Chapter 1 Photosynthesis
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Lecture 29 Spring 2007
Geol. 656 Isotope Geochemistry Lecture 29 Spring 2007 ISOTOPE FRACTIONATION IN THE BIOSPHERE INTRODUCTION As we noted, biological processes often involve large isotopic fractionations. Indeed, biological proc- esses are the most important cause of variations in the isotope composition of carbon, nitrogen, and sul- fur. For the most part, the largest fractionations occur during the initial production of organic matter by the so-called primary producers, or autotrophs. These include all plants and many kinds of bacteria. The most important means of production of organic matter is photosynthesis, but organic matter may also be produced by chemosynthesis, for example at mid-ocean ridge hydrothermal vents. Large frac- tions of both carbon and nitrogen occur during primary production. Additional fractionations also oc- cur in subsequent reactions and up through the food chain as hetrotrophs consume primary producers, but these are generally smaller. CARBON ISOTOPE FRACTIONATION DURING PHOTOSYNTHESIS The most important of process producing isotopic fractionation of carbon is photosynthesis. As we earlier noted, photosynthetic fractionation of carbon isotopes is primarily kinetic. The early work of Park and Epstein (1960) suggested fractionation occurred in several steps. Subsequent work has eluci- dated the fractionations involved in these steps, which we will consider in more detail here. For terrestrial plants (those utilizing atmospheric CO2), the first step is diffusion of CO2 into the boundary layer surrounding the leaf, through the stomata, and internally in the leaf. The average δ13C of various species of plants has been correlated with the stomatal conductance (Delucia et al., 1988), in- dicating that diffusion into the plant is indeed important in fractionating carbon isotopes. -
Light Pollution and the Impacts on Biodiversity, Species and Their Habitats P
LIGHT POLLUTION AND THE IMPACTS ON BIODIVERSITY, SPECIES AND THEIR HABITATS P. DEDA, I. ELBERTZHAGEN, M. KLUSSMANN Secretariat of the Convention on the Conservation of Migratory Species of Wild Animals (UNEP-CMS) What is ecological light pollution? Longcore and Rich describe artificial light that alters the natural patterns of light and dark in ecosystems as “ecological light pollution”.7 Ecological light pollution comprises direct glare, chronically increased illumination and temporary, unexpected fluctuations in lighting. The sources of ecological light pol- lution are very various and found in nearly every ecosystem in the form of “sky glow, illuminated buildings and towers, streetlights, fishing boats, security lights, lights on vehicles, flares on offshore oil platforms, and even lights on undersea research ves- sels”.7 Impacts of light pollution Because the study of light pollution is still in its early days the impacts of this prob- lem are not fully understood. While the increased brightness of the night sky is the most familiar of the many effects of light pollution (it is the most obvious and astronomers recognized it many years ago) many other alarming aspects are still unexplored: for example, the fact that light pollution leads to a great wastage of energy. On a global scale, approximately 19% of all electricity used produces light at night.18 The by-prod- uct of electric illumination generated by the burning of fossil fuels, is the discharge of greenhouse gases. These gases are responsible for global warming and the exhaustion of non-renewable resources. Light pollution produces many other impacts on the environment. Harmful effects involve the animal kingdom, the vegetable kingdom and mankind. -
Vitamin a Deficiency and Night Blindness by John E
VITAMIN A DEFICIENCY AND NIGHT BLINDNESS BY JOHN E. DOWLING AND GEORGE WALD* BIOLOGICAL LABORATORIES OF HARVARD UNIVERSITY, CAMBRIDGE Communicated May 16, 1958 One of the oldest diseases known to man is nutritional night blindness. Its descriptions go back to the ancient Egyptian medical papyri and are already ac- companied by the correct prescription for its cure, the eating of liver. Toward the end of World War I the factor in liver which cures night blindness was identified with the then newly discovered vitamin A.1 Vitamin A is the precursor in the retina of the visual pigments of the rods and cones.2 It seems reasonable to suppose that on a diet deficient in this factor the retina eventually synthesizes subnormal amounts of visual pigment, with the corresponding decline of visual sensitivity that constitutes night blindness. Some of the first studies of experimental human night blindness seemed to reveal such a simple and direct relationship.' In two subjects deprived of vitamin A, the visual thresholds of both rods and cones began at once to rise, until a mild night blindness had been established.4 On oral administration of vitamin A or carotene, the thresholds of both rod and cone vision returned to normal within 2-3 hours. It looked for a time, therefore, as though this might be an exemplary instance of the origin and cure of a biochemical disease, all elements of which were well under- stood. Further studies, however, exposed two major discrepancies: (1) Though in some subjects placed on a vitamin A-deficient diet the visual threshold began at once to rise, in a larger number it remained unchanged for periods ranging from several months5 to, in one instance, 2 years.6 (2) Among the subjects who developed night blindness, some were completely cured within a few hours after receiving vitamin A, whereas others, though showing some immediate improvement, took months of vitamin A supplementation to return to normal. -
Shedding New Light on the Generation of the Visual Chromophore PERSPECTIVE Krzysztof Palczewskia,B,C,1 and Philip D
PERSPECTIVE Shedding new light on the generation of the visual chromophore PERSPECTIVE Krzysztof Palczewskia,b,c,1 and Philip D. Kiserb,d Edited by Jeremy Nathans, Johns Hopkins University School of Medicine, Baltimore, MD, and approved July 9, 2020 (received for review May 16, 2020) The visual phototransduction cascade begins with a cis–trans photoisomerization of a retinylidene chro- mophore associated with the visual pigments of rod and cone photoreceptors. Visual opsins release their all-trans-retinal chromophore following photoactivation, which necessitates the existence of pathways that produce 11-cis-retinal for continued formation of visual pigments and sustained vision. Proteins in the retinal pigment epithelium (RPE), a cell layer adjacent to the photoreceptor outer segments, form the well- established “dark” regeneration pathway known as the classical visual cycle. This pathway is sufficient to maintain continuous rod function and support cone photoreceptors as well although its throughput has to be augmented by additional mechanism(s) to maintain pigment levels in the face of high rates of photon capture. Recent studies indicate that the classical visual cycle works together with light-dependent pro- cesses in both the RPE and neural retina to ensure adequate 11-cis-retinal production under natural illu- minances that can span ten orders of magnitude. Further elucidation of the interplay between these complementary systems is fundamental to understanding how cone-mediated vision is sustained in vivo. Here, we describe recent -
A Dicarboxylate/4-Hydroxybutyrate Autotrophic Carbon Assimilation Cycle in the Hyperthermophilic Archaeum Ignicoccus Hospitalis
A dicarboxylate/4-hydroxybutyrate autotrophic carbon assimilation cycle in the hyperthermophilic Archaeum Ignicoccus hospitalis Harald Huber*†, Martin Gallenberger*, Ulrike Jahn*, Eva Eylert‡, Ivan A. Berg§, Daniel Kockelkorn§, Wolfgang Eisenreich‡, and Georg Fuchs§ *Lehrstuhl fu¨r Mikrobiologie und Archaeenzentrum, Universita¨t Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany; ‡Lehrstuhl fu¨r Biochemie, Department Chemie, Technische Universita¨t Mu¨ nchen, Lichtenbergstrasse 4, D-85748 Garching, Germany; and §Lehrstuhl fu¨r Mikrobiologie, Universita¨t Freiburg, Scha¨nzlestrasse 1, D-79104 Freiburg, Germany Edited by Dieter So¨ll, Yale University, New Haven, CT, and approved April 1, 2008 (received for review February 1, 2008) Ignicoccus hospitalis is an anaerobic, autotrophic, hyperthermophilic starting from acetyl-CoA (4). On the basis of these data, pyruvate Archaeum that serves as a host for the symbiotic/parasitic Archaeum synthase and phosphoenolpyruvate (PEP) carboxylase were pos- Nanoarchaeum equitans. It uses a yet unsolved autotrophic CO2 tulated as CO2 fixing enzymes, with PEP carboxylase serving as the fixation pathway that starts from acetyl-CoA (CoA), which is reduc- only enzyme used for oxaloacetate synthesis. In addition, the tively carboxylated to pyruvate. Pyruvate is converted to phosphoe- operation of an incomplete ‘‘horseshoe-type’’ citric acid cycle, in nol-pyruvate (PEP), from which glucogenesis as well as oxaloacetate which 2-oxoglutarate oxidation does not take place, was demon- formation branch off. Here, we present the complete metabolic cycle strated. Enzyme and labeling data indicated a conventional glu- by which the primary CO2 acceptor molecule acetyl-CoA is regener- coneogenesis, but with some enzymes unrelated to those of the ated. Oxaloacetate is reduced to succinyl-CoA by an incomplete classical pathway. -
Lecture 7 - the Calvin Cycle and the Pentose Phosphate Pathway
Lecture 7 - The Calvin Cycle and the Pentose Phosphate Pathway Chem 454: Regulatory Mechanisms in Biochemistry University of Wisconsin-Eau Claire 1 Introduction The Calvin cycle Text The dark reactions of photosynthesis in green plants Reduces carbon from CO2 to hexose (C6H12O6) Requires ATP for free energy and NADPH as a reducing agent. 2 2 Introduction NADH versus Text NADPH 3 3 Introduction The Pentose Phosphate Pathway Used in all organisms Glucose is oxidized and decarboxylated to produce reduced NADPH Used for the synthesis and degradation of pentoses Shares reactions with the Calvin cycle 4 4 1. The Calvin Cycle Source of carbon is CO2 Text Takes place in the stroma of the chloroplasts Comprises three stages Fixation of CO2 by ribulose 1,5-bisphosphate to form two 3-phosphoglycerate molecules Reduction of 3-phosphoglycerate to produce hexose sugars Regeneration of ribulose 1,5-bisphosphate 5 5 1. Calvin Cycle Three stages 6 6 1.1 Stage I: Fixation Incorporation of CO2 into 3-phosphoglycerate 7 7 1.1 Stage I: Fixation Rubisco: Ribulose 1,5- bisphosphate carboxylase/ oxygenase 8 8 1.1 Stage I: Fixation Active site contains a divalent metal ion 9 9 1.2 Rubisco Oxygenase Activity Rubisco also catalyzes a wasteful oxygenase reaction: 10 10 1.3 State II: Formation of Hexoses Reactions similar to those of gluconeogenesis But they take place in the chloroplasts And use NADPH instead of NADH 11 11 1.3 State III: Regeneration of Ribulose 1,5-Bisphosphosphate Involves a sequence of transketolase and aldolase reactions. 12 12 1.3 State III: -
A Molecular Perspective of Human Circadian Rhythm Disorders Nicolas Cermakian* , Diane B
Brain Research Reviews 42 (2003) 204–220 www.elsevier.com/locate/brainresrev Review A molecular perspective of human circadian rhythm disorders Nicolas Cermakian* , Diane B. Boivin Douglas Hospital Research Center, McGill University, 6875 LaSalle boulevard, Montreal, Quebec H4H 1R3, Canada Accepted 10 March 2003 Abstract A large number of physiological variables display 24-h or circadian rhythms. Genes dedicated to the generation and regulation of physiological circadian rhythms have now been identified in several species, including humans. These clock genes are involved in transcriptional regulatory feedback loops. The mutation of these genes in animals leads to abnormal rhythms or even to arrhythmicity in constant conditions. In this view, and given the similarities between the circadian system of humans and rodents, it is expected that mutations of clock genes in humans may give rise to health problems, in particular sleep and mood disorders. Here we first review the present knowledge of molecular mechanisms underlying circadian rhythmicity, and we then revisit human circadian rhythm syndromes in light of the molecular data. 2003 Elsevier Science B.V. All rights reserved. Theme: Neural basis of behavior Topic: Biological rhythms and sleep Keywords: Circadian rhythm; Clock gene; Sleep disorder; Suprachiasmatic nucleus Contents 1 . Introduction ............................................................................................................................................................................................ 205 -
Recreating Ancient Metabolic Pathways Before Enzymes Kamila B
Recreating ancient metabolic pathways before enzymes Kamila B. Muchowska, Elodie Chevallot-Beroux, Joseph Moran To cite this version: Kamila B. Muchowska, Elodie Chevallot-Beroux, Joseph Moran. Recreating ancient metabolic path- ways before enzymes. Bioorganic and Medicinal Chemistry, Elsevier, 2019, 27 (12), pp.2292-2297. 10.1016/j.bmc.2019.03.012. hal-02516541 HAL Id: hal-02516541 https://hal.archives-ouvertes.fr/hal-02516541 Submitted on 23 Mar 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Graphical Abstract To create your abstract, type over the instructions in the template box below. Fonts or abstract dimensions should not be changed or altered. Recreating ancient metabolic pathways Leave this area blank for abstract info. before enzymes Kamila B. Muchowskaa* , Elodie Chevallot-Berouxa, and Joseph Morana* University of Strasbourg, CNRS, ISIS UMR 7006, 67000 Strasbourg, France Bioorganic & Medicinal Chemistry journal homepage: www.elsevier.com Recreating ancient metabolic pathways before enzymes Kamila B. Muchowska,a* Elodie Chevallot-Beroux,a and Joseph Morana* a University of Strasbourg, CNRS, ISIS UMR 7006, 67000 Strasbourg, France. ARTICLE INFO ABSTRACT Article history: The biochemistry of all living organisms uses complex, enzyme-catalyzed metabolic reaction Received networks. -
Scotobiology: the Biology of the Dark
SCOTOBIOLOGY: THE BIOLOGY OF THE DARK An outline for public information prepared by Dr. R.G.S. Bidwell, Wallace, NS What is Scotobiology? The concept of scotobiology as a science was developed at a conference on light pollution held in Muskoka, Ontario, in 2003. It was recognized that the underlying principle was the deleterious effect of light pollution on the operation of biological systems, ranging from their biochemistry and physiology to their social behaviour. Scotobiology is the study of biological systems that require nightly darkness for their effective performance; systems that are inhibited or prevented from operating by light. Why is Scotobiology important? Virtually all biological systems evolved in an environment of alternating light and darkness. Furthermore, the light/dark periods in temperate zones vary with the seasons. Organisms have evolved to use the variations in the length of day and night to integrate their physiological and social behaviour with the seasons. Many organisms measure specifically the length of the night, and light pollution may prevent them from determining the season, with serious of deadly consequences. For this reason light pollution is recognized as being a major component of global pollution, and scotobiology, the study of its specific effects on organisms, has now become an important branch of biological research. Summary of specific scotobiological responses Insects: Insects tend to fly towards light. Light pollution thus causes insects to concentrate around bright lights at night with several serious consequences. First, they become easy prey for birds and predacious insects. Insect numbers are reduced by their disorientation and death around lights, and also because they are concentrated where natural predators have an unnatural advantage to capture them. -
Artificial Light in the Environment
Published by TSO (The Stationery Office) and available from: Online www.tsoshop.co.uk Mail, Telephone Fax & E-Mail TSO PO Box 29, Norwich, NR3 1GN Telephone orders/General enquiries 0870 600 5522 Order through the Parliamentary Hotline Lo-Call 0845 7 023474 Fax orders: 0870 600 5533 E-mail: [email protected] Textphone: 0870 240 3701 The Parliamentary Bookshop 12 Bridge Street, Parliament Square, London SW1A 2JX Telephone orders/ General enquiries: 020 7219 3890 Fax orders: 020 7219 3866 Email: [email protected] Internet: http://www.bookshop.parliament.uk TSO@Blackwell and other Accredited Agents Customers can also order publications from TSO Ireland 16 Arthur Street, Belfast BT1 4GD 028 9023 8451 Fax 028 9023 5401 ISBN 978-0-10-850854-7 9 780108 508547 Artificial Light in the Environment £14.35 © Crown Copyright 2009 The text in this document (excluding the Royal Arms and other departmental or agency logos) may be reproduced free of charge in any format or medium providing it is reproduced accurately and not used in a misleading context. The material must be acknowledged as Crown copyright and the title of the document specified. Where we have identified any third party copyright material you will need to obtain permission from the copyright holders concerned. For any other use of this material please contact the Office of Public Sector Information, Information Policy Team, Kew, Richmond, Surrey TW9 4DU or e-mail: [email protected]. ISBN: 9780108508547 Printed in the UK by The Stationery Office Limited on behalf of the Controller of Her Majesty’s Stationery Office ID 2328242 11/09 Printed on paper containing 75% recycled fibre content minimum. -
Introduction; Environment & Review of Eyes in Different Species
The Biological Vision System: Introduction; Environment & Review of Eyes in Different Species James T. Fulton https://neuronresearch.net/vision/ Abstract: Keywords: Biological, Human, Vision, phylogeny, vitamin A, Electrolytic Theory of the Neuron, liquid crystal, Activa, anatomy, histology, cytology PROCESSES IN BIOLOGICAL VISION: including, ELECTROCHEMISTRY OF THE NEURON Introduction 1- 1 1 Introduction, Phylogeny & Generic Forms 1 “Vision is the process of discovering from images what is present in the world, and where it is” (Marr, 1985) ***When encountering a citation to a Section number in the following material, the first numeric is a chapter number. All cited chapters can be found at https://neuronresearch.net/vision/document.htm *** 1.1 Introduction While the material in this work is designed for the graduate student undertaking independent study of the vision sensory modality of the biological system, with a certain amount of mathematical sophistication on the part of the reader, the major emphasis is on specific models down to specific circuits used within the neuron. The Chapters are written to stand-alone as much as possible following the block diagram in Section 1.5. However, this requires frequent cross-references to other Chapters as the analyses proceed. The results can be followed by anyone with a college degree in Science. However, to replicate the (photon) Excitation/De-excitation Equation, a background in differential equations and integration-by-parts is required. Some background in semiconductor physics is necessary to understand how the active element within a neuron operates and the unique character of liquid-crystalline water (the backbone of the neural system). The level of sophistication in the animal vision system is quite remarkable. -
Reproductive Seasonality in Captive Wild Ruminants: Implications for Biogeographical Adaptation, Photoperiodic Control, and Life History
Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2012 Reproductive seasonality in captive wild ruminants: implications for biogeographical adaptation, photoperiodic control, and life history Zerbe, Philipp Abstract: Zur quantitativen Beschreibung der Reproduktionsmuster wurden Daten von 110 Wildwiederkäuer- arten aus Zoos der gemässigten Zone verwendet (dabei wurde die Anzahl Tage, an denen 80% aller Geburten stattfanden, als Geburtenpeak-Breite [BPB] definiert). Diese Muster wurden mit verschiede- nen biologischen Charakteristika verknüpft und mit denen von freilebenden Tieren verglichen. Der Bre- itengrad des natürlichen Verbreitungsgebietes korreliert stark mit dem in Menschenobhut beobachteten BPB. Nur 11% der Spezies wechselten ihr reproduktives Muster zwischen Wildnis und Gefangenschaft, wobei für saisonale Spezies die errechnete Tageslichtlänge zum Zeitpunkt der Konzeption für freilebende und in Menschenobhut gehaltene Populationen gleich war. Reproduktive Saisonalität erklärt zusätzliche Varianzen im Verhältnis von Körpergewicht und Tragzeit, wobei saisonalere Spezies für ihr Körpergewicht eine kürzere Tragzeit aufweisen. Rückschliessend ist festzuhalten, dass Photoperiodik, speziell die abso- lute Tageslichtlänge, genetisch fixierter Auslöser für die Fortpflanzung ist, und dass die Plastizität der Tragzeit unterstützend auf die erfolgreiche Verbreitung der Wiederkäuer in höheren Breitengraden wirkte. A dataset on 110 wild ruminant species kept in captivity in temperate-zone zoos was used to describe their reproductive patterns quantitatively (determining the birth peak breadth BPB as the number of days in which 80% of all births occur); then this pattern was linked to various biological characteristics, and compared with free-ranging animals. Globally, latitude of natural origin highly correlates with BPB observed in captivity, with species being more seasonal originating from higher latitudes.