Cyclohexane conformation
A cyclohexane conformation is any of several three-dimensional shapes that a cyclohexane molecule can assume while maintaining the integrity of its chemical bonds. The internal angles of a flat regular hexagon are 120°, while the preferred angle between successive bonds in a carbon chain is about 109.5°, the tetrahedral angle. Therefore, the cyclohexane ring tends to assume certain non-planar conformations, which have all angles closer to 109.5° and therefore a lower strain energy than the flat hexagonal shape. The most important shapes are called chair, half-chair and twist-boat; the molecule can switch between these conformations, only two of them—chair and twist-boat—can be isolated in pure form. Cyclohexane conformations have been extensively studied in organic chemistry because they are the classical example of conformational isomerism and have noticeable influence on the physical and chemical properties of cyclohexane. In 1890, Hermann Sachse, a 28-year-old assistant in Berlin, published instructions for folding a piece of paper to represent two forms of cyclohexane he called symmetrical and unsymmetrical.
He understood that these forms had two positions for the hydrogen atoms, that two chairs would interconvert, how certain substituents might favor one of the chair forms. Because he expressed all this in mathematical language, few chemists of the time understood his arguments, he had several attempts at publishing these ideas, but none succeeded in capturing the imagination of chemists. His death in 1893 at the age of 31 meant, it was only in 1918 when Ernst Mohr, based on the molecular structure of diamond, solved using the very new technique of x-ray crystallography, was able to argue that Sachse's chair was the pivotal motif. Derek Barton and Odd Hassel shared the 1969 Nobel Prize for work on the conformations of cyclohexane and various other molecules; the carbon-carbon bonds along the cyclohexane ring are sp³ hybrid orbitals, which have tetrahedral symmetry. Therefore, the angles between bonds of a tetravalent carbon atom have a preferred value θ ≈ 109.5°. The bonds have a fixed bond length λ.
On the other hand, adjacent carbon atoms are free to rotate about the axis of the bond. Therefore, a ring, warped so that the bond lengths and angles are close to those ideal values will have less strain energy than a flat ring with 120° angles. For each particular conformation of the carbon ring, the directions of the 12 carbon-hydrogen bonds are fixed. There are eight warped polygons with six distinguished corners that have all internal angles equal to θ and all sides equal to λ, they comprise two ideal chair conformations, where the carbons alternately lie above and below the mean ring plane. In theory, a molecule with any of those ring conformations would be free of angle strain. However, due to interactions between the hydrogen atoms, the angles and bond lengths of the actual chair forms are different from the nominal values. For the same reasons, the actual boat forms have higher energy than the chair forms. Indeed, the boat forms are unstable, deform spontaneously to twist-boat conformations that are local minima of the total energy, therefore stable.
Each of the stable ring conformations can be transformed into any other without breaking the ring. However, such transformations must go through other states with stressed rings. In particular, they must go through unstable states where four successive carbon atoms lie on the same plane; these shapes are called half-chair conformations. In 2011, Donna Nelson and Christopher Brammer surveyed comprehensive undergraduate organic chemistry textbooks in use at that time, in order to determine consistency among the textbooks and with research literature; the two chair conformations have the lowest total energy, are therefore the most stable, have D3d symmetry. In the basic chair conformation, the carbons C1 through C6 alternate between two parallel planes, one with C1, C3 and C5, the other with C2, C4, C6; the molecule has a symmetry axis perpendicular to these two planes, is congruent to itself after a rotation of 120° about that axis. The two chair conformations have the same shape; the perpendicular projection of the ring onto its mean plane is a regular hexagon.
All C-C bonds are tilted relative to the mean plane. As a consequence of the ring warping, six of the 12 carbon-hydrogen bonds end up perpendicular to the mean plane and parallel to the symmetry axis, with alternating directions, are said to be axial; the other six C-H bonds lie parallel to the mean plane, are said to be equatorial. The precise angles are such that the two C-H bonds in each carbon, one axial and one equatorial, point in opposite senses relative to the symmetry axis. Thus, in a chair conformation, there are three C-H bonds of each kind — axial "up", axial "down", equatorial "up", equatorial "down"; the hydrogens in successive carbons are thus staggered. This geometry is preserved when the hydrogen atoms are replaced by halogens or other simple
Carbohydrate
A carbohydrate is a biomolecule consisting of carbon and oxygen atoms with a hydrogen–oxygen atom ratio of 2:1 and thus with the empirical formula Cmn. This formula holds true for monosaccharides; some exceptions exist. The carbohydrates are technically hydrates of carbon; the term is most common in biochemistry, where it is a synonym of saccharide, a group that includes sugars and cellulose. The saccharides are divided into four chemical groups: monosaccharides, disaccharides and polysaccharides. Monosaccharides and disaccharides, the smallest carbohydrates, are referred to as sugars; the word saccharide comes from the Greek word σάκχαρον, meaning "sugar". While the scientific nomenclature of carbohydrates is complex, the names of the monosaccharides and disaccharides often end in the suffix -ose, as in the monosaccharides fructose and glucose and the disaccharides sucrose and lactose. Carbohydrates perform numerous roles in living organisms. Polysaccharides serve as structural components; the 5-carbon monosaccharide ribose is an important component of coenzymes and the backbone of the genetic molecule known as RNA.
The related deoxyribose is a component of DNA. Saccharides and their derivatives include many other important biomolecules that play key roles in the immune system, preventing pathogenesis, blood clotting, development, they are found in a wide variety of processed foods. Starch is a polysaccharide, it is abundant in cereals and processed food based on cereal flour, such as bread, pizza or pasta. Sugars appear in human diet as table sugar, lactose and fructose, both of which occur in honey, many fruits, some vegetables. Table sugar, milk, or honey are added to drinks and many prepared foods such as jam and cakes. Cellulose, a polysaccharide found in the cell walls of all plants, is one of the main components of insoluble dietary fiber. Although it is not digestible, insoluble dietary fiber helps to maintain a healthy digestive system by easing defecation. Other polysaccharides contained in dietary fiber include resistant starch and inulin, which feed some bacteria in the microbiota of the large intestine, are metabolized by these bacteria to yield short-chain fatty acids.
In scientific literature, the term "carbohydrate" has many synonyms, like "sugar", "saccharide", "ose", "glucide", "hydrate of carbon" or "polyhydroxy compounds with aldehyde or ketone". Some of these terms, specially "carbohydrate" and "sugar", are used with other meanings. In food science and in many informal contexts, the term "carbohydrate" means any food, rich in the complex carbohydrate starch or simple carbohydrates, such as sugar. In lists of nutritional information, such as the USDA National Nutrient Database, the term "carbohydrate" is used for everything other than water, fat and ethanol; this includes chemical compounds such as acetic or lactic acid, which are not considered carbohydrates. It includes dietary fiber, a carbohydrate but which does not contribute much in the way of food energy though it is included in the calculation of total food energy just as though it were a sugar. In the strict sense, "sugar" is applied for sweet, soluble carbohydrates, many of which are used in food.
The name "carbohydrate" was used in chemistry for any compound with the formula Cm n. Following this definition, some chemists considered formaldehyde to be the simplest carbohydrate, while others claimed that title for glycolaldehyde. Today, the term is understood in the biochemistry sense, which excludes compounds with only one or two carbons and includes many biological carbohydrates which deviate from this formula. For example, while the above representative formulas would seem to capture the known carbohydrates and abundant carbohydrates deviate from this. For example, carbohydrates display chemical groups such as: N-acetyl, carboxylic acid and deoxy modifications. Natural saccharides are built of simple carbohydrates called monosaccharides with general formula n where n is three or more. A typical monosaccharide has the structure H–x–y–H, that is, an aldehyde or ketone with many hydroxyl groups added one on each carbon atom, not part of the aldehyde or ketone functional group. Examples of monosaccharides are glucose and glyceraldehydes.
However, some biological substances called "monosaccharides" do not conform to this formula and there are many chemicals that do conform to this formula but are not considered to be monosaccharides. The open-chain form of a monosaccharide coexists with a closed ring form where the aldehyde/ketone carbonyl group carbon and hydroxyl group react forming a hemiacetal with a new C–O–C bridge. Monosaccharides can be linked togeth
Golgi apparatus
The Golgi apparatus known as the Golgi complex, Golgi body, or the Golgi, is an organelle found in most eukaryotic cells. It was identified in 1897 by the Italian scientist Camillo Golgi and named after him in 1898. Part of the endomembrane system in the cytoplasm, the Golgi apparatus packages proteins into membrane-bound vesicles inside the cell before the vesicles are sent to their destination; the Golgi apparatus resides at the intersection of the secretory and endocytic pathways. It is of particular importance in processing proteins for secretion, containing a set of glycosylation enzymes that attach various sugar monomers to proteins as the proteins move through the apparatus. Owing to its large size and distinctive structure, the Golgi apparatus was one of the first organelles to be discovered and observed in detail, it was discovered in 1898 by Italian physician Camillo Golgi during an investigation of the nervous system. After first observing it under his microscope, he termed the structure as apparato reticolare interno.
Some doubted the discovery at first, arguing that the appearance of the structure was an optical illusion created by the observation technique used by Golgi. With the development of modern microscopes in the 20th century, the discovery was confirmed. Early references to the Golgi apparatus referred to it by various names including the "Golgi–Holmgren apparatus", "Golgi–Holmgren ducts", "Golgi–Kopsch apparatus"; the term "Golgi apparatus" was used in 1910 and first appeared in the scientific literature in 1913, while "Golgi complex" was introduced in 1956. The subcellular localization of the Golgi apparatus varies among eukaryotes. In mammals, a single Golgi apparatus is located near the cell nucleus, close to the centrosome. Tubular connections are responsible for linking the stacks together. Localization and tubular connections of the Golgi apparatus are dependent on microtubules. In experiments it is seen that as microtubules are depolymerized the Golgi apparatuses lose mutual connections and become individual stacks throughout the cytoplasm.
In yeast, multiple Golgi apparatuses are scattered throughout the cytoplasm. In plants, Golgi stacks are not concentrated at the centrosomal region and do not form Golgi ribbons. Organization of the plant Golgi depends on actin cables and not microtubules; the common feature among Golgi is. In most eukaryotes, the Golgi apparatus is made up of a series of compartments and is a collection of fused, flattened membrane-enclosed disks known as cisternae, originating from vesicular clusters that bud off the endoplasmic reticulum. A mammalian cell contains 40 to 100 stacks of cisternae. Between four and eight cisternae are present in a stack; this collection of cisternae is broken down into cis and trans compartments, making up two main networks: the cis Golgi network and the trans Golgi network. The CGN is the first cisternal structure, the TGN is the final, from which proteins are packaged into vesicles destined to lysosomes, secretory vesicles, or the cell surface; the TGN is positioned adjacent to the stack, but can be separate from it.
The TGN may act as an early endosome in yeast and plants. There are organizational differences in the Golgi apparatus among eukaryotes. In some yeasts, Golgi stacking is not observed. Pichia pastoris does have stacked Golgi. In plants, the individual stacks of the Golgi apparatus seem to operate independently; the Golgi apparatus tends to be larger and more numerous in cells that synthesize and secrete large amounts of substances. In all eukaryotes, each cisternal stack has a trans exit face; these faces are characterized by unique biochemistry. Within individual stacks are assortments of enzymes responsible for selectively modifying protein cargo; these modifications influence the fate of the protein. The compartmentalization of the Golgi apparatus is advantageous for separating enzymes, thereby maintaining consecutive and selective processing steps: enzymes catalyzing early modifications are gathered in the cis face cisternae, enzymes catalyzing modifications are found in trans face cisternae of the Golgi stacks.
The Golgi apparatus is a major collection and dispatch station of protein products received from the endoplasmic reticulum. Proteins synthesized in the ER are packaged into vesicles, which fuse with the Golgi apparatus; these cargo proteins are destined for secretion via exocytosis or for use in the cell. In this respect, the Golgi can be thought of as similar to a post office: it packages and labels items which it sends to different parts of the cell or to the extracellular space; the Golgi apparatus is involved in lipid transport and lysosome formation. The structure and function of the Golgi apparatus are intimately linked. Individual stacks have different assortments of enzymes, allowing for progressive processing of cargo proteins as they travel from the cisternae to the trans Golgi face. Enzymatic reactions within the Golgi stacks occur near its membrane surfaces, where enzymes are anchored; this feature is in contrast to the ER, which has soluble enzymes in its lumen. Much of the enzymatic processing is post-translational modification of proteins.
For example, phosphorylation of oligosaccharides on lysosomal proteins occurs in the early CGN. Cis cisterna are associ
Cellulase
Cellulase is any of several enzymes produced chiefly by fungi and protozoans that catalyze cellulolysis, the decomposition of cellulose and of some related polysaccharides. The name is used for any occurring mixture or complex of various such enzymes, that act serially or synergistically to decompose cellulosic material. Cellulases break down the cellulose molecule into monosaccharides such as beta-glucose, or shorter polysaccharides and oligosaccharides. Cellulose breakdown is of considerable economic importance, because it makes a major constituent of plants available for consumption and use in chemical reactions; the specific reaction involved is the hydrolysis of the 1,4-beta-D-glycosidic linkages in cellulose, hemicellulose and cereal beta-D-glucans. Because cellulose molecules bind to each other, cellulolysis is difficult compared to the breakdown of other polysaccharides such as starch. Most mammals have only limited ability to digest dietary fibres such as cellulose by themselves. In many herbivorous animals such as ruminants like cattle and sheep and hindgut fermenters like horses, cellulases are produced by symbiotic bacteria.
Cellulases are produced by a few types of animals, such as some termites and earthworms. Several different kinds of cellulases are known, which differ mechanistically. Synonyms and specific enzymes associated with the name "cellulase" include endo-1,4-beta-D-glucanase, carboxymethyl cellulase, celludextrinase, cellulase A, cellulosin AP, alkali cellulase, cellulase A 3, 9.5 cellulase, pancellase SS. Enzymes that cleave lignin have been called cellulases, but this old usage is deprecated. Five general types of cellulases based on the type of reaction catalyzed: Endocellulases randomly cleave internal bonds at amorphous sites that create new chain ends. Exocellulases or cellobiohydrolases cleave two to four units from the ends of the exposed chains produced by endocellulase, resulting in tetrasaccharides or disaccharides, such as cellobiose. Exocellulases are further classified into type I, that work processively from the reducing end of the cellulose chain, type II, that work processively from the nonreducing end.
Cellobiases or beta-glucosidases hydrolyse the exocellulase product into individual monosaccharides. Oxidative cellulases depolymerize cellulose by radical reactions, as for instance cellobiose dehydrogenase. Cellulose phosphorylases depolymerize cellulose using phosphates instead of water. Avicelase has exclusively exo-cellulase activity, since avicel is a micro-crystalline substrate. Within the above types there are progressive and nonprogressive types. Progressive cellulase will continue to interact with a single polysaccharide strand, nonprogressive cellulase will interact once disengage and engage another polysaccharide strand. Cellulase action is considered to be synergistic as all three classes of cellulase can yield much more sugar than the addition of all three separately. Aside from ruminants, most animals do not produce cellulase in their bodies and can only break down cellulose through fermentation, limiting their ability to use energy in fibrous plant material. Most fungal cellulases have a two-domain structure, with one catalytic domain and one cellulose binding domain, that are connected by a flexible linker.
This structure is adapted for working on an insoluble substrate, it allows the enzyme to diffuse two-dimensionally on a surface in a caterpillar-like fashion. However, there are cellulases that lack cellulose binding domains. Both binding of substrates and catalysis depend on the three-dimensional structure of the enzyme which arises as a consequence of the level of protein folding; the amino acid sequence and arrangement of their residues that occur within the active site, the position where the substrate binds, may influence factors like binding affinity of ligands, stabilization of substrates within the active site and catalysis. The substrate structure is complementary to the precise active site structure of enzyme. Changes in the position of residues may result in distortion of one or more of these interactions. Additional factors like temperature, pH and metal ions influence the non-covalent interactions between enzyme structure; the Thermotoga maritima species make cellulases consisting of 2 beta-sheets surrounding a central catalytic region, the active-site.
The enzyme is categorised as an endoglucanase, which internally cleaves β-1,4 -glycosydic bonds in cellulose chains facilitating further degradation of the polymer. Different species in the same family as T. Maritima make cellulases with different structures. Cellulases produced by the species Coprinopsis Cinerea consists of seven protein strands in the shape of an enclosed tunnel called a beta/alpha barrel; these enzymes hydrolyse the substrate carboxymethyl cellulose. Binding of the substrate in the active site induces a change in conformation which allows degradation of the molecule. In many bacteria, cellulases in-vivo are complex enzyme structures organized in supramolecular complexes, the cellulosomes, they can contain, but are not limited to, five different enzymatic subunits representing namely endocellulases, cellobiases, oxidative cellulases and cellulose phosphorylases wherein only endocellulases and cellobiases participate in the actual hydrolysis of the β linkage. The number of sub-units making up cellulosomes can determine the r
Cellulose
Cellulose is an organic compound with the formula n, a polysaccharide consisting of a linear chain of several hundred to many thousands of β linked D-glucose units. Cellulose is an important structural component of the primary cell wall of green plants, many forms of algae and the oomycetes; some species of bacteria secrete it to form biofilms. Cellulose is the most abundant organic polymer on Earth; the cellulose content of cotton fiber is 90%, that of wood is 40–50%, that of dried hemp is 57%. Cellulose is used to produce paperboard and paper. Smaller quantities are converted into a wide variety of derivative products such as cellophane and rayon. Conversion of cellulose from energy crops into biofuels such as cellulosic ethanol is under development as a renewable fuel source. Cellulose for industrial use is obtained from wood pulp and cotton; some animals ruminants and termites, can digest cellulose with the help of symbiotic micro-organisms that live in their guts, such as Trichonympha. In human nutrition, cellulose is a non-digestible constituent of insoluble dietary fiber, acting as a hydrophilic bulking agent for feces and aiding in defecation.
Cellulose was discovered in 1838 by the French chemist Anselme Payen, who isolated it from plant matter and determined its chemical formula. Cellulose was used to produce the first successful thermoplastic polymer, celluloid, by Hyatt Manufacturing Company in 1870. Production of rayon from cellulose began in the 1890s and cellophane was invented in 1912. Hermann Staudinger determined the polymer structure of cellulose in 1920; the compound was first chemically synthesized by Kobayashi and Shoda. Cellulose has no taste, is odorless, is hydrophilic with the contact angle of 20–30 degrees, is insoluble in water and most organic solvents, is chiral and is biodegradable, it was shown to melt at 467 °C in 2016. It can be broken down chemically into its glucose units by treating it with concentrated mineral acids at high temperature. Cellulose is derived from D-glucose units; this linkage motif contrasts with that for α-glycosidic bonds present in glycogen. Cellulose is a straight chain polymer. Unlike starch, no coiling or branching occurs and the molecule adopts an extended and rather stiff rod-like conformation, aided by the equatorial conformation of the glucose residues.
The multiple hydroxyl groups on the glucose from one chain form hydrogen bonds with oxygen atoms on the same or on a neighbor chain, holding the chains together side-by-side and forming microfibrils with high tensile strength. This confers tensile strength in cell walls, where cellulose microfibrils are meshed into a polysaccharide matrix. Compared to starch, cellulose is much more crystalline. Whereas starch undergoes a crystalline to amorphous transition when heated beyond 60–70 °C in water, cellulose requires a temperature of 320 °C and pressure of 25 MPa to become amorphous in water. Several different crystalline structures of cellulose are known, corresponding to the location of hydrogen bonds between and within strands. Natural cellulose is cellulose I, with structures Iα and Iβ. Cellulose produced by bacteria and algae is enriched in Iα while cellulose of higher plants consists of Iβ. Cellulose in regenerated cellulose fibers is cellulose II; the conversion of cellulose I to cellulose II is irreversible, suggesting that cellulose I is metastable and cellulose II is stable.
With various chemical treatments it is possible to produce the structures cellulose III and cellulose IV. Many properties of cellulose depend on its chain length or degree of polymerization, the number of glucose units that make up one polymer molecule. Cellulose from wood pulp has typical chain lengths between 1700 units. Molecules with small chain length resulting from the breakdown of cellulose are known as cellodextrins. Cellulose contains 44.44% carbon, 6.17% hydrogen, 49.39% oxygen. The chemical formula of cellulose is n where n is the degree of polymerization and represents the number of glucose groups. Plant-derived cellulose is found in a mixture with hemicellulose, lignin and other substances, while bacterial cellulose is quite pure, has a much higher water content and higher tensile strength due to higher chain lengths. Cellulose is soluble in Schweizer's reagent, cupriethylenediamine, cadmiumethylenediamine, N-methylmorpholine N-oxide, lithium chloride / dimethylacetamide; this is used in the production of regenerated celluloses from dissolving pulp.
Cellulose is soluble in many kinds of ionic liquids. Cellulose consists of amorphous regions. By treating it with strong acid, the amorphous regions can be broken up, thereby producing nanocrystalline cellulose, a novel material with many desirable properties. Nanocrystalline cellulose was used as the filler phase in bio-based polymer matrices to produce nanocomposites with superior thermal and mechanical properties. Given a cellulose-containing material, the carbohydrate portion that does not dissolve in a 17.5% solution of sodium hydroxide at 20 °C is α cellulose, true cellulose. Acidification of the extract precipitates β cellulose; the portion that dissolves in base but does not precipitate with acid is γ cellulose. Cellulose can be assayed using a method described by Updegraff in 1969, where the fiber is dissolved in acetic and nitric acid to remov
Polymer
A polymer is a large molecule, or macromolecule, composed of many repeated subunits. Due to their broad range of properties, both synthetic and natural polymers play essential and ubiquitous roles in everyday life. Polymers range from familiar synthetic plastics such as polystyrene to natural biopolymers such as DNA and proteins that are fundamental to biological structure and function. Polymers, both natural and synthetic, are created via polymerization of many small molecules, known as monomers, their large molecular mass relative to small molecule compounds produces unique physical properties, including toughness, a tendency to form glasses and semicrystalline structures rather than crystals. The terms polymer and resin are synonymous with plastic; the term "polymer" derives from the Greek word πολύς and μέρος, refers to a molecule whose structure is composed of multiple repeating units, from which originates a characteristic of high relative molecular mass and attendant properties. The units composing polymers derive or conceptually, from molecules of low relative molecular mass.
The term was coined in 1833 by Jöns Jacob Berzelius, though with a definition distinct from the modern IUPAC definition. The modern concept of polymers as covalently bonded macromolecular structures was proposed in 1920 by Hermann Staudinger, who spent the next decade finding experimental evidence for this hypothesis. Polymers are studied in the fields of biophysics and macromolecular science, polymer science. Products arising from the linkage of repeating units by covalent chemical bonds have been the primary focus of polymer science. Polyisoprene of latex rubber is an example of a natural/biological polymer, the polystyrene of styrofoam is an example of a synthetic polymer. In biological contexts all biological macromolecules—i.e. Proteins, nucleic acids, polysaccharides—are purely polymeric, or are composed in large part of polymeric components—e.g. Isoprenylated/lipid-modified glycoproteins, where small lipidic molecules and oligosaccharide modifications occur on the polyamide backbone of the protein.
The simplest theoretical models for polymers are ideal chains. Polymers are of two types: occurring and synthetic or man made. Natural polymeric materials such as hemp, amber, wool and natural rubber have been used for centuries. A variety of other natural polymers exist, such as cellulose, the main constituent of wood and paper; the list of synthetic polymers in order of worldwide demand, includes polyethylene, polystyrene, polyvinyl chloride, synthetic rubber, phenol formaldehyde resin, nylon, polyacrylonitrile, PVB, many more. More than 330 million tons of these polymers are made every year. Most the continuously linked backbone of a polymer used for the preparation of plastics consists of carbon atoms. A simple example is polyethylene. Many other structures do exist. Oxygen is commonly present in polymer backbones, such as those of polyethylene glycol, DNA. Polymerization is the process of combining many small molecules known as monomers into a covalently bonded chain or network. During the polymerization process, some chemical groups may be lost from each monomer.
This happens in the polymerization of PET polyester. The monomers are terephthalic acid and ethylene glycol but the repeating unit is —OC—C6H4—COO—CH2—CH2—O—, which corresponds to the combination of the two monomers with the loss of two water molecules; the distinct piece of each monomer, incorporated into the polymer is known as a repeat unit or monomer residue. Laboratory synthetic methods are divided into two categories, step-growth polymerization and chain-growth polymerization; the essential difference between the two is that in chain growth polymerization, monomers are added to the chain one at a time only, such as in polyethylene, whereas in step-growth polymerization chains of monomers may combine with one another directly, such as in polyester. Newer methods, such as plasma polymerization do not fit neatly into either category. Synthetic polymerization reactions may be carried out without a catalyst. Laboratory synthesis of biopolymers of proteins, is an area of intensive research. There are three main classes of biopolymers: polysaccharides and polynucleotides.
In living cells, they may be synthesized by enzyme-mediated processes, such as the formation of DNA catalyzed by DNA polymerase. The synthesis of proteins involves multiple enzyme-mediated processes to transcribe genetic information from the DNA to RNA and subsequently translate that information to synthesize the specified protein from amino acids; the protein may be modified further following translation in order to provide appropriate structure and functioning. There are other biopolymers such as rubber, suberin and lignin. Occurring polymers such as cotton and rubber were familiar materials for years before synthetic polymers such as polyethene and perspex appeared on the market. Many commercially important polymers are synthesized by chemical modification of occurring polymers. Prominent examples inclu
Acid
An acid is a molecule or ion capable of donating a hydron, or, capable of forming a covalent bond with an electron pair. The first category of acids is the proton donors or Brønsted acids. In the special case of aqueous solutions, proton donors form the hydronium ion H3O+ and are known as Arrhenius acids. Brønsted and Lowry generalized the Arrhenius theory to include non-aqueous solvents. A Brønsted or Arrhenius acid contains a hydrogen atom bonded to a chemical structure, still energetically favorable after loss of H+. Aqueous Arrhenius acids have characteristic properties which provide a practical description of an acid. Acids form aqueous solutions with a sour taste, can turn blue litmus red, react with bases and certain metals to form salts; the word acid is derived from the Latin acidus/acēre meaning sour. An aqueous solution of an acid has a pH less than 7 and is colloquially referred to as'acid', while the strict definition refers only to the solute. A lower pH means a higher acidity, thus a higher concentration of positive hydrogen ions in the solution.
Chemicals or substances having the property of an acid are said to be acidic. Common aqueous acids include hydrochloric acid, acetic acid, sulfuric acid, citric acid; as these examples show, acids can be solutions or pure substances, can be derived from acids that are solids, liquids, or gases. Strong acids and some concentrated weak acids are corrosive, but there are exceptions such as carboranes and boric acid; the second category of acids are Lewis acids. An example is boron trifluoride, whose boron atom has a vacant orbital which can form a covalent bond by sharing a lone pair of electrons on an atom in a base, for example the nitrogen atom in ammonia. Lewis considered this as a generalization of the Brønsted definition, so that an acid is a chemical species that accepts electron pairs either directly or by releasing protons into the solution, which accept electron pairs. However, hydrogen chloride, acetic acid, most other Brønsted-Lowry acids cannot form a covalent bond with an electron pair and are therefore not Lewis acids.
Conversely, many Lewis acids are not Brønsted-Lowry acids. In modern terminology, an acid is implicitly a Brønsted acid and not a Lewis acid, since chemists always refer to a Lewis acid explicitly as a Lewis acid. Modern definitions are concerned with the fundamental chemical reactions common to all acids. Most acids encountered in everyday life are aqueous solutions, or can be dissolved in water, so the Arrhenius and Brønsted-Lowry definitions are the most relevant; the Brønsted-Lowry definition is the most used definition. Hydronium ions are acids according to all three definitions. Although alcohols and amines can be Brønsted-Lowry acids, they can function as Lewis bases due to the lone pairs of electrons on their oxygen and nitrogen atoms; the Swedish chemist Svante Arrhenius attributed the properties of acidity to hydrogen ions or protons in 1884. An Arrhenius acid is a substance that, when added to water, increases the concentration of H+ ions in the water. Note that chemists write H+ and refer to the hydrogen ion when describing acid-base reactions but the free hydrogen nucleus, a proton, does not exist alone in water, it exists as the hydronium ion, H3O+.
Thus, an Arrhenius acid can be described as a substance that increases the concentration of hydronium ions when added to water. Examples include molecular substances such as acetic acid. An Arrhenius base, on the other hand, is a substance which increases the concentration of hydroxide ions when dissolved in water; this decreases the concentration of hydronium because the ions react to form H2O molecules: H3O+ + OH− ⇌ H2O + H2ODue to this equilibrium, any increase in the concentration of hydronium is accompanied by a decrease in the concentration of hydroxide. Thus, an Arrhenius acid could be said to be one that decreases hydroxide concentration, while an Arrhenius base increases it. In an acidic solution, the concentration of hydronium ions is greater than 10−7 moles per liter. Since pH is defined as the negative logarithm of the concentration of hydronium ions, acidic solutions thus have a pH of less than 7. While the Arrhenius concept is useful for describing many reactions, it is quite limited in its scope.
In 1923 chemists Johannes Nicolaus Brønsted and Thomas Martin Lowry independently recognized that acid-base reactions involve the transfer of a proton. A Brønsted-Lowry acid is a species. Brønsted-Lowry acid-base theory has several advantages over Arrhenius theory. Consider the following reactions of acetic acid, the organic acid that gives vinegar its characteristic taste: CH3COOH + H2O ⇌ CH3COO− + H3O+ CH3COOH + NH3 ⇌ CH3COO− + NH+4Both theories describe the first reaction: CH3COOH acts as an Arrhenius acid because it acts as a source of H3O+ when dissolved in water, it acts as a Brønsted acid by donating a proton to water. In the second example CH3COOH undergoes the same transformation, in this case donating a proton to ammonia, but does not relate to the Arrhenius definition of an acid because the reaction does not produce hydronium. CH3COOH is
