DOCSLIB.ORG

Amino Sugars and Muramic Acid—Biomarkers for Soil Microbial Community Structure Analysis

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Amino Sugars and Muramic Acid—Biomarkers for Soil Microbial Community Structure Analysis Soil Biology & Biochemistry 36 (2004) 399–407 www.elsevier.com/locate/soilbio Amino sugars and muramic acid—biomarkers for soil microbial community structure analysis Bruno Glasera,*, Marı´a-Bele´n Turrio´nb, Kassem Alefc aInstitute of Soil Science and Soil Geography, University of Bayreuth, Bayreuth D-95440, Germany bArea of Soil Science and Soil Chemistry, ETSIIAA, University of Valladolid, Palencia 34004, Spain cUmwelt und Technologie Consulting, Bayreuth D-95448, Germany Received 13 December 2002; received in revised form 22 July 2003; accepted 7 October 2003 Abstract Characterizing functional and phylogenetic microbial community structure in soil is important for understanding the fate of microbially- derived compounds during the decomposition and turn-over of soil organic matter. This study was conducted to test whether amino sugars and muramic acid are suitable biomarkers to trace bacterial, fungal, and actinomycetal residues in soil. For this aim, we investigated the pattern, amounts, and dynamics of three amino sugars (glucosamine, mannosamine and galactosamine) and muramic acid in the total microbial biomass and selectively cultivated bacteria, fungi, and actinomycetes offive different soils amended with and without glucose. Our results revealed that total amino sugar and muramic acid concentrations in microbial biomass, extracted from soil after chloroform fumigation varied between 1 and 27 mg kg21 soil. In all soils investigated, glucose addition resulted in a 50–360% increase of these values. In reference to soil microbial biomass-C, the total amino sugar- and muramic acid-C concentrations ranged from 1–71 g C kg21 biomass-C. After an initial lag phase, the cultivated microbes revealed similar amino sugar concentrations of about 35, 27 and 17 g glucosamine-C kg21 TOC in bacteria, fungi, and actinomycetes, respectively. Mannosamine and galactosamine concentrations were lower than those for glucosamine. Mannosamine was not found in actinomycete cultures. The highest muramic acid concentrations were found in bacteria, but small amounts were also found in actinomycete cultures. The concentrations of the three amino sugars studied and muramic acid differed significantly between bacteria and the other phylogenetic microbial groups under investigation (fungi and actinomycetes). Comparison between the amino sugar and muramic acid concentrations in soil microbial biomass, extracted after chloroform fumigation, and total concentrations in the soil showed that living microbial biomass contributed negligible amounts to total amino sugar contents in the soil, being at least two orders of magnitude greater in the soils than in the soil inherent microbial biomass. Thus, amino sugars are significantly stabilized in soil. q 2003 Elsevier Ltd. All rights reserved. Keywords: Biomarker; Amino sugar; Muramic acid; Microbial community structure; Microbial biomass; Microbial necromass 1. Introduction is known that a diversity of populations with different Microbial biomass has been defined as the part of soil biochemical characteristics are present. organic matter (SOM) which constitutes living microorgan- Several methods have been applied to estimate the isms smaller than 5–10 mm3. It contributes between 1 and microbial biomass in soil (Alef and Nannipieri, 1995). The 5% of SOM (Alef and Nannipieri, 1995). The importance of chloroform fumigation extraction (CFE) method has several estimating soil microbial biomass is related to its function as advantages in comparison with other methods such as time a pool for the delivery of plant nutrients, its role in soil and resource intensity of the analysis (Joergensen, 1996), structure formation and stabilization and as a marker for soil being applicable immediately after substrate addition to a fertility and sustainability (Smith and Paul, 1990). Esti- soil, in the organic layers of soils, in acid soils and in water- mations of the microbial biomass have usually involved logged soils. With the CFE method, soil microorganisms die treatment of the biomass as a single component, although it after their cell membranes are attacked by chloroform fume. Microbial constituents, especially in the cytoplasm, are * Corresponding author. Tel.: þ49-921-552254; fax: þ49-921-552246. degraded by enzymatic autolysis and transformed into E-mail address: [email protected] (B. Glaser). extractable components. 0038-0717/$ - see front matter q 2003 Elsevier Ltd. All rights reserved. doi:10.1016/j.soilbio.2003.10.013 400 B. Glaser et al. / Soil Biology & Biochemistry 36 (2004) 399–407 Strategies for community structure analysis comprise among five different soil samples under pasture vegetation, laboratory cultivation techniques and those based on direct whereas in the present paper the data shown correspond only extraction and analysis of indicator molecules (Ogram and to one soil sample which was incubated with and without Feng, 1997). We used amino sugars as biomarkers because glucose. these compounds are part of the cell wall of bacteria, fungi and actinomycetes (Amelung, 2001; Joergensen et al., 1995; Kandeler et al., 2000). Bacterial cell walls contain a 2.2. Selective cultivation of bacteria, fungi, actinomycetes peptidoglycan, constructed of the glucose derivatives N- and soil microbial community acetyl glucosamine and muramic acid. The peptidoglycan structure is present only in prokaryotes, and has never been We consulted the bibliography about the determination found in eukaryotic cells. In gram-positive bacteria, as much of microbial biomass, and there was ambiguity about the as 90% of the cell wall consists of peptidoglycan, whereas in time of pre-incubation of soils. To determine microbial gram-negative bacteria this figure is only 5–20% (Brock biomass several authors have pre-incubated the soils only and Madigan, 1988). It is thought that fungi contain only for 1 week (Beck et al., 1997; Tsai et al., 1997) observing a glucosamine and galactosamine (Cochran and Vercellotti, complete recovery of the microbial biomass. Additionally, it 1978). Also, invertebrate exoskeletons contain chitin, an was not clear whether there was enough labile SOM in the N-acetyl glucosamine polymer (Chantigny et al., 1997). non-glucose-amended soils for 2 weeks of incubation. Moreover, glucosamine has been found in earthworm gut Therefore, prior to the extraction of extractable and viable lining, nematode egg shells, mollusc polysacharides, and in microbes, the air-dried soil (,2 mm) was incubated at field snail gelatin (Amelung, 2001). Nevertheless, the concen- capacity and room temperature (25 8C) for 1 week. Moist trations of amino sugars and muramic acid are routinely soil (10 g) was then extracted with 90 ml of 50 mM Tris applied to indicate microbial contributions to SOM (Zhang buffer at pH 7.5 by ultrasonication using a total energy input et al., 1999; Amelung, 2001; Solomon et al., 2001; Turrio´n of 4500 J, as suggested by Ramsay (1984). An aliquot (1 ml) et al., 2002). Furthermore, the ratios of amino sugars and of each soil suspension was spread over the surface of agar muramic acid have been used to characterize the contri- plates which contained different growth media and incu- bution of microbial residues to SOM. As examples, the ratio bated at 36 8C in five replicates. All microbes were of glucosamine to galactosamine was used to indicate the cultivated on solid media containing 10 ml of a trace relative contribution of fungal-derived sugars, whilst the element solution per liter as proposed by Alef and ratio of glucosamine to muramic acid was used to eva- Nannipieri (1995). A standard II agar with actidione luate the fate of bacterial-derived SOM (Amelung et al., (cycloheximide; 100 mg dm23) to inhibit fungal growth 1999; Amelung, 2001). However, up to now it remains was used as a selective media for the cultivation of bacteria. unclear whether applying these ratios is valid. Fungi were selectively grown on Sabouraud 2% glucose Therefore, the objectives of this study were (1) to agar containing 100 mg dm23 streptomycin as a bactericide. ascertain if amino sugars are suitable indicators for the Actinomycetes were grown on a chitinous mineral salt agar determination of microbial biomass and/or necromass in 23 23 23 (1 g dm chitin, 1 g dm NH4Cl, 0.1 g dm MgCl2, soil, (2) to investigate whether amino sugar patterns allow a 20 mM phosphate buffer adjusted to pH 6.8). Rose bengal differentiation between bacterial, fungal and actinomycetal (40 mg dm23), actidione (100 mg dm23) and streptomycin contributions in soil, and (3) to evaluate the variability of (100 mg dm23) were added to suppress bacterial and fungal these indicator concentrations in microbial biomass isolated growth. from different soil types. 2.3. Chloroform fumigation extraction (CFE) 2. Materials and methods Previous to the extraction of the microbial biomass, air 2.1. Selected soils dried soil (,2 mm) was incubated at field capacity and room temperature (25 8C) for 1 week. A second sample set To cover a wide range of different soil habitats, the upper was prepared by the addition of 100 mg glucose, to 10 cm of five well characterized soils differing in basic soil stimulate microbial activity. Chloroform fumigation of the properties (Table 1) were used. Soil 1 was a Vertisol from soils released microbial cytoplasm into the soil environ- the North American Great Plains (Amelung et al., 1997). ment. After subsequent extraction of the cell material with Soils 2 and 3 were highly weathered soils of the humid 0.5 M K2SO4 (Vance et al., 1987), total organic carbon tropics (Glaser et al., 2000a, 2001). Soil 4 represented a (TOC) was quantified as a reference for the microbial typical central European Hortisol (Glaser et al., 1998) and biomass. The microbial biomass was calculated by biomass ¼ = ; Soil 5 was from a high mountain ecosystem of Central Asia C EC kEC where EC is the organic C extracted from (Glaser et al., 2000b; Turrio´n et al., 2000, 2002). The amino fumigated soil minus that extracted from non-fumigated soil sugar results that appear in Turrio´n et al. (2002) are the mean and kEC is the extractable part of microbial biomass C after B.
Load more

Recommended publications
  • Liquid Chromatography with Electrospray Ionization And
    Hindawi Publishing Corporation International Journal of Analytical Chemistry Volume 2016, Article ID 9269357, 8 pages http://dx.doi.org/10.1155/2016/9269357 Research Article Liquid Chromatography with Electrospray Ionization and Tandem Mass Spectrometry Applied in the Quantitative Analysis of Chitin-Derived Glucosamine for a Rapid Estimation of Fungal Biomass in Soil Madelen A. Olofsson and Dan Bylund DepartmentofNaturalSciences,MidSwedenUniversity,85170Sundsvall,Sweden Correspondence should be addressed to Madelen A. Olofsson; [email protected] Received 2 September 2015; Accepted 12 January 2016 Academic Editor: Frantisek Foret Copyright © 2016 M. A. Olofsson and D. Bylund. This 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. This method employs liquid chromatography-tandem mass spectrometry to rapidly quantify chitin-derived glucosamine for estimating fungal biomass. Analyte retention was achieved using hydrophilic interaction liquid chromatography, with a zwitter- ionic stationary phase (ZIC-HILIC), and isocratic elution using 60% 5 mM ammonium formate buffer (pH 3.0) and 40% ACN. Inclusion of muramic acid and its chromatographic separation from glucosamine enabled calculation of the bacterial contribution to the latter. Galactosamine, an isobaric isomer to glucosamine, found in significant amounts in soil samples, was also investigated. Thetwoisomersformthesameprecursorandproductionsandcouldnotbechromatographicallyseparatedusingthisrapid method. Instead, glucosamine and galactosamine were distinguished mathematically, using the linear relationships describing the differences in product ion intensities for the two analytes. The m/z transitions of 180 → 72 and 180 → 84 were applied for the detection of glucosamine and galactosamine and that of 252 → 126 for muramic acid.
    [Show full text]
  • 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:
    [Show full text]
  • Supplementary Data
    Metabolomics in cancer research: Supplementary data 1 Supplementary Data 2 Supplementary methods 3 Additional information regarding the search strategy used in the main paper 4 Supplementary tables 5 Supplementary Table 1: List of reported metabolites to be altered in human cancers 6 Supplementary figures 7 Supplementary Figure 1: General overview over the metabolomics workflow 8 1 Metabolomics in cancer research: Supplementary data 9 Supplementary methods 10 Search strategy 11 The search strategy was described in the main paper. For the Web of Knowledge search an 12 additional refinement step was necessary to reduce irrelevant findings. The following research 13 areas of low relevance were excluded: 14 Plant Science, Biophysics, Agriculture, Environmental Sciences Ecology, Microbiology, 15 Computer Science, Mathematics, Cardiology, Engineering, Automation control Systems, 16 Marine Freshwater Biology, Behavioral Science, Physics, Developmental Biology, Zoology, 17 Psychiatry, Energy Fuels, Infectious Disease, Parasitology, Mycology, Rheumatology, 18 Psychology, Veterinary Sciences, Dentistry, Legal Medicine, Polymer Science, 19 Anesthesiology, Robotics, Sports Science, Forestry, Tropical Medicine, Virology, Water 20 Resources, Electrochemistry, Evolutionary Biology, Fisheries, Materials Science, 21 Oceanography, Substance Abuse, Geology, Nuclear Science Technology, Operations 22 Research Management, Orthopedics, Allergy, Biodiversity, Educational Research, 23 Metallurgy, Optics, Emergency Medicine, Geochemistry, History philosophy of science, 24 Mathematical methods in Social sciences, Mechanics, Social Issues, Thermodynamics 25 Additionally the abstracts had to contain one of the following keywords: 26 “MS” OR “mass spectrometry” OR “patients”. 2 Metabolomics in cancer research: Supplementary data 27 Supplementary tables 28 Supplementary Table 1: List of reported metabolites altered in human cancers. Metabolites in bold were reported from a study that validated 29 findings within an independent study population.
    [Show full text]
  • Xorox Univerelty Microfilms
    INFORMATION TO USERS This material was producad from a microfilm copy of the original document. While the moit advanced technological meant to photograph and reproduce thii document have been used, the quality it heavily dependent upon the quality of the original submitted. The following explanation of techniques is provided to help ou understand markings or patterns which may appear on this reproduction. 1. The sign or "target" for pages apparently lacking from the document photographed is "Missing Page(s)". If it was possible to ob tain the mining page(s) or section, they are spliced into the film along w ith: adjacent pages, This may have necessitated cutting thru an image and dupli eating adjacent pages to insure you complete continuity. 2. When an image on the film is obliterated with a large round black mark, it is an indication that the photographer suspected that the copy may have moved during exposure and thus cause a blurred image, fou will find a good image of the page in the adjacent frame. 3. When a map, drawing or chart, etc., was part of the material being photographed the photographer followed a definite method in "sectioning” the material. It is customary to begin photoi ig at the upper left hand comer of a large dieet and to continue photoi ig from left to right in equal sections with a small overlap. If necessary, sectioning is continued agein — beginning below the first row and continuing on until complete. 4. The majority of users indicate that the textual content is of greatest value, however, a somewhat higher quality reproduction could be made from "photographs" if essential to the understanding of the dissertation.
    [Show full text]
  • Analysis of Proteomic Responses of Freeze-Dried Oenococcus Oeni to Access the Molecular Mechanism of Acid Acclimation on Cell Freeze-Drying Resistance
    Accepted Manuscript Analysis of proteomic responses of freeze-dried Oenococcus oeni to access the molecular mechanism of acid acclimation on cell freeze-drying resistance Kun Yang, Yang Zhu, Yiman Qi, Tingjing Zhang, Miaomiao Liu, Jie Zhang, Xinyuan Wei, Mingtao Fan, Guoqiang Zhang PII: S0308-8146(19)30188-8 DOI: https://doi.org/10.1016/j.foodchem.2019.01.120 Reference: FOCH 24215 To appear in: Food Chemistry Received Date: 2 October 2018 Revised Date: 24 December 2018 Accepted Date: 17 January 2019 Please cite this article as: Yang, K., Zhu, Y., Qi, Y., Zhang, T., Liu, M., Zhang, J., Wei, X., Fan, M., Zhang, G., Analysis of proteomic responses of freeze-dried Oenococcus oeni to access the molecular mechanism of acid acclimation on cell freeze-drying resistance, Food Chemistry (2019), doi: https://doi.org/10.1016/j.foodchem. 2019.01.120 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Analysis of proteomic responses of freeze-dried Oenococcus oeni to access the molecular mechanism of acid acclimation on cell freeze-drying resistance Kun Yang1,2, Yang Zhu3, Yiman Qi2,Tingjing Zhang4, Miaomiao Liu2, Jie Zhang2, Xinyuan Wei2, Mingtao Fan2,*, Guoqiang Zhang1,* 1 College of Biological and Chemical Engineering, Anhui Polytechnic University, Wuhu, 241000, China 2 College of Food Science and Engineering, Northwest A ＆ F University, Yangling, 712100, China 3 School of Agriculture and Food Sciences, University of Queensland, QLD, 4046, Australia 4 College of Food Science and Technology, Henan University of Technology, Zhenzhou, 450001, China * Corresponding author: 1.
    [Show full text]
  • The Metabolic Building Blocks of a Minimal Cell Supplementary
    The metabolic building blocks of a minimal cell Mariana Reyes-Prieto, Rosario Gil, Mercè Llabrés, Pere Palmer and Andrés Moya Supplementary material. Table S1. List of enzymes and reactions modified from Gabaldon et. al. (2007). n.i.: non identified. E.C. Name Reaction Gil et. al. 2004 Glass et. al. 2006 number 2.7.1.69 phosphotransferase system glc + pep → g6p + pyr PTS MG041, 069, 429 5.3.1.9 glucose-6-phosphate isomerase g6p ↔ f6p PGI MG111 2.7.1.11 6-phosphofructokinase f6p + atp → fbp + adp PFK MG215 4.1.2.13 fructose-1,6-bisphosphate aldolase fbp ↔ gdp + dhp FBA MG023 5.3.1.1 triose-phosphate isomerase gdp ↔ dhp TPI MG431 glyceraldehyde-3-phosphate gdp + nad + p ↔ bpg + 1.2.1.12 GAP MG301 dehydrogenase nadh 2.7.2.3 phosphoglycerate kinase bpg + adp ↔ 3pg + atp PGK MG300 5.4.2.1 phosphoglycerate mutase 3pg ↔ 2pg GPM MG430 4.2.1.11 enolase 2pg ↔ pep ENO MG407 2.7.1.40 pyruvate kinase pep + adp → pyr + atp PYK MG216 1.1.1.27 lactate dehydrogenase pyr + nadh ↔ lac + nad LDH MG460 1.1.1.94 sn-glycerol-3-phosphate dehydrogenase dhp + nadh → g3p + nad GPS n.i. 2.3.1.15 sn-glycerol-3-phosphate acyltransferase g3p + pal → mag PLSb n.i. 2.3.1.51 1-acyl-sn-glycerol-3-phosphate mag + pal → dag PLSc MG212 acyltransferase 2.7.7.41 phosphatidate cytidyltransferase dag + ctp → cdp-dag + pp CDS MG437 cdp-dag + ser → pser + 2.7.8.8 phosphatidylserine synthase PSS n.i. cmp 4.1.1.65 phosphatidylserine decarboxylase pser → peta PSD n.i.
    [Show full text]
  • NMR Spectroscopy and MD Simulations of Carbohydrates
    NMR spectroscopy and MD simul ations of carbohydrates Elin Säwén © Elin Säwén, Stockholm 2011 Cover picture: Five repeating units of the exopolysaccharide produced by Streptococcus thermophilus ST1 and a 1H NMR spectrum of the same exopolysaccharide. ISSN XXXX-XXXX ISBN XXX-XX-XXXXX-XX-X Printed in Sweden by US-AB, Stockholm 2011 Distributor: Department of Organic Chemistry, Stockholm University Till Ingrid Abstract Knowledge about the structure, conformation and dynamics of carbohydrates is important in our understanding of the way carbohydrates function in bio- logical systems, for example in intermolecular signaling and recognition. This thesis is a summary of five papers studying these properties in carbohy- drate-containing molecules with NMR spectroscopy and molecular dynamics simulations. In paper I, the ring-conformations of the six-membered rings of two car- baiduronic analogs were investigated. These carbasugars could potentially be used as hydrolytically stable mimics of iduronic acid in drugs. The study 4 showed that the equilibrium is entirely shifted towards the C1 conformation. Paper II is an investigation of the conformational flexibility and dynamics of two (1 →6)-linked disaccharides related to an oligosaccharide epitope expressed on malignant tumor cells. In paper III, the conformational space of the glycosidic linkage of the di- saccharide α-D-Man p-(1 →2)-α-D-Man p-OMe, which is present in N- and O- linked glycoproteins, was studied. A maximum entropy analysis using dif- ferent priors as background information was used and four new Karplus 3 3 equations for JC,C and JC,H coupling constants, related to the glycosidic linkage, were presented.
    [Show full text]
  • Synthesis and Sorting of Proteoglycans
    Journal of Cell Science 113, 193-205 (2000) 193 Printed in Great Britain © The Company of Biologists Limited 2000 JCS0690 COMMENTARY Synthesis and sorting of proteoglycans Kristian Prydz1,* and Knut Tomas Dalen2 1Department of Biochemistry and 2Institute for Nutrition Research, University of Oslo, Norway *Author for correspondence (e-mail: [email protected]) Published on WWW 13 January 2000 SUMMARY Proteoglycans are widely expressed in animal cells. type, which is acquired by use of particular Ser-Gly sites in Interactions between negatively charged glycosaminoglycan the protein core, might therefore be important for post- chains and molecules such as growth factors are essential for synthesis sorting. This links regulation of glycosaminoglycan differentiation of cells during development and maintenance synthesis to the post-Golgi fate of proteoglycans. of tissue organisation. We propose that glycosaminoglycan chains play a role in targeting of proteoglycans to their proper cellular or extracellular location. The variability seen Key words: Proteoglycan, Glycosaminoglycan, Sorting, Polarised in glycosaminoglycan chain structure from cell type to cell cell, Epithelial cell, Glycan INTRODUCTION VARIATION IN PROTEOGLYCAN COMPOSITION Proteoglycans (PGs) consist of a protein portion and long, PGs were initially grouped together because of the high unbranched polysaccharides (glycosaminoglycans or GAGs). negative charges of their GAG chains, which make separation The latter have a high negative charge, owing to the presence from other molecules by ion-exchange chromatography easy. of acidic sugar residues and/or modification by sulphate PGs are, however, not that similar. The core protein size ranges groups. The acidic sugar alternates with an amino sugar in from 10 kDa to >500 kDa, and the number of GAG chains repeated disaccharide units.
    [Show full text]
  • Pentose Phosphate Pathway and the Synthesis of Glycosides, Lactose, Glycoproteins, and Glycolipids
    Chapter 27 Pentose Phosphate Pathway and the Synthesis of Glycosides, Lactose, Glycoproteins, and Glycolipids Human Biochemistry • The pentose phosphate pathway (also known as the hexose monophosphate shunt [HMP shunt]) consists of both oxidative and nonoxidative components. • In the oxidative pathway, glucose 6- phosphate (glucose 6-P) is oxidized to ribulose 5-phosphate (ribulose 5-P), CO2, and NADPH. Ribulose 5-P, a pentose, can be converted to ribose 5-phosphate (ribose 5-P) for nucleotide biosynthesis. • The second stage of the pentose Overview of the pentose phosphate pathway. phosphate pathway generates ribose 5-P The pentose phosphate pathway generates NADPH and converts unused intermediates to for reactions that require reducing equivalents fructose 6-P and glyceraldehyde 3-P in (electrons) or ribose 5-P for nucleotide biosynthesis. the glycolytic pathway. Glucose 6-P is a substrate for both the pentose phosphate pathway and glycolysis. The five-carbon sugar intermediates of the pentose phosphate pathway are reversibly interconverted to intermediates of glycolysis. The portion of glycolysis that is not part of the pentose phosphate pathway is shown in red. • In the oxidative, first phase of the pentose phosphate pathway, glucose 6-P undergoes and oxidation and decarboxylation to a pentose sugar, ribulose 5-phosphate (ribulose 5-P). • The first enzyme of this pathway, glucose-6-phosphate dehydrogenase, oxidizes the aldehyde at carbon 1 and reduces NADP to NADPH. • The gluconolactone that is formed is rapidly hydrolyzed to 6- phosphogluconate, a sugar acid with a carboxylic acid group at carbon 1. • The next oxidation step releases this carboxyl group as CO2, with the electrons being transferred to NADP.
    [Show full text]
  • Salemcity, A.J Carbohydrate Chemistry Lecture
    BCM 210 LECTURE SALEMCITY, A.J CARBOHYDRATE CHEMISTRY • Carbohydrates (saccharides) are a large family of naturally occurring compounds including sugars, starches, and cellulose, as well as materials found in bacterial cell walls and insect exoskeletons. • Carbohydrates, in general, contain a C-C skeletal monomers bearing C=O and OH (and sometimes NH2) functional groups. SUGAR DERIVATIVES OF BIOLOGICAL IMPORTANCE • Monosaccharides undergo various reactions to form biologically important derivatives. • The important functional groups present in monosaccharides are hydroxyl and carbonyl groups. • The hydroxyl group forms phosphodiester bond, usually with phosphoric acid or is replaced by a hydrogen or amino group. • The carbonyl group undergoes reduction or oxidation to produce number of derived monosaccharides. • These derivatives include amino sugar, sugar acids, sugar phosphates, deoxy sugars, and sugar amides etc. Amino Sugars and N-acetylated sugars • The hydroxyl group, usually at C-2, is replaced by an amino group to produce amino sugars such as glucosamine, galactosamine and mannosamine. • The amino group may be condensed with acetic acid to produce N-acetyl amino sugars, for example, N-acetyl glucosamine. • This glucosamine derivative is important constituent of many structural polymers (chitin, bacterial cell wall polysaccharides etc.). Glucosamine: the systemic name is 2-Amino-2- deoxy-D-glucose. • Glucosamine is an amino sugar derived from glucose, produced in the body from the sugar glucose and the amino acid glutamine through the action of the enzyme glucosamine synthetase. • Glucosamine stimulates the synthesis of proteoglycans, glycosaminoglycans (also called mucopolysaccharides), and collagen. • Glycosaminoglycans are a major component of joint cartilage, supplemental glucosamine may help to rebuild cartilage and treat arthritis.
    [Show full text]
  • Biochemistry Introductory Lecture Dr
    Biochemistry Introductory lecture Dr. Munaf S. Daoud Carbohydrates (CHO) Definition: Aldehyde or Ketone derivatives of the higher polyhydric alcohols or compounds which yield these derivatives on hydrolysis. Classification: (mono, di, oligo, poly) saccharide. Monosaccharides: Can be classified as trioses, tetroses, pentoses, hexoses and heptoses depending upon the number of carbon atoms, and as aldoses or ketoses, depending upon whether they have an aldehyde or ketone group. Aldehyde (-CHO) Aldoses Ketone (-C=O) Ketoses Polysaccharides (glycans): Homopolysaccharides (homoglycans): e.g. starch, glycogen, inulin, cellulose, dextrins, dextrans. Heteropolysaccharides (heteroglycans): e.g. mucopolysaccharides (MPS) or glycosaminoglycans. Function of CHO: 1) Chief source of energy (immediate and stored energy). 2) Constituent of compound lipids and conjugated protein. 3) Structural element like cellulose. 4) Drugs like cardiac glycosides and antibodies. 5) Lactating mammary gland (Lactose in milk). 6) Synthesis of other substances like fatty acids, cholesterol, amino acids…etc. by their degradation products. 7) Constituent of mucopolysaccharides. 1 1) Stereo-isomerism Stereo-isomers: D-form, L-form 2) Optical isomers (optical activity) Enantiomers: dextrorotatory (d or + sign) Levorotatory (l or – sign) Racemic (d l) 3) Cyclic structures or open chain 4) Anomers and Anomeric carbon OH on carbon number 1, if below the plane then its -form, if above the plane then -form. Mutarotation: the changes of the initial optical rotation that takes place
    [Show full text]
  • Chemical Modification of Glycosaminoglycan Polysaccharides
    molecules Review Chemical Modification of Glycosaminoglycan Polysaccharides Lais C. G. F. Palhares 1 , James A. London 2 , Aleksandra M. Kozlowski 3, Emiliano Esposito 4, Suely F. Chavante 1, Minghong Ni 4 and Edwin A. Yates 2,* 1 Programa de Pós-graduação em Bioquímica e Biologia Molecular, Departamento de Bioquímica, Universidade do Rio Grande do Norte (UFRN), Natal 59012-570, Brazil; [email protected] (L.C.G.F.P.); [email protected] (S.F.C.) 2 Department of Biochemistry and Systems Biology, ISMIB, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK; [email protected] 3 Department of Chemistry and Chemical Engineering, Forest Products and Chemical Engineering, Chalmers University of Technology, Kemigården 4, 412 58 Göteborg, Sweden; [email protected] 4 Instituto di Richerche Chemiche e Biochemiche, ‘G.Ronzoni’, Via G Colombo 81, 20133 Milano, Italy; [email protected] (E.E.); [email protected] (M.N.) * Correspondence: [email protected] or [email protected]; Tel.: +44-151-795-4429 Abstract: The linear anionic class of polysaccharides, glycosaminoglycans (GAGs), are critical throughout the animal kingdom for developmental processes and the maintenance of healthy tissues. They are also of interest as a means of influencing biochemical processes. One member of the GAG family, heparin, is exploited globally as a major anticoagulant pharmaceutical and there is a growing interest in the potential of other GAGs for diverse applications ranging from skin care to the treatment of neurodegenerative conditions, and from the treatment and prevention of microbial infection to biotechnology. To realize the potential of GAGs, however, it is necessary to develop effective tools that are able to exploit the chemical manipulations to which GAGs are susceptible.
    [Show full text]