-encompassing than the Arrhenius model. The calculation of pH under the Arrhenius model depended on alkalis (bases) dissolving in water (aqueous solution). The Brønsted–Lowry model expanded what could be pH tested using insoluble and soluble solutions (gas, liquid, solid). The general formula for acid–base reactions according to the Brønsted–Lowry definition is: where HA represents the acid, B represents the base, BH represents the conjugate acid of B, and A represents the conjugate base of HA. For example, a Brønsted-Lowry model for the dissociation of hydrochloric acid (HCl) in aqueous solution would be the following: The removal of H from the HCl produces the chloride ion, Cl, the conjugate base of the acid. The addition of H to the HO (acting as a base) forms the hydronium ion, HO, the conjugate acid of the base. Water is amphoteric—that is, it can act as both an acid and a base. The Brønsted-Lowry model explains this, showing the dissociation of water into low concentrations of hydronium and hydroxide ions: This equation is demonstrated in the image below: Here, one molecule of water acts as an acid, donating an H and forming the conjugate base, OH, and a second molecule of water acts as a base, accepting the H ion and forming the conjugate acid, HO. As an example of water acting as an acid, consider an aqueous solution of pyridine, CHN | https://en.wikipedia.org/wiki?curid=3038 |
Acid–base reaction In this example, a water molecule is split into a hydrogen ion, which is donated to a pyridine molecule, and an hydroxide ion. In the Brønsted-Lowry model, the solvent does not necessarily have to be water that is required by the Arrhenius Acid-Base model. For example, consider what happens when acetic acid, CHCOOH, dissolves in liquid ammonia. An H ion is removed from acetic acid, forming its conjugate base, the acetate ion, CHCOO. The addition of an H ion to an ammonia molecule of the solvent creates its conjugate acid, the ammonium ion, . The Brønsted–Lowry model calls hydrogen-containing substances (like HCl) acids. Thus, some substances, which many chemists considered to be acids, such as SO or BCl, are excluded from this classification due to lack of hydrogen. Gilbert N. Lewis wrote in 1938, "To restrict the group of acids to those substances that contain hydrogen interferes as seriously with the systematic understanding of chemistry as would the restriction of the term oxidizing agent to substances containing oxygen." Furthermore, KOH and KNH are not considered Brønsted bases, but rather salts containing the bases OH and . The hydrogen requirement of Arrhenius and Brønsted–Lowry was removed by the Lewis definition of acid–base reactions, devised by Gilbert N. Lewis in 1923, in the same year as Brønsted–Lowry, but it was not elaborated by him until 1938 | https://en.wikipedia.org/wiki?curid=3038 |
Acid–base reaction Instead of defining acid–base reactions in terms of protons or other bonded substances, the Lewis definition defines a base (referred to as a "Lewis base") to be a compound that can donate an "electron pair", and an acid (a "Lewis acid") to be a compound that can receive this electron pair. For example, boron trifluoride, BF is a typical Lewis acid. It can accept a pair of electrons as it has a vacancy in its octet. The fluoride ion has a full octet and can donate a pair of electrons. Thus is a typical Lewis acid, Lewis base reaction. All compounds of group 13 elements with a formula AX can behave as Lewis acids. Similarly, compounds of group 15 elements with a formula DY, such as amines, NR, and phosphines, PR, can behave as Lewis bases. Adducts between them have the formula XA←DY with a dative covalent bond, shown symbolically as ←, between the atoms A (acceptor) and D (donor). Compounds of group 16 with a formula DX may also act as Lewis bases; in this way, a compound like an ether, RO, or a thioether, RS, can act as a Lewis base. The Lewis definition is not limited to these examples. For instance, carbon monoxide acts as a Lewis base when it forms an adduct with boron trifluoride, of formula FB←CO. Adducts involving metal ions are referred to as co-ordination compounds; each ligand donates a pair of electrons to the metal ion | https://en.wikipedia.org/wiki?curid=3038 |
Acid–base reaction The reaction can be seen as an acid–base reaction in which a stronger base (ammonia) replaces a weaker one (water) The Lewis and Brønsted–Lowry definitions are consistent with each other since the reaction is an acid–base reaction in both theories. One of the limitations of the Arrhenius definition is its reliance on water solutions. Edward Curtis Franklin studied the acid–base reactions in liquid ammonia in 1905 and pointed out the similarities to the water-based Arrhenius theory. Albert F.O. Germann, working with liquid phosgene, , formulated the solvent-based theory in 1925, thereby generalizing the Arrhenius definition to cover aprotic solvents. Germann pointed out that in many solutions, there are ions in equilibrium with the neutral solvent molecules: For example, water and ammonia undergo such dissociation into hydronium and hydroxide, and ammonium and amide, respectively: Some aprotic systems also undergo such dissociation, such as dinitrogen tetroxide into nitrosonium and nitrate, antimony trichloride into dichloroantimonium and tetrachloroantimonate, and phosgene into chlorocarboxonium and chloride: A solute that causes an increase in the concentration of the solvonium ions and a decrease in the concentration of solvate ions is defined as an "acid". A solute that causes an increase in the concentration of the solvate ions and a decrease in the concentration of the solvonium ions is defined as a "base". Thus, in liquid ammonia, (supplying ) is a strong base, and (supplying ) is a strong acid | https://en.wikipedia.org/wiki?curid=3038 |
Acid–base reaction In liquid sulfur dioxide (), thionyl compounds (supplying ) behave as acids, and sulfites (supplying ) behave as bases. The non-aqueous acid–base reactions in liquid ammonia are similar to the reactions in water: Nitric acid can be a base in liquid sulfuric acid: The unique strength of this definition shows in describing the reactions in aprotic solvents; for example, in liquid : Because the solvent system definition depends on the solute as well as on the solvent itself, a particular solute can be either an acid or a base depending on the choice of the solvent: is a strong acid in water, a weak acid in acetic acid, and a weak base in fluorosulfonic acid; this characteristic of the theory has been seen as both a strength and a weakness, because some substances (such as and ) have been seen to be acidic or basic on their own right. On the other hand, solvent system theory has been criticized as being too general to be useful. Also, it has been thought that there is something intrinsically acidic about hydrogen compounds, a property not shared by non-hydrogenic solvonium salts. This acid–base theory was a revival of oxygen theory of acids and bases, proposed by German chemist Hermann Lux in 1939, further improved by Håkon Flood circa 1947 and is still used in modern geochemistry and electrochemistry of molten salts. This definition describes an acid as an oxide ion () acceptor and a base as an oxide ion donor | https://en.wikipedia.org/wiki?curid=3038 |
Acid–base reaction For example: This theory is also useful in the systematisation of the reactions of noble gas compounds, especially the xenon oxides, fluorides, and oxofluorides. Mikhail Usanovich developed a general theory that does not restrict acidity to hydrogen-containing compounds, but his approach, published in 1938, was even more general than Lewis theory. Usanovich's theory can be summarized as defining an acid as anything that accepts negative species or donates positive ones, and a base as the reverse. This defined the concept of redox (oxidation-reduction) as a special case of acid–base reactions Some examples of Usanovich acid–base reactions include: In 1963, Ralph Pearson proposed a qualitative concept known as the Hard and Soft Acids and Bases principle. later made quantitative with help of Robert Parr in 1984. 'Hard' applies to species that are small, have high charge states, and are weakly polarizable. 'Soft' applies to species that are large, have low charge states and are strongly polarizable. Acids and bases interact, and the most stable interactions are hard–hard and soft–soft. This theory has found use in organic and inorganic chemistry. The ECW model created by Russell S. Drago is a quantitative model that describes and predicts the strength of Lewis acid base interactions, −Δ"H". The model assigned "E" and "C" parameters to many Lewis acids and bases. Each acid is characterized by an "E" and a "C". Each base is likewise characterized by its own "E" and "C" | https://en.wikipedia.org/wiki?curid=3038 |
Acid–base reaction The "E" and "C" parameters refer, respectively, to the electrostatic and covalent contributions to the strength of the bonds that the acid and base will form. The equation is The "W" term represents a constant energy contribution for acid–base reaction such as the cleavage of a dimeric acid or base. The equation predicts reversal of acids and base strengths. The graphical presentations of the equation show that there is no single order of Lewis base strengths or Lewis acid strengths. The reaction of a strong acid with a strong base is essentially a quantitative reaction. For example, In this reaction both the sodium and chloride ions are spectators as the neutralization reaction, does not involve them. With weak bases addition of acid is not quantitative because a solution of a weak base is a buffer solution. A solution of a weak acid is also a buffer solution. When a weak acid reacts with a weak base an equilibrium mixture is produced. For example, adenine, written as AH, can react with a hydrogen phosphate ion, . The equilibrium constant for this reaction can be derived from the acid dissociation constants of adenine and of the dihydrogen phosphate ion. The notation [X] signifies "concentration of X". When these two equations are combined by eliminating the hydrogen ion concentration, an expression for the equilibrium constant, "K" is obtained. An acid–alkali reaction is a special case of an acid–base reaction, where the base used is also an alkali | https://en.wikipedia.org/wiki?curid=3038 |
Acid–base reaction When an acid reacts with an alkali salt (a metal hydroxide), the product is a metal salt and water. Acid–alkali reactions are also neutralization reactions. In general, acid–alkali reactions can be simplified to by omitting spectator ions. Acids are in general pure substances that contain hydrogen cations () or cause them to be produced in solutions. Hydrochloric acid () and sulfuric acid () are common examples. In water, these break apart into ions: The alkali breaks apart in water, yielding dissolved hydroxide ions: | https://en.wikipedia.org/wiki?curid=3038 |
Afterglow An afterglow is a broad arch of whitish or pinkish sunlight in the sky that is scattered by fine particulates, like dust, suspended in the atmosphere. An afterglow may appear above the highest clouds in the hour of fading twilight or be reflected off high snowfields in mountain regions long after sunset. The particles produce a scattering effect upon the component parts of white light. The opposite of an afterglow is a foreglow, which occurs before sunrise. True alpenglow, which occurs long after sunset or long before sunrise, is caused by the backscattering of red sunlight by aerosols and fine dust particles low in the atmosphere. After sunset, alpenglow is an afterglow caused by the illumination of atmospheric particles by sunlight as it gets refracted and scattered through the Earth's atmosphere. The high-energy and high-frequency light is scattered out the most, while the remaining low-energy and -frequency light reaches the observer on the horizon at twilight. The backscattering of this light further turns it pinkish to reddish. This period of time is referred to as blue hour and is widely treasured by photographers and painters. The afterglow persists until the Earth's shadow (terminator line) overtakes the sky above the observer as night falls and the stars appear, with Venus (the second-brightest celestial object after the Moon in the night sky) visible above the horizon opposite of the Belt of Venus around the antisolar point | https://en.wikipedia.org/wiki?curid=3124 |
Afterglow After the 1883 eruption of the volcano Krakatoa, a remarkable series of red sunsets appeared worldwide. An enormous amount of exceedingly fine dust were blown to a great height by the volcano's explosion, and then globally diffused by the high atmospheric winds. Edvard Munch's painting "The Scream" possibly depicts an afterglow during this period. | https://en.wikipedia.org/wiki?curid=3124 |
Biochemistry Biochemistry, sometimes called biological chemistry, is the study of chemical processes within and relating to living organisms. Biochemical processes give rise to the complexity of life. A sub-discipline of both biology and chemistry, biochemistry can be divided into three fields; structural biology, enzymology, and metabolism. Over the last decades of the 20th century, biochemistry has become successful at explaining living processes through these three disciplines. Almost all areas of the life sciences are being uncovered and developed by biochemical methodology and research. focuses on understanding the chemical basis which allows biological molecules to give rise to the processes that occur within living cells and between cells, which in turn relates greatly to the study and understanding of tissues and organs, as well as organism structure and function. is closely related to molecular biology, the study of the molecular mechanisms of biological phenomena. Much of biochemistry deals with the structures, functions, and interactions of biological macromolecules, such as proteins, nucleic acids, carbohydrates, and lipids, which provide the structure of cells and perform many of the functions associated with life. The chemistry of the cell also depends on the reactions of smaller molecules and ions. These can be inorganic (for example, water and metal ions) or organic (for example, the amino acids, which are used to synthesize proteins) | https://en.wikipedia.org/wiki?curid=3954 |
Biochemistry The mechanisms by which cells harness energy from their environment via chemical reactions are known as metabolism. The findings of biochemistry are applied primarily in medicine, nutrition, and agriculture. In medicine, biochemists investigate the causes and cures of diseases. In nutrition, they study how to maintain health and wellness and study the effects of nutritional deficiencies. In agriculture, biochemists investigate soil and fertilizers. They also try to discover ways to improve crop cultivation, crop storage, and pest control. At its broadest definition, biochemistry can be seen as a study of the components and composition of living things and how they come together to become life. In this sense, the history of biochemistry may therefore go back as far as the ancient Greeks. However, biochemistry as a specific scientific discipline began sometime in the 19th century, or a little earlier, depending on which aspect of biochemistry is being focused on. Some argued that the beginning of biochemistry may have been the discovery of the first enzyme, diastase (today called amylase), in 1833 by Anselme Payen, while others considered Eduard Buchner's first demonstration of a complex biochemical process alcoholic fermentation in cell-free extracts in 1897 to be the birth of biochemistry | https://en.wikipedia.org/wiki?curid=3954 |
Biochemistry Some might also point as its beginning to the influential 1842 work by Justus von Liebig, "Animal chemistry, or, Organic chemistry in its applications to physiology and pathology", which presented a chemical theory of metabolism, or even earlier to the 18th century studies on fermentation and respiration by Antoine Lavoisier. Many other pioneers in the field who helped to uncover the layers of complexity of biochemistry have been proclaimed founders of modern biochemistry. Emil Fischer, who studied the chemistry of proteins, and F. Gowland Hopkins, who studied enzymes and the dynamic nature of biochemistry, represent two examples of early biochemists. The term "biochemistry" itself is derived from a combination of biology and chemistry. In 1877, Felix Hoppe-Seyler used the term ("biochemie" in German) as a synonym for physiological chemistry in the foreword to the first issue of "Zeitschrift für Physiologische Chemie" (Journal of Physiological Chemistry) where he argued for the setting up of institutes dedicated to this field of study. The German chemist Carl Neuberg however is often cited to have coined the word in 1903, while some credited it to Franz Hofmeister. It was once generally believed that life and its materials had some essential property or substance (often referred to as the "vital principle") distinct from any found in non-living matter, and it was thought that only living beings could produce the molecules of life | https://en.wikipedia.org/wiki?curid=3954 |
Biochemistry Then, in 1828, Friedrich Wöhler published a paper on the synthesis of urea, proving that organic compounds can be created artificially. Since then, biochemistry has advanced, especially since the mid-20th century, with the development of new techniques such as chromatography, X-ray diffraction, dual polarisation interferometry, NMR spectroscopy, radioisotopic labeling, electron microscopy, and molecular dynamics simulations. These techniques allowed for the discovery and detailed analysis of many molecules and metabolic pathways of the cell, such as glycolysis and the Krebs cycle (citric acid cycle), and led to an understanding of biochemistry on a molecular level. Philip Randle is well known for his discovery in diabetes research is possibly the glucose-fatty acid cycle in 1963. He confirmed that fatty acids reduce oxidation of sugar by the muscle. High fat oxidation was responsible for the insulin resistance. Another significant historic event in biochemistry is the discovery of the gene, and its role in the transfer of information in the cell. In the 1950s, James D. Watson, Francis Crick, Rosalind Franklin, and Maurice Wilkins were instrumental in solving DNA structure and suggesting its relationship with the genetic transfer of information. In 1958, George Beadle and Edward Tatum received the Nobel Prize for work in fungi showing that one gene produces one enzyme. In 1988, Colin Pitchfork was the first person convicted of murder with DNA evidence, which led to the growth of forensic science | https://en.wikipedia.org/wiki?curid=3954 |
Biochemistry More recently, Andrew Z. Fire and Craig C. Mello received the 2006 Nobel Prize for discovering the role of RNA interference (RNAi), in the silencing of gene expression. Around two dozen chemical elements are essential to various kinds of biological life. Most rare elements on Earth are not needed by life (exceptions being selenium and iodine), while a few common ones (aluminum and titanium) are not used. Most organisms share element needs, but there are a few differences between plants and animals. For example, ocean algae use bromine, but land plants and animals seem to need none. All animals require sodium, but some plants do not. Plants need boron and silicon, but animals may not (or may need ultra-small amounts). Just six elements—carbon, hydrogen, nitrogen, oxygen, calcium, and phosphorus—make up almost 99% of the mass of living cells, including those in the human body (see composition of the human body for a complete list). In addition to the six major elements that compose most of the human body, humans require smaller amounts of possibly 18 more. The four main classes of molecules in biochemistry (often called biomolecules) are carbohydrates, lipids, proteins, and nucleic acids. Many biological molecules are polymers: in this terminology, monomers are relatively small macromolecules that are linked together to create large macromolecules known as polymers. When monomers are linked together to synthesize a biological polymer, they undergo a process called dehydration synthesis | https://en.wikipedia.org/wiki?curid=3954 |
Biochemistry Different macromolecules can assemble in larger complexes, often needed for biological activity. Two of the main functions of carbohydrates are energy storage and providing structure. Sugars are carbohydrates, but not all carbohydrates are sugars. There are more carbohydrates on Earth than any other known type of biomolecule; they are used to store energy and genetic information, as well as play important roles in cell to cell interactions and communications. The simplest type of carbohydrate is a monosaccharide, which among other properties contains carbon, hydrogen, and oxygen, mostly in a ratio of 1:2:1 (generalized formula CHO, where "n" is at least 3). Glucose (CHO) is one of the most important carbohydrates; others include fructose (CHO), the sugar commonly associated with the sweet taste of fruits, and deoxyribose (CHO), a component of DNA. A monosaccharide can switch between acyclic (open-chain) form and a cyclic form. The open-chain form can be turned into a ring of carbon atoms bridged by an oxygen atom created from the carbonyl group of one end and the hydroxyl group of another. The cyclic molecule has a hemiacetal or hemiketal group, depending on whether the linear form was an aldose or a ketose. In these cyclic forms, the ring usually has 5 or 6 atoms. These forms are called furanoses and pyranoses, respectively—by analogy with furan and pyran, the simplest compounds with the same carbon-oxygen ring (although they lack the carbon-carbon double bonds of these two molecules) | https://en.wikipedia.org/wiki?curid=3954 |
Biochemistry For example, the aldohexose glucose may form a hemiacetal linkage between the hydroxyl on carbon 1 and the oxygen on carbon 4, yielding a molecule with a 5-membered ring, called glucofuranose. The same reaction can take place between carbons 1 and 5 to form a molecule with a 6-membered ring, called glucopyranose. Cyclic forms with a 7-atom ring called heptoses are rare. Two monosaccharides can be joined together by a glycosidic or ether bond into a "disaccharide" through a dehydration reaction during which a molecule of water is released. The reverse reaction in which the glycosidic bond of a disaccharide is broken into two monosaccharides is termed "hydrolysis". The best-known disaccharide is sucrose or ordinary sugar, which consists of a glucose molecule and a fructose molecule joined together. Another important disaccharide is lactose found in milk, consisting of a glucose molecule and a galactose molecule. Lactose may be hydrolysed by lactase, and deficiency in this enzyme results in lactose intolerance. When a few (around three to six) monosaccharides are joined, it is called an "oligosaccharide" ("oligo-" meaning "few"). These molecules tend to be used as markers and signals, as well as having some other uses. Many monosaccharides joined together form a polysaccharide. They can be joined together in one long linear chain, or they may be branched. Two of the most common polysaccharides are cellulose and glycogen, both consisting of repeating glucose monomers | https://en.wikipedia.org/wiki?curid=3954 |
Biochemistry "Cellulose" is an important structural component of plant's cell walls and "glycogen" is used as a form of energy storage in animals. Sugar can be characterized by having reducing or non-reducing ends. A reducing end of a carbohydrate is a carbon atom that can be in equilibrium with the open-chain aldehyde (aldose) or keto form (ketose). If the joining of monomers takes place at such a carbon atom, the free hydroxy group of the pyranose or furanose form is exchanged with an OH-side-chain of another sugar, yielding a full acetal. This prevents opening of the chain to the aldehyde or keto form and renders the modified residue non-reducing. Lactose contains a reducing end at its glucose moiety, whereas the galactose moiety forms a full acetal with the C4-OH group of glucose. Saccharose does not have a reducing end because of full acetal formation between the aldehyde carbon of glucose (C1) and the keto carbon of fructose (C2). Lipids comprise a diverse range of molecules and to some extent is a catchall for relatively water-insoluble or nonpolar compounds of biological origin, including waxes, fatty acids, fatty-acid derived phospholipids, sphingolipids, glycolipids, and terpenoids (e.g., retinoids and steroids). Some lipids are linear, open-chain aliphatic molecules, while others have ring structures. Some are aromatic (with a cyclic [ring] and planar [flat] structure) while others are not. Some are flexible, while others are rigid | https://en.wikipedia.org/wiki?curid=3954 |
Biochemistry Lipids are usually made from one molecule of glycerol combined with other molecules. In triglycerides, the main group of bulk lipids, there is one molecule of glycerol and three fatty acids. Fatty acids are considered the monomer in that case, and may be saturated (no double bonds in the carbon chain) or unsaturated (one or more double bonds in the carbon chain). Most lipids have some polar character in addition to being largely nonpolar. In general, the bulk of their structure is nonpolar or hydrophobic ("water-fearing"), meaning that it does not interact well with polar solvents like water. Another part of their structure is polar or hydrophilic ("water-loving") and will tend to associate with polar solvents like water. This makes them amphiphilic molecules (having both hydrophobic and hydrophilic portions). In the case of cholesterol, the polar group is a mere –OH (hydroxyl or alcohol). In the case of phospholipids, the polar groups are considerably larger and more polar, as described below. Lipids are an integral part of our daily diet. Most oils and milk products that we use for cooking and eating like butter, cheese, ghee etc., are composed of fats. Vegetable oils are rich in various polyunsaturated fatty acids (PUFA). Lipid-containing foods undergo digestion within the body and are broken into fatty acids and glycerol, which are the final degradation products of fats and lipids. Lipids, especially phospholipids, are also used in various pharmaceutical products, either as co-solubilisers (e.g | https://en.wikipedia.org/wiki?curid=3954 |
Biochemistry , in parenteral infusions) or else as drug carrier components (e.g., in a liposome or transfersome). Proteins are very large molecules—macro-biopolymers—made from monomers called amino acids. An amino acid consists of an alpha carbon atom attached to an amino group, –NH, a carboxylic acid group, –COOH (although these exist as –NH and –COO under physiologic conditions), a simple hydrogen atom, and a side chain commonly denoted as "–R". The side chain "R" is different for each amino acid of which there are 20 standard ones. It is this "R" group that made each amino acid different, and the properties of the side-chains greatly influence the overall three-dimensional conformation of a protein. Some amino acids have functions by themselves or in a modified form; for instance, glutamate functions as an important neurotransmitter. Amino acids can be joined via a peptide bond. In this dehydration synthesis, a water molecule is removed and the peptide bond connects the nitrogen of one amino acid's amino group to the carbon of the other's carboxylic acid group. The resulting molecule is called a "dipeptide", and short stretches of amino acids (usually, fewer than thirty) are called "peptides" or polypeptides. Longer stretches merit the title "proteins". As an example, the important blood serum protein albumin contains 585 amino acid residues. Proteins can have structural and/or functional roles. For instance, movements of the proteins actin and myosin ultimately are responsible for the contraction of skeletal muscle | https://en.wikipedia.org/wiki?curid=3954 |
Biochemistry One property many proteins have is that they specifically bind to a certain molecule or class of molecules—they may be "extremely" selective in what they bind. Antibodies are an example of proteins that attach to one specific type of molecule. Antibodies are composed of heavy and light chains. Two heavy chains would be linked to two light chains through disulfide linkages between their amino acids. Antibodies are specific through variation based on differences in the N-terminal domain. The enzyme-linked immunosorbent assay (ELISA), which uses antibodies, is one of the most sensitive tests modern medicine uses to detect various biomolecules. Probably the most important proteins, however, are the enzymes. Virtually every reaction in a living cell requires an enzyme to lower the activation energy of the reaction. These molecules recognize specific reactant molecules called "substrates"; they then catalyze the reaction between them. By lowering the activation energy, the enzyme speeds up that reaction by a rate of 10 or more; a reaction that would normally take over 3,000 years to complete spontaneously might take less than a second with an enzyme. The enzyme itself is not used up in the process and is free to catalyze the same reaction with a new set of substrates. Using various modifiers, the activity of the enzyme can be regulated, enabling control of the biochemistry of the cell as a whole. The structure of proteins is traditionally described in a hierarchy of four levels | https://en.wikipedia.org/wiki?curid=3954 |
Biochemistry The primary structure of a protein consists of its linear sequence of amino acids; for instance, "alanine-glycine-tryptophan-serine-glutamate-asparagine-glycine-lysine-…". Secondary structure is concerned with local morphology (morphology being the study of structure). Some combinations of amino acids will tend to curl up in a coil called an α-helix or into a sheet called a β-sheet; some α-helixes can be seen in the hemoglobin schematic above. Tertiary structure is the entire three-dimensional shape of the protein. This shape is determined by the sequence of amino acids. In fact, a single change can change the entire structure. The alpha chain of hemoglobin contains 146 amino acid residues; substitution of the glutamate residue at position 6 with a valine residue changes the behavior of hemoglobin so much that it results in sickle-cell disease. Finally, quaternary structure is concerned with the structure of a protein with multiple peptide subunits, like hemoglobin with its four subunits. Not all proteins have more than one subunit. Ingested proteins are usually broken up into single amino acids or dipeptides in the small intestine and then absorbed. They can then be joined to form new proteins. Intermediate products of glycolysis, the citric acid cycle, and the pentose phosphate pathway can be used to form all twenty amino acids, and most bacteria and plants possess all the necessary enzymes to synthesize them. Humans and other mammals, however, can synthesize only half of them | https://en.wikipedia.org/wiki?curid=3954 |
Biochemistry They cannot synthesize isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. Because they must be ingested, these are the essential amino acids. Mammals do possess the enzymes to synthesize alanine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline, serine, and tyrosine, the nonessential amino acids. While they can synthesize arginine and histidine, they cannot produce it in sufficient amounts for young, growing animals, and so these are often considered essential amino acids. If the amino group is removed from an amino acid, it leaves behind a carbon skeleton called an α-keto acid. Enzymes called transaminases can easily transfer the amino group from one amino acid (making it an α-keto acid) to another α-keto acid (making it an amino acid). This is important in the biosynthesis of amino acids, as for many of the pathways, intermediates from other biochemical pathways are converted to the α-keto acid skeleton, and then an amino group is added, often via transamination. The amino acids may then be linked together to form a protein. A similar process is used to break down proteins. It is first hydrolyzed into its component amino acids. Free ammonia (NH3), existing as the ammonium ion (NH4+) in blood, is toxic to life forms. A suitable method for excreting it must therefore exist. Different tactics have evolved in different animals, depending on the animals' needs. Unicellular organisms simply release the ammonia into the environment | https://en.wikipedia.org/wiki?curid=3954 |
Biochemistry Likewise, bony fish can release the ammonia into the water where it is quickly diluted. In general, mammals convert the ammonia into urea, via the urea cycle. In order to determine whether two proteins are related, or in other words to decide whether they are homologous or not, scientists use sequence-comparison methods. Methods like sequence alignments and structural alignments are powerful tools that help scientists identify homologies between related molecules. The relevance of finding homologies among proteins goes beyond forming an evolutionary pattern of protein families. By finding how similar two protein sequences are, we acquire knowledge about their structure and therefore their function. Nucleic acids, so-called because of their prevalence in cellular nuclei, is the generic name of the family of biopolymers. They are complex, high-molecular-weight biochemical macromolecules that can convey genetic information in all living cells and viruses. The monomers are called nucleotides, and each consists of three components: a nitrogenous heterocyclic base (either a purine or a pyrimidine), a pentose sugar, and a phosphate group. The most common nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The phosphate group and the sugar of each nucleotide bond with each other to form the backbone of the nucleic acid, while the sequence of nitrogenous bases stores the information. The most common nitrogenous bases are adenine, cytosine, guanine, thymine, and uracil | https://en.wikipedia.org/wiki?curid=3954 |
Biochemistry The nitrogenous bases of each strand of a nucleic acid will form hydrogen bonds with certain other nitrogenous bases in a complementary strand of nucleic acid (similar to a zipper). Adenine binds with thymine and uracil, thymine binds only with adenine, and cytosine and guanine can bind only with one another. Aside from the genetic material of the cell, nucleic acids often play a role as second messengers, as well as forming the base molecule for adenosine triphosphate (ATP), the primary energy-carrier molecule found in all living organisms. Also, the nitrogenous bases possible in the two nucleic acids are different: adenine, cytosine, and guanine occur in both RNA and DNA, while thymine occurs only in DNA and uracil occurs in RNA. Glucose is an energy source in most life forms. For instance, polysaccharides are broken down into their monomers by enzymes (glycogen phosphorylase removes glucose residues from glycogen, a polysaccharide). Disaccharides like lactose or sucrose are cleaved into their two component monosaccharides. Glucose is mainly metabolized by a very important ten-step pathway called glycolysis, the net result of which is to break down one molecule of glucose into two molecules of pyruvate. This also produces a net two molecules of ATP, the energy currency of cells, along with two reducing equivalents of converting NAD (nicotinamide adenine dinucleotide: oxidized form) to NADH (nicotinamide adenine dinucleotide: reduced form) | https://en.wikipedia.org/wiki?curid=3954 |
Biochemistry This does not require oxygen; if no oxygen is available (or the cell cannot use oxygen), the NAD is restored by converting the pyruvate to lactate (lactic acid) (e.g., in humans) or to ethanol plus carbon dioxide (e.g., in yeast). Other monosaccharides like galactose and fructose can be converted into intermediates of the glycolytic pathway. In aerobic cells with sufficient oxygen, as in most human cells, the pyruvate is further metabolized. It is irreversibly converted to acetyl-CoA, giving off one carbon atom as the waste product carbon dioxide, generating another reducing equivalent as NADH. The two molecules acetyl-CoA (from one molecule of glucose) then enter the citric acid cycle, producing two molecules of ATP, six more NADH molecules and two reduced (ubi)quinones (via FADH as enzyme-bound cofactor), and releasing the remaining carbon atoms as carbon dioxide. The produced NADH and quinol molecules then feed into the enzyme complexes of the respiratory chain, an electron transport system transferring the electrons ultimately to oxygen and conserving the released energy in the form of a proton gradient over a membrane (inner mitochondrial membrane in eukaryotes). Thus, oxygen is reduced to water and the original electron acceptors NAD and quinone are regenerated. This is why humans breathe in oxygen and breathe out carbon dioxide. The energy released from transferring the electrons from high-energy states in NADH and quinol is conserved first as proton gradient and converted to ATP via ATP synthase | https://en.wikipedia.org/wiki?curid=3954 |
Biochemistry This generates an additional "28" molecules of ATP (24 from the 8 NADH + 4 from the 2 quinols), totaling to 32 molecules of ATP conserved per degraded glucose (two from glycolysis + two from the citrate cycle). It is clear that using oxygen to completely oxidize glucose provides an organism with far more energy than any oxygen-independent metabolic feature, and this is thought to be the reason why complex life appeared only after Earth's atmosphere accumulated large amounts of oxygen. In vertebrates, vigorously contracting skeletal muscles (during weightlifting or sprinting, for example) do not receive enough oxygen to meet the energy demand, and so they shift to anaerobic metabolism, converting glucose to lactate. The combination of glucose from noncarbohydrates origin , such as fat and proteins. This only happens when glycogen supplies in the liver are worn out. The pathway is a crucial reversal of glycolysis from pyruvate to glucose and it can utilize many sources like amino acids , glycerol and Krebs Cycle. Large scale protein and fat catabolism usually occur when those suffer from starvation or certain endocrine disorders. The liver regenerates the glucose, using a process called gluconeogenesis. This process is not quite the opposite of glycolysis, and actually requires three times the amount of energy gained from glycolysis (six molecules of ATP are used, compared to the two gained in glycolysis) | https://en.wikipedia.org/wiki?curid=3954 |
Biochemistry Analogous to the above reactions, the glucose produced can then undergo glycolysis in tissues that need energy, be stored as glycogen (or starch in plants), or be converted to other monosaccharides or joined into di- or oligosaccharides. The combined pathways of glycolysis during exercise, lactate's crossing via the bloodstream to the liver, subsequent gluconeogenesis and release of glucose into the bloodstream is called the Cori cycle. Researchers in biochemistry use specific techniques native to biochemistry, but increasingly combine these with techniques and ideas developed in the fields of genetics, molecular biology, and biophysics. There is not a defined line between these disciplines. studies the chemistry required for biological activity of molecules, molecular biology studies their biological activity, genetics studies their heredity, which happens to be carried by their genome. This is shown in the following schematic that depicts one possible view of the relationships between the fields: Extremophiles are microorganisms that live in extreme conditions, some of which may provide some exceptions or variations on some of the natural laws cited above. For example, in July 2019, a scientific study of Kidd Mine in Canada discovered sulfur-breathing organisms that live 7900 feet below the surface and absorb sulfur instead of oxygen to facilitate cellular respiration. These organisms are also remarkable due to eating rocks such as pyrite as their regular food source | https://en.wikipedia.org/wiki?curid=3954 |
Biochemistry The DNA polimerase of the thermophile bacteria "Thermus aquaticus", extracted in 1968 and named "Taq" polymerase, is a biochemical DNA replicator resistant to relative high temperatures (50-80 °C), which has allowed molecular biologists to ease complications in the PCR (Polymerase Chain Reaction) method. a. Fructose is not the only sugar found in fruits. Glucose and sucrose are also found in varying quantities in various fruits, and sometimes exceed the fructose present. For example, 32% of the edible portion of a date is glucose, compared with 24% fructose and 8% sucrose. However, peaches contain more sucrose (6.66%) than they do fructose (0.93%) or glucose (1.47%). | https://en.wikipedia.org/wiki?curid=3954 |
Bioleaching is the extraction of metals from their ores through the use of living organisms. This is much cleaner than the traditional heap leaching using cyanide. is one of several applications within biohydrometallurgy and several methods are used to recover copper, zinc, lead, arsenic, antimony, nickel, molybdenum, gold, silver, and cobalt. can involve numerous ferrous iron and sulfur oxidizing bacteria, including "Acidithiobacillus ferrooxidans" (formerly known as "Thiobacillus ferrooxidans") and "Acidithiobacillus thiooxidans " (formerly known as "Thiobacillus thiooxidans"). As a general principle, Fe ions are used to oxidize the ore. This step is entirely independent of microbes. The role of the bacteria is the further oxidation of the ore, but also the regeneration of the chemical oxidant Fe from Fe. For example, bacteria catalyse the breakdown of the mineral pyrite (FeS) by oxidising the sulfur and metal (in this case ferrous iron, (Fe)) using oxygen. This yields soluble products that can be further purified and refined to yield the desired metal | https://en.wikipedia.org/wiki?curid=4111 |
Bioleaching Pyrite leaching (FeS): In the first step, disulfide is spontaneously oxidized to thiosulfate by ferric ion (Fe), which in turn is reduced to give ferrous ion (Fe): The ferrous ion is then oxidized by bacteria using oxygen: Thiosulfate is also oxidized by bacteria to give sulfate: The ferric ion produced in reaction (2) oxidized more sulfide as in reaction (1), closing the cycle and given the net reaction: The net products of the reaction are soluble ferrous sulfate and sulfuric acid. The microbial oxidation process occurs at the cell membrane of the bacteria. The electrons pass into the cells and are used in biochemical processes to produce energy for the bacteria while reducing oxygen to water. The critical reaction is the oxidation of sulfide by ferric iron. The main role of the bacterial step is the regeneration of this reactant. The process for copper is very similar, but the efficiency and kinetics depend on the copper mineralogy. The most efficient minerals are supergene minerals such as chalcocite, CuS and covellite, CuS. The main copper mineral chalcopyrite (CuFeS) is not leached very efficiently, which is why the dominant copper-producing technology remains flotation, followed by smelting and refining. The leaching of CuFeS follows the two stages of being dissolved and then further oxidised, with Cu ions being left in solution | https://en.wikipedia.org/wiki?curid=4111 |
Bioleaching Chalcopyrite leaching: net reaction: In general, sulfides are first oxidized to elemental sulfur, whereas disulfides are oxidized to give thiosulfate, and the processes above can be applied to other sulfidic ores. of non-sulfidic ores such as pitchblende also uses ferric iron as an oxidant (e.g., UO + 2 Fe ==> UO + 2 Fe). In this case, the sole purpose of the bacterial step is the regeneration of Fe. Sulfidic iron ores can be added to speed up the process and provide a source of iron. of non-sulfidic ores by layering of waste sulfides and elemental sulfur, colonized by "Acidithiobacillus" spp., has been accomplished, which provides a strategy for accelerated leaching of materials that do not contain sulfide minerals. The dissolved copper (Cu) ions are removed from the solution by ligand exchange solvent extraction, which leaves other ions in the solution. The copper is removed by bonding to a ligand, which is a large molecule consisting of a number of smaller groups, each possessing a lone electron pair. The ligand-copper complex is extracted from the solution using an organic solvent such as kerosene: The ligand donates electrons to the copper, producing a complex - a central metal atom (copper) bonded to the ligand. Because this complex has no charge, it is no longer attracted to polar water molecules and dissolves in the kerosene, which is then easily separated from the solution. Because the initial reaction is reversible, it is determined by pH | https://en.wikipedia.org/wiki?curid=4111 |
Bioleaching Adding concentrated acid reverses the equation, and the copper ions go back into an aqueous solution. Then the copper is passed through an electro-winning process to increase its purity: An electric current is passed through the resulting solution of copper ions. Because copper ions have a 2+ charge, they are attracted to the negative cathodes and collect there. The copper can also be concentrated and separated by displacing the copper with Fe from scrap iron: The electrons lost by the iron are taken up by the copper. Copper is the oxidising agent (it accepts electrons), and iron is the reducing agent (it loses electrons). Traces of precious metals such as gold may be left in the original solution. Treating the mixture with sodium cyanide in the presence of free oxygen dissolves the gold. The gold is removed from the solution by adsorbing (taking it up on the surface) to charcoal. Several species of fungi can be used for bioleaching. Fungi can be grown on many different substrates, such as electronic scrap, catalytic converters, and fly ash from municipal waste incineration. Experiments have shown that two fungal strains ("Aspergillus niger, Penicillium simplicissimum") were able to mobilize Cu and Sn by 65%, and Al, Ni, Pb, and Zn by more than 95%. "Aspergillus niger" can produce some organic acids such as citric acid. This form of leaching does not rely on microbial oxidation of metal but rather uses microbial metabolism as source of acids that directly dissolve the metal | https://en.wikipedia.org/wiki?curid=4111 |
Bioleaching Extractions involve many expensive steps such as roasting, pressure oxidation, and smelting, which require sufficient concentrations of elements in ores and are environmentally unfriendly. Low concentrations are not a problem for bacteria because they simply ignore the waste that surrounds the metals, attaining extraction yields of over 90% in some cases. These microorganisms actually gain energy by breaking down minerals into their constituent elements. The company simply collects the ions out of the solution after the bacteria have finished. There is a limited amount of ores. At the current time, it is more economical to smelt copper ore rather than to use bioleaching, since the concentration of copper in its ore is in general quite high. The profit obtained from the speed and yield of smelting justifies its cost. Nonetheless, at the largest copper mine of the world, Escondida in Chile the process seems to be favorable. However, the concentration of gold in its ore is in general very low. In this case, the lower cost of bacterial leaching outweighs the time it takes to extract the metal. Economically it is also very expensive and many companies once started can not keep up with the demand and end up in debt. Projects like Finnish Talvivaara proved to be environmentally and economically disastrous. | https://en.wikipedia.org/wiki?curid=4111 |
Bacteriophage A bacteriophage (), also known informally as a phage (), is a virus that infects and replicates within bacteria and archaea. The term was derived from "bacteria" and the Greek φαγεῖν (""), meaning "to devour". Bacteriophages are composed of proteins that encapsulate a DNA or RNA genome, and may have structures that are either simple or elaborate. Their genomes may encode as few as four genes (e.g. MS2) and as many as hundreds of genes. Phages replicate within the bacterium following the injection of their genome into its cytoplasm. Bacteriophages are among the most common and diverse entities in the biosphere. Bacteriophages are ubiquitous viruses, found wherever bacteria exist. It is estimated there are more than 10 bacteriophages on the planet, more than every other organism on Earth, including bacteria, combined. One of the densest natural sources for phages and other viruses is seawater, where up to 9x10 virions per millilitre have been found in microbial mats at the surface, and up to 70% of marine bacteria may be infected by phages. Phages have been used since the late 19th century as an alternative to antibiotics in the former Soviet Union and Central Europe, as well as in France. They are seen as a possible therapy against multi-drug-resistant strains of many bacteria (see phage therapy). Phages of "Inoviridae" have been shown to complicate biofilms involved in pneumonia and cystic fibrosis and to shelter the bacteria from drugs meant to eradicate disease, thus promoting persistent infection | https://en.wikipedia.org/wiki?curid=4185 |
Bacteriophage Bacteriophages occur abundantly in the biosphere, with different genomes, and lifestyles. Phages are classified by the International Committee on Taxonomy of Viruses (ICTV) according to morphology and nucleic acid. Nineteen families are currently recognized by the ICTV that infect bacteria and archaea. Of these, only two families have RNA genomes, and only five families are surrounded by an envelope. Of the viral families with DNA genomes, only two have single-stranded genomes. Eight of the viral families with DNA genomes have circular genomes, while nine have linear genomes. Nine families infect bacteria only, nine infect archaea only, and one ("Tectiviridae") infects both bacteria and archaea. It has been suggested that members of "Picobirnaviridae" infect bacteria, but not mammals. In 1896, Ernest Hanbury Hankin reported that something in the waters of the Ganges and Yamuna rivers in India had a marked antibacterial action against cholera and it could pass through a very fine porcelain filter. In 1915, British bacteriologist Frederick Twort, superintendent of the Brown Institution of London, discovered a small agent that infected and killed bacteria. He believed the agent must be one of the following: Twort's research was interrupted by the onset of World War I, as well as a shortage of funding and the discoveries of antibiotics | https://en.wikipedia.org/wiki?curid=4185 |
Bacteriophage Independently, French-Canadian microbiologist Félix d'Hérelle, working at the Pasteur Institute in Paris, announced on 3 September 1917, that he had discovered "an invisible, antagonistic microbe of the dysentery bacillus". For d’Hérelle, there was no question as to the nature of his discovery: "In a flash I had understood: what caused my clear spots was in fact an invisible microbe … a virus parasitic on bacteria." D'Hérelle called the virus a bacteriophage, a bacteria-eater (from the Greek "" meaning "to devour"). He also recorded a dramatic account of a man suffering from dysentery who was restored to good health by the bacteriophages. It was D'Herelle who conducted much research into bacteriophages and introduced the concept of phage therapy. More than a half a century later, in 1969, Max Delbrück, Alfred Hershey, and Salvador Luria were awarded the Nobel Prize in Physiology or Medicine for their discoveries of the replication of viruses and their genetic structure. Phages were discovered to be antibacterial agents and were used in the former Soviet Republic of Georgia (pioneered there by Giorgi Eliava with help from the co-discoverer of bacteriophages, Félix d'Herelle) during the 1920s and 1930s for treating bacterial infections. They had widespread use, including treatment of soldiers in the Red Army. However, they were abandoned for general use in the West for several reasons: The use of phages has continued since the end of the Cold War in Russia, Georgia and elsewhere in Central and Eastern Europe | https://en.wikipedia.org/wiki?curid=4185 |
Bacteriophage The first regulated, randomized, double-blind clinical trial was reported in the Journal of Wound Care in June 2009, which evaluated the safety and efficacy of a bacteriophage cocktail to treat infected venous ulcers of the leg in human patients. The FDA approved the study as a Phase I clinical trial. The study's results demonstrated the safety of therapeutic application of bacteriophages, but did not show efficacy. The authors explained that the use of certain chemicals that are part of standard wound care (e.g. lactoferrin or silver) may have interfered with bacteriophage viability. Shortly after that, another controlled clinical trial in Western Europe (treatment of ear infections caused by "Pseudomonas aeruginosa") was reported in the journal Clinical Otolaryngology in August 2009. The study concludes that bacteriophage preparations were safe and effective for treatment of chronic ear infections in humans. Additionally, there have been numerous animal and other experimental clinical trials evaluating the efficacy of bacteriophages for various diseases, such as infected burns and wounds, and cystic fibrosis associated lung infections, among others. Meanwhile, bacteriophage researchers have been developing engineered viruses to overcome antibiotic resistance, and engineering the phage genes responsible for coding enzymes that degrade the biofilm matrix, phage structural proteins, and the enzymes responsible for lysis of the bacterial cell wall | https://en.wikipedia.org/wiki?curid=4185 |
Bacteriophage There have been results showing that T4 phages that are small in size and short-tailed, can be helpful in detecting "E.coli" in the human body. Therapeutic efficacy of a phage cocktail was evaluated in a mice model with nasal infection of multidrug-resistant (MDR) "A. baumannii". Mice treated with the phage cocktail showed a 2.3-fold higher survival rate than those untreated in seven days post infection. In 2017 a patient with a pancreas compromised by MDR "A. baumannii" was put on several antibiotics, despite this the patient's health continued to deteriorate during a four-month period. Without effective antibiotics the patient was subjected to phage therapy using a phage cocktail containing nine different phages that had been demonstrated to be effective against MDR "A. baumannii". Once on this therapy the patient's downward clinical trajectory reversed, and returned to health. D'Herelle "quickly learned that bacteriophages are found wherever bacteria thrive: in sewers, in rivers that catch waste runoff from pipes, and in the stools of convalescent patients." This includes rivers traditionally thought to have healing powers, including India's Ganges River. Food industry - Since 2006, the United States Food and Drug Administration (FDA) and United States Department of Agriculture (USDA) have approved several bacteriophage products. LMP-102 (Intralytix) was approved for treating ready-to-eat (RTE) poultry and meat products | https://en.wikipedia.org/wiki?curid=4185 |
Bacteriophage In that same year, the FDA approved LISTEX (developed and produced by Micreos) using bacteriophages on cheese to kill "Listeria monocytogenes" bacteria, in order to give them generally recognized as safe (GRAS) status. In July 2007, the same bacteriophage were approved for use on all food products. In 2011 USDA confirmed that LISTEX is a clean label processing aid and is included in USDA. Research in the field of food safety is continuing to see if lytic phages are a viable option to control other food-borne pathogens in various food products. Dairy industry – Bacteriophages present in the environment can cause fermentation failures of cheese starter cultures. In order to avoid this, mixed-strain starter cultures and culture rotation regimes can be used. Diagnostics - In 2011, the FDA cleared the first bacteriophage-based product for in vitro diagnostic use. The KeyPath MRSA/MSSA Blood Culture Test uses a cocktail of bacteriophage to detect "Staphylococcus aureus" in positive blood cultures and determine methicillin resistance or susceptibility. The test returns results in about five hours, compared to two to three days for standard microbial identification and susceptibility test methods. It was the first accelerated antibiotic-susceptibility test approved by the FDA | https://en.wikipedia.org/wiki?curid=4185 |
Bacteriophage Counteracting bioweapons and toxins – Government agencies in the West have for several years been looking to Georgia and the former Soviet Union for help with exploiting phages for counteracting bioweapons and toxins, such as anthrax and botulism. Developments are continuing among research groups in the U.S. Other uses include spray application in horticulture for protecting plants and vegetable produce from decay and the spread of bacterial disease. Other applications for bacteriophages are as biocides for environmental surfaces, e.g., in hospitals, and as preventative treatments for catheters and medical devices before use in clinical settings. The technology for phages to be applied to dry surfaces, e.g., uniforms, curtains, or even sutures for surgery now exists. Clinical trials reported in "Clinical Otolaryngology" show success in veterinary treatment of pet dogs with otitis. The SEPTIC bacterium sensing and identification method uses the ion emission and its dynamics during phage infection and offers high specificity and speed for detection. Phage display is a different use of phages involving a library of phages with a variable peptide linked to a surface protein. Each phage genome encodes the variant of the protein displayed on its surface (hence the name), providing a link between the peptide variant and its encoding gene. Variant phages from the library may be selected through their binding affinity to an immobilized molecule (e.g., botulism toxin) to neutralize it | https://en.wikipedia.org/wiki?curid=4185 |
Bacteriophage The bound, selected phages can be multiplied by reinfecting a susceptible bacterial strain, thus allowing them to retrieve the peptides encoded in them for further study. Antimicrobial drug discovery - Phage proteins often have antimicrobial activity and may serve as leads for peptidomimetics, i.e. drugs that mimic peptides. Phage-ligand technology makes use of phage proteins for various applications, such as binding of bacteria and bacterial components (e.g. endotoxin) and lysis of bacteria. Basic research – Bacteriophages are important model organisms for studying principles of evolution and ecology. Bacteriophages may have a lytic cycle or a lysogenic cycle. With "lytic phages" such as the T4 phage, bacterial cells are broken open (lysed) and destroyed after immediate replication of the virion. As soon as the cell is destroyed, the phage progeny can find new hosts to infect. Lytic phages are more suitable for phage therapy. Some lytic phages undergo a phenomenon known as lysis inhibition, where completed phage progeny will not immediately lyse out of the cell if extracellular phage concentrations are high. This mechanism is not identical to that of temperate phage going dormant and usually, is temporary. In contrast, the "lysogenic cycle" does not result in immediate lysing of the host cell. Those phages able to undergo lysogeny are known as temperate phages. Their viral genome will integrate with host DNA and replicate along with it, relatively harmlessly, or may even become established as a plasmid | https://en.wikipedia.org/wiki?curid=4185 |
Bacteriophage The virus remains dormant until host conditions deteriorate, perhaps due to depletion of nutrients, then, the endogenous phages (known as prophages) become active. At this point they initiate the reproductive cycle, resulting in lysis of the host cell. As the lysogenic cycle allows the host cell to continue to survive and reproduce, the virus is replicated in all offspring of the cell. An example of a bacteriophage known to follow the lysogenic cycle and the lytic cycle is the phage lambda of "E. coli." Sometimes prophages may provide benefits to the host bacterium while they are dormant by adding new functions to the bacterial genome, in a phenomenon called lysogenic conversion. Examples are the conversion of harmless strains of "Corynebacterium diphtheriae" or "Vibrio cholerae" by bacteriophages, to highly virulent ones that cause diphtheria or cholera, respectively. Strategies to combat certain bacterial infections by targeting these toxin-encoding prophages have been proposed. Bacterial cells are protected by a cell wall of polysaccharides, which are important virulence factors protecting bacterial cells against both immune host defenses and antibiotics. To enter a host cell, bacteriophages attach to specific receptors on the surface of bacteria, including lipopolysaccharides, teichoic acids, proteins, or even flagella. This specificity means a bacteriophage can infect only certain bacteria bearing receptors to which they can bind, which in turn, determines the phage's host range | https://en.wikipedia.org/wiki?curid=4185 |
Bacteriophage Polysaccharide-degrading enzymes, like endolysins are virion-associated proteins to enzymatically degrade the capsular outer layer of their hosts, at the initial step of a tightly programmed phage infection process. Host growth conditions also influence the ability of the phage to attach and invade them. As phage virions do not move independently, they must rely on random encounters with the correct receptors when in solution, such as blood, lymphatic circulation, irrigation, soil water, etc. Myovirus bacteriophages use a hypodermic syringe-like motion to inject their genetic material into the cell. After contacting the appropriate receptor, the tail fibers flex to bring the base plate closer to the surface of the cell. This is known as reversible binding. Once attached completely, irreversible binding is initiated and the tail contracts, possibly with the help of ATP, present in the tail, injecting genetic material through the bacterial membrane. The injection is accomplished through a sort of bending motion in the shaft by going to the side, contracting closer to the cell and pushing back up. Podoviruses lack an elongated tail sheath like that of a myovirus, so instead, they use their small, tooth-like tail fibers enzymatically to degrade a portion of the cell membrane before inserting their genetic material. Within minutes, bacterial ribosomes start translating viral mRNA into protein. For RNA-based phages, RNA replicase is synthesized early in the process | https://en.wikipedia.org/wiki?curid=4185 |
Bacteriophage Proteins modify the bacterial RNA polymerase so it preferentially transcribes viral mRNA. The host's normal synthesis of proteins and nucleic acids is disrupted, and it is forced to manufacture viral products instead. These products go on to become part of new virions within the cell, helper proteins that contribute to the assemblage of new virions, or proteins involved in cell lysis. In 1972, Walter Fiers (University of Ghent, Belgium) was the first to establish the complete nucleotide sequence of a gene and in 1976, of the viral genome of bacteriophage MS2. Some dsDNA bacteriophages encode ribosomal proteins, which are thought to modulate protein translation during phage infection. In the case of the T4 phage, the construction of new virus particles involves the assistance of helper proteins. The base plates are assembled first, with the tails being built upon them afterward. The head capsids, constructed separately, will spontaneously assemble with the tails. The DNA is packed efficiently within the heads. The whole process takes about 15 minutes. Phages may be released via cell lysis, by extrusion, or, in a few cases, by budding. Lysis, by tailed phages, is achieved by an enzyme called endolysin, which attacks and breaks down the cell wall peptidoglycan. An altogether different phage type, the filamentous phage, make the host cell continually secrete new virus particles. Released virions are described as free, and, unless defective, are capable of infecting a new bacterium | https://en.wikipedia.org/wiki?curid=4185 |
Bacteriophage Budding is associated with certain "Mycoplasma" phages. In contrast to virion release, phages displaying a lysogenic cycle do not kill the host but, rather, become long-term residents as prophage. Research in 2017 revealed that the bacteriophage Φ3T makes a short viral protein that signals other bacteriophages to lie dormant instead of killing the host bacterium. Arbitrium is the name given to this protein by the researchers who discovered it. Given the millions of different phages in the environment, phage genomes come in a variety of forms and sizes. RNA phage such as MS2 have the smallest genomes, of only a few kilobases. However, some DNA phage such as T4 may have large genomes with hundreds of genes; the size and shape of the capsid varies along with the size of the genome. The largest bacteriophage genomes reach a size of 735 kb. genomes can be highly mosaic, i.e. the genome of many phage species appear to be composed of numerous individual modules. These modules may be found in other phage species in different arrangements. Mycobacteriophages, bacteriophages with mycobacterial hosts, have provided excellent examples of this mosaicism. In these mycobacteriophages, genetic assortment may be the result of repeated instances of site-specific recombination and illegitimate recombination (the result of phage genome acquisition of bacterial host genetic sequences) | https://en.wikipedia.org/wiki?curid=4185 |
Bacteriophage Evolutionary mechanisms shaping the genomes of bacterial viruses vary between different families and depend upon the type of the nucleic acid, characteristics of the virion structure, as well as the mode of the viral life cycle. Phages often have dramatic effects on their hosts. As a consequence, the transcription pattern of the infected bacterium may change considerably. For instance, infection of "Pseudomonas aeruginosa" by the temperate phage PaP3 changed the expression of 38% (2160/5633) of its host's genes. Many of these effects are probably indirect, hence the challenge becomes to identify the direct interactions among bacteria and phage. Several attempts have been made to map protein–protein interactions among phage and their host. For instance, bacteriophage lambda was found to interact with its host, E. coli, by 31 interactions. However, a large-scale study revealed 62 interactions, most of which were new. Again, the significance of many of these interactions remains unclear, but these studies suggest that there most likely are several key interactions and many indirect interactions whose role remains uncharacterized. Metagenomics has allowed the in-water detection of bacteriophages that was not possible previously. Also, bacteriophages have been used in hydrological tracing and modelling in river systems, especially where surface water and groundwater interactions occur | https://en.wikipedia.org/wiki?curid=4185 |
Bacteriophage The use of phages is preferred to the more conventional dye marker because they are significantly less absorbed when passing through ground waters and they are readily detected at very low concentrations. Non-polluted water may contain approximately 2×10 bacteriophages per ml. Bacteriophages are thought to contribute extensively to horizontal gene transfer in natural environments, principally via transduction, but also via transformation. Metagenomics-based studies also have revealed that viromes from a variety of environments harbor antibiotic-resistance genes, including those that could confer multidrug resistance. The following bacteriophages are extensively studied: | https://en.wikipedia.org/wiki?curid=4185 |
Bacterial conjugation is the transfer of genetic material between bacterial cells by direct cell-to-cell contact or by a bridge-like connection between two cells. This takes place through a pilus. It is a mechanism of horizontal gene transfer as are transformation and transduction although these two other mechanisms do not involve cell-to-cell contact. Classical "E. coli" bacterial conjugation is often regarded as the bacterial equivalent of sexual reproduction or mating since it involves the exchange of genetic material. However, it is not sexual reproduction, since no exchange of gamete occurs, and indeed no generation of a new organism: instead an existing organism is transformed. During classical "E. coli" conjugation the "donor" cell provides a conjugative or mobilizable genetic element that is most often a plasmid or transposon. Most conjugative plasmids have systems ensuring that the "recipient" cell does not already contain a similar element. The genetic information transferred is often beneficial to the recipient. Benefits may include antibiotic resistance, xenobiotic tolerance or the ability to use new metabolites. Such beneficial plasmids may be considered bacterial endosymbionts. Other elements, however, may be viewed as bacterial parasites and conjugation as a mechanism evolved by them to allow for their spread. Conjugation in "Escherichia coli" by spontaneous zygogenesis and in "Mycobacterium smegmatis" by distributive conjugal transfer differ from the more well studied classical "E | https://en.wikipedia.org/wiki?curid=4460 |
Bacterial conjugation coli" conjugation in that these cases involve substantial blending of the parental genomes. The process was discovered by Joshua Lederberg and Edward Tatum in 1946. Conjugation diagram The F-plasmid is an episome (a plasmid that can integrate itself into the bacterial chromosome by homologous recombination) with a length of about 100 kb. It carries its own origin of replication, the "oriV", and an origin of transfer, or "oriT". There can only be one copy of the F-plasmid in a given bacterium, either free or integrated, and bacteria that possess a copy are called "F-positive" or "F-plus" (denoted F). Cells that lack F plasmids are called "F-negative" or "F-minus" (F) and as such can function as recipient cells. Among other genetic information, the F-plasmid carries a "tra" and "trb" locus, which together are about 33 kb long and consist of about 40 genes. The "tra" locus includes the "pilin" gene and regulatory genes, which together form pili on the cell surface. The locus also includes the genes for the proteins that attach themselves to the surface of F bacteria and initiate conjugation. Though there is some debate on the exact mechanism of conjugation it seems that the pili are not the structures through which DNA exchange occurs. This has been shown in experiments where the pilus are allowed to make contact, but then are denatured with SDS and yet DNA transformation still proceeds | https://en.wikipedia.org/wiki?curid=4460 |
Bacterial conjugation Several proteins coded for in the "tra" or "trb" locus seem to open a channel between the bacteria and it is thought that the traD enzyme, located at the base of the pilus, initiates membrane fusion. When conjugation is initiated by a signal the relaxase enzyme creates a nick in one of the strands of the conjugative plasmid at the "oriT". Relaxase may work alone or in a complex of over a dozen proteins known collectively as a relaxosome. In the F-plasmid system the relaxase enzyme is called TraI and the relaxosome consists of TraI, TraY, TraM and the integrated host factor IHF. The nicked strand, or "T-strand", is then unwound from the unbroken strand and transferred to the recipient cell in a 5'-terminus to 3'-terminus direction. The remaining strand is replicated either independent of conjugative action (vegetative replication beginning at the "oriV") or in concert with conjugation (conjugative replication similar to the rolling circle replication of lambda phage). Conjugative replication may require a second nick before successful transfer can occur. A recent report claims to have inhibited conjugation with chemicals that mimic an intermediate step of this second nicking event. If the F-plasmid that is transferred has previously been integrated into the donor's genome (producing an Hfr strain ["High Frequency of Recombination"]) some of the donor's chromosomal DNA may also be transferred with the plasmid DNA | https://en.wikipedia.org/wiki?curid=4460 |
Bacterial conjugation The amount of chromosomal DNA that is transferred depends on how long the two conjugating bacteria remain in contact. In common laboratory strains of "E. coli" the transfer of the entire bacterial chromosome takes about 100 minutes. The transferred DNA can then be integrated into the recipient genome via homologous recombination. A cell culture that contains in its population cells with non-integrated F-plasmids usually also contains a few cells that have accidentally integrated their plasmids. It is these cells that are responsible for the low-frequency chromosomal gene transfers that occur in such cultures. Some strains of bacteria with an integrated F-plasmid can be isolated and grown in pure culture. Because such strains transfer chromosomal genes very efficiently they are called Hfr (high frequency of recombination). The "E. coli" genome was originally mapped by interrupted mating experiments in which various Hfr cells in the process of conjugation were sheared from recipients after less than 100 minutes (initially using a Waring blender). The genes that were transferred were then investigated. Since integration of the F-plasmid into the "E. coli" chromosome is a rare spontaneous occurrence, and since the numerous genes promoting DNA transfer are in the plasmid genome rather than in the bacterial genome, it has been argued that conjugative bacterial gene transfer, as it occurs in the "E. coli" Hfr system, is not an evolutionary adaptation of the bacterial host, nor is it likely ancestral to eukaryotic sex | https://en.wikipedia.org/wiki?curid=4460 |
Bacterial conjugation Spontaneous zygogenesis in "E. coli" In addition to classical bacterial conjugation described above for "E. coli", a form of conjugation referred to as spontaneous zygogenesis (Z-mating for short) is observed in certain strains of "E. coli". In Z-mating there is complete genetic mixing, and unstable diploids are formed that throw off phenotypically haploid cells, of which some show a parental phenotype and some are true recombinants. Conjugation in "Mycobacteria smegmatis", like conjugation in "E. coli", requires stable and extended contact between a donor and a recipient strain, is DNase resistant, and the transferred DNA is incorporated into the recipient chromosome by homologous recombination. However, unlike "E. coli" Hfr conjugation, mycobacterial conjugation is chromosome rather than plasmid based. Furthermore, in contrast to "E. coli" Hfr conjugation, in "M. smegmatis" all regions of the chromosome are transferred with comparable efficiencies. The lengths of the donor segments vary widely, but have an average length of 44.2kb. Since a mean of 13 tracts are transferred, the average total of transferred DNA per genome is 575kb. This process is referred to as "Distributive conjugal transfer." Gray et al. found substantial blending of the parental genomes as a result of conjugation and regarded this blending as reminiscent of that seen in the meiotic products of sexual reproduction. Bacteria related to the nitrogen fixing "Rhizobia" are an interesting case of inter-kingdom conjugation | https://en.wikipedia.org/wiki?curid=4460 |
Bacterial conjugation For example, the tumor-inducing (Ti) plasmid of "Agrobacterium" and the root-tumor inducing (Ri) plasmid of "A. rhizogenes" contain genes that are capable of transferring to plant cells. The expression of these genes effectively transforms the plant cells into opine-producing factories. Opines are used by the bacteria as sources of nitrogen and energy. Infected cells form crown gall or root tumors. The Ti and Ri plasmids are thus endosymbionts of the bacteria, which are in turn endosymbionts (or parasites) of the infected plant. The Ti and Ri plasmids can also be transferred between bacteria using a system (the "tra", or transfer, operon) that is different and independent of the system used for inter-kingdom transfer (the "vir", or virulence, operon). Such transfers create virulent strains from previously avirulent strains. Conjugation is a convenient means for transferring genetic material to a variety of targets. In laboratories, successful transfers have been reported from bacteria to yeast, plants, mammalian cells, diatoms and isolated mammalian mitochondria. Conjugation has advantages over other forms of genetic transfer including minimal disruption of the target's cellular envelope and the ability to transfer relatively large amounts of genetic material (see the above discussion of "E. coli" chromosome transfer). In plant engineering, "Agrobacterium"-like conjugation complements other standard vehicles such as tobacco mosaic virus (TMV) | https://en.wikipedia.org/wiki?curid=4460 |
Bacterial conjugation While TMV is capable of infecting many plant families these are primarily herbaceous dicots. "Agrobacterium"-like conjugation is also primarily used for dicots, but monocot recipients are not uncommon. | https://en.wikipedia.org/wiki?curid=4460 |
Biotechnology is the broad area of biology, involving living systems and organisms to develop or make products. Depending on the tools and applications, it often overlaps with related scientific fields. In the late 20th and early 21st centuries, biotechnology has expanded to include new and diverse sciences, such as genomics, recombinant gene techniques, applied immunology, and development of pharmaceutical therapies and diagnostic tests. The wide concept of "biotech" or "biotechnology" encompasses a wide range of procedures for modifying living organisms according to human purposes, going back to domestication of animals, cultivation of the plants, and "improvements" to these through breeding programs that employ artificial selection and hybridization. Modern usage also includes genetic engineering as well as cell and tissue culture technologies. The American Chemical Society defines biotechnology as the application of biological organisms, systems, or processes by various industries to learning about the science of life and the improvement of the value of materials and organisms such as pharmaceuticals, crops, and livestock. Per the European Federation of Biotechnology, biotechnology is the integration of natural science and organisms, cells, parts thereof, and molecular analogues for products and services. is based on the basic biological sciences (e.g. molecular biology, biochemistry, cell biology, embryology, genetics, microbiology) and conversely provides methods to support and perform basic research in biology | https://en.wikipedia.org/wiki?curid=4502 |
Biotechnology is the research and development in the laboratory using bioinformatics for exploration, extraction, exploitation and production from any living organisms and any source of biomass by means of biochemical engineering where high value-added products could be planned (reproduced by biosynthesis, for example), forecasted, formulated, developed, manufactured, and marketed for the purpose of sustainable operations (for the return from bottomless initial investment on R & D) and gaining durable patents rights (for exclusives rights for sales, and prior to this to receive national and international approval from the results on animal experiment and human experiment, especially on the pharmaceutical branch of biotechnology to prevent any undetected side-effects or safety concerns by using the products). The utilization of biological processes, organisms or systems to produce products that are anticipated to improve human lives is termed biotechnology. By contrast, bioengineering is generally thought of as a related field that more heavily emphasizes higher systems approaches (not necessarily the altering or using of biological materials "directly") for interfacing with and utilizing living things. Bioengineering is the application of the principles of engineering and natural sciences to tissues, cells and molecules. This can be considered as the use of knowledge from working with and manipulating biology to achieve a result that can improve functions in plants and animals | https://en.wikipedia.org/wiki?curid=4502 |
Biotechnology Relatedly, biomedical engineering is an overlapping field that often draws upon and applies "biotechnology" (by various definitions), especially in certain sub-fields of biomedical or chemical engineering such as tissue engineering, biopharmaceutical engineering, and genetic engineering. Although not normally what first comes to mind, many forms of human-derived agriculture clearly fit the broad definition of "'utilizing a biotechnological system to make products". Indeed, the cultivation of plants may be viewed as the earliest biotechnological enterprise. Agriculture has been theorized to have become the dominant way of producing food since the Neolithic Revolution. Through early biotechnology, the earliest farmers selected and bred the best suited crops, having the highest yields, to produce enough food to support a growing population. As crops and fields became increasingly large and difficult to maintain, it was discovered that specific organisms and their by-products could effectively fertilize, restore nitrogen, and control pests. Throughout the history of agriculture, farmers have inadvertently altered the genetics of their crops through introducing them to new environments and breeding them with other plants — one of the first forms of biotechnology. These processes also were included in early fermentation of beer. These processes were introduced in early Mesopotamia, Egypt, China and India, and still use the same basic biological methods | https://en.wikipedia.org/wiki?curid=4502 |
Biotechnology In brewing, malted grains (containing enzymes) convert starch from grains into sugar and then adding specific yeasts to produce beer. In this process, carbohydrates in the grains broke down into alcohols, such as ethanol. Later, other cultures produced the process of lactic acid fermentation, which produced other preserved foods, such as soy sauce. Fermentation was also used in this time period to produce leavened bread. Although the process of fermentation was not fully understood until Louis Pasteur's work in 1857, it is still the first use of biotechnology to convert a food source into another form. Before the time of Charles Darwin's work and life, animal and plant scientists had already used selective breeding. Darwin added to that body of work with his scientific observations about the ability of science to change species. These accounts contributed to Darwin's theory of natural selection. For thousands of years, humans have used selective breeding to improve production of crops and livestock to use them for food. In selective breeding, organisms with desirable characteristics are mated to produce offspring with the same characteristics. For example, this technique was used with corn to produce the largest and sweetest crops. In the early twentieth century scientists gained a greater understanding of microbiology and explored ways of manufacturing specific products | https://en.wikipedia.org/wiki?curid=4502 |
Biotechnology In 1917, Chaim Weizmann first used a pure microbiological culture in an industrial process, that of manufacturing corn starch using "Clostridium acetobutylicum," to produce acetone, which the United Kingdom desperately needed to manufacture explosives during World War I. has also led to the development of antibiotics. In 1928, Alexander Fleming discovered the mold "Penicillium". His work led to the purification of the antibiotic compound formed by the mold by Howard Florey, Ernst Boris Chain and Norman Heatley – to form what we today know as penicillin. In 1940, penicillin became available for medicinal use to treat bacterial infections in humans. The field of modern biotechnology is generally thought of as having been born in 1971 when Paul Berg's (Stanford) experiments in gene splicing had early success. Herbert W. Boyer (Univ. Calif. at San Francisco) and Stanley N. Cohen (Stanford) significantly advanced the new technology in 1972 by transferring genetic material into a bacterium, such that the imported material would be reproduced. The commercial viability of a biotechnology industry was significantly expanded on June 16, 1980, when the United States Supreme Court ruled that a genetically modified microorganism could be patented in the case of "Diamond v. Chakrabarty". Indian-born Ananda Chakrabarty, working for General Electric, had modified a bacterium (of the genus "Pseudomonas") capable of breaking down crude oil, which he proposed to use in treating oil spills | https://en.wikipedia.org/wiki?curid=4502 |
Biotechnology (Chakrabarty's work did not involve gene manipulation but rather the transfer of entire organelles between strains of the "Pseudomonas" bacterium. The MOSFET (metal-oxide-semiconductor field-effect transistor) was invented by Mohamed M. Atalla and Dawon Kahng in 1959. Two years later, Leland C. Clark and Champ Lyons invented the first biosensor in 1962. Biosensor MOSFETs were later developed, and they have since been widely used to measure physical, chemical, biological and environmental parameters. The first BioFET was the ion-sensitive field-effect transistor (ISFET), invented by Piet Bergveld in 1970. It is a special type of MOSFET, where the metal gate is replaced by an ion-sensitive membrane, electrolyte solution and reference electrode. The ISFET is widely used in biomedical applications, such as the detection of DNA hybridization, biomarker detection from blood, antibody detection, glucose measurement, pH sensing, and genetic technology. By the mid-1980s, other BioFETs had been developed, including the gas sensor FET (GASFET), pressure sensor FET (PRESSFET), chemical field-effect transistor (ChemFET), reference ISFET (REFET), enzyme-modified FET (ENFET) and immunologically modified FET (IMFET). By the early 2000s, BioFETs such as the DNA field-effect transistor (DNAFET), gene-modified FET (GenFET) and cell-potential BioFET (CPFET) had been developed | https://en.wikipedia.org/wiki?curid=4502 |
Biotechnology A factor influencing the biotechnology sector's success is improved intellectual property rights legislation—and enforcement—worldwide, as well as strengthened demand for medical and pharmaceutical products to cope with an ageing, and ailing, U.S. population. Rising demand for biofuels is expected to be good news for the biotechnology sector, with the Department of Energy estimating ethanol usage could reduce U.S. petroleum-derived fuel consumption by up to 30% by 2030. The biotechnology sector has allowed the U.S. farming industry to rapidly increase its supply of corn and soybeans—the main inputs into biofuels—by developing genetically modified seeds that resist pests and drought. By increasing farm productivity, biotechnology boosts biofuel production. has applications in four major industrial areas, including health care (medical), crop production and agriculture, non-food (industrial) uses of crops and other products (e.g. biodegradable plastics, vegetable oil, biofuels), and environmental uses. For example, one application of biotechnology is the directed use of microorganisms for the manufacture of organic products (examples include beer and milk products). Another example is using naturally present bacteria by the mining industry in bioleaching. is also used to recycle, treat waste, clean up sites contaminated by industrial activities (bioremediation), and also to produce biological weapons | https://en.wikipedia.org/wiki?curid=4502 |
Biotechnology A series of derived terms have been coined to identify several branches of biotechnology, for example: In medicine, modern biotechnology has many applications in areas such as pharmaceutical drug discoveries and production, pharmacogenomics, and genetic testing (or genetic screening). Pharmacogenomics (a combination of pharmacology and genomics) is the technology that analyses how genetic makeup affects an individual's response to drugs. Researchers in the field investigate the influence of genetic variation on drug responses in patients by correlating gene expression or single-nucleotide polymorphisms with a drug's efficacy or toxicity. The purpose of pharmacogenomics is to develop rational means to optimize drug therapy, with respect to the patients' genotype, to ensure maximum efficacy with minimal adverse effects. Such approaches promise the advent of "personalized medicine"; in which drugs and drug combinations are optimized for each individual's unique genetic makeup. has contributed to the discovery and manufacturing of traditional small molecule pharmaceutical drugs as well as drugs that are the product of biotechnology – biopharmaceutics. Modern biotechnology can be used to manufacture existing medicines relatively easily and cheaply. The first genetically engineered products were medicines designed to treat human diseases. To cite one example, in 1978 Genentech developed synthetic humanized insulin by joining its gene with a plasmid vector inserted into the bacterium "Escherichia coli" | https://en.wikipedia.org/wiki?curid=4502 |
Biotechnology Insulin, widely used for the treatment of diabetes, was previously extracted from the pancreas of abattoir animals (cattle or pigs). The genetically engineered bacteria are able to produce large quantities of synthetic human insulin at relatively low cost. has also enabled emerging therapeutics like gene therapy. The application of biotechnology to basic science (for example through the Human Genome Project) has also dramatically improved our understanding of biology and as our scientific knowledge of normal and disease biology has increased, our ability to develop new medicines to treat previously untreatable diseases has increased as well. Genetic testing allows the genetic diagnosis of vulnerabilities to inherited diseases, and can also be used to determine a child's parentage (genetic mother and father) or in general a person's ancestry. In addition to studying chromosomes to the level of individual genes, genetic testing in a broader sense includes biochemical tests for the possible presence of genetic diseases, or mutant forms of genes associated with increased risk of developing genetic disorders. Genetic testing identifies changes in chromosomes, genes, or proteins. Most of the time, testing is used to find changes that are associated with inherited disorders. The results of a genetic test can confirm or rule out a suspected genetic condition or help determine a person's chance of developing or passing on a genetic disorder. As of 2011 several hundred genetic tests were in use | https://en.wikipedia.org/wiki?curid=4502 |
Biotechnology Since genetic testing may open up ethical or psychological problems, genetic testing is often accompanied by genetic counseling. Genetically modified crops ("GM crops", or "biotech crops") are plants used in agriculture, the DNA of which has been modified with genetic engineering techniques. In most cases, the main aim is to introduce a new trait that does not occur naturally in the species. firms can contribute to future food security by improving the nutrition and viability of urban agriculture. Furthermore, the protection of intellectual property rights encourages private sector investment in agrobiotechnology. For example, in Illinois FARM Illinois (Food and Agriculture RoadMap for Illinois) is an initiative to develop and coordinate farmers, industry, research institutions, government, and nonprofits in pursuit of food and agriculture innovation. In addition, the Illinois Industry Organization (iBIO) is a life sciences industry association with more than 500 life sciences companies, universities, academic institutions, service providers and others as members. The association describes its members as "dedicated to making Illinois and the surrounding Midwest one of the world’s top life sciences centers." Examples in food crops include resistance to certain pests, diseases, stressful environmental conditions, resistance to chemical treatments (e.g. resistance to a herbicide), reduction of spoilage, or improving the nutrient profile of the crop | https://en.wikipedia.org/wiki?curid=4502 |
Biotechnology Examples in non-food crops include production of pharmaceutical agents, biofuels, and other industrially useful goods, as well as for bioremediation. Farmers have widely adopted GM technology. Between 1996 and 2011, the total surface area of land cultivated with GM crops had increased by a factor of 94, from to 1,600,000 km (395 million acres). 10% of the world's crop lands were planted with GM crops in 2010. As of 2011, 11 different transgenic crops were grown commercially on 395 million acres (160 million hectares) in 29 countries such as the US, Brazil, Argentina, India, Canada, China, Paraguay, Pakistan, South Africa, Uruguay, Bolivia, Australia, Philippines, Myanmar, Burkina Faso, Mexico and Spain. Genetically modified foods are foods produced from organisms that have had specific changes introduced into their DNA with the methods of genetic engineering. These techniques have allowed for the introduction of new crop traits as well as a far greater control over a food's genetic structure than previously afforded by methods such as selective breeding and mutation breeding. Commercial sale of genetically modified foods began in 1994, when Calgene first marketed its Flavr Savr delayed ripening tomato. To date most genetic modification of foods have primarily focused on cash crops in high demand by farmers such as soybean, corn, canola, and cotton seed oil. These have been engineered for resistance to pathogens and herbicides and better nutrient profiles | https://en.wikipedia.org/wiki?curid=4502 |
Biotechnology GM livestock have also been experimentally developed; in November 2013 none were available on the market, but in 2015 the FDA approved the first GM salmon for commercial production and consumption. There is a scientific consensus that currently available food derived from GM crops poses no greater risk to human health than conventional food, but that each GM food needs to be tested on a case-by-case basis before introduction. Nonetheless, members of the public are much less likely than scientists to perceive GM foods as safe. The legal and regulatory status of GM foods varies by country, with some nations banning or restricting them, and others permitting them with widely differing degrees of regulation. GM crops also provide a number of ecological benefits, if not used in excess. However, opponents have objected to GM crops per se on several grounds, including environmental concerns, whether food produced from GM crops is safe, whether GM crops are needed to address the world's food needs, and economic concerns raised by the fact these organisms are subject to intellectual property law. Industrial biotechnology (known mainly in Europe as white biotechnology) is the application of biotechnology for industrial purposes, including industrial fermentation. It includes the practice of using cells such as microorganisms, or components of cells like enzymes, to generate industrially useful products in sectors such as chemicals, food and feed, detergents, paper and pulp, textiles and biofuels | https://en.wikipedia.org/wiki?curid=4502 |
Biotechnology In the current decades, significant progress has been done in creating genetically modified organisms (GMOs) that enhance the diversity of applications and economical viability of industrial biotechnology. By using renewable raw materials to produce a variety of chemicals and fuels, industrial biotechnology is actively advancing towards lowering greenhouse gas emissions and moving away from a petrochemical-based economy. The environment can be affected by biotechnologies, both positively and adversely. Vallero and others have argued that the difference between beneficial biotechnology (e.g.bioremediation is to clean up an oil spill or hazard chemical leak) versus the adverse effects stemming from biotechnological enterprises (e.g. flow of genetic material from transgenic organisms into wild strains) can be seen as applications and implications, respectively. Cleaning up environmental wastes is an example of an application of environmental biotechnology; whereas loss of biodiversity or loss of containment of a harmful microbe are examples of environmental implications of biotechnology. The regulation of genetic engineering concerns approaches taken by governments to assess and manage the risks associated with the use of genetic engineering technology, and the development and release of genetically modified organisms (GMO), including genetically modified crops and genetically modified fish | https://en.wikipedia.org/wiki?curid=4502 |
Biotechnology There are differences in the regulation of GMOs between countries, with some of the most marked differences occurring between the US and Europe. Regulation varies in a given country depending on the intended use of the products of the genetic engineering. For example, a crop not intended for food use is generally not reviewed by authorities responsible for food safety. The European Union differentiates between approval for cultivation within the EU and approval for import and processing. While only a few GMOs have been approved for cultivation in the EU a number of GMOs have been approved for import and processing. The cultivation of GMOs has triggered a debate about coexistence of GM and non GM crops. Depending on the coexistence regulations, incentives for cultivation of GM crops differ. In 1988, after prompting from the United States Congress, the National Institute of General Medical Sciences (National Institutes of Health) (NIGMS) instituted a funding mechanism for biotechnology training. Universities nationwide compete for these funds to establish Training Programs (BTPs). Each successful application is generally funded for five years then must be competitively renewed. Graduate students in turn compete for acceptance into a BTP; if accepted, then stipend, tuition and health insurance support is provided for two or three years during the course of their Ph.D. thesis work. Nineteen institutions offer NIGMS supported BTPs. training is also offered at the undergraduate level and in community colleges. | https://en.wikipedia.org/wiki?curid=4502 |
Chemistry is the scientific discipline involved with elements and compounds composed of atoms, molecules and ions: their composition, structure, properties, behavior and the changes they undergo during a reaction with other substances. In the scope of its subject, chemistry occupies an intermediate position between physics and biology. It is sometimes called the central science because it provides a foundation for understanding both basic and applied scientific disciplines at a fundamental level. For example, chemistry explains aspects of plant chemistry (botany), the formation of igneous rocks (geology), how atmospheric ozone is formed and how environmental pollutants are degraded (ecology), the properties of the soil on the moon (astrophysics), how medications work (pharmacology), and how to collect DNA evidence at a crime scene (forensics). addresses topics such as how atoms and molecules interact via chemical bonds to form new chemical compounds. There are four types of chemical bonds: covalent bonds, in which compounds share one or more electron(s); ionic bonds, in which a compound donates one or more electrons to another compound to produce ions (cations and anions); hydrogen bonds; and Van der Waals force bonds. The word "chemistry" comes from "alchemy," which referred to an earlier set of practices that encompassed elements of chemistry, metallurgy, philosophy, astrology, astronomy, mysticism and medicine | https://en.wikipedia.org/wiki?curid=5180 |
Chemistry It is often seen as linked to the quest to turn lead or another common starting material into gold, though in ancient times, the study encompassed many of the questions of modern chemistry being defined as the study of the composition of waters, movement, growth, embodying, disembodying, drawing the spirits from bodies and bonding the spirits within bodies by the early 4th century Greek-Egyptian alchemist Zosimos. An alchemist was called a 'chemist' in popular speech, and later the suffix "-ry" was added to this to describe the art of the chemist as "chemistry". The modern word "alchemy" in turn is derived from the Arabic word "al-kīmīā" (الكیمیاء). In origin, the term is borrowed from the Greek χημία or χημεία. This may have Egyptian origins since "al-kīmīā" is derived from the Greek χημία, which is in turn derived from the word Kemet, which is the ancient name of Egypt in the Egyptian language. Alternately, "al-kīmīā" may derive from χημεία, meaning "cast together". The current model of atomic structure is the quantum mechanical model. Traditional chemistry starts with the study of elementary particles, atoms, molecules, substances, metals, crystals and other aggregates of matter. Matter can be studied in solid, liquid, gas and plasma states, in isolation or in combination. The interactions, reactions and transformations that are studied in chemistry are usually the result of interactions between atoms, leading to rearrangements of the chemical bonds which hold atoms together | https://en.wikipedia.org/wiki?curid=5180 |
Chemistry Such behaviors are studied in a chemistry laboratory. The chemistry laboratory stereotypically uses various forms of laboratory glassware. However glassware is not central to chemistry, and a great deal of experimental (as well as applied/industrial) chemistry is done without it. A chemical reaction is a transformation of some substances into one or more different substances. The basis of such a chemical transformation is the rearrangement of electrons in the chemical bonds between atoms. It can be symbolically depicted through a chemical equation, which usually involves atoms as subjects. The number of atoms on the left and the right in the equation for a chemical transformation is equal. (When the number of atoms on either side is unequal, the transformation is referred to as a nuclear reaction or radioactive decay.) The type of chemical reactions a substance may undergo and the energy changes that may accompany it are constrained by certain basic rules, known as chemical laws. Energy and entropy considerations are invariably important in almost all chemical studies. Chemical substances are classified in terms of their structure, phase, as well as their chemical compositions. They can be analyzed using the tools of chemical analysis, e.g. spectroscopy and chromatography. Scientists engaged in chemical research are known as chemists. Most chemists specialize in one or more sub-disciplines | https://en.wikipedia.org/wiki?curid=5180 |
Chemistry Several concepts are essential for the study of chemistry; some of them are: In chemistry, matter is defined as anything that has rest mass and volume (it takes up space) and is made up of particles. The particles that make up matter have rest mass as well – not all particles have rest mass, such as the photon. Matter can be a pure chemical substance or a mixture of substances. The atom is the basic unit of chemistry. It consists of a dense core called the atomic nucleus surrounded by a space occupied by an electron cloud. The nucleus is made up of positively charged protons and uncharged neutrons (together called nucleons), while the electron cloud consists of negatively charged electrons which orbit the nucleus. In a neutral atom, the negatively charged electrons balance out the positive charge of the protons. The nucleus is dense; the mass of a nucleon is approximately 1,836 times that of an electron, yet the radius of an atom is about 10,000 times that of its nucleus. The atom is also the smallest entity that can be envisaged to retain the chemical properties of the element, such as electronegativity, ionization potential, preferred oxidation state(s), coordination number, and preferred types of bonds to form (e.g., metallic, ionic, covalent). A chemical element is a pure substance which is composed of a single type of atom, characterized by its particular number of protons in the nuclei of its atoms, known as the atomic number and represented by the symbol "Z" | https://en.wikipedia.org/wiki?curid=5180 |
Chemistry The mass number is the sum of the number of protons and neutrons in a nucleus. Although all the nuclei of all atoms belonging to one element will have the same atomic number, they may not necessarily have the same mass number; atoms of an element which have different mass numbers are known as isotopes. For example, all atoms with 6 protons in their nuclei are atoms of the chemical element carbon, but atoms of carbon may have mass numbers of 12 or 13. The standard presentation of the chemical elements is in the periodic table, which orders elements by atomic number. The periodic table is arranged in groups, or columns, and periods, or rows. The periodic table is useful in identifying periodic trends. A "compound" is a pure chemical substance composed of more than one element. The properties of a compound bear little similarity to those of its elements. The standard nomenclature of compounds is set by the International Union of Pure and Applied (IUPAC). Organic compounds are named according to the organic nomenclature system. The names for inorganic compounds are created according to the inorganic nomenclature system. When a compound has more than one component, then they are divided into two classes, the electropositive and the electronegative components. In addition the Chemical Abstracts Service has devised a method to index chemical substances. In this scheme each chemical substance is identifiable by a number known as its CAS registry number | https://en.wikipedia.org/wiki?curid=5180 |
Chemistry A "molecule" is the smallest indivisible portion of a pure chemical substance that has its unique set of chemical properties, that is, its potential to undergo a certain set of chemical reactions with other substances. However, this definition only works well for substances that are composed of molecules, which is not true of many substances (see below). Molecules are typically a set of atoms bound together by covalent bonds, such that the structure is electrically neutral and all valence electrons are paired with other electrons either in bonds or in lone pairs. Thus, molecules exist as electrically neutral units, unlike ions. When this rule is broken, giving the "molecule" a charge, the result is sometimes named a molecular ion or a polyatomic ion. However, the discrete and separate nature of the molecular concept usually requires that molecular ions be present only in well-separated form, such as a directed beam in a vacuum in a mass spectrometer. Charged polyatomic collections residing in solids (for example, common sulfate or nitrate ions) are generally not considered "molecules" in chemistry. Some molecules contain one or more unpaired electrons, creating radicals. Most radicals are comparatively reactive, but some, such as nitric oxide (NO) can be stable | https://en.wikipedia.org/wiki?curid=5180 |
Chemistry The "inert" or noble gas elements (helium, neon, argon, krypton, xenon and radon) are composed of lone atoms as their smallest discrete unit, but the other isolated chemical elements consist of either molecules or networks of atoms bonded to each other in some way. Identifiable molecules compose familiar substances such as water, air, and many organic compounds like alcohol, sugar, gasoline, and the various pharmaceuticals. However, not all substances or chemical compounds consist of discrete molecules, and indeed most of the solid substances that make up the solid crust, mantle, and core of the Earth are chemical compounds without molecules. These other types of substances, such as ionic compounds and network solids, are organized in such a way as to lack the existence of identifiable molecules "per se". Instead, these substances are discussed in terms of formula units or unit cells as the smallest repeating structure within the substance. Examples of such substances are mineral salts (such as table salt), solids like carbon and diamond, metals, and familiar silica and silicate minerals such as quartz and granite. One of the main characteristics of a molecule is its geometry often called its structure. While the structure of diatomic, triatomic or tetra-atomic molecules may be trivial, (linear, angular pyramidal etc.) the structure of polyatomic molecules, that are constituted of more than six atoms (of several elements) can be crucial for its chemical nature | https://en.wikipedia.org/wiki?curid=5180 |
Chemistry A chemical substance is a kind of matter with a definite composition and set of properties. A collection of substances is called a mixture. Examples of mixtures are air and alloys. The mole is a unit of measurement that denotes an amount of substance (also called chemical amount). The mole is defined as the number of atoms found in exactly 0.012 kilogram (or 12 grams) of carbon-12, where the carbon-12 atoms are unbound, at rest and in their ground state. The number of entities per mole is known as the Avogadro constant, and is determined empirically to be approximately 6.022 mol. Molar concentration is the amount of a particular substance per volume of solution, and is commonly reported in mol/dm. In addition to the specific chemical properties that distinguish different chemical classifications, chemicals can exist in several phases. For the most part, the chemical classifications are independent of these bulk phase classifications; however, some more exotic phases are incompatible with certain chemical properties. A "phase" is a set of states of a chemical system that have similar bulk structural properties, over a range of conditions, such as pressure or temperature. Physical properties, such as density and refractive index tend to fall within values characteristic of the phase. The phase of matter is defined by the "phase transition", which is when energy put into or taken out of the system goes into rearranging the structure of the system, instead of changing the bulk conditions | https://en.wikipedia.org/wiki?curid=5180 |
Chemistry Sometimes the distinction between phases can be continuous instead of having a discrete boundary' in this case the matter is considered to be in a supercritical state. When three states meet based on the conditions, it is known as a triple point and since this is invariant, it is a convenient way to define a set of conditions. The most familiar examples of phases are solids, liquids, and gases. Many substances exhibit multiple solid phases. For example, there are three phases of solid iron (alpha, gamma, and delta) that vary based on temperature and pressure. A principal difference between solid phases is the crystal structure, or arrangement, of the atoms. Another phase commonly encountered in the study of chemistry is the "aqueous" phase, which is the state of substances dissolved in aqueous solution (that is, in water). Less familiar phases include plasmas, Bose–Einstein condensates and fermionic condensates and the paramagnetic and ferromagnetic phases of magnetic materials. While most familiar phases deal with three-dimensional systems, it is also possible to define analogs in two-dimensional systems, which has received attention for its relevance to systems in biology. Atoms sticking together in molecules or crystals are said to be bonded with one another. A chemical bond may be visualized as the multipole balance between the positive charges in the nuclei and the negative charges oscillating about them | https://en.wikipedia.org/wiki?curid=5180 |
Chemistry More than simple attraction and repulsion, the energies and distributions characterize the availability of an electron to bond to another atom. A chemical bond can be a covalent bond, an ionic bond, a hydrogen bond or just because of Van der Waals force. Each of these kinds of bonds is ascribed to some potential. These potentials create the interactions which hold atoms together in molecules or crystals. In many simple compounds, valence bond theory, the Valence Shell Electron Pair Repulsion model (VSEPR), and the concept of oxidation number can be used to explain molecular structure and composition. An ionic bond is formed when a metal loses one or more of its electrons, becoming a positively charged cation, and the electrons are then gained by the non-metal atom, becoming a negatively charged anion. The two oppositely charged ions attract one another, and the ionic bond is the electrostatic force of attraction between them. For example, sodium (Na), a metal, loses one electron to become an Na cation while chlorine (Cl), a non-metal, gains this electron to become Cl. The ions are held together due to electrostatic attraction, and that compound sodium chloride (NaCl), or common table salt, is formed. In a covalent bond, one or more pairs of valence electrons are shared by two atoms: the resulting electrically neutral group of bonded atoms is termed a molecule | https://en.wikipedia.org/wiki?curid=5180 |
Chemistry Atoms will share valence electrons in such a way as to create a noble gas electron configuration (eight electrons in their outermost shell) for each atom. Atoms that tend to combine in such a way that they each have eight electrons in their valence shell are said to follow the octet rule. However, some elements like hydrogen and lithium need only two electrons in their outermost shell to attain this stable configuration; these atoms are said to follow the "duet rule", and in this way they are reaching the electron configuration of the noble gas helium, which has two electrons in its outer shell. Similarly, theories from classical physics can be used to predict many ionic structures. With more complicated compounds, such as metal complexes, valence bond theory is less applicable and alternative approaches, such as the molecular orbital theory, are generally used. See diagram on electronic orbitals. In the context of chemistry, energy is an attribute of a substance as a consequence of its atomic, molecular or aggregate structure. Since a chemical transformation is accompanied by a change in one or more of these kinds of structures, it is invariably accompanied by an increase or decrease of energy of the substances involved. Some energy is transferred between the surroundings and the reactants of the reaction in the form of heat or light; thus the products of a reaction may have more or less energy than the reactants | https://en.wikipedia.org/wiki?curid=5180 |
Chemistry A reaction is said to be exergonic if the final state is lower on the energy scale than the initial state; in the case of endergonic reactions the situation is the reverse. A reaction is said to be exothermic if the reaction releases heat to the surroundings; in the case of endothermic reactions, the reaction absorbs heat from the surroundings. Chemical reactions are invariably not possible unless the reactants surmount an energy barrier known as the activation energy. The "speed" of a chemical reaction (at given temperature T) is related to the activation energy E, by the Boltzmann's population factor formula_1 – that is the probability of a molecule to have energy greater than or equal to E at the given temperature T. This exponential dependence of a reaction rate on temperature is known as the Arrhenius equation. The activation energy necessary for a chemical reaction to occur can be in the form of heat, light, electricity or mechanical force in the form of ultrasound. A related concept free energy, which also incorporates entropy considerations, is a very useful means for predicting the feasibility of a reaction and determining the state of equilibrium of a chemical reaction, in chemical thermodynamics. A reaction is feasible only if the total change in the Gibbs free energy is negative, formula_2; if it is equal to zero the chemical reaction is said to be at equilibrium. There exist only limited possible states of energy for electrons, atoms and molecules | https://en.wikipedia.org/wiki?curid=5180 |
Chemistry These are determined by the rules of quantum mechanics, which require quantization of energy of a bound system. The atoms/molecules in a higher energy state are said to be excited. The molecules/atoms of substance in an excited energy state are often much more reactive; that is, more amenable to chemical reactions. The phase of a substance is invariably determined by its energy and the energy of its surroundings. When the intermolecular forces of a substance are such that the energy of the surroundings is not sufficient to overcome them, it occurs in a more ordered phase like liquid or solid as is the case with water (HO); a liquid at room temperature because its molecules are bound by hydrogen bonds. Whereas hydrogen sulfide (HS) is a gas at room temperature and standard pressure, as its molecules are bound by weaker dipole-dipole interactions. The transfer of energy from one chemical substance to another depends on the "size" of energy quanta emitted from one substance. However, heat energy is often transferred more easily from almost any substance to another because the phonons responsible for vibrational and rotational energy levels in a substance have much less energy than photons invoked for the electronic energy transfer. Thus, because vibrational and rotational energy levels are more closely spaced than electronic energy levels, heat is more easily transferred between substances relative to light or other forms of electronic energy | https://en.wikipedia.org/wiki?curid=5180 |
Chemistry For example, ultraviolet electromagnetic radiation is not transferred with as much efficacy from one substance to another as thermal or electrical energy. The existence of characteristic energy levels for different chemical substances is useful for their identification by the analysis of spectral lines. Different kinds of spectra are often used in chemical spectroscopy, e.g. IR, microwave, NMR, ESR, etc. Spectroscopy is also used to identify the composition of remote objects – like stars and distant galaxies – by analyzing their radiation spectra. The term chemical energy is often used to indicate the potential of a chemical substance to undergo a transformation through a chemical reaction or to transform other chemical substances. When a chemical substance is transformed as a result of its interaction with another substance or with energy, a chemical reaction is said to have occurred. A "chemical reaction" is therefore a concept related to the "reaction" of a substance when it comes in close contact with another, whether as a mixture or a solution; exposure to some form of energy, or both. It results in some energy exchange between the constituents of the reaction as well as with the system environment, which may be designed vessels—often laboratory glassware. Chemical reactions can result in the formation or dissociation of molecules, that is, molecules breaking apart to form two or more molecules or rearrangement of atoms within or across molecules | https://en.wikipedia.org/wiki?curid=5180 |
Chemistry Chemical reactions usually involve the making or breaking of chemical bonds. Oxidation, reduction, dissociation, acid-base neutralization and molecular rearrangement are some of the commonly used kinds of chemical reactions. A chemical reaction can be symbolically depicted through a chemical equation. While in a non-nuclear chemical reaction the number and kind of atoms on both sides of the equation are equal, for a nuclear reaction this holds true only for the nuclear particles viz. protons and neutrons. The sequence of steps in which the reorganization of chemical bonds may be taking place in the course of a chemical reaction is called its mechanism. A chemical reaction can be envisioned to take place in a number of steps, each of which may have a different speed. Many reaction intermediates with variable stability can thus be envisaged during the course of a reaction. Reaction mechanisms are proposed to explain the kinetics and the relative product mix of a reaction. Many physical chemists specialize in exploring and proposing the mechanisms of various chemical reactions. Several empirical rules, like the Woodward–Hoffmann rules often come in handy while proposing a mechanism for a chemical reaction. According to the IUPAC gold book, a chemical reaction is "a process that results in the interconversion of chemical species." Accordingly, a chemical reaction may be an elementary reaction or a stepwise reaction | https://en.wikipedia.org/wiki?curid=5180 |
Chemistry An additional caveat is made, in that this definition includes cases where the interconversion of conformers is experimentally observable. Such detectable chemical reactions normally involve sets of molecular entities as indicated by this definition, but it is often conceptually convenient to use the term also for changes involving single molecular entities (i.e. 'microscopic chemical events'). An "ion" is a charged species, an atom or a molecule, that has lost or gained one or more electrons. When an atom loses an electron and thus has more protons than electrons, the atom is a positively charged ion or cation. When an atom gains an electron and thus has more electrons than protons, the atom is a negatively charged ion or anion. Cations and anions can form a crystalline lattice of neutral salts, such as the Na and Cl ions forming sodium chloride, or NaCl. Examples of polyatomic ions that do not split up during acid-base reactions are hydroxide (OH) and phosphate (PO). Plasma is composed of gaseous matter that has been completely ionized, usually through high temperature. A substance can often be classified as an acid or a base. There are several different theories which explain acid-base behavior. The simplest is Arrhenius theory, which states that acid is a substance that produces hydronium ions when it is dissolved in water, and a base is one that produces hydroxide ions when dissolved in water | https://en.wikipedia.org/wiki?curid=5180 |
Chemistry According to Brønsted–Lowry acid-base theory, acids are substances that donate a positive hydrogen ion to another substance in a chemical reaction; by extension, a base is the substance which receives that hydrogen ion. A third common theory is Lewis acid-base theory, which is based on the formation of new chemical bonds. Lewis theory explains that an acid is a substance which is capable of accepting a pair of electrons from another substance during the process of bond formation, while a base is a substance which can provide a pair of electrons to form a new bond. According to this theory, the crucial things being exchanged are charges. There are several other ways in which a substance may be classified as an acid or a base, as is evident in the history of this concept. Acid strength is commonly measured by two methods. One measurement, based on the Arrhenius definition of acidity, is pH, which is a measurement of the hydronium ion concentration in a solution, as expressed on a negative logarithmic scale. Thus, solutions that have a low pH have a high hydronium ion concentration and can be said to be more acidic. The other measurement, based on the Brønsted–Lowry definition, is the acid dissociation constant (K), which measures the relative ability of a substance to act as an acid under the Brønsted–Lowry definition of an acid. That is, substances with a higher K are more likely to donate hydrogen ions in chemical reactions than those with lower K values | https://en.wikipedia.org/wiki?curid=5180 |
Chemistry Redox ("red"uction-"ox"idation) reactions include all chemical reactions in which atoms have their oxidation state changed by either gaining electrons (reduction) or losing electrons (oxidation). Substances that have the ability to oxidize other substances are said to be oxidative and are known as oxidizing agents, oxidants or oxidizers. An oxidant removes electrons from another substance. Similarly, substances that have the ability to reduce other substances are said to be reductive and are known as reducing agents, reductants, or reducers. A reductant transfers electrons to another substance and is thus oxidized itself. And because it "donates" electrons it is also called an electron donor. Oxidation and reduction properly refer to a change in oxidation number—the actual transfer of electrons may never occur. Thus, oxidation is better defined as an increase in oxidation number, and reduction as a decrease in oxidation number. Although the concept of equilibrium is widely used across sciences, in the context of chemistry, it arises whenever a number of different states of the chemical composition are possible, as for example, in a mixture of several chemical compounds that can react with one another, or when a substance can be present in more than one kind of phase. A system of chemical substances at equilibrium, even though having an unchanging composition, is most often not static; molecules of the substances continue to react with one another thus giving rise to a dynamic equilibrium | https://en.wikipedia.org/wiki?curid=5180 |
Chemistry Thus the concept describes the state in which the parameters such as chemical composition remain unchanged over time. Chemical reactions are governed by certain laws, which have become fundamental concepts in chemistry. Some of them are: The history of chemistry spans a period from very old times to the present. Since several millennia BC, civilizations were using technologies that would eventually form the basis of the various branches of chemistry. Examples include extracting metals from ores, making pottery and glazes, fermenting beer and wine, extracting chemicals from plants for medicine and perfume, rendering fat into soap, making glass, and making alloys like bronze. was preceded by its protoscience, alchemy, which is an intuitive but non-scientific approach to understanding the constituents of matter and their interactions. It was unsuccessful in explaining the nature of matter and its transformations, but, by performing experiments and recording the results, alchemists set the stage for modern chemistry. as a body of knowledge distinct from alchemy began to emerge when a clear differentiation was made between them by Robert Boyle in his work "The Sceptical Chymist" (1661). While both alchemy and chemistry are concerned with matter and its transformations, the crucial difference was given by the scientific method that chemists employed in their work | https://en.wikipedia.org/wiki?curid=5180 |
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