Chapter 6 Fueling

Chapter 6: Fueling Overview of Fueling Reactions 1. The metabolic route to making a new cell starts with fueling, the ensemble of reactions supplying the need of the cell—the 13 precursor metabolites, reducing power, and energy—are the fueling reactions of the cell. 2. Microbes have evolved a variety of ways to get energy and make metabolites. 3. For heterotrophic microbes (use of organic source of carbon) fueling reactions can be conveniently sorted into three stages: entry process, which move organic and inorganic food substrate from the environment into cell; feeder pathways, which converts food into one another metabolite; central metabolism, produce all precursor metabolite, 4. For autotrophic microbes, those that use CO2 as the main source of carbon, where CO2 fixation and generation of energy from light or inorganic chemicals are the defining process, pathways are used solely to provide precursor metabolites and feeder pathways are designed to lead from the products of CO2 fixation to central metabolism. Getting Energy and Reducing Power I. Driving Force and its Generation 1. All energy of in living system is derived from the movement of electron down an energy gradient to produce two forms of usable energy; 1. high energy phosphoryl bonds of ATP [metabolism reactions is driven by coupling to ATP hydrolysis] and 2. transmembrane ion gradient [drive cellular processes], both interconvertible 2. Electrons are derived rom oxidation reactions, many of which involve dehydrogenation [removal of hydrogen atom from organic molecules], which are transferred to either NAD+ or NADP+, where there reduced forms NADH and NADPH are sources for many metabolic reactions, commonly in biosynthesis. 3. Two means to make ATP, substrate level phosphorylation and harvesting a transmembrane gradient to make ATP via a membrane bound ATP synthase. II. Substrate Level Phosphorylation and Fermentation 1. Organic substrate become phosphorylated with inorganic phosphate (requires no energy) which is then oxidized trapping the energy in that bond where the high energy phosphoryl bond is transfer to ADP to make ATP. 2. Many microbes can live indefinitely using that mode of ATP generation is a process called fermentation, which remove the protons and electrons from one substrate in oxidation reaction to reduce a second organic molecule, usually a product of the metabolism of the first using only NADH (oxidized to NAD+).. 3. In fermentation, NADH oxidation is accomplished by dehydrogenases, but some bacteria have an enzyme called hydrogenases that can oxidize NADH and other reduced cofactors to produce hydrogen gas. 4. Fermentative modes of fueling is restricted to heterotrophs. III, Transmembrane Ion Gradient 1. Most microbial energy generation involves the use of an ion gradient across the cell membrane where the membrane is energized by proton motive force, where ATPase or F1FO synthase use the energy to create ATP or the opposite to pump protons out to create a tansmembrane ion gradient. (oxidative phosphorylation) 2. Bacteria living in high alkaline or high sodium environment cannot establish a proton gradient because it would react with hydroxyl ions, so it employ a gradient of another cation Na+, which constitute a sodium motive force. 3. Ion graded can be used for secondary active transport [ion- couple transport] across cell membrane, maintaining cell’s turgor (water pressure), maintainf cell’s interior pH, turning flagella and driving a reverse flow of electrons though respiration chain to reduce NAD+ when NADH supply is low. A. Respiration 1. Process by which electrons are passed from electron donor (reductant) to a terminal electron acceptor (oxidant), it reaches the oxidant through a number of membrane-bound electron carriers that uses the energy to pump H+ out of cell, export H+ during electron-to-hydrogen transfer and scalar rxn. [electron transport system]

2. Proteons are taken from the cytosol by reduction of a H+ carrier on the inside of the membrane and are release outside the cell by reducing of an electron carrier on the outside of the membrane,. [yields about 30 ATPs] 3. When O2 is the acceptor resulting in reduction to water, it is aerobic respiration and when the final acceptor is some other molecule it is anaerobic respiration. 4. Important for life where anaerobic respiration, uses nitrate for acceptor, which yield nitrite, which is uses as a acceptor by other, which yields nitric oxide, which is used to give nitrous, and finally N2 gas in armosphere. 5. The CO2-fixing pathways by which autotrophs makes precursor metabolites do not yield energy or reducing power because they use both. 6. Chemoautotrops obtain these essential driving forces by oxidizing inorganic compounds [employ same respiratory mechanism as chemoheterotroph] and photoautotrophs obtain them by harvesting energy from light. 7. The uniqueness of chemautotrophs lies in their ability to feed electron transport chain from inorganic sources, where most can carry out aerobic respiration as well anaerobic. 8. Anaerobic respiration and chemoautotrophic fueling are complementary variation of aerobic respiration, where anaerobic respiration differs in terminal electron acceptor of ETS and chemoautotrophic differs in the primary electron donor to ETS. B. Photosynthesis 1. Light energy activates an electron from chlorophyll to flow back down through an electron transport chain to the original ground state chlorophyll [cyclic photophosphorylation that generates ATP, but no reducind power] or to NADP+[ non-cyclic photophosphorylation] and if it is the second more must be supplied to chlorophyll; the sources can be water or sulfur compounds. 2. Some bacteria are photoheterotrophs deriving precursor metabolite from organic compounds and the driving force others are autotrophs, (H2A + CO2 > A + carbohydrate, where A can be O, S, or other element) 3. One group of photoautotrophic bacteria is the cyanobacteria that uses the same oxygen system of photpsynthesis, where oxygen is produce by stripping electrons from waterm and the other group carry out anoxygenic photosynthesis because they use a compound other than water to supply reducing power. 4. Anoxygenic photosynthesis is an anaerobic process but the bacteria called purple nonsulfur bacteria are capable chemoheterotrophic growth on presence of oxygen, they are facultative autotrophs. 5. Photosynthesis generates proton motive force by passing electron down an electron chemical gradient leading to extrusion of protons across cell membrane. C. Enzyme Pump 1. Membrane proteins that are not part of ETS, but functions independently to pump protons or other ions across the membrane, creating a gradient that can be used for the usual energy-requiring processes. D. Scalar Reaction 1. Is one in which the substrates and products are in the same location or comportment, which directly or indirectly create a transmembrane ion gradient without moving ions where some of these reactions are associated with ETS, but other exist separately. 2. Establish proton gradient by decarboxylating materials or by proton symport. IV. Oxygen and Life 1, Oxygen is toxic to cells, the interior of cell has low concentration or no oxygen at all, but O2 is effective terminal electron acceptor in biological redox reaction whether the energy source is organic or inorganic. 2. Ability of cell to withstand effect of oxygen depends on two factors, whether enzymes are sensitive to oxygen and whether cell is able to break down two high metabolic products of oxygen, hydrogen peroxide and superoxide anion [O2-]. 3. Organism that can tolerate oxygen have protective enzymes including catalase, which converts H2O2 to H2O and O2 and superoxide dismutase, which converts superoxide to oxygen and hydrogen peroxide. Making Precursor Metabolites: Heterotrophy

I. Acquiring Nutrients 1. Food must enter at a high rate, but the cell membrane but exclude substance that are potentially harmful to vital cell machinery. A. Transport Through the Outer Membrane of Gram-Negative Bacteria 1. Thick murein lattice of gram-positive cells is readily permeable to water and solutes, in gram-negative, it is porin-formed channels allow material to get into cell, as long they are hydrophilic and 600-700 Da and the concentration of substrate has to be lower in the cell. [other preferentially pores] B. Transport Through the Cell Membrane 1. Passive transport relies on diffusion, uses no energy, and operates only when solutes is at higher concentration outside than inside the cell, where simple diffusion occurs for few nutrients that is not fast or selective, facilitated diffusion is, and channel protein form selective channels for passage of specific molecules. 2. Active transport mediates the entry of all nutrients, which uses energy to pump molecules at high rates against concentration gradient, where ion-coupled transport is driven by electrochemical gradient established by electron transport or hydrolysis of ATP by ATPase [symport, uniport, antiport drive solute in]. 3. ABC transport employs ATP directly to pump solutes into the cell, where specific binding proteins confer specificity by carrying their particular ligand to a protein complex on the membrane, where hydrolysis of ATP open the membrane pore allowing unidirectional movement. 4. Phosphotransferase system, where transport occurs by chemically modifying the solute where it is phosphorylated as it transverse the membrane so the molecule is trapped in the cell by being membrane impermeable. [common in anaerobic bacteria]. 5. Bacteria secrete a powerful chelators called siderophores that bind to Fe in the environment and the Fesiderophore complex is taken by up by the cell actively. II. Feeder Pathways 1. Once imported, carbon compounds will serve as the basic for making precursor metabolite and generating driving force need to be introduced into the central pathways of fueling reactions. 2. Feeder pathways convert this enormous variety of substances into one or another of the metabolites of the central pathways, from which the cell can make the 13 precursor metabolites and driving force for biosynthesis. 3. Organic compounds imported as food for fueling must be converted, by however many sequential reactions it takes, to derivatives that can enter at least one of the three interconnected pathway of central metabolism. III. Central Metabolism 1. Consists of three common and a number of species specific auxiliary pathway. A. Common Pathways of Central Metabolism 1. Glycolysis pathway yield pyruvate, three other precursor metabolite, reducing power in form of NADH, and net of two molecules of ATP. 2. Pentose phosphate pathway is alternate pathway to convert glucose-6-phosphate to triosephosphate and play role in supping two metabolites, and two molecules of reducing power in the form of NADPH, commonly used in biosynthesis. 3. TCA cycle [link from glycolysis by pyruvate & acetyl CoA], which forms three precursor of metabolites and four units of reducing power while producing two molecules of CO2. [anaerobes have portion of cycle where it does produce NADH] B. Auxiliary Pathways of Central Metabolism 1. Entner-Doudoroff pathway is an alternative link between an intermediate of the pentose-phosphate pathway and two compounds of glycolysis where the value is other pathways from a number of sugar acids feeds into its single intermediate. [So it serves as collector of metabolites of other feeder pathways] 2. Glyoxylate cycle is modification of TCA cycle, where the pathway is actually a bypass or short-circuiting of two of the decarboxylation reaction of part of TCA cycle, enable organism to grow on acetate or fatty acids.

3. Fermentation pathways. C, Diversity and Flexibity of Central Metabolism 1. Depending on the environmental circumstance central pathways must operate in the forward or reverse direction because the precursor metabolite must be generated no matter where a feeder pathway pour metabolites into a particular central pathway. 2. The modification in the operation of central pathways that enable many prokaryotes to grow aerobically, anaerobically, and in situations requiring gluconeogenesis (synthesis of hexose from 1,2,3,4-carbon substrate) Making Precursor Metabolites: Autotrophy 1. Defining characteristic of autotrophs is their ability to fix (convert into organic compounds) sufficient CO2 to supply carbon for their precursor metabolite and hence all their cellular constituents and to do so rapidly enough to permit growth at a reasonable rate. I. The Calvin Cycle 1. Majority of autotrophs fix CO2 via ribulose bisphosphate carboxylase (RuBisCo), which catalyze the addition of CO2 to the five-carbon sugar phosphate ribulose bisphosphate, producing a six-carbon intermediate, which splits into two 3-phosphoglycerate. 2. This cycle along aith pathways of central metabolism is sufficient to synthesize all the precursor metabolits from CO2. 3. RuBisCo, is a inefficient enzyme that had difficulty distinguishing CO2 and O2, when it fixes O2 it produces a useless toxic product that must be eliminated using energy, where some organism evolved mechanism to increased intracellular CO2. II. Other CO2-Fixing Cycles 1. The reductive TCA cycle and the hydroxypropionate pathway, which are restricted to small amounts of prokaryotes and fourth that make acetate from CO2 and H2. 2. All pathways for CO2 fixation produce one or another metabolite of the central pathways or some compound easily converted to a central metabolite.

Schaechter, M., Ingtaham, J., & Neidhardt, F. C. (2006). Microbe. Washington, D.C.: ASM Press.