Monosaccharides and Their Derivatives in Carbonaceous Meteorites: a Scenario for Their Synthesis and Onset of Enantiomeric Excesses
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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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder. -
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: -
Deoxyketohexose Isomerase and Method for Producing Deoxyketohexose and Derivative Thereof Using the Same
(19) & (11) EP 2 161 332 A1 (12) EUROPEAN PATENT APPLICATION published in accordance with Art. 153(4) EPC (43) Date of publication: (51) Int Cl.: 10.03.2010 Bulletin 2010/10 C12N 9/90 (2006.01) C07H 3/02 (2006.01) C12P 19/24 (2006.01) C12N 15/09 (2006.01) (21) Application number: 07832172.6 (86) International application number: (22) Date of filing: 20.11.2007 PCT/JP2007/072442 (87) International publication number: WO 2008/062780 (29.05.2008 Gazette 2008/22) (84) Designated Contracting States: (72) Inventors: AT BE BG CH CY CZ DE DK EE ES FI FR GB GR • IZUMORI, Ken HU IE IS IT LI LT LU LV MC MT NL PL PT RO SE Kita-gun SI SK TR Kagawa 761-0793 (JP) • TOKUDA, Masaaki (30) Priority: 20.11.2006 JP 2006313671 Kita-gun Kagawa 761-0793 (JP) (71) Applicants: • FLEET, George • National University Corporation Kagawa OX27NB (GB) University • TSUJISAKA, Yoshio Takamatsu-shi, Kagawa 760-8521 (JP) Kita-gun • Rare Sugar Production Technical Kagawa 761-0615 (JP) Research Laboratories, LLC • TAKESHITA, Kei Mikicho Marugame-Shi Kita-gun Kagawa 763-8605 (JP) Kagawa 761-0615 (JP) • TSUSAKI, Keiji • Kabushiki Kaisha Hayashibara Seibutsu Okayama-Shi Kagaku Kenkyujo Okayama 712-8046 (JP) Okayama-shi • OKUMA, Kazuhiro Okayama 700-0907 (JP) Itami-shi • Matsutani Chemical Industry Co., Ltd. Hyogo 664-8508 (JP) Itami-shi, Hyogo 664-8508 (JP) (74) Representative: TBK-Patent Bavariaring 4-6 80336 München (DE) (54) DEOXYKETOHEXOSE ISOMERASE AND METHOD FOR PRODUCING DEOXYKETOHEXOSE AND DERIVATIVE THEREOF USING THE SAME (57) Providing 1- or 6-deoxy products corresponding to all of aldohexoses, ketohexoses and sugar alcohols, as based on Deoxy-Izumoring, as well as a method for systematically producing those products. -
Abstract Sugars and Related Polyols Are Critical Components of All
/ /) f t_/ 1 Abstract Sugars and related polyols are critical components of all organisms and may have been necessary for the origin of life. To date, this class of organic compounds had not been definitively identified in meteorites. This study was undertaken to determine if polyols were present in the early Solar System as constituents of carbonaceous meteorites. Results of analyses of the Murchison and Murray meteorites indicate that formaldehyde and sugar chemistry niay be responsible for the presence of a variety of polyols. We conclude that polyols were present on the early Earth through delivery by asteroids and possibly comets. .-) Sugar-Related Organic Compounds in Carbonaceous Meteorites George Cooper*, Novelle Kimmich, Warren Belisle, Josh Sarinana, Katrina Brabham, Laurence Garrel, G. Cooper, N. Kimmich, J. Sarinana, K. Brabham, W. Belisle, NASA Ames Research Center, Moffett Field, CA 94035 USA L. Garrel, current address, International Research Sch ool of Planetary Sciences (IRSPS), Universita' d'Annunzio Viale Pindaro, 42 65127 Pescara, Italy Carbonaceous meteorites contain a diverse suite of soluble organic compounds. To date, these compounds provide the only record available for the laboratory study of organic chemical processes in the early Solar System. The Murchison meteorite is the best-characterized carbonaceous meteorite with respect to organic chemistry. The study of its organic compounds has been important in understanding aqueous processes on carbonaceous meteorite parent bodies chemistry as well as the formation of compounds of potential importance for the origin of life. Among the classes of organic compounds found in Murchison are amino acids, amides, carboxylic acids, hydroxy acids, sulfonic acids, phosphonic acids, purines and pyrimidines (1). -
Photosynthetic Productivity: Can Plants Do Better?
3 Photosynthetic Productivity: Can Plants do Better? John B. Skillman1, Kevin L. Griffin2, Sonya Earll1 and Mitsuru Kusama1 1Department of Biology, California State University, San Bernardino, California 2Lamont-Doherty Earth Observatory, Columbia University, New York, New York USA 1. Introduction By the time you finish this paragraph you will be a changed person. Change, of course, takes a variety of forms, from eroding mountains and melting snowflakes to the major changes we experience in our own lives - birth, growth, reproduction, and death. Less tangible, but changes nonetheless, are the small shifts in perspective that occur as we go through our days - new ideas, new feelings, and new understandings. But, as the Second Law of Thermodynamics reminds us, these varied and seemingly unrelated expressions of change do, in fact have a common source. All change arises from the decay of order - an increase in entropy. Sometimes the increased disarray that defines change is obvious, as when a crystalline cube of ice turns into a higgledy-piggledy puddle of water. Other times, the increased disorder is less obvious. Indeed, in living systems, change often seems to be associated with an increase in order. The gradual recovery of a lush and materially diverse living forest in the years following a catastrophic fire would seem to represent a net increase in order. The sequential nature of biological development, from zygote to adult, or from acorn to ancient oak, would seem to represent a net increase in order. The regulated changes in neuronal connectivity and brain architecture that occurs as the mind grasps new insights would seem to represent a net increase in order. -
Sigma Sugars and Carbohydrates
Sigma Sugars and Carbohydrates Library Listing – 614 spectra This library represents a material-specific subset of the larger Sigma Biochemical Condensed Phase Library relating to sugars and carbohydrates found in the Sigma Biochemicals and Reagents catalog. Spectra acquired by Sigma-Aldrich Co. which were examined and processed at Thermo Fisher Scientific. The spectra include compound name, molecular formula, CAS (Chemical Abstract Service) registry number, and Sigma catalog number. Sigma Sugars and Carbohydrates Index Compound Name Index Compound Name 255 (+/-)-Epi-inosose-2 475 2,3,4,6-Tetra-O-methyl-D-glucopyranose 468 1,2,3,4-Tetra-O-acetyl-6- 487 2,3,5-Tri-O-benzoyl-1-O-p-nitrobenzoyl diphenylphosphoryl-b-D-manopyranose D-ribofuranoside 471 1,2,3,4-Tetra-O-acetyl-b-D- 490 2,3,5-Tri-O-benzyl-1-O-p-nitrobenzoyl- glucopyranose D-arabinofuranoside 472 1,2,3,5-Tetra-O-acetyl-b-D-ribofuranose 488 2,3,5-Tri-O-benzyl-b-D-arabinofuranose 473 1,2,3,5-Tetra-O-benzoyl-a-D- 489 2,3,5-Tri-O-benzyl-b-L-arabinofuranose xylofuranose 107 2,3-Dehydro-2-deoxy-N- 258 1,2-O-Isopropylidene-3-O-benzyl-rac- acetylneuraminic acid glycerol 142 2,3-Diphospho-D-glyceric acid, 261 1,2-O-Isopropylidene-5-O-p-tosyl-a-D- penta(CHA) salt xylofuranose 143 2,3-Diphospho-D-glyceric acid, 259 1,2-O-Isopropylidene-D-glucofuranose pentasodium salt 262 1,2-O-Isopropylidene-D-xylofuranose 144 2,3-Diphospho-D-glyceric acid, tris salt 135 1,2:3,4-Di-O-isopropylidene-D- 260 2,3-O-Isopropylidene-b-D- galactopyranose ribofuranosylamine, tosylate salt 141 1,2:3,5-Di-O-isopropylidene-D- -
The Clinical Significance of the Organic Acids Test
The Clinical Significance of the Organic Acids Test The Organic Acids Test (OAT) provides an accurate metabolic snapshot of what is going on in the body. Besides offering the most complete and accurate evaluation of intestinal yeast and bacteria, it also provides information on important neurotransmitters, nutritional markers, glutathione status, oxalate metabolism, and much more. The test includes 76 urinary metabolite markers that can be very useful for discovering underlying causes of chronic illness. Patients and physicians report that treating yeast and bacterial abnormalities reduces fatigue, increases alertness and energy, improves sleep, normalizes bowel function, and reduces hyperactivity and abdominal pain. The OAT Assists in Evaluating: ■ Krebs Cycle Abnormalities ■ Neurotransmitter Levels ■ Nutritional Deficiencies ■ Antioxidant Deficiencies ■ Yeast and Clostridia Overgrowth ■ Fatty Acid Metabolism ■ Oxalate Levels ■ And More! The OAT Pairs Well with the Following Tests: ■ GPL-TOX: Toxic Non-Metal Chemical Profile ■ IgG Food Allergy + Candida ■ MycoTOX Profile ■ Phospholipase A2 Activity Test Learn how to better integrate the OAT into your practice, along with our other top tests by attending one of our GPL Academy Practitioner Workshops! Visit www.GPLWorkshops.com for workshop dates and locations. The following pages list the 75 metabolite markers of the Organic Acids Test. Included is the name of the metabolic marker, its clinical significance, and usual initial treatment. INTESTINAL MICROBIAL OVERGROWTH Yeast and Fungal Markers Elevated citramalic acid is produced mainly by Saccharomyces species or Propionibacteria Citramalic Acid overgrowth. High-potency, multi-strain probiotics may help rebalance GI flora. A metabolite produced by Aspergillus and possibly other fungal species in the GI tract. 5-Hydroxy-methyl- Prescription or natural antifungals, along with high-potency, multi-strain probiotics, furoic Acid may reduce overgrowth levels. -
Inhibition of Fucosylation of Cell Wall Components by 2-Fluoro 2-Deoxy-L
The Plant Journal (2015) 84, 1137–1151 doi: 10.1111/tpj.13071 Inhibition of fucosylation of cell wall components by 2-fluoro 2-deoxy-L-fucose induces defects in root cell elongation Marie Dumont1, Arnaud Lehner1, Muriel Bardor1, Carole Burel1, Boris Vauzeilles2,3,4, Olivier Lerouxel5, Charles T. Anderson6, Jean-Claude Mollet1 and Patrice Lerouge1,* 1Laboratoire Glycobiologie et Matrice Extracellulaire Veg etale, EA 4358, IRIB, VASI, Normandie Universite, 76821 Mont-Saint-Aignan, France, 2Institut de Chimie Moleculaire et des Materiaux d’Orsay (ICMMO) UMR CNRS 8182, Universite de Paris Sud, 91405 Orsay, France, 3Institut de Chimie des Substances Naturelles (ICSN) UPR CNRS 2301, 91198 Gif-sur-Yvette, France, 4Click4Tag, Zone Luminy Biotech, Case 922, 163 Avenue de Luminy, 13009 Marseille, France, 5Centre de Recherches sur les Macromolecules Veg etales (CERMAV) – CNRS BP 53, 38041 Grenoble Cedex 9, France, and 6Department of Biology and Center for Lignocellulose Structure and Formation, Pennsylvania State University, University Park, Pennsylvania, USA Received 21 September 2015; revised 26 October 2015; accepted 3 November 2015; published online 13 November 2015. *For correspondence (e-mail [email protected]). SUMMARY Screening of commercially available fluoro monosaccharides as putative growth inhibitors in Arabidopsis thaliana revealed that 2-fluoro 2-L-fucose (2F-Fuc) reduces root growth at micromolar concentrations. The inability of 2F-Fuc to affect an Atfkgp mutant that is defective in the fucose salvage pathway indicates that 2F-Fuc must be converted to its cognate GDP nucleotide sugar in order to inhibit root growth. Chemical analysis of cell wall polysaccharides and glycoproteins demonstrated that fucosylation of xyloglucans and of N-linked glycans is fully inhibited by 10 lM 2F-Fuc in Arabidopsis seedling roots, but genetic evidence indicates that these alterations are not responsible for the inhibition of root development by 2F-Fuc. -
Research Article a Urine Metabonomics Study of Rat Bladder Cancer by Combining Gas Chromatography-Mass Spectrometry with Random Forest Algorithm
Hindawi International Journal of Analytical Chemistry Volume 2020, Article ID 8839215, 9 pages https://doi.org/10.1155/2020/8839215 Research Article A Urine Metabonomics Study of Rat Bladder Cancer by Combining Gas Chromatography-Mass Spectrometry with Random Forest Algorithm MengchanFang,1 FanLiu,2 LinglingHuang,1 LiqingWu,3 LanGuo ,1,2 andYiqunWan 1,2 1College of Chemistry, Nanchang University, Nanchang 330031, China 2Jiangxi Province Key Laboratory of Modern Analytical Science, Nanchang University, Nanchang 330031, China 3Department of Pathology, 3rd Affiliated Hospital of Nanchang University, Nanchang 330008, China Correspondence should be addressed to Lan Guo; [email protected] and Yiqun Wan; [email protected] Received 15 June 2020; Revised 6 September 2020; Accepted 9 September 2020; Published 21 September 2020 Academic Editor: David M. Lubman Copyright © 2020 Mengchan Fang et al. .is is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. A urine metabolomics study based on gas chromatography-mass spectrometry (GC-MS) and multivariate statistical analysis was applied to distinguish rat bladder cancer. Urine samples with different stages were collected from animal models, i.e., the early stage, medium stage, and advanced stage of the bladder cancer model group and healthy group. After resolving urea with urease, the urine samples were extracted with methanol and, then, derived with N, O-Bis(trimethylsilyl) trifluoroacetamide and tri- methylchlorosilane (BSTFA + TMCS, 99 :1, v/v), before analyzed by GC-MS. .ree classification models, i.e., healthy control vs. early- and middle-stage groups, healthy control vs. -
Chapter 11 Lecture Notes: Carbohydrates
Chapter 11 Lecture Notes: Carbohydrates Educational Goals 1. Given a Fischer projection of a monosaccharide, classify it as either aldoses or ketoses. 2. Given a Fischer projection of a monosaccharide, classify it by the number of carbons it contains. 3. Given a Fischer projection of a monosaccharide, identify it as a D-sugar or L-sugar. 4. Given a Fischer projection of a monosaccharide, identify chiral carbons and determine the number of stereoisomers that are possible. 5. Identify four common types of monosaccharide derivatives. 6. Predict the products when a monosaccharide reacts with a reducing agent or with Benedict’s reagent. 7. Define the term anomer and explain the difference between α and β anomers. 8. Understand and describe mutarotation. 9. Given its Haworth projection, identify a monosaccharide either a pyranose or a furanose. 10. Identify the anomeric carbon in Haworth structures. 11. Compare and contrast monosaccharides, disaccharides, oligosaccharides, and polysaccharides. 12. Given the structure of an oligosaccharide or polysaccharide, identify the glycosidic bond(s) and characterize the glycosidic linkage by the bonding pattern [for example: β(1⟶4)]. 13. Given the Haworth structures of two monosaccharides, be able to draw the disaccharide that is formed when they are connected by a glycosidic bond. 14. Understand the difference between homopolysaccharides and heteropolysaccharides. 15. Compare and contrast the two components of starch. 16. Compare and contrast amylopectin and glycogen. 17. Identify acetal and hemiacetal bonding patterns in carbohydrates. An Introduction to Carbohydrates Carbohydrates are quite abundant in nature. More than half of the carbon found in living organisms is contained in carbohydrate molecules, most of which are contained in plants. -
The Role of Glycerol and Its Derivatives in the Biochemistry of Living Organisms, and Their Prebiotic Origin and Significance in the Evolution of Life
catalysts Review The Role of Glycerol and Its Derivatives in the Biochemistry of Living Organisms, and Their Prebiotic Origin and Significance in the Evolution of Life Maheen Gull * and Matthew A. Pasek School of Geosciences, University of South Florida, 4202 E Fowler Ave., NES 204, Tampa, FL 33620, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-813-974-8979 Abstract: The emergence and evolution of prebiotic biomolecules on the early Earth remain a question that is considered crucial to understanding the chemistry of the origin of life. Amongst prebiotic molecules, glycerol is significant due to its ubiquity in biochemistry. In this review, we discuss the significance of glycerol and its various derivatives in biochemistry, their plausible roles in the origin and evolution of early cell membranes, and significance in the biochemistry of extremophiles, followed by their prebiotic origin on the early Earth and associated catalytic processes that led to the origin of these compounds. We also discuss various scenarios for the prebiotic syntheses of glycerol and its derivates and evaluate these to determine their relevance to early Earth biochemistry and geochemistry, and recapitulate the utilization of various minerals (including clays), condensation agents, and solvents that could have led to the successful prebiotic genesis of these biomolecules. Furthermore, important prebiotic events such as meteoritic delivery and prebiotic synthesis reactions under astrophysical conditions are also discussed. Finally, we have also highlighted some novel features of glycerol, including glycerol nucleic acid (GNA), in the origin and evolution of the life. Citation: Gull, M.; Pasek, M.A. The Keywords: glycerol; phosphorylation; catalysis; prebiotic syntheses; origin of life; evolution of cell Role of Glycerol and Its Derivatives in membranes; deep eutectic solvents; extremophiles; glycerol biochemistry; phospholipids; early Earth the Biochemistry of Living Organisms, and Their Prebiotic Origin and Significance in the Evolution of Life. -
PATHWAY of SERINE FORMATION from CARBOHYDRATE in RAT LIVER* by AKIRA Ichiharat and DAVID M
Proceedings of the NATIONAL ACADEMY OF SCIENCES Volume 41 Number 9 September 15, 1955 PATHWAY OF SERINE FORMATION FROM CARBOHYDRATE IN RAT LIVER* BY AKIRA ICHIHARAt AND DAVID M. GREENBERG DEPARTMENT OF PHYSIOLOGICAL CHEMISTRY, UNIVERSITY OF CALIFORNIA SCHOOL OF MEDICINE, BERKELEY Communicated by H. A. Barker, June 3, 1955 There are a number of reports on the formation of serine from glucose in animal tissues,1-3 but experimental evidence for the steps in the main pathway of serine formation has not been available up to now. Sallach4 has recently reported the presence of a transaminase between 3-hydroxypyruvic acid and alanine and has presented a possible pathway of serine formation from D-glyceric acid through 3- hydroxypyruvic acid. This paper reports the formation of serine from glucose, D-glyceric acid, 3-phosphoglyceric acid, and 3-phosphohydroxypyruvic acid by a rat-liver enzyme system and presents an alternative pathway of serine formation. EXPERIMENTAL Preparation of Enzyme System.-The livers from male rats, weighing 250-300 gm., were homogenized with 2 volumes of 0.1 M phosphate buffer (pH 7.4) in a Waring Blendor for 40 seconds. The homogenate was then centrifuged at 600 X g for 10 minutes and the supernatant fluid recentrifuged at 105,400 X g for 30 minutes in the Spinco preparative ultracentrifuge. The supernatant fluid from this was fractionated with saturated (NH4)2SO4, and the enzyme activity was found in the fraction precipitating between 33-66 per cent saturation. This was dissolved in 0.1 M phosphate buffer and dialyzed against 0.03 M phosphate buffer, both at pH 7.4, for 6 hours.