In enzymology, a ribokinase is an enzyme that catalyzes the chemical reaction ATP + D-ribose ⇌ ADP + D-ribose 5-phosphateThus, the two substrates of this enzyme are ATP and D-ribose, whereas its two products are ADP and D-ribose 5-phosphate. The systematic name of this enzyme class is ATP:D-ribose 5-phosphotransferase. Other names in common use include deoxyribokinase, D-ribokinase; this enzyme participates in pentose phosphate pathway. Ribokinase belongs to the phosphofructokinase B family of sugar kinases. Other members of this family include adenosine kinase, inosine-guanosine kinase, 1-phosphofructokinase; the members of the PfkB/RK family are identified by the presence of three conserved sequence motifs and the enzymatic activity of this family of protein shows a dependence on the presence of pentavalent ions. The conserved NXXE motif, a distinctive property of the PfkB family of proteins, is involved in pentavalent ion dependency; the structures of RK and several other PfK family of proteins have been determined from a number of organisms.
Despite low sequence similarity between AdK and other PfkB family of proteins, these proteins are quite similar at structural levels. As of late 2007, 7 structures have been solved for this class of enzymes, with PDB accession codes 1GQT, 1RK2, 1RKA, 1RKD, 1RKS, 1VM7, 2FV7
Hermann Emil Louis Fischer FRS FRSE FCS was a German chemist and 1902 recipient of the Nobel Prize in Chemistry. He discovered the Fischer esterification, he developed the Fischer projection, a symbolic way of drawing asymmetric carbon atoms. He never used his first given name, was known throughout his life as Emil Fischer. Fischer was born in Euskirchen, near Cologne, the son of Laurenz Fischer, a businessman, his wife Julie Poensgen. After graduating he wished to study natural sciences, but his father compelled him to work in the family business until determining that his son was unsuitable. Fischer attended the University of Bonn in 1871, but switched to the University of Strasbourg in 1872, he earned his doctorate in 1874 under Adolf von Baeyer with his study of phthaleins and was appointed to a position at the university. Fischer is noted for his work on sugars: among other work, the organic synthesis of D--glucose and purines. Fischer was instrumental in the discovery of barbiturates, a class of sedative drugs used for insomnia, epilepsy and anesthesia.
Along with the physician Josef von Mering, he helped to launch the first barbiturate sedative, barbital, in 1904. In 1897 he put forward the idea to create the International Atomic Weights Commission. Fischer was elected a Foreign Member of the Royal Society in 1899. Many names of chemical reactions and concepts are named after him: Nobel Lecture Syntheses in the Purine and Sugar Group from Nobelprize.org website Eminent Chemists of Our Time By Benjamin Harrow pages 216–239, published 1920 by Von Nostrand Company at books.google.com. Guide to the Emil Fischer Papers at The Bancroft Library Text-book of Physiological Chemistry in Thirty Lectures by Emil Abderhalden, translated by William Thomas Hall and George Defren. American Journal of Diseases of Children 1911 volume 2 by the American Medical Association refers to Fischer's work. An Introduction to the History of Medicine: With Medical Chronology by Fielding Hudson Garrison, page 708 refers to Fischer and Merings discovery of the drugs veronal and proponal, published 1921 by Saunders Company.
1914 Year Book of the American Pharmaceutical Association, page 438 abstracts Fischer and Strauss's work on Phenol-Glucosides – Synthetic Production from Berlin d. D Chem. Germany, page 45 No. 12. Texts on Wikisource: "Fischer, Emil". New International Encyclopedia. 1905. "Fischer, Emil". Encyclopædia Britannica. 1911. "Fischer, Emil". Encyclopedia Americana. 1920
In chemistry, phosphorylation of a molecule is the attachment of a phosphoryl group. Together with its counterpart, dephosphorylation, it is critical for many cellular processes in biology. Phosphorylation is important for protein function. Many proteins are phosphorylated temporarily, as are many sugars and other molecules. Protein phosphorylation is considered the most abundant post-translational modification in eukaryotes. Phosphorylation can occur on serine and tyrosine side chains through phosphoester bond formation, on histidine and arginine through phosphoramidate bonds, on aspartic acid and glutamic acid through mixed anhydride linkages. Recent evidence confirms widespread histidine phosphorylation at both the 1 and 3 N-atoms of the imidazole ring Recent work from 2017 suggests widespread human protein phosphorylation on multiple non-canonical amino acids, including motifs containing phosphorylated histidine, glutamate and lysine in HeLa cell extracts. Due to the chemical lability of these phosphorylated residues, in marked contrast to Ser and Tyr phosphorylation, the analysis of phosphorylated histidine using standard biochemical and mass spectrometric approaches is much more challenging and special procedures and separation techniques are required for their preservation alongside classical Ser and Tyr phosphorylation.
The prominent role of protein phosphorylation in biochemistry is illustrated by the huge body of studies published on the subject. Phosphorylation of sugars is the first stage in their catabolism. Phosphorylation allows cells to accumulate sugars because the phosphate group prevents the molecules from diffusing back across their transporter. Phosphorylation of glucose is a key reaction in sugar metabolism because many sugars are first converted to glucose before they are metabolized further; the chemical equation for the conversion of D-glucose to D-glucose-6-phosphate in the first step of glycolysis is given by D-glucose + ATP → D-glucose-6-phosphate + ADPΔG° = −16.7 kJ/mol Researcher D. G. Walker of the University of Birmingham determined the presence of two specific enzymes in adult guinea pig liver, both of which catalyze the phosphorylation of glucose to glucose 6 phosphate; the two enzymes have been identified as a specific non-specific hexokinase. Hepatic cell is permeable to glucose, the initial rate of phosphorylation of glucose is the rate-limiting step in glucose metabolism by the liver and non-specific hexokinase.
The role of glucose 6-phosphate in glycogen synthase: High blood glucose concentration causes an increase in intracellular levels of glucose 6 phosphate in liver, skeletal muscle and fat tissue. And non-specific hexokinase. In liver, synthesis of glycogen is directly correlated by blood glucose concentration and in skeletal muscle and adipocytes, glucose has a minor effect on glycogen synthase. High blood glucose releases insulin, stimulating the trans location of specific glucose transporters to the cell membrane; the liver’s crucial role in controlling blood sugar concentrations by breaking down glucose into carbon dioxide and glycogen is characterized by the negative delta G value, which indicates that this is a point of regulation with. The hexokinase enzyme has a low Km, indicating a high affinity for glucose, so this initial phosphorylation can proceed when glucose levels at nanoscopic scale within the blood; the phosphorylation of glucose can be enhanced by the binding of Fructose-6-phosphate, lessened by the binding fructose-1-phosphate.
Fructose consumed in the diet is converted to F1P in the liver. This negates the action of F6P on glucokinase, which favors the forward reaction; the capacity of liver cells to phosphorylate fructose exceeds capacity to metabolize fructose-1-phosphate. Consuming excess fructose results in an imbalance in liver metabolism, which indirectly exhausts the liver cell’s supply of ATP. Allosteric activation by glucose 6 phosphate, which acts as an effector, stimulates glycogen synthase, glucose 6 phosphate may inhibit the phosphorylation of glycogen synthase by cyclic AMP-stimulated protein kinase. Phosphorylation of glucose is imperative in processes within the body. For example, phosphorylating glucose is necessary for insulin-dependent mechanistic target of rapamycin pathway activity within the heart; this further suggests a link between cardiac growth. Reversible phosphorylation of proteins is an important regulatory mechanism that occurs in both prokaryotic and eukaryotic organisms, it is estimated that 230,000, 156,000 and 40,000 phosphorylation sites exist in human and yeast, respectively.
Kinases phosphorylate proteins and phosphatases dephosphorylate proteins. Many enzymes and receptors "off" by phosphorylation and dephosphorylation. Reversible phosphorylation results in a conformational change in the structure in many enzymes and receptors, causing them to become activated or deactivated. Phosphorylation occurs on serine, threonine and histidine residues in eukaryotic proteins. Histidine phosphorylation of eukaryotic proteins appears to be much more frequent than tyrosine phos
Metabolism is the set of life-sustaining chemical reactions in organisms. The three main purposes of metabolism are: the conversion of food to energy to run cellular processes; these enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, respond to their environments.. Metabolic reactions may be categorized as catabolic - the breaking down of compounds. Catabolism releases energy, anabolism consumes energy; the chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed through a series of steps into another chemical, each step being facilitated by a specific enzyme. Enzymes are crucial to metabolism because they allow organisms to drive desirable reactions that require energy that will not occur by themselves, by coupling them to spontaneous reactions that release energy. Enzymes act as catalysts - they allow a reaction to proceed more - and they allow the regulation of the rate of a metabolic reaction, for example in response to changes in the cell's environment or to signals from other cells.
The metabolic system of a particular organism determines which substances it will find nutritious and which poisonous. For example, some prokaryotes use hydrogen sulfide as a nutrient, yet this gas is poisonous to animals; the basal metabolic rate of an organism is the measure of the amount of energy consumed by all of these chemical reactions. A striking feature of metabolism is the similarity of the basic metabolic pathways among vastly different species. For example, the set of carboxylic acids that are best known as the intermediates in the citric acid cycle are present in all known organisms, being found in species as diverse as the unicellular bacterium Escherichia coli and huge multicellular organisms like elephants; these similarities in metabolic pathways are due to their early appearance in evolutionary history, their retention because of their efficacy. Most of the structures that make up animals and microbes are made from three basic classes of molecule: amino acids and lipids; as these molecules are vital for life, metabolic reactions either focus on making these molecules during the construction of cells and tissues, or by breaking them down and using them as a source of energy, by their digestion.
These biochemicals can be joined together to make polymers such as DNA and proteins, essential macromolecules of life. Proteins are made of amino acids arranged in a linear chain joined together by peptide bonds. Many proteins are enzymes. Other proteins have structural or mechanical functions, such as those that form the cytoskeleton, a system of scaffolding that maintains the cell shape. Proteins are important in cell signaling, immune responses, cell adhesion, active transport across membranes, the cell cycle. Amino acids contribute to cellular energy metabolism by providing a carbon source for entry into the citric acid cycle when a primary source of energy, such as glucose, is scarce, or when cells undergo metabolic stress. Lipids are the most diverse group of biochemicals, their main structural uses are as part of biological membranes both internal and external, such as the cell membrane, or as a source of energy. Lipids are defined as hydrophobic or amphipathic biological molecules but will dissolve in organic solvents such as benzene or chloroform.
The fats are a large group of compounds that contain fatty glycerol. Several variations on this basic structure exist, including alternate backbones such as sphingosine in the sphingolipids, hydrophilic groups such as phosphate as in phospholipids. Steroids such as cholesterol are another major class of lipids. Carbohydrates are aldehydes or ketones, with many hydroxyl groups attached, that can exist as straight chains or rings. Carbohydrates are the most abundant biological molecules, fill numerous roles, such as the storage and transport of energy and structural components; the basic carbohydrate units are called monosaccharides and include galactose and most glucose. Monosaccharides can be linked together to form polysaccharides in limitless ways; the two nucleic acids, DNA and RNA, are polymers of nucleotides. Each nucleotide is composed of a phosphate attached to a ribose or deoxyribose sugar group, attached to a nitrogenous base. Nucleic acids are critical for the storage and use of genetic information, its interpretation through the processes of transcription and protein biosynthesis.
This information is propagated through DNA replication. Many viruses have an RNA genome, such as HIV, which uses reverse transcription to create a DNA template from its viral RNA genome. RNA in ribozymes such as spliceosomes and ribosomes is similar to enzymes as it can catalyze chemical reactions. Individual nucleosides are made
Ribonucleic acid is a polymeric molecule essential in various biological roles in coding, decoding and expression of genes. RNA and DNA are nucleic acids, along with lipids and carbohydrates, constitute the four major macromolecules essential for all known forms of life. Like DNA, RNA is assembled as a chain of nucleotides, but unlike DNA it is more found in nature as a single-strand folded onto itself, rather than a paired double-strand. Cellular organisms use messenger RNA to convey genetic information that directs synthesis of specific proteins. Many viruses encode their genetic information using an RNA genome; some RNA molecules play an active role within cells by catalyzing biological reactions, controlling gene expression, or sensing and communicating responses to cellular signals. One of these active processes is protein synthesis, a universal function in which RNA molecules direct the assembly of proteins on ribosomes; this process uses transfer RNA molecules to deliver amino acids to the ribosome, where ribosomal RNA links amino acids together to form proteins.
Like DNA, most biologically active RNAs, including mRNA, tRNA, rRNA, snRNAs, other non-coding RNAs, contain self-complementary sequences that allow parts of the RNA to fold and pair with itself to form double helices. Analysis of these RNAs has revealed that they are structured. Unlike DNA, their structures do not consist of long double helices, but rather collections of short helices packed together into structures akin to proteins. In this fashion, RNAs can achieve chemical catalysis. For instance, determination of the structure of the ribosome—an RNA-protein complex that catalyzes peptide bond formation—revealed that its active site is composed of RNA; each nucleotide in RNA contains a ribose sugar, with carbons numbered 1' through 5'. A base is attached to the 1' position, in general, cytosine, guanine, or uracil. Adenine and guanine are purines and uracil are pyrimidines. A phosphate group is attached to the 5' position of the next; the phosphate groups have a negative charge each. The bases form hydrogen bonds between cytosine and guanine, between adenine and uracil and between guanine and uracil.
However, other interactions are possible, such as a group of adenine bases binding to each other in a bulge, or the GNRA tetraloop that has a guanine–adenine base-pair. An important structural component of RNA that distinguishes it from DNA is the presence of a hydroxyl group at the 2' position of the ribose sugar; the presence of this functional group causes the helix to take the A-form geometry, although in single strand dinucleotide contexts, RNA can also adopt the B-form most observed in DNA. The A-form geometry results in a deep and narrow major groove and a shallow and wide minor groove. A second consequence of the presence of the 2'-hydroxyl group is that in conformationally flexible regions of an RNA molecule, it can chemically attack the adjacent phosphodiester bond to cleave the backbone. RNA is transcribed with only four bases, but these bases and attached sugars can be modified in numerous ways as the RNAs mature. Pseudouridine, in which the linkage between uracil and ribose is changed from a C–N bond to a C–C bond, ribothymidine are found in various places.
Another notable modified base is hypoxanthine, a deaminated adenine base whose nucleoside is called inosine. Inosine plays a key role in the wobble hypothesis of the genetic code. There are more than 100 other occurring modified nucleosides; the greatest structural diversity of modifications can be found in tRNA, while pseudouridine and nucleosides with 2'-O-methylribose present in rRNA are the most common. The specific roles of many of these modifications in RNA are not understood. However, it is notable that, in ribosomal RNA, many of the post-transcriptional modifications occur in functional regions, such as the peptidyl transferase center and the subunit interface, implying that they are important for normal function; the functional form of single-stranded RNA molecules, just like proteins requires a specific tertiary structure. The scaffold for this structure is provided by secondary structural elements that are hydrogen bonds within the molecule; this leads to several recognizable "domains" of secondary structure like hairpin loops and internal loops.
Since RNA is charged, metal ions such as Mg2+ are needed to stabilise many secondary and tertiary structures. The occurring enantiomer of RNA is D-RNA composed of D-ribonucleotides. All chirality centers are located in the D-ribose. By the use of L-ribose or rather L-ribonucleotides, L-RNA can be synthesized. L-RNA is much more stable against degradation by RNase. Like other structured biopolymers such as proteins, one can define topology of a folded RNA molecule; this is done based on arrangement of intra-chain contacts within a folded RNA, termed as circuit topology. Synthesis of RNA is catalyzed by an enzyme—RNA polymerase—using DNA as a template, a process known as transcription. Initiation of transcription begins with the binding of the enzyme to a promoter sequence in the DNA; the DNA double helix is unwound by the helicase activity of the enzyme. The enzyme progresses along the template strand in the 3’ to 5’ direction, synthesizing a complementary RNA molecule with elongation occ
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
Carbon is a chemical element with symbol C and atomic number 6. It is nonmetallic and tetravalent—making four electrons available to form covalent chemical bonds, it belongs to group 14 of the periodic table. Three isotopes occur 12C and 13C being stable, while 14C is a radionuclide, decaying with a half-life of about 5,730 years. Carbon is one of the few elements known since antiquity. Carbon is the 15th most abundant element in the Earth's crust, the fourth most abundant element in the universe by mass after hydrogen and oxygen. Carbon's abundance, its unique diversity of organic compounds, its unusual ability to form polymers at the temperatures encountered on Earth enables this element to serve as a common element of all known life, it is the second most abundant element in the human body by mass after oxygen. The atoms of carbon can bond together in different ways, termed allotropes of carbon; the best known are graphite and amorphous carbon. The physical properties of carbon vary with the allotropic form.
For example, graphite is opaque and black while diamond is transparent. Graphite is soft enough to form a streak on paper, while diamond is the hardest occurring material known. Graphite is a good electrical conductor. Under normal conditions, carbon nanotubes, graphene have the highest thermal conductivities of all known materials. All carbon allotropes are solids under normal conditions, with graphite being the most thermodynamically stable form at standard temperature and pressure, they are chemically resistant and require high temperature to react with oxygen. The most common oxidation state of carbon in inorganic compounds is +4, while +2 is found in carbon monoxide and transition metal carbonyl complexes; the largest sources of inorganic carbon are limestones and carbon dioxide, but significant quantities occur in organic deposits of coal, peat and methane clathrates. Carbon forms a vast number of compounds, more than any other element, with ten million compounds described to date, yet that number is but a fraction of the number of theoretically possible compounds under standard conditions.
For this reason, carbon has been referred to as the "king of the elements". The allotropes of carbon include graphite, one of the softest known substances, diamond, the hardest occurring substance, it bonds with other small atoms, including other carbon atoms, is capable of forming multiple stable covalent bonds with suitable multivalent atoms. Carbon is known to form ten million different compounds, a large majority of all chemical compounds. Carbon has the highest sublimation point of all elements. At atmospheric pressure it has no melting point, as its triple point is at 10.8±0.2 MPa and 4,600 ± 300 K, so it sublimes at about 3,900 K. Graphite is much more reactive than diamond at standard conditions, despite being more thermodynamically stable, as its delocalised pi system is much more vulnerable to attack. For example, graphite can be oxidised by hot concentrated nitric acid at standard conditions to mellitic acid, C66, which preserves the hexagonal units of graphite while breaking up the larger structure.
Carbon sublimes in a carbon arc, which has a temperature of about 5800 K. Thus, irrespective of its allotropic form, carbon remains solid at higher temperatures than the highest-melting-point metals such as tungsten or rhenium. Although thermodynamically prone to oxidation, carbon resists oxidation more than elements such as iron and copper, which are weaker reducing agents at room temperature. Carbon is the sixth element, with a ground-state electron configuration of 1s22s22p2, of which the four outer electrons are valence electrons, its first four ionisation energies, 1086.5, 2352.6, 4620.5 and 6222.7 kJ/mol, are much higher than those of the heavier group-14 elements. The electronegativity of carbon is 2.5 higher than the heavier group-14 elements, but close to most of the nearby nonmetals, as well as some of the second- and third-row transition metals. Carbon's covalent radii are taken as 77.2 pm, 66.7 pm and 60.3 pm, although these may vary depending on coordination number and what the carbon is bonded to.
In general, covalent radius decreases with higher bond order. Carbon compounds form the basis of all known life on Earth, the carbon–nitrogen cycle provides some of the energy produced by the Sun and other stars. Although it forms an extraordinary variety of compounds, most forms of carbon are comparatively unreactive under normal conditions. At standard temperature and pressure, it resists all but the strongest oxidizers, it does not react with hydrochloric acid, chlorine or any alkalis. At elevated temperatures, carbon reacts with oxygen to form carbon oxides and will rob oxygen from metal oxides to leave the elemental metal; this exothermic reaction is used in the iron and steel industry to smelt iron and to control the carbon content of steel: Fe3O4 + 4 C → 3 Fe + 4 COCarbon monoxide can be recycled to smelt more iron: Fe3O4 + 4 CO → 3 Fe + 4 CO2with sulfur to form carbon disulfide and with steam in the coal-gas reaction: C + H2O → CO + H2. Carbon combines with some metals at high temperatures to form metallic carbides, such as the iron carbide cementite in steel and tungsten carbide used as an abrasive and for making hard tips for cutting tools.
The system of carbon allotropes spans a range of extremes: Atomic carbon is a ver