Photorespiration: the Futile Cycle?
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Biomolecules
CHAPTER 3 Biomolecules 3.1 Carbohydrates In the previous chapter you have learnt about the cell and 3.2 Fatty Acids and its organelles. Each organelle has distinct structure and Lipids therefore performs different function. For example, cell membrane is made up of lipids and proteins. Cell wall is 3.3 Amino Acids made up of carbohydrates. Chromosomes are made up of 3.4 Protein Structure protein and nucleic acid, i.e., DNA and ribosomes are made 3.5 Nucleic Acids up of protein and nucleic acids, i.e., RNA. These ingredients of cellular organelles are also called macromolecules or biomolecules. There are four major types of biomolecules— carbohydrates, proteins, lipids and nucleic acids. Apart from being structural entities of the cell, these biomolecules play important functions in cellular processes. In this chapter you will study the structure and functions of these biomolecules. 3.1 CARBOHYDRATES Carbohydrates are one of the most abundant classes of biomolecules in nature and found widely distributed in all life forms. Chemically, they are aldehyde and ketone derivatives of the polyhydric alcohols. Major role of carbohydrates in living organisms is to function as a primary source of energy. These molecules also serve as energy stores, 2021-22 Chapter 3 Carbohydrade Final 30.018.2018.indd 50 11/14/2019 10:11:16 AM 51 BIOMOLECULES metabolic intermediates, and one of the major components of bacterial and plant cell wall. Also, these are part of DNA and RNA, which you will study later in this chapter. The cell walls of bacteria and plants are made up of polymers of carbohydrates. -
PLGG1, a Plastidic Glycolate Glycerate Transporter, Is Required for Photorespiration and Defines a Unique Class of Metabolite Transporters
PLGG1, a plastidic glycolate glycerate transporter, is required for photorespiration and defines a unique class of metabolite transporters Thea R. Picka,1, Andrea Bräutigama,1, Matthias A. Schulza, Toshihiro Obatab, Alisdair R. Fernieb, and Andreas P. M. Webera,2 aInstitute of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich Heine University, 40225 Düsseldorf, Germany; and bMax-Planck Institute for Molecular Plant Physiology, Department of Molecular Physiology, 14476 Potsdam-Golm, Germany Edited by Wolf B. Frommer, Carnegie Institution for Science, Stanford, CA, and accepted by the Editorial Board January 8, 2013 (received for review September 4, 2012) Photorespiratory carbon flux reaches up to a third of photosyn- (PGLP). Glycolate is exported from the chloroplasts to the per- thetic flux, thus contributes massively to the global carbon cycle. oxisomes, where it is oxidized to glyoxylate by glycolate oxidase The pathway recycles glycolate-2-phosphate, the most abundant (GOX) and transaminated to glycine by Ser:glyoxylate and Glu: byproduct of RubisCO reactions. This oxygenation reaction of glyoxylate aminotransferase (SGT and GGT, respectively). Glycine RubisCO and subsequent photorespiration significantly limit the leaves the peroxisomes and enters the mitochondria, where two biomass gains of many crop plants. Although photorespiration is molecules of glycine are deaminated and decarboxylated by the a compartmentalized process with enzymatic reactions in the glycine decarboxylase complex (GDC) and serine hydroxymethyl- chloroplast, the peroxisomes, the mitochondria, and the cytosol, transferase (SHMT) to form one molecule each of serine, ammo- nia, and carbon dioxide. Serine is exported from the mitochondria no transporter required for the core photorespiratory cycle has to the peroxisomes, where it is predominantly converted to glyc- been identified at the molecular level to date. -
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. -
The Self-Inhibitory Nature of Metabolic Networks and Its Alleviation Through Compartmentalization
ARTICLE Received 30 Oct 2016 | Accepted 23 May 2017 | Published 10 Jul 2017 DOI: 10.1038/ncomms16018 OPEN The self-inhibitory nature of metabolic networks and its alleviation through compartmentalization Mohammad Tauqeer Alam1,2, Viridiana Olin-Sandoval1,3, Anna Stincone1,w, Markus A. Keller1,4, Aleksej Zelezniak1,5,6, Ben F. Luisi1 & Markus Ralser1,5 Metabolites can inhibit the enzymes that generate them. To explore the general nature of metabolic self-inhibition, we surveyed enzymological data accrued from a century of experimentation and generated a genome-scale enzyme-inhibition network. Enzyme inhibition is often driven by essential metabolites, affects the majority of biochemical processes, and is executed by a structured network whose topological organization is reflecting chemical similarities that exist between metabolites. Most inhibitory interactions are competitive, emerge in the close neighbourhood of the inhibited enzymes, and result from structural similarities between substrate and inhibitors. Structural constraints also explain one-third of allosteric inhibitors, a finding rationalized by crystallographic analysis of allosterically inhibited L-lactate dehydrogenase. Our findings suggest that the primary cause of metabolic enzyme inhibition is not the evolution of regulatory metabolite–enzyme interactions, but a finite structural diversity prevalent within the metabolome. In eukaryotes, compartmentalization minimizes inevitable enzyme inhibition and alleviates constraints that self-inhibition places on metabolism. 1 Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK. 2 Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK. 3 Department of Food Science and Technology, Instituto Nacional de Ciencias Me´dicas y Nutricio´n Salvador Zubira´n, Vasco de Quiroga 15, Tlalpan, 14080 Mexico City, Mexico. -
A New Insight Into Role of Phosphoketolase Pathway in Synechocystis Sp
www.nature.com/scientificreports OPEN A new insight into role of phosphoketolase pathway in Synechocystis sp. PCC 6803 Anushree Bachhar & Jiri Jablonsky* Phosphoketolase (PKET) pathway is predominant in cyanobacteria (around 98%) but current opinion is that it is virtually inactive under autotrophic ambient CO2 condition (AC-auto). This creates an evolutionary paradox due to the existence of PKET pathway in obligatory photoautotrophs. We aim to answer the paradox with the aid of bioinformatic analysis along with metabolic, transcriptomic, fuxomic and mutant data integrated into a multi-level kinetic model. We discussed the problems linked to neglected isozyme, pket2 (sll0529) and inconsistencies towards the explanation of residual fux via PKET pathway in the case of silenced pket1 (slr0453) in Synechocystis sp. PCC 6803. Our in silico analysis showed: (1) 17% fux reduction via RuBisCO for Δpket1 under AC-auto, (2) 11.2–14.3% growth decrease for Δpket2 in turbulent AC-auto, and (3) fux via PKET pathway reaching up to 252% of the fux via phosphoglycerate mutase under AC-auto. All results imply that PKET pathway plays a crucial role under AC-auto by mitigating the decarboxylation occurring in OPP pathway and conversion of pyruvate to acetyl CoA linked to EMP glycolysis under the carbon scarce environment. Finally, our model predicted that PKETs have low afnity to S7P as a substrate. Metabolic engineering of cyanobacteria provides many options for producing valuable compounds, e.g., acetone from Synechococcus elongatus PCC 79421 and butanol from Synechocystis sp. strain PCC 68032. However, certain metabolites or overproduction of intermediates can be lethal. Tere is also a possibility that required mutation(s) might be unstable or the target bacterium may even be able to maintain the fux distribution for optimal growth balance due to redundancies in the metabolic network, such as alternative pathways. -
Sugars As the Source of Energized Carbon for Abiogenesis
Astrobiology Science Conference 2010 (2010) 5095.pdf SUGARS AS THE SOURCE OF ENERGIZED CARBON FOR ABIOGENESIS. A. L. Weber, SETI Institute, NASA Ames Research Center, Mail Stop 239-4, Moffett Field, CA, 94035-1000, [email protected] Abstract: As shown in Figure 1, abiogenesis has sev- eral requirements: (A) a source of organic substrates and chemical energy that drives the synthesis of (B) useful small molecules (ammonia, monomers, metabo- lites, energy molecules), and (C) a second synthetic processs that yields large replicating and catalytic polymers that control (D) the growth and maintenance of a primitive protocell. Furthermore, the required chemical energy must be sustained and effectively coupled to individual reactions to drive biosynthesis at a rate that counters chemical degradation. Energy coupling would have been especially difficult during the origin of life before the development of powerful enzyme catalysts with 3-D active sites. To solve this energy coupling problem we have investigated abio- genesis using sugar substrates whose energized carbon groups drive spontaneous synthetic self-transformation reactions that yield: biometabolites, catalytic mole- cules, energy-rich thioesters, amino acids, plausible alternative nucleobases and cell-like microstructures [1-8]. Recently, we demonstrated that sugars drive the synthesis of ammonia from nitrite [9]. The ability of sugars to drive ammonia synthesis provides a way to generate ammonia at microscopic sites of sugar-based origins processes, thereby eliminating the need for a planet-wide source of photochemically unstable am- monia. Figure 1. Major Synthetic Processes of Abiogenesis. [1] Weber A. L. (1998) Orig. Life Evol. Biosph., 28, 259-270. [2] Weber A. -
An Overview of Biosynthesis Pathways – Inspiration for Pharmaceutical and Agrochemical Discovery
An Overview of Biosynthesis Pathways – Inspiration for Pharmaceutical and Agrochemical Discovery Alan C. Spivey [email protected] 19th Oct 2019 Lessons in Synthesis - Azadirachtin • Azadirachtin is a potent insect anti-feedant from the Indian neem tree: – exact biogenesis unknown but certainly via steroid modification: O MeO C OAc O 2 H O OH O H O OH 12 O O C 11 O 14 OH oxidative 8 O H 7 cleavage highly hindered C-C bond HO OH AcO OH AcO OH for synthesis! H H of C ring H MeO2C O AcO H tirucallol azadirachtanin A azadirachtin (cf. lanosterol) (a limanoid = tetra-nor-triterpenoid) – Intense synhtetic efforts by the groups of Nicolaou, Watanabe, Ley and others since structural elucidation in 1987. –1st total synthesis achieved in 2007 by Ley following 22 yrs of effort – ~40 researchers and over 100 person-years of research! – 64-step synthesis – Veitch Angew. Chem. Int. Ed. 2007, 46, 7629 (DOI) & Veitch Angew. Chem. Int. Ed. 2007, 46, 7633 (DOI) – Review ‘The azadirachtin story’ see: Veitch Angew. Chem. Int. Ed. 2008, 47, 9402 (DOI) Format & Scope of Presentation • Metabolism & Biosynthesis – some definitions, 1° & 2° metabolites • Shikimate Metabolites – photosynthesis & glycolysis → shikimate formation → shikimate metabolites – Glyphosate – a non-selective herbicide • Alkaloids – acetylCoA & the citric acid cycle → -amino acids → alkaloids – Opioids – powerful pain killers • Fatty Acids and Polyketides –acetylCoA → malonylCoA → fatty acids, prostaglandins, polyketides, macrolide antibiotics – NSAIDs – anti-inflammatory’s • Isoprenoids/terpenes -
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: -
Bioinorganic Chemistry Content
Bioinorganic Chemistry Content 1. What is bioinorganic chemistry? 2. Evolution of elements 3. Elements and molecules of life 4. Phylogeny 5. Metals in biochemistry 6. Ligands in biochemistry 7. Principals of coordination chemistry 8. Properties of bio molecules 9. Biochemistry of main group elements 10. Biochemistry of transition metals 11. Biochemistry of lanthanides and actinides 12. Modell complexes 13. Analytical methods in bioinorganic 14. Applications areas of bioinorganic chemistry "Simplicity is the ultimate sophistication" Leonardo Da Vinci Bioinorganic Chemistry Slide 1 Prof. Dr. Thomas Jüstel Literature • C. Elschenbroich, A. Salzer, Organometallchemie, 2. Auflage, Teubner, 1988 • S.J. Lippard, J.N. Berg, Bioinorganic Chemistry, Spektrum Akademischer Verlag, 1995 • J.E. Huheey, E. Keiter, R. Keiter, Anorganische Chemie – Prinzipien von Struktur und Reaktivität, 3. Auflage, Walter de Gruyter, 2003 • W. Kaim, B. Schwederski: Bioinorganic Chemistry, 4. Auflage, Vieweg-Teubner, 2005 • H. Rauchfuß, Chemische Evolution und der Ursprung des Lebens, Springer, 2005 • A.F. Hollemann, N. Wiberg, Lehrbuch der Anorganischen Chemie, 102. Auflage, de Gruyter, 2007 • I. Bertini, H.B. Gray, E.I. Stiefel, J.S. Valentine, Biological Chemistry, University Science Books, 2007 • N. Metzler-Nolte, U. Schatzschneier, Bioinorganic Chemistry: A Practical Course, Walter de Gruyter, 2009 • W. Ternes, Biochemie der Elemente, Springer, 2013 • D. Rabinovich, Bioinorganic Chemistry, Walter de Gruyter, 2020 Bioinorganic Chemistry Slide 2 Prof. Dr. Thomas Jüstel 1. What is Bioinorganic Chemistry? A Highly Interdisciplinary Science at the Verge of Biology, Chemistry, Physics, and Medicine Biochemistry Inorganic Chemistry (Micro)- Physics & Biology Spectroscopy Bioinorganic Chemistry Pharmacy & Medicine & Toxicology Physiology Diagnostics Bioinorganic Chemistry Slide 3 Prof. Dr. Thomas Jüstel 2. Evolution of the Elements Most Abundant Elements in the Universe According to Atomic Fraction Are: 1. -
UV-B Induced Stress Responses in Three Rice Cultivars
BIOLOGIA PLANTARUM 54 (3): 571-574, 2010 BRIEF COMMUNICATION UV-B induced stress responses in three rice cultivars I. FEDINA1*, J. HIDEMA2, M. VELITCHKOVA3, K. GEORGIEVA1 and D. NEDEVA1 Institute of Plant Physiology1 and Institute of Biophysics3, Bulgarian Academy of Sciences, Academic Georgi Bonchev Street, Building 21, Sofia 1113, Bulgaria Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan2 Abstract UV-B responses of three rice (Oryza sativa L.) cultivars (Sasanishiki, Norin 1 and Surjamkhi) with different photolyase activity were investigated. Carbon dioxide assimilation data support that Sasanishiki was less sensitive to UV-B than Norin 1 and Surjamkhi. UV-B radiation sharply decreased the content of Rubisco protein in Surjamkhi and has no effect in Sasanishiki. The photochemical activities of photosystem (PS) 1 and PS 2 was slightly affected by UV-B treatment. The content of H2O2 and the activities of antioxidant enzymes, catalase (CAT), peroxides (POX) and superoxide dismutase (SOD) were enhanced after UV-B treatment. The activities of CAT and POX isoenzymes in Sasanishiki were more enhanced by UV-B radiation than those in Norin 1 and Surjamkhi. 14 Additional key words: catalase, CO2 fixation, hydrogen peroxide, peroxidase, Rubisco, superoxide dismutase. ⎯⎯⎯⎯ UV-B sensitivity of plants is determined by the balance of Furthermore, transgenic rice plants in which the CPD damage incurred and by the efficiency of repair processes photolyase was overexpressed had higher CPD photolyase that can restore the impaired functions. This balance is activity and showed significantly greater resistance to influenced by several factors, including the genetic UV-B than wild plants (Hidema et al. -
Physiology, Biochemistry, and Pharmacology of Transporters for Organic Cations
International Journal of Molecular Sciences Editorial Physiology, Biochemistry, and Pharmacology of Transporters for Organic Cations Giuliano Ciarimboli Experimental Nephrology, Department of Internal Medicine D, University Hospital Münster, 48149 Münster, Germany; [email protected] This editorial summarizes the 13 scientific papers published in the Special Issue “Physiology, Biochemistry, and Pharmacology of Transporters for Organic Cations” of the International Journal of Molecular Sciences. In this Special Issue, the readers will find integrative information on transporters for organic cations. Besides reviews on physi- ology, pharmacology, and toxicology of these transporters [1–3], which offer a concise overview of the field, the readers will find original research work focusing on specific transporter aspects. Specifically, the review “Organic Cation Transporters in Human Physiology, Phar- macology, and Toxicology” by Samodelov et al. [1] summarizes well the general as- pects of physiology, pharmacology, and toxicology of transporter for organic cations. The other review “Organic Cation Transporters in the Lung—Current and Emerging (Patho)Physiological and Pharmacological Concepts” by Ali Selo et al. [2] focuses on these aspects of transporters for organic cations in the lung, an important but often ne- glected field. In the paper “Systems Biology Analysis Reveals Eight SLC22 Transporter Subgroups, Including OATs, OCTs, and OCTNs”, by performing a system biology analysis of SLC22 transporters, Engelhart et al. [4] suggest the existence of a transporter–metabolite network. They propose that, in this network, mono-, oligo-, and multi-specific SLC22 transporters Citation: Ciarimboli, G. Physiology, interact to regulate concentrations and fluxes of many metabolites and signaling molecules. Biochemistry, and Pharmacology of In particular, the organic cation transporters (OCT) subgroup seems to be associated with Transporters for Organic Cations. -
BIOCHEMISTRY MAJOR the Biochemistry Major Is Offered Through the Department of Chemistry
BIOCHEMISTRY MAJOR The Biochemistry major is offered through the Department of Chemistry. This sequence is recommended for students planning entry into graduate school in Biochemistry, Pharmacology, or related subjects. It is also strongly recommend for those desiring to pursue medical or dental school. NOTE: This course sequence may be modified to include a Senior Capstone Experience. FIRST YEAR Fall Semester Credits Spring Semester Credits General Chemistry I for Majors (CHE111) 3 General Chemistry II for Majors (CHE112) 3 General Chemistry I Lab for Majors (CHE111L) 1 General Chemistry II Lab for Majors (CHE112L) 1 General Chemistry I Récitation (CHE111R) 0 General Chemistry II Récitation (CHE112R) 0 Precalculus (MAT116 or MAT120) 3-4 Calculus I (MAT231) 4 First Year Composition (ENG103) 4 Foreign Language (FL201) 4 African Diaspora/World I (ADW111) 4 African Diaspora/World II (ADW112) 4 First Year Experience (FYE 101-Chemistry) 1 First Year Experience (FYE 102-Chemistry) 1 First Year Seminar in Chemistry (CHE101) 0 Big Questions Colloquia (BQC) 1 TOTAL HOURS 16-17 TOTAL HOURS 18 SOPHOMORE YEAR Fall Semester Credits Spring Semester Credits Organic Chemistry I for Majors (CHE231) 4 Organic Chemistry II for Majors (CHE232) 4 Organic Chemistry I Lab (CHE233L) 1 Organic Chemistry II Lab (CHE234L) 1 Organic Chemistry I Récitation (CHE233R) 0 Organic Chemistry II Récitation (CHE234R) 0 Biology of the Cell (BIO120) 4 Organismal Form and Function(BIO115) 4 Calculus II (MAT 232) 4 Physics I: Mechanics & Lab (PHY151) 4 Foreign Language (FL202)