Photosynthesis and Respiration
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Lipid Analysis of CO2-Rich Subsurface Aquifers Suggests an Autotrophy-Based Deep Biosphere with Lysolipids Enriched in CPR Bacteria
The ISME Journal (2020) 14:1547–1560 https://doi.org/10.1038/s41396-020-0624-4 ARTICLE Lipid analysis of CO2-rich subsurface aquifers suggests an autotrophy-based deep biosphere with lysolipids enriched in CPR bacteria 1,2 3,4 1,3 3 3 Alexander J. Probst ● Felix J. Elling ● Cindy J. Castelle ● Qingzeng Zhu ● Marcus Elvert ● 5,6 6 1 7,9 7 Giovanni Birarda ● Hoi-Ying N. Holman ● Katherine R. Lane ● Bethany Ladd ● M. Cathryn Ryan ● 8 3 1 Tanja Woyke ● Kai-Uwe Hinrichs ● Jillian F. Banfield Received: 20 November 2018 / Revised: 5 February 2020 / Accepted: 25 February 2020 / Published online: 13 March 2020 © The Author(s) 2020. This article is published with open access Abstract Sediment-hosted CO2-rich aquifers deep below the Colorado Plateau (USA) contain a remarkable diversity of uncultivated microorganisms, including Candidate Phyla Radiation (CPR) bacteria that are putative symbionts unable to synthesize membrane lipids. The origin of organic carbon in these ecosystems is unknown and the source of CPR membrane lipids remains elusive. We collected cells from deep groundwater brought to the surface by eruptions of Crystal Geyser, sequenced 1234567890();,: 1234567890();,: the community, and analyzed the whole community lipidome over time. Characteristic stable carbon isotopic compositions of microbial lipids suggest that bacterial and archaeal CO2 fixation ongoing in the deep subsurface provides organic carbon for the complex communities that reside there. Coupled lipidomic-metagenomic analysis indicates that CPR bacteria lack complete lipid biosynthesis pathways but still possess regular lipid membranes. These lipids may therefore originate from other community members, which also adapt to high in situ pressure by increasing fatty acid unsaturation. -
Carlson Udel 0060D 13047.Pdf
SYNTHETIC CARBON FIXATION FOR IMPROVED MICROBIAL FERMENTATION YIELDS by Ellinor Dorothee Carlson A dissertation submitted to the Faculty of the University of Delaware in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Chemical Engineering Summer 2017 © 2017 Ellinor Dorothee Carlson All Rights Reserved SYNTHETIC CARBON FIXATION FOR IMPROVED MICROBIAL FERMENTATION YIELDS by Ellinor Dorothee Carlson Approved: __________________________________________________________ Abraham M. Lenhoff, Ph.D. Chair of the Department of Chemical & Biomolecular Engineering Approved: __________________________________________________________ Babatunde A. Ogunnaike, Ph.D. Dean of the College of Engineering Approved: __________________________________________________________ Ann L. Ardis, Ph.D. Senior Vice Provost for Graduate and Professional Education I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: __________________________________________________________ Eleftherios T. Papoutsakis, Ph.D. Professor in charge of dissertation I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: __________________________________________________________ Maciek R. Antoniewicz, Ph.D. Member of dissertation committee I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: __________________________________________________________ Wilfred Chen, Ph.D. Member of dissertation committee I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. -
Photosynthesis and Cellular Respiration
Unit 4 - Photosynthesis and Cellular Respiration Topic Products and Reactants Best and Worst Colors for Photos nthesis " Light Dependent vs. Light Independent Reaction Organelles Responsible ADP VS. ATP Products and Reactants Photosynthesis Cellular Respiration Aerobic: C6H120 6 + O2 ~C02 + H20 + 36 ATP Anaerobic: Human: C6H1206~ CO 2 + lactic acid + 4ATP • Yeast: C6H1206~ CO 2 + ethyl alcohol + 4ATP Best and Worst • Colors for . Photosynthesis i Light Dependent vs. Light Independent Reaction Organelles Responsible ADP vs. AlP 8986 - 1 - Page 1 Nanre: _______________________________________ In animal cells, the energy to convert ADP to AlP comes directly from A) organic molecules C) sunlight B) inorganic molecules D) hormones 2) Which statement correctly describes part ofthe photosynthetic process in plants? A) Water is spili in the light reactions. B) Alcohol is produced by the light reactions. C) Oxygen is used in the dark reactions. D) Carbon dioxide is released in the dark reactions. 3) Which statement best describes one ofthe events taking p1ace in the ,chemical reaction represented below? ATPase H 0 + ATP --------~) ADP + P + energy 2 A) Photosynthesis is taking place, resulting in the storage ofenergy. B) Energy is being stored as a result ofaerobic respiratioIt C) Energy is being released fur metabolic activities. D) Fermentation is taking place, resulting in the synthesis ofAlP. 4) Which process results in muscle fatigue and cramping in humans? A) aerobic respiration C) lactic acid fermentation B) photosynthesis D) alcoholic fermentation -
24 Biological Energy Transfer Cellular Respiration Involves the Stepwise Transfer of Energy and Electrons
contents Principles of Biology 24 Biological Energy Transfer Cellular respiration involves the stepwise transfer of energy and electrons. Large-scale municipal composting. The steam emitted from the compost as it is being turned is evidence of trillions of microorganisms performing cellular respiration, breaking down molecules in the compost and generating energy, some in the form of heat. Nancy J. Pierce/Science Source. Topics Covered in this Module How Do Organisms Obtain Energy? Redox Reactions An Outline of the Stages in Cellular Respiration Major Objectives of this Module Describe the relationships among photosynthesis, respiration, producers, and consumers. Explain how reduction-oxidation (redox) reactions work. Describe how aerobic cellular respiration breaks down fuel molecules and releases energy for cellular work. page 121 of 989 4 pages left in this module contents Principles of Biology 24 Biological Energy Transfer How Do Organisms Obtain Energy? No matter how wealthy you become in life, you will always work for a living. That is, your cells will always be working to keep you alive. From synthesizing proteins to producing gametes to chasing down prey, living cells are constantly at work, and all that work requires energy. Where does that energy come from? Ultimately it comes from our Sun as light energy. Energy flows through all living systems. Plants, algae, and photosynthetic bacteria use energy from sunlight to generate sugar molecules through the process of photosynthesis. Such organisms, known as photoautotrophic producers, convert the radiant energy of sunlight into chemical energy that they store in sugars and other organic compounds. Other organisms, termed heterotrophic consumers, must acquire the chemical energy they need by ingesting or absorbing organic molecules from other organisms. -
The Formation of a Gluconeogenesis System and Reductive Pentose Phosphate Pathway of CO2 Fixation in Ancient Hydrothermal Systems Sergey A
: O tics pe ge n r A e c n c e Marakushev and Belonogova, Bioenergetics 2016, e o s i s B 5:2 Bioenergetics: Open Access DOI: 10.4172/2167-7662.1000141 ISSN: 2167-7662 Research Article Open Access The Emergence of Bioenergetics: The Formation of a Gluconeogenesis System and Reductive Pentose Phosphate Pathway of CO2 Fixation in Ancient Hydrothermal Systems Sergey A. Marakushev* and Ol’ga V. Belonogova Institute of Problems of Chemical Physics, Russian Academy of Sciences, Chernogolovka, Moscow Region, Russia *Corresponding author: Marakushev SA, Institute of Problems of Chemical Physics, Russian Academy of Sciences, Chernogolovka, Russia, Tel: 496-522-7772; E-mail: [email protected] Rec date: Apr 18, 2016; Acc date: Nov 08, 2016; Pub date: Nov 11, 2016 Copyright: © 2016 Marakushev SA et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Abstract The origin of phosphorus metabolism is one of the central problems in the context of the emergence of life on Earth. It has been shown that the C–H–O system can be transformed into a four- component C–H–O–P system with the formation of a gluconeogenesis path in a possible Archean hydrothermal condition under the influence of a phosphorus chemical potential. This system became the energy supply basis for protometabolism, and facilitated the formation of a new CO2 fixation cycle (the reductive pentose phosphate pathway). The modular design of central metabolism in the C–H–O–P system is derived from the parageneses (associations) of certain substances, and the emerging modules in turn associate with each other in certain physical and chemical hydrothermal conditions. -
Cellular Biology 1
Cellular biology 1 INTRODUCTION • Specialized intracellular membrane-bound organelles (Fig. 1.2), such as mitochondria, Golgi apparatus, endoplasmic reticulum (ER). This chapter is an overview of eukaryotic cells, addressing • Large size (relative to prokaryotic cells). their intracellular organelles and structural components. A basic appreciation of cellular structure and function is important for an understanding of the following chapters’ information concerning metabolism and nutrition. For fur- ther detailed information in this subject area, please refer to EUKARYOTIC ORGANELLES a reference textbook. Nucleus The eukaryotic cell The nucleus is surrounded by a double membrane (nuclear Humans are multicellular eukaryotic organisms. All eukary- envelope). The envelope has multiple pores to allow tran- otic organisms are composed of eukaryotic cells. Eukaryotic sit of material between the nucleus and the cytoplasm. The cells (Fig. 1.1) are defined by the following features: nucleus contains the cell’s genetic material, DNA, organized • A membrane-limited nucleus (the key feature into linear structures known as chromosomes. As well as differentiating eukaryotic cells from prokaryotic cells) chromosomes, irregular zones of densely staining material that contains the cell’s genetic material. are also present. These are the nucleoli, which are responsible Inner nuclear Nucleus membrane Nucleolus Inner Outer Outer mitochondrial nuclear mitochondrial membrane membrane membrane Ribosome Intermembrane space Chromatin Mitochondrial Rough matrix Mitochondrial Nuclear endoplasmic ribosome pore reticulum Crista Mitochondrial mRNA Smooth Vesicle endoplasmic Mitochondrion Circular reticulum mitochondrial Proteins of the DNA Vesicle budding electron transport off rough ER Vesicles fusing system with trans face of Cytoplasm Golgi apparatus ‘Cis’ face + discharging protein/lipid Golgi apparatus ‘Trans’ face Lysosome Vesicles leaving Golgi with modified protein/lipid cargo Cell membrane Fig. -
A Survey of Carbon Fixation Pathways Through a Quantitative Lens
Journal of Experimental Botany, Vol. 63, No. 6, pp. 2325–2342, 2012 doi:10.1093/jxb/err417 Advance Access publication 26 December, 2011 REVIEW PAPER A survey of carbon fixation pathways through a quantitative lens Arren Bar-Even, Elad Noor and Ron Milo* Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel * To whom correspondence should be addressed. E-mail: [email protected] Received 15 August 2011; Revised 4 November 2011; Accepted 8 November 2011 Downloaded from Abstract While the reductive pentose phosphate cycle is responsible for the fixation of most of the carbon in the biosphere, it http://jxb.oxfordjournals.org/ has several natural substitutes. In fact, due to the characterization of three new carbon fixation pathways in the last decade, the diversity of known metabolic solutions for autotrophic growth has doubled. In this review, the different pathways are analysed and compared according to various criteria, trying to connect each of the different metabolic alternatives to suitable environments or metabolic goals. The different roles of carbon fixation are discussed; in addition to sustaining autotrophic growth it can also be used for energy conservation and as an electron sink for the recycling of reduced electron carriers. Our main focus in this review is on thermodynamic and kinetic aspects, including thermodynamically challenging reactions, the ATP requirement of each pathway, energetic constraints on carbon fixation, and factors that are expected to limit the rate of the pathways. Finally, possible metabolic structures at Weizmann Institute of Science on July 3, 2016 of yet unknown carbon fixation pathways are suggested and discussed. -
Evolution of the First Metabolic Cycles
Proc. Natl. Acad. Sci. USA Vol. 87, pp. 200-204, January 1990 Evolution Evolution of the first metabolic cycles (chemoautotrophy/reductive citric acid cycle/origin of life/pyrite) GUNTER WACHTERSHAUSER 8000 Munich 2, Tal 29, Federal Republic of Germany Communicated by Karl Popper, October 12, 1989 (received for review February 28, 1989) ABSTRACT There are two alternatives concerning the genobacter thermophilus (13), and Desulfobacter hydro- origin of life: the origin may be heterotrophic or autotrophic. genophilus (14) and also in the sulfur-associated archaebac- The central problem within the theory of an autotrophic origin teria Thermoproteus neutrophilus (15) and, partly demon- is the first process of carbon fixation. I here propose the strated, in Sulfolobus brierleyi (16). As suggested by Kandler hypothesis that this process is an autocatalytic cycle that can be and Stetter (16) and previously by Hartmann (17), it may be retrodictively constructed from the extant reductive citric acid considered to be of great antiquity and the evolutionary cycle by replacing thioesters by thioacids and by assuming that precursor ofthe oxidative Krebs cycle. It is here conjectured the required reducing power is obtained from the oxidative to be the extant candidate for the reconstruction of the formation of pyrite (FeS2). This archaic cycle is strictly archaic autocatalytic cycle of carbon fixation. chemoautotrophic: photoautotrophy is not required. The cycle The presently accepted form of the extant reductive citric is catalytic for pyrite formation and autocatalytic for its own acid cycle is shown in Fig. 1 in a somewhat unusual repre- multiplication. It is a consequence of this hypothesis that the sentation, twisted in an 8. -
Passive and Active Transport
Passive and Active Transport 1. Thermodynamics of transport 2. Passive-mediated transport 3. Active transport neuron, membrane potential, ion transport Membranes • Provide barrier function – Extracellular – Organelles • Barrier can be overcome by „transport proteins“ – To mediate transmembrane movements of ions, Na+, K+ – Nutrients, glucose, amino acids etc. – Water (aquaporins) 1) Thermodynamics of Transport • Aout <-> Ain (ressembles a chemical equilibration) o‘ • GA - G A = RT ln [A] • ∆GA = GA(in) - GA(out) = RT ln ([A]in/[A]out) • GA: chemical potential of A o‘ • G A: chemical potential of standard state of A • If membrane has a potential, i.e., plasma membrane: -100mV (inside negative) then GA is termed the electrochemical potential of A Two types of transport across a membrane: o Nonmediated transport occurs by passive diffusion, i.e., O2, CO2 driven by chemical potential gradient, i.e. cannot occur against a concentration gradient o Mediated transport occurs by dedicated transport proteins 1. Passive-mediated transport/facilitated diffusion: [high] -> [low] 2. Active transport: [low] -> [high] May require energy in form of ATP or in form of a membrane potential 2) Passive-mediated transport Substances that are too large or too polar to diffuse across the bilayer must be transported by proteins: carriers, permeases, channels and transporters A) Ionophores B) Porins C) Ion Channels D) Aquaporins E) Transport Proteins A) Ionophores Organic molecules of divers types, often of bacterial origin => Increase the permeability of a target membrane for ions, frequently antibiotic, result in collapse of target membrane potential by ion equilibration 1. Carrier Ionophore, make ion soluble in membrane, i.e. valinomycin, 104 K+/sec 2. -
Evidence for a Respiratory Chain in the Chloroplast
Proc. NatL Acad. Sci. USA Vol. 79, pp. 4352-4356, July 1982 Cell Biology Evidence for a respiratory chain in the chloroplast (photosynthesis/respiration/starch degradation/evolution) PIERRE BENNOUN Institut de Biologie Physico-Chimique, 13, rue Pierre et Marie Curie, 75005, Paris, France Communicated by Pierre Joliot, April 12, 1982 ABSTRACT Evidence is given for the existence ofan electron in 20 ml of 20 mM N-tris(hydroxymethyl)methylglycine(Tri- transport pathway to oxygen in the thylakoid membranes ofchlo- cine)/KOH, pH 7.8/10 mM NaCl/10 mM MgCl2/1 mM K2- roplasts (chlororespiration). Plastoquinone is shown to be a redox HPO4/0.1 M sucrose/5% Ficoll. The cell suspension was carrier common to both photosynthetic and chlororespiratory passed through a Yeda press operated at 90 kg/cm2, diluted pathways. It is shown that, in dark-adapted chloroplasts, an elec- with 200 ml of Ficoll-lacking buffer, and centrifuged, and the trochemical gradient is built up across the thylakoid membrane pellet was suspended in the same buffer. by transfer of electrons through the chlororespiratory chain as Chlorophyll fluorescence kinetics and luminescence mea- well as by reverse functioning of the chloroplast ATPases. It is surements were performed as described (9). proposed that these mechanisms ensure recycling ofthe ATP and NAD(P)H generated by the glycolytic pathway converting starch into triose phosphates. Chlororespiration is thus an 02-uptake RESULTS process distinct from photorespiration and the Mehler reaction. The plastoquinone (PQ) pool ofchloroplast is a redox carrier of The evolutionary significance of chlororespiration is discussed. the photosynthetic electron transport chain. -
The Electrochemical Gradient of Protons and Its Relationship to Active Transport in Escherichia Coli Membrane Vesicles
Proc. Natl. Acad. Sci. USA Vol. 73, No. 6, pp. 1892-1896, June 1976 Biochemistry The electrochemical gradient of protons and its relationship to active transport in Escherichia coli membrane vesicles (flow dialysis/membrane potential/energy transduction/lipophilic cations/weak acids) SOFIA RAMOS, SHIMON SCHULDINER*, AND H. RONALD KABACK The Roche Institute of Molecular Biology, Nutley, New Jersey 07110 Communicated by B. L. Horecker, March 17, 1976 ABSTRACT Membrane vesicles isolated from E. coli gen- presence of valinomycin), a respiration-dependent membrane erate a trans-membrane proton gradient of 2 pH units under potential (AI, interior negative) of approximately -75 mV in appropriate conditions when assayed by flow dialysis. Using E. coli membrane vesicles has been documented (6, 13, 14). the distribution of weak acids to measure the proton gradient (ApH) and the distribution of the lipophilic cation triphenyl- Moreover it has been shown that the potential causes the ap- methylphosphonium to measure the electrical potential across pearance of high affinity binding sites for dansyl- and azido- the membrane (AI), the vesicles are shown to generate an phenylgalactosides on the outer surface of the membrane (4, electrochemical proton gradient (AiH+) of approximately -180 15) and that the potential is partially dissipated as a result of mV at pH 5.5 in the presence of ascorbate and phenazine lactose accumulation (6). Although these findings provide ev- methosulfate, the major component of which is a ApH of about idence for the chemiosmotic hypothesis, it has also been dem- -110 mV. As external pH is increased, ApH decreases, reaching o at pH 7.5 and above, while AI remains at about -75 mV and onstrated (6, 16) that vesicles are able to accumulate lactose and internal pH remains at pH 7.5. -
Glycolysis-Gluconeogenesis (Hsa00010), B
A. TITLE:Glycolysis / Gluconeogenesis Starch and sucrose metabolism K01085... Cori ester PGM1 G6PC K02777... Glucose HK1 K00886 alpha-D-Glucose GCK ADPGK alpha-D-Glucose 6-phosphate GALM K01792 GPI GPI HK1 K00886 GPI beta-D-Glucose GCK ADPGKbeta-D-Glucose 6-phosphate beta-D-Fructose 6-phosphate FBP1 PFKL K00918 K00895... Pentose phosphate pathway K02777... K01222... Ursin Arbutin-6P K02777... K01222... beta-D-Fructose 1,6-bisphosphate Salicin Salicin-6P ALDOA TPI1 Glycerone phosphate Glyceraldehyde 3-phosphate GAPDH K00150 K00131 K11389 BPGM 1,3-Bisphospho-D-glycerate K18978 PGK1 DPG Carbon fixation in BPGM photosynthetic organisms 3-Phosphoglycerate PGAM4 K15633... MINPP1 2-Phospho-D-glycerate ENO1 PCK1 Oxaloacetate K01610 PEP Pyruvate metabolism PKLR K00169... Citrate cycle (TCA cycle) K00174... TPP PDHA1 DLAT PDHA1 LDHAL6A Acetyl-CoA S-Acetyldihydrolipoamide-E 2-Hydroxyethyl-ThPP K01568 Pyruvate L-Lactate DLD ACSS2 K01905... Dihydrolipoamide-E Lipoamide-E K01568 Propanoate metabolism ADH1A ALDH2 AKR1A1 K14028... Acetate ALDH3A1 K00138 Ethanal K04022 Ethanol K00114 B. B. TITLE:Citrate cycle (TCA cycle) PCK1 Glycolysis / Gluconeogenesis K01610 PEP Fatty acid biosynthesis K00169... Fatty acid elongation K00174... Valine TPP Fatty acid degradation DLAT PDHA1 PDHA1 Acetyl-CoA S-Acetyldihydrolipoamide-E 2-Hydroxyethyl-ThPP Pyruvate Alanine PC DLD Dihydrolipoamide-E Lipoamide-E Glyoxylate and dicarboxylate metabolism CS MDH1 ACO1 ACO1 Oxaloacetate ACLY Citrate cis-Aconitate Isocitrate K00116 Malate IDH1 FH Tyrosine metabolism Oxalosuccinate IDH3A K17753 Arginine biosynthesis Fumarate IDH1 K00244... SDHA TPP SUCLG2 SUCLG2 DLST OGDH OGDH Arginine biosynthesis Succinate Succinyl-CoA S-Succinyldihydrolipoamide-E 3-Carboxy-1-hydroxypropyl-ThPP 2-Oxoglutarate K18118 Ascorbate and aldarate DLD metabolism Dihydrolipoamide-E Lipoamide-E Valine K00174..