Organic Chemistry/Fourth Edition: E-Text
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Synechococcus Elongatus
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.30.424818; this version posted December 31, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 5-Deoxyadenosine Salvage by Promiscuous Enzyme Activity 2 leads to Bioactive Deoxy-Sugar Synthesis in 3 Synechococcus elongatus 4 5 Running title: Unusual 5-deoxyadenosine salvage in S. elongatus 6 7 Johanna Rappa, Pascal Rathb, Joachim Kilianc, Klaus Brilisauera, Stephanie Grondb, Karl 8 Forchhammera# 9 aInterfaculty Institute of Microbiology and Infection Medicine, Microbiology/Organismic Interactions, Eberhard 10 Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany. 11 bInstitute of Organic Chemistry, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, 12 Germany. 13 cCenter for Plant Molecular Biology, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 32, 72076 14 Tübingen, Germany. 15 16 #corresponding author ([email protected], Tel.: +49 (7071) 29- 72096) 17 18 Abbreviations: SAM: S-Adenosylmethionine; MTA: Methylthioadenosine; 5dAdo: 19 5-Deoxyadenosine; MSP: Methionine salvage pathway; 5dR: 5-Deoxyribose; 7dSh: 20 7-Deoxysedoheptulose; 5dR-1P: 5-Deoxyribose 1-phosphate; 5dRu-1P: 5-Deoxyribulose 21 1-phosphate; MTRI: Methylthioribose 1-phosphate isomerase; MTR: Methylthioribose 22 23 Keywords: 5-Deoxyadenosine salvage, 5-deoxyribose, 7-deoxysedoheptulose, 7dSh 24 biosynthesis; enzyme promiscuity, S-adenosylmethionine, radical SAM enzymes, 25 cyanobacteria 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.12.30.424818; this version posted December 31, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. -
Monosaccharides and Their Derivatives in Carbonaceous Meteorites: a Scenario for Their Synthesis and Onset of Enantiomeric Excesses
life Review Monosaccharides and Their Derivatives in Carbonaceous Meteorites: A Scenario for Their Synthesis and Onset of Enantiomeric Excesses George Cooper 1,*, Andro C. Rios 1,2,* and Michel Nuevo 1,3 ID 1 NASA-Ames Research Center, Moffett Field, CA 94035, USA; [email protected] 2 Blue Marble Space, 1001 4th Ave, Ste 3201, Seattle, WA 98154, USA 3 Bay Area Environmental Research Institute, NASA Research Park, Moffett Field, CA 94035, USA * Correspondence: [email protected] (G.C.); [email protected] (A.C.R.) Received: 5 June 2018; Accepted: 22 August 2018; Published: 27 August 2018 Abstract: Carbonaceous meteorites provide the best glimpse into the solar system’s earliest physical and chemical processes. These ancient objects, ~4.56 billion years old, contain evidence of phenomena ranging from solar system formation to the synthesis of organic compounds by aqueous and (likely) low-temperature photolytic reactions. Collectively, chemical reactions resulted in an insoluble kerogen-like carbon phase and a complex mixture of discrete soluble compounds including amino acids, nucleobases, and monosaccharide (or “sugar”) derivatives. This review presents the documented search for sugars and their derivatives in carbonaceous meteorites. We examine early papers, published in the early 1960s, and note the analytical methods used for meteorite analysis as well as conclusions on the results. We then present the recent finding of sugar derivatives including sugar alcohols and several sugar acids: The latter compounds were found to possess unusual “D” enantiomeric (mirror-image) excesses. After discussions on the possible roles of interstellar grain chemistry and meteorite parent body aqueous activity in the synthesis of sugar derivatives, we present a scenario that suggests that most of Earth’s extraterrestrial sugar alcohols (e.g., glycerol) were synthesized by interstellar irradiation and/or cold grain chemistry and that the early solar disk was the location of the initial enantiomeric excesses in meteoritic sugar derivatives. -
Basics of Kraft Pulping
Lignin Wood is composed of many chemical components, primarily extractives, carbohydrates, and lignin, which are distributed nonuniformly as the result of anatomical structure. Lignin is derived from the Latin term lignum, which means wood.1 Anselme Payen (1838) was the first to recognize the composite nature of wood and referred to a carbon- rich substance as the “encrusting material” which embedded cellulose in the wood. Schulze (1865) later defined this encrusting material as lignin. Lignin has been described as a random, three-dimensional network polymer comprised of variously linked phenylpropane units.2 Lignin is the second most abundant biological material on the planet, exceeded only by cellulose and hemicellulose, and comprises 15-25% of the dry weight of woody plants. This macromolecule plays a vital role in providing mechanical support to bind plant fibers together. Lignin also decreases the permeation of water through the cell walls of the xylem, thereby playing an intricate role in the transport of water and nutrients. Finally, lignin plays an important function in a plant’s natural defense against degradation by impeding penetration of destructive enzymes through the cell wall. Although lignin is necessary to trees, it is undesirable in most chemical papermaking fibers and is removed by pulping and bleaching processes. 1.1.1 Biosynthesis Plant lignins can be broadly divided into three classes: softwood (gymnosperm), hardwood (angiosperm) and grass or annual plant (graminaceous) lignin.3 Three different phenylpropane units, or monolignols, are responsible for lignin biosynthesis.4 Guaiacyl lignin is composed principally of coniferyl alcohol units, while guaiacyl-syringyl lignin contains monomeric units from coniferyl and sinapyl alcohol. -
Hereditary Galactokinase Deficiency J
Arch Dis Child: first published as 10.1136/adc.46.248.465 on 1 August 1971. Downloaded from Alrchives of Disease in Childhood, 1971, 46, 465. Hereditary Galactokinase Deficiency J. G. H. COOK, N. A. DON, and TREVOR P. MANN From the Royal Alexandra Hospital for Sick Children, Brighton, Sussex Cook, J. G. H., Don, N. A., and Mann, T. P. (1971). Archives of Disease in Childhood, 46, 465. Hereditary galactokinase deficiency. A baby with galactokinase deficiency, a recessive inborn error of galactose metabolism, is des- cribed. The case is exceptional in that there was no evidence of gypsy blood in the family concerned. The investigation of neonatal hyperbilirubinaemia led to the discovery of galactosuria. As noted by others, the paucity of presenting features makes early diagnosis difficult, and detection by biochemical screening seems desirable. Cataract formation, of early onset, appears to be the only severe persisting complication and may be due to the biosynthesis and accumulation of galactitol in the lens. Ophthalmic surgeons need to be aware of this enzyme defect, because with early diagnosis and dietary treatment these lens changes should be reversible. Galactokinase catalyses the conversion of galac- and galactose diabetes had been made in this tose to galactose-l-phosphate, the first of three patient (Fanconi, 1933). In adulthood he was steps in the pathway by which galactose is converted found to have glycosuria as well as galactosuria, and copyright. to glucose (Fig.). an unexpectedly high level of urinary galactitol was detected. He was of average intelligence, and his handicaps, apart from poor vision, appeared to be (1) Galactose Gackinase Galactose-I-phosphate due to neurofibromatosis. -
Chapter 12 Slides
11/15/17 CHAPTER 12: Carbohydrates: Structure and Function OUTLINE • 12.1 Role of Carbohydrates • 12.2 Monosaccharides • 12.3 Complex Carbohydrates • 12.4 Carbohydrate Catabolism • 12.5 Oligosaccharides as Cell Markers CHAPTER 12: Carbohydrates: Structure and Function WHAT ARE CARBOHYDRATES? • Glucose and its derivatives are carbohydrates: Ø Carbohydrates are simple organic molecules that have a shared basic chemical Formula: Cn(H2O)n Ø The name “carbo + hydrate” represents that Fact that they are made from CO2 and H2O by photosynthesis • About halF oF all earth’s solid carbon is Found in two polymers of glucose found in plants: Ø Starch = major energy storage molecule Ø Cellulose = major structural component oF the plant cell wall (aka. “fiber”) CHAPTER 12: Carbohydrates: Structure and Function THE SIMPLEST CARBOHYDRATES • Monosaccharides are carbohydrates that cannot be hydrolyZed into simpler carbohydrates: Ø These are the Fundamental building blocks For all other carbohydrates (oFten called “simple sugars”) Ø All have Formulas of based on the basic pattern: Cn(H2O)n • Monosaccharides have speciFic Functional groups: 1. An aldehyde OR a ketone (not both!) 2. Several (two or more) alcohol (-OH) groups 1 11/15/17 CHAPTER 12: Carbohydrates: Structure and Function STRUCTURE & NOMENCLATURE OF MONOSACCHARIDES • Monosaccharides are classiFied by two features: 1. Length of their main carbon chain (utilize standard IUPAC naming For # oF carbons) 2. Whether they contain an aldehyde or ketone group • Names always end with –ose • Two common hexoses: -
In Silico Screening of Sugar Alcohol Compounds to Inhibit Viral Matrix Protein VP40 of Ebola Virus
Molecular Biology Reports (2019) 46:3315–3324 https://doi.org/10.1007/s11033-019-04792-w ORIGINAL ARTICLE In silico screening of sugar alcohol compounds to inhibit viral matrix protein VP40 of Ebola virus Nagasundaram Nagarajan1 · Edward K. Y. Yapp2 · Nguyen Quoc Khanh Le1 · Hui‑Yuan Yeh1 Received: 28 December 2018 / Accepted: 28 March 2019 / Published online: 13 April 2019 © Springer Nature B.V. 2019 Abstract Ebola virus is a virulent pathogen that causes highly lethal hemorrhagic fever in human and non-human species. The rapid growth of this virus infection has made the scenario increasingly complicated to control the disease. Receptor viral matrix protein (VP40) is highly responsible for the replication and budding of progeny virus. The binding of RNA to VP40 could be the crucial factor for the successful lifecycle of the Ebola virus. In this study, we aimed to identify the potential drug that could inhibit VP40. Sugar alcohols were enrich with antiviral properties used to inhibit VP40. Virtual screening analysis was perform for the 48 sugar alcohol compounds, of which the following three compounds show the best binding afnity: Sorbitol, Mannitol and Galactitol. To understand the perfect binding orientation and the strength of non-bonded interactions, individual molecular docking studies were perform for the best hits. Further molecular dynamics studies were conduct to analyze the efcacy between the protein–ligand complexes and it was identify that Sorbitol obtains the highest efcacy. The best-screened compounds obtained drug-like property and were less toxic, which could be use as a potential lead compound to develop anti-Ebola drugs. -
Polyols Have a Variety of Functional Properties That Make Them Useful Alternatives to Sugars in Applications Including Baked Goods
Polyols have a variety of functional properties that make them useful alternatives to sugars in applications including baked goods. Photo © iStockphoto.com/Synergee pg 22 09.12 • www.ift.org BY LYN NABORS and THERESA HEDRICK SUGAR REDUCTION WITH Polyols Polyols are in a unique position to assist with reduced-sugar or sugar-free reformulations since they can reduce calories and complement sugar’s functionality. ugar reduction will be an important goal over the of the product’s original characteristics may still be main- next few years as consumers, government, and in- tained with the replacement of those sugars by polyols. Sdustry alike have expressed interest in lower-calorie In addition, excellent, good-tasting sugar-free products and lower-sugar foods. The 2010 Dietary Guidelines for can be developed by using polyols. Polyols are in a unique Americans put a strong emphasis on consuming fewer position to assist with reduced-sugar or sugar-free refor- calories and reducing intake of added sugars. The In- mulations; since they are only partially digested and ab- stitute of Medicine (IOM) held a public workshop in sorbed, they can reduce calories and complement sugar’s November 2010 to discuss ways the food industry can functionality. Polyols provide the same bulk as sugars and use contemporary and innovative food processing tech- other carbohydrates. Additionally, polyols have a clean, nologies to reduce calorie intake in an effort to reduce sweet taste, which is important since consumers are not and prevent obesity, and in October 2011 recommended likely to sacrifice taste for perceived health benefits. Poly- front-of-package labeling that includes rating the product ols have a host of other functional properties that make based on added sugars content. -
Biovalorisation of Crude Glycerol and Xylose Into Xylitol by Oleaginous Yeast Yarrowia Lipolytica
Biovalorisation of crude glycerol and xylose into xylitol by oleaginous yeast Yarrowia lipolytica Ashish Prabhu Craneld University Dominic J Thomas Craneld University Rodrigo Ledesma- Amaro Imperial College London Gary A Leeke University of Birmingham Angel Medina Vaya Craneld University Carol Verheecke-Vaessen Craneld University Frederic Coulon Craneld University Vinod Kumar ( [email protected] ) Craneld University https://orcid.org/0000-0001-8967-6119 Research Keywords: Glycerol, Xylose, Yarrowia lipolytica, Biotransformation, Xylitol Posted Date: March 26th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-19009/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Version of Record: A version of this preprint was published at Microbial Cell Factories on June 3rd, 2020. See the published version at https://doi.org/10.1186/s12934-020-01378-1. Page 1/28 Abstract Background: Xylitol is a commercially important chemical with multiple applications in food and pharmaceutical industries. According to the US Department of Energy, xylitol is among the twelve platform chemicals that can be produced from biomass. The chemical method for xylitol synthesis is however expensive and energy intensive. In contrast, the biological route involving microbial cell factories offers a potential cost-effective alternative process. The bioprocess occurs under ambient conditions and makes use of biocatalysts which can be sourced from renewable carbon coming from a variety of cheap feedstocks classied as wastes. Result: In this study, biotransformation of xylose to xylitol was investigated using Yarrowia lipolytica an oleaginous yeast grown on glycerol/glucose screening of primary carbon source, media optimisation in shake ask, scale up in bioreactor and downstream processing of xylitol were carried out. -
Hemicellulose Arabinogalactan Hydrolytic Hydrogenation Over Ru-Modified H-USY Zeolites
Research Collection Journal Article Hemicellulose arabinogalactan hydrolytic hydrogenation over Ru-modified H-USY zeolites Author(s): Murzin, Dmitry; Kusema, Bright; Murzina, Elena V.; Aho, Atte; Tokarev, Anton; Boymirzaev, Azamat S.; Wärnå, Johan; Dapsens, Pierre Y.; Mondelli, Cecilia; Pérez-Ramírez, Javier; Salmi, Tapio Publication Date: 2015-10 Permanent Link: https://doi.org/10.3929/ethz-a-010792434 Originally published in: Journal of Catalysis 330, http://doi.org/10.1016/j.jcat.2015.06.022 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library Hemicellulose arabinogalactan hydrolytic hydrogenation over Ru-modified H-USY zeolites Dmitry Yu. Murzin1*, Bright Kusema2, Elena V. Murzina1, Atte Aho1, Anton Tokarev1, Azamat S. Boymirzaev3, Johan Wärnå1,4, Pierre Y. Dapsens2, Cecilia Mondelli2, Javier Pérez-Ramírez2, Tapio Salmi1 1Laboratory of Industrial Chemistry and Reaction Engineering, Process Chemistry Centre, Department of Chemical Engineering, Åbo Akademi University, FI-20500 Åbo/Turku, Finland, E-mail: [email protected] 2Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1, CH-8093 Zurich, Switzerland 3Namangan Institute of Engineering and Technology, Department of Chemical Technology, Namangan, 160115, Uzbekistan 4University of Umeå, Umeä, Sweden ABSTRACT The hydrolytic hydrogenation of hemicellulose arabinogalactan was investigated in the presence of protonic and Ru (1-5 wt.%)-modified USY zeolites (Si/Al ratio = 15 and 30). The use of the purely acidic materials was effective in depolymerizing the macromolecule into free sugars. While the latter partly dehydrated into 5- hydroxymethylfurfural and furfural, the generation of high molecular-weight compounds (aggregates of sugars and humins) was not favored, in contrast to previous evidences over beta zeolites. -
Sugar Alcohols a Sugar Alcohol Is a Kind of Alcohol Prepared from Sugars
Sweeteners, Good, Bad, or Something even Worse. (Part 8) These are Low calorie sweeteners - not non-calorie sweeteners Sugar Alcohols A sugar alcohol is a kind of alcohol prepared from sugars. These organic compounds are a class of polyols, also called polyhydric alcohol, polyalcohol, or glycitol. They are white, water-soluble solids that occur naturally and are used widely in the food industry as thickeners and sweeteners. In commercial foodstuffs, sugar alcohols are commonly used in place of table sugar (sucrose), often in combination with high intensity artificial sweeteners to counter the low sweetness of the sugar alcohols. Unlike sugars, sugar alcohols do not contribute to the formation of tooth cavities. Common Sugar Alcohols Arabitol, Erythritol, Ethylene glycol, Fucitol, Galactitol, Glycerol, Hydrogenated Starch – Hydrolysate (HSH), Iditol, Inositol, Isomalt, Lactitol, Maltitol, Maltotetraitol, Maltotriitol, Mannitol, Methanol, Polyglycitol, Polydextrose, Ribitol, Sorbitol, Threitol, Volemitol, Xylitol, Of these, xylitol is perhaps the most popular due to its similarity to sucrose in visual appearance and sweetness. Sugar alcohols do not contribute to tooth decay. However, consumption of sugar alcohols does affect blood sugar levels, although less than that of "regular" sugar (sucrose). Sugar alcohols may also cause bloating and diarrhea when consumed in excessive amounts. Erythritol Also labeled as: Sugar alcohol Zerose ZSweet Erythritol is a sugar alcohol (or polyol) that has been approved for use as a food additive in the United States and throughout much of the world. It was discovered in 1848 by British chemist John Stenhouse. It occurs naturally in some fruits and fermented foods. At the industrial level, it is produced from glucose by fermentation with a yeast, Moniliella pollinis. -
Oleaginous Yeasts for the Production of Sugar Alcohols Sujit S Jagtap1,2
Oleaginous Yeasts for the Production of Sugar Alcohols Sujit S Jagtap1,2* ([email protected]), Ashwini A Bedekar2, Jing-Jing Liu1, Anshu Deewan1,2, and Christopher V Rao1,2 1DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Illinois. 2Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Illinois. https://cabbi.bio/ Project Goal: The goal of this project is to investigate sugar alcohol production from plant- based sugars and glycerol in the oleaginous yeasts Rhodosporidium toruloides and Yarrowia lipolytica. We are also interested in understanding the mechanism of sugar alcohol production and the key genes involved in the polyol synthesis process. Sugar alcohols are commonly used as low-calorie, natural sweeteners. They have also been proposed by the Department of Energy as potential building blocks for bio-based chemicals. They can be used to produce polymers with applications in medicine and as precursors to anti-cancer drugs 1. Production of these sugar alcohols by yeast often results, from redox imbalances associated with growth on different sugars, accumulation of toxic intermediates, and as a cell response to the high osmotic pressure of the environment 2-3. The ability of yeast to naturally produce these sugar alcohols from simple sugars provides a potentially safer and more sustainable alternative to traditional chemical hydrogenation. In our study, we found that the oleaginous yeast R. toruloides IFO0880 produces D-arabitol during growth on xylose in nitrogen-rich medium 3. Efficient xylose utilization was a prerequisite for extracellular D-arabitol production. D-arabitol is an overflow metabolite associated with transient redox imbalances during growth on xylose. -
Xylitol Production Process Partnering Opportunity
2225 W. Harrison St., Suite F Chicago, IL 60612 312-997-2150 telephone 312-997-2160 fax Xylitol Production Process Partnering Opportunity About zuChem zuChem is a biotechnology company specializing in the development of proprietary bioprocesses for the production of unique carbohydrates and glycochemicals for the food and pharmaceutical markets. The Company has offices in Chicago, Illinois as well as research facilities in Peoria, Illinois. Xylitol Xylitol is a naturally occurring sugar polyol that has a sweetening property matching that of sucrose, but contributes one- third less calories. It is used extensively in a variety of confectionary products such as candies and gums. Xylitol has been implicated in the prevention of dental caries, and is thought by many to be anti-cariogenic thus making it the best nutritive sugar substitute with respect to the prevention of dental cavities. Xylitol growth has been severely limited because of price and, more importantly, supply constraints. Current processes for the manufacture of xylitol require pure xylose, which is expensive and in limited supply. This in turn has made xylitol end users reluctant to launch new products containing xylitol. If price and supply limitations were to be removed, it has been estimated that the market for xylitol could grow significantly, particularly in the U.S. zuChem’s proprietary process has been designed to overcome the supply constraint by removing the requirement for pure xylose, while also providing a significant cost of goods advantage. The zuChem Process zuChem has developed a fermentation process for the production of xylitol using a hemicellulose (i.e. a C5/C6 sugar mixture) feedstock instead of the purified xylose required by traditional chemical manufacturing methods.