A hydroxy or hydroxyl group is the entity with the formula OH. It contains oxygen bonded to hydrogen. In organic chemistry and carboxylic acids contain hydroxy groups; the anion, called hydroxide, consists of a hydroxyl group. According to IUPAC rules, the term hydroxyl refers to the radical OH only, while the functional group −OH is called hydroxy group. Water, carboxylic acids, many other hydroxy-containing compounds can be deprotonated readily; this behavior is rationalized by the disparate electronegativities of hydrogen. Hydroxy-containing compounds engage in hydrogen bonding, which causes them to stick together, leading to higher boiling and melting points than found for compounds that lack this functional group. Organic compounds, which are poorly soluble in water, become water-soluble when they contain two or more hydroxy groups, as illustrated by sugars and amino acid; the hydroxy group is pervasive in biochemistry. Many inorganic compounds contain hydroxy groups, including sulfuric acid, the chemical compound produced on the largest scale industrially.
Hydroxy groups participate in the dehydration reactions that link simple biological molecules into long chains. The joining of a fatty acid to glycerol to form a triacylglycerol removes the −OH from the carboxy end of the fatty acid; the joining of two aldehyde sugars to form a disaccharide removes the −OH from the carboxy group at the aldehyde end of one sugar. The creation of a peptide bond to link two amino acids to make a protein removes the −OH from the carboxy group of one amino acid. Hydroxyl radicals are reactive and undergo chemical reactions that make them short-lived; when biological systems are exposed to hydroxyl radicals, they can cause damage to cells, including those in humans, where they can react with DNA, proteins. In 2009, India's Chandrayaan-1 satellite, NASA's Cassini spacecraft and the Deep Impact probe have each detected the presence of water by evidence of hydroxyl fragments on the Moon; as reported by Richard Kerr, "A spectrometer detected an infrared absorption at a wavelength of 3.0 micrometers that only water or hydroxyl—a hydrogen and an oxygen bound together—could have created."
NASA reported in 2009 that the LCROSS probe revealed an ultraviolet emission spectrum consistent with hydroxyl presence. The Venus Express orbiter sent back Venus science data from April 2006 until December 2014. Results from Venus Express include the detection of hydroxyl in the atmosphere. Hydronium Ion Oxide Reece, Jane. "Unit 1, Chapter 4 &5." In Campbell Biology. Berge, Susan. San Francisco: Pearson Benjamin Cummings. ISBN 978-0-321-55823-7
Phenylalanine is an essential α-amino acid with the formula C9H11NO2. It can be viewed as a benzyl group substituted for the methyl group of alanine, or a phenyl group in place of a terminal hydrogen of alanine; this essential amino acid is classified as neutral, nonpolar because of the inert and hydrophobic nature of the benzyl side chain. The L-isomer is used to biochemically form proteins, coded for by DNA. Phenylalanine is a precursor for tyrosine, the monoamine neurotransmitters dopamine and epinephrine, the skin pigment melanin, it is encoded by the codons UUU and UUC. Phenylalanine is found in the breast milk of mammals, it is used in the manufacture of food and drink products and sold as a nutritional supplement for its reputed analgesic and antidepressant effects. It is a direct precursor to the neuromodulator phenethylamine, a used dietary supplement; as an essential amino acid, phenylalanine is not synthesized de novo in humans and other animals, who must ingest phenylalanine or phenylalanine-containing proteins.
The first description of phenylalanine was made in 1879, when Schulze and Barbieri identified a compound with the empirical formula, C9H11NO2, in yellow lupine seedlings. In 1882, Erlenmeyer and Lipp first synthesized phenylalanine from phenylacetaldehyde, hydrogen cyanide, ammonia; the genetic codon for phenylalanine was first discovered by J. Heinrich Matthaei and Marshall W. Nirenberg in 1961, they showed that by using mRNA to insert multiple uracil repeats into the genome of the bacterium E. coli, they could cause the bacterium to produce a polypeptide consisting of repeated phenylalanine amino acids. This discovery helped to establish the nature of the coding relationship that links information stored in genomic nucleic acid with protein expression in the living cell. Good sources of phenylalanine are eggs, liver, beef and soybeans; the Food and Nutrition Board of the U. S. Institute of Medicine set Recommended Dietary Allowances for essential amino acids in 2002. For phenylalanine plus tyrosine, for adults 19 years and older, 33 mg/kg body weight/day.
L-Phenylalanine is biologically converted into L-tyrosine, another one of the DNA-encoded amino acids. L-tyrosine in turn is converted into L-DOPA, further converted into dopamine and epinephrine; the latter three are known as the catecholamines. Phenylalanine uses the same active transport channel as tryptophan to cross the blood–brain barrier. In excessive quantities, supplementation can interfere with the production of serotonin and other aromatic amino acids as well as nitric oxide due to the overuse of the associated cofactors, iron or tetrahydrobiopterin; the corresponding enzymes in for those compounds are the aromatic amino acid hydroxylase family and nitric oxide synthase. Phenylalanine is the starting compound used in the synthesis of flavonoids. Lignan is derived from tyrosine. Phenylalanine is converted to cinnamic acid by the enzyme phenylalanine ammonia-lyase; the genetic disorder phenylketonuria is the inability to metabolize phenylalanine because of a lack of the enzyme phenylalanine hydroxylase.
Individuals with this disorder are known as "phenylketonurics" and must regulate their intake of phenylalanine. Phenylketonurics use blood tests to monitor the amount of phenylalanine in their blood. Lab results may report phenylalanine levels using either mg/dL and μmol/L. One mg/dL of phenylalanine is equivalent to 60 μmol/L. A "variant form" of phenylketonuria called hyperphenylalaninemia is caused by the inability to synthesize a cofactor called tetrahydrobiopterin, which can be supplemented. Pregnant women with hyperphenylalaninemia may show similar symptoms of the disorder, but these indicators will disappear at the end of gestation. Pregnant women with PKU must control their blood phenylalanine levels if the fetus is heterozygous for the defective gene because the fetus could be adversely affected due to hepatic immaturity. A non-food source of phenylalanine is the artificial sweetener aspartame; this compound is metabolized by the body into several chemical byproducts including phenylalanine.
The breakdown problems phenylketonurics have with the buildup of phenylalanine in the body occurs with the ingestion of aspartame, although to a lesser degree. Accordingly, all products in Australia, the U. S. and Canada that contain aspartame must be labeled: "Phenylketonurics: Contains phenylalanine." In the UK, foods containing aspartame must carry ingredient panels that refer to the presence of "aspartame or E951" and they must be labeled with a warning "Contains a source of phenylalanine." In Brazil, the label "Contém Fenilalanina" is mandatory in products which contain it. These warnings are placed to help individuals avoid such foods. Geneticists sequenced the genome of macaques in 2007, their investigations found "some instances where the normal form of the macaque protein looked like the diseased human protein" including markers for PKU. The stereoisomer D-phenylalanine can be produced by conventional organic synthesis, either as a single enantiomer or as a component of the racemic mixture.
It does not participate in protein biosynthesis although it is found in proteins in small amounts - aged proteins and food proteins that have been processed. The biological functions of D-amino acids remain unclear, although D-phenylalanine has pharmacological activity at niacin receptor 2. DL-Phenylalanine is marketed as a nutritional supplement for its purported analgesic and antidepressant activ
The Jmol applet, among other abilities, offers an alternative to the Chime plug-in, no longer under active development. While Jmol has many features that Chime lacks, it does not claim to reproduce all Chime functions, most notably, the Sculpt mode. Chime requires plug-in installation and Internet Explorer 6.0 or Firefox 2.0 on Microsoft Windows, or Netscape Communicator 4.8 on Mac OS 9. Jmol operates on a wide variety of platforms. For example, Jmol is functional in Mozilla Firefox, Internet Explorer, Google Chrome, Safari. Chemistry Development Kit Comparison of software for molecular mechanics modeling Jmol extension for MediaWiki List of molecular graphics systems Molecular graphics Molecule editor Proteopedia PyMOL SAMSON Official website Wiki with listings of websites and moodles Willighagen, Egon. "Fast and Scriptable Molecular Graphics in Web Browsers without Java3D". Doi:10.1038/npre.2007.50.1
Coffee is a brewed drink prepared from roasted coffee beans, the seeds of berries from certain Coffea species. The genus Coffea is native to tropical Africa and Madagascar, the Comoros, Réunion in the Indian Ocean. Coffee plants are now cultivated in over 70 countries in the equatorial regions of the Americas, Southeast Asia, Indian subcontinent, Africa; the two most grown are C. arabica and C. robusta. Once ripe, coffee berries are picked and dried. Dried coffee seeds are roasted to varying degrees, depending on the desired flavor. Roasted beans are ground and brewed with near-boiling water to produce the beverage known as coffee. Coffee is darkly colored, bitter acidic and has a stimulating effect in humans due to its caffeine content, it is one of the most popular drinks in the world, it can be prepared and presented in a variety of ways. It is served hot, although iced coffee is a popular alternative. Clinical studies indicate that moderate coffee consumption is benign or mildly beneficial in healthy adults, with continuing research on whether long-term consumption lowers the risk of some diseases, although those long-term studies are of poor quality.
The earliest credible evidence of coffee-drinking appears in modern-day Yemen in southern Arabia in the middle of the 15th century in Sufi shrines. It was here in Arabia that coffee seeds were first roasted and brewed in a similar way to how it is now prepared, but the coffee seeds had to be first exported from East Africa to Yemen, as the Coffea arabica plant is thought to have been indigenous to the former. The Yemenis began to cultivate the seed. By the 16th century, the drink had reached Persia and North Africa. From there, it spread to the rest of the world; as of 2016, Brazil was the leading grower of producing one-third of the world total. Coffee is a major export commodity, it is one of the most valuable commodities exported by developing countries. Green, unroasted coffee is one of the most traded agricultural commodities in the world; some controversy has been associated with coffee cultivation and the way developed countries trade with developing nations, as well as the impact on the environment with regards to the clearing of land for coffee-growing and water use.
The markets for fair trade and organic coffee are expanding, notably in the USA. The word coffee appears to have derived from the name of the region where coffee beans were first used by a herder in the 6th or 9th century: kaffa derived from Kaffa Province, the name of the region in ancient Abyssinia; the word "coffee" entered the English language in 1582 via the Dutch koffie, borrowed from the Ottoman Turkish kahve, borrowed in turn from the Arabic qahwah. The Arabic word qahwah was traditionally held to refer to a type of wine whose etymology is given by Arab lexicographers as deriving from the verb qahiya, "to lack hunger", in reference to the drink's reputation as an appetite suppressant, it has been proposed that the source may be the Proto-Central Semitic root q-h-h meaning "dark". The term "coffee pot" dates from 1705; the expression "coffee break" was first attested in 1952. According to legend, ancestors of today's Oromo people in a region of Kaffa in Ethiopia were believed to have been the first to recognize the energizing effect of the coffee plant.
However, there is no direct evidence, found earlier than the 15th century indicating where in Africa coffee first grew or who among the native populations might have used it as a stimulant. The story of Kaldi, the 9th-century Ethiopian goatherd who discovered coffee when he noticed how excited his goats became after eating the beans from a coffee plant, did not appear in writing until 1671 and is apocryphal. Other accounts attribute the discovery of coffee to Sheikh Omar. According to an ancient chronicle, known for his ability to cure the sick through prayer, was once exiled from Mocha in Yemen to a desert cave near Ousab. Starving, Omar found them to be bitter, he tried roasting the seeds to improve the flavor. He tried boiling them to soften the seed, which resulted in a fragrant brown liquid. Upon drinking the liquid Omar was sustained for days; as stories of this "miracle drug" reached Mocha, Omar was made a saint. The earliest credible evidence of coffee-drinking or knowledge of the coffee tree appears in the middle of the 15th century in the accounts of Ahmed al-Ghaffar in Yemen.
It was here in Arabia that coffee seeds were first roasted and brewed, in a similar way to how it is prepared now. Coffee was used by Sufi circles to stay awake for their religious rituals. Accounts differ on the origin of the coffee plant prior to its appearance in Yemen. From Ethiopia, coffee could have been introduced to Yemen via trade across the Red Sea. One account credits Muhammad Ibn Sa'd for bringing the beverage to Aden from the African coast. Other early accounts say Ali ben Omar of the Shadhili Sufi order was the first to introduce coffee to Arabia. According to al Shardi, Ali ben Omar may have encountered coffee during his stay with the Adal king Sadadin's companions in 1401. Famous 16th-century Islamic scholar Ibn Hajar al-Haytami notes in his
3-Deoxy-D-arabino-heptulosonic acid 7-phosphate
3-Deoxy-D-arabino-heptulosonic acid 7-phosphate is a 7-carbon ulonic acid. This compound is found in the shikimic acid biosynthesis pathway and is an intermediate in the production of aromatic amino acids. Phosphoenolpyruvate and erythrose-4-phosphate react to form 3-deoxy-D-arabinoheptulosonate-7-phosphate, in a reaction catalyzed by the enzyme DAHP synthase. DAHP is transformed to 3-dehydroquinate, in a reaction catalyzed by DHQ synthase. Although this reaction requires nicotinamide adenine dinucleotide as a cofactor, the enzymic mechanism regenerates it, resulting in the net use of no NAD; the mechanism of ring closure is complex, but involves an aldol condensation at C-2 and C-7. Metabolic engineering has improved production of DAHP by Escherichia coli; the first step, condensation of 3-deoxy-D-arabino-heptulosonic acid 7-phosphate from PEP/E4P, uses three isoenzymes AroF, AroG, AroH. Each one of these has its synthesis regulated from tyrosine and tryptophan, respectively; these isoenzymes all have the ability to help regulate synthesis of DAHP by the method of feedback inhibition.
This acts in the cell by monitoring the concentrations of each of the three aromatic amino acids. When there is too much of any one of them, that one will allosterically control the DAHP synthetase by “turning it off”. With the first step of the common pathway shut off, synthesis of the three amino acids can not proceed; the rest of the enzymes is in the common pathway. Webby, Celia J.. "The Structure of 3-Deoxy-d-arabino-heptulosonate 7-phosphate Synthase from Mycobacterium tuberculosis Reveals a Common Catalytic Scaffold and Ancestry for Type I and Type II Enzymes". Journal of Molecular Biology. 354: 927–39. Doi:10.1016/j.jmb.2005.09.093. PMID 16288916
In chemistry in biochemistry, a fatty acid is a carboxylic acid with a long aliphatic chain, either saturated or unsaturated. Most occurring fatty acids have an unbranched chain of an number of carbon atoms, from 4 to 28. Fatty acids are not found in organisms, but instead as three main classes of esters: triglycerides and cholesterol esters. In any of these forms, fatty acids are both important dietary sources of fuel for animals and they are important structural components for cells; the concept of fatty acid was introduced by Michel Eugène Chevreul, though he used some variant terms: graisse acide and acide huileux. Fatty acids differ by length categorized as short to long. Short-chain fatty acids are fatty acids with aliphatic tails of five or fewer carbons. Medium-chain fatty acids are fatty acids with aliphatic tails of 6 to 12 carbons, which can form medium-chain triglycerides. Long-chain fatty acids are fatty acids with aliphatic tails of 13 to 21 carbons. Long chain fatty acids are fatty acids with aliphatic tails of 22 or more carbons.
Saturated fatty acids have no C=C double bonds. They have the same formula CH3nCOOH, with variations in "n". An important saturated fatty acid is stearic acid, which when neutralized with lye is the most common form of soap. Unsaturated fatty acids have one or more C=C double bonds; the C=C double bonds can give either cis or trans isomers. Cis A cis configuration means that the two hydrogen atoms adjacent to the double bond stick out on the same side of the chain; the rigidity of the double bond freezes its conformation and, in the case of the cis isomer, causes the chain to bend and restricts the conformational freedom of the fatty acid. The more double bonds the chain has in the cis configuration, the less flexibility it has; when a chain has many cis bonds, it becomes quite curved in its most accessible conformations. For example, oleic acid, with one double bond, has a "kink" in it, whereas linoleic acid, with two double bonds, has a more pronounced bend. Α-Linolenic acid, with three double bonds, favors a hooked shape.
The effect of this is that, in restricted environments, such as when fatty acids are part of a phospholipid in a lipid bilayer, or triglycerides in lipid droplets, cis bonds limit the ability of fatty acids to be packed, therefore can affect the melting temperature of the membrane or of the fat. Trans A trans configuration, by contrast, means that the adjacent two hydrogen atoms lie on opposite sides of the chain; as a result, they do not cause the chain to bend much, their shape is similar to straight saturated fatty acids. In most occurring unsaturated fatty acids, each double bond has three n carbon atoms after it, for some n, all are cis bonds. Most fatty acids in the trans configuration are not found in nature and are the result of human processing; the differences in geometry between the various types of unsaturated fatty acids, as well as between saturated and unsaturated fatty acids, play an important role in biological processes, in the construction of biological structures. The position of the carbon atoms in a fatty acid can be indicated from the −COOH end, or from the −CH3 end.
If indicated from the −COOH end the C-1, C-2, C-3, …. Notation is used. If the position is counted from the other, −CH3, end the position is indicated by the ω-n notation; the positions of the double bonds in a fatty acid chain can, therefore, be indicated in two ways, using the C-n or the ω-n notation. Thus, in an 18 carbon fatty acid, a double bond between C-12 and C-13 is reported either as Δ12 if counted from the −COOH end, or as ω-6 if counting from the −CH3 end; the "Δ" is the Greek letter delta. Omega is the last letter in the Greek alphabet, is therefore used to indicate the “last” carbon atom in the fatty acid chain. Since the ω-n notation is used exclusively to indicate the positions of the double bonds close to the −CH3 end in essential fatty acids, there is no necessity for an equivalent “Δ”-like notation - the use of the “ω-n” notation always refers to the position of a double bond. Fatty acids with an odd number of carbon atoms are called odd-chain fatty acids, whereas the rest are even-chain fatty acids.
The difference is relevant to gluconeogenesis. The following table describes the most common systems of naming fatty acids; when circulating in the plasma are not in their ester, fatty acids are known as non-esterified fatty acids or free fatty acids. FFAs are always bound to a transport protein, such as albumin. Fatty acids are produced industrially by the hydrolysis of triglycerides, with the removal of glycerol. Phospholipids represent another source; some fatty acids are produced synthetically by hydrocarboxylation of alkenes. Template:Says whom? In animals, fatty acids are formed from carbohydrates predominantly in the liver, adipose tissue, the mammary glands during lactation. Carbohydrates are converted into pyruvate by glycolysis as the first important step in the conversion of carbohydrates into fatty acids. Pyruvate is decarboxylated to form acetyl-CoA in the mitochondrion. However, this acetyl CoA needs to be transported into cytosol where the synthesis of fatty acids occurs; this cannot occur directly.
To obtain cytosol
Transamination, a chemical reaction that transfers an amino group to a ketoacid to form new amino acids. This pathway is responsible for the deamination of most amino acids; this is one of the major degradation pathways which convert essential amino acids to nonessential amino acids. Transamination in biochemistry is accomplished by enzymes called aminotransferases. Α-ketoglutarate acts as the predominant amino-group acceptor and produces glutamate as the new amino acid. Aminoacid + α-ketoglutarate ↔ α-keto acid + GlutamateGlutamate's amino group, in turn, is transferred to oxaloacetate in a second transamination reaction yielding aspartate. Glutamate + oxaloacetate ↔ α-ketoglutarate + aspartate Transamination catalyzed by aminotransferase occurs in two stages. In the first step, the α amino group of an aminoacid is transferred to the enzyme, producing the corresponding α-keto acid and the aminated enzyme. During the second stage, the amino group is transferred to the keto acid acceptor, forming the amino acid product while regenerating the enzyme.
The chirality of an amino acid is determined during transamination. For the reaction to complete, aminotransferases require participation of aldehyde containing coenzyme, pyridoxal-5'-phosphate, a derivative of Pyridoxine; the amino group is accommodated by conversion of this coenzyme to pyridoxamine-5'-phosphate. PLP is covalently attached to the enzyme via a Schiff Base linkage formed by the condensation of its aldehyde group with the ε-amino group of an enzymatic Lys residue; the Schiff base, conjugated to the enzymes pyridinium ring is the focus of the coenzyme activity. The product of transamination reactions depend on the availability of α-keto acids; the products are either alanine, aspartate or glutamate, since their corresponding alpha-keto acids are produced through metabolism of fuels. Being a major degradative aminoacid pathway, lysine and threonine are the only three amino acids that do not always undergo transamination and rather use respective dehydrogenase. Alternative Mechanism A second type of transamination reaction can be described as a nucleophilic substitution of one amine or amide anion on an amine or ammonium salt.
For example, the attack of a primary amine by a primary amide anion can be used to prepare secondary amines: RNH2 + R'NH− → RR'NH + NH2− Symmetric secondary amines can be prepared using Raney nickel. And quaternary ammonium salts can be dealkylated using ethanolamine: R4N+ + NH2CH2CH2OH → R3N + RN+H2CH2CH2OH Aminonaphthalenes undergo transaminations. Transamination is mediated by several different aminotransferase enzymes; these may be specific for individual amino acids, or they may be able to process a group of chemically similar ones. The latter applies to the group of the branched-chain amino acids, which comprises leucine and valine; the two common types of aminotransferases are Alanine aminotransferase and Aspartate aminotransferase. • Smith, M. B. and March, J. Advanced Organic Chemistry: Reactions and Structure, 5th ed. Wiley, 2001, p. 503. ISBN 0-471-58589-0 • Gerald Booth "Naphthalene Derivatives" in Ullmann's Encyclopedia of Industrial Chemistry, 2005, Wiley-VCH, Weinheim. Doi:10.1002/14356007.a17_009 Voet & Voet.
"Biochemistry" Fourth edition Amino Acid Biosynthesis The chemical logic behind aminoacid degradation and the urea cycle