Metabolism: Catabolism. Metabolism. Energy & Carbon sources. Chapter 5 Metabolism: Overview. Obtaining Carbon. Obtaining Energy

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1 Metabolism: Chapter 5 Metabolism: Overview Lecture Exam #1 is Monday. Bring Scantron 882 form! See website for review. You will only be tested on material covered in lecture. Dr. Amy Rogers Fall 2006 Lectures: MW Noon Office Hours: Mon. & Wed AM Sequoia 530 All the chemical processes carried out by living things Anabolism: reactions that require energy to synthesize complex molecules from simpler ones X + Y + energy X Y endergonic reaction Needed for growth, reproduction, repair, movement, transport, etc. Where does the energy come from? Catabolism Reactions that release energy by breaking complex molecules into simpler ones Metabolism as a cycle of synthesis (anabolism) and degradation (catabolism), with energy tranferred & consumed along the way X Y X + Y + energy exergonic reaction Energy is captured / stored in high energy bonds of ATP & similar molecules Involves electron transfer (oxidation-reduction) Energy & Carbon sources All living things need energy All living things need Carbon Why? To synthesize all organic molecules Microbes are extremely versatile in the ways in which they acquire energy & carbon. {Some bug somewhere can eat just about anything: see this week s news articles!} Obtaining Carbon Auto- (self) get carbon from CO 2 to synthesize organic molecules Hetero- (other) get carbon from pre-made organic sources Obtaining Energy Photo- capture the energy of light Chemo- capture energy from chemicals 1

2 Metabolism: Categories of energy capturing Photoautotrophs Do not generally cause disease Many perform photosynthesis Cyanobacteria, algae, plants light energy 6 CO H 2 O C 6 H 12 O O 2 Carbon water chlorophyll glucose oxygen dioxide Energy from sunlight Carbon from inorganic carbon dioxide Produce organic energy source (glucose) Oxygen gas is a waste product Photoautotrophs: Green & Purple Sulfur Bacteria use a more primitive form of photosynthesis, evolved when the earth s atmosphere did not contain free O 2 (but was rich in hydrogen gas) Strict anaerobes Use H 2 S instead of H 2 O Produce elemental S or sulfuric acid instead of oxygen gas Chemoheterotrophs Nearly all pathogenic microbes 3 principle pathways for catabolizing food (glucose): 1. Glycolysis 2. Fermentation 3. Aerobic respiration Do not require oxygen Oxygen required Chemoheterotrophs Photosynthesis & Respiration form a cycle Complete oxidation of glucose by glycolysis & aerobic respiration: C 6 H 12 O O 2 6 CO H 2 O + energy Glucose oxygen carbon water dioxide Energy from organic compound Carbon from organic compound Energy for anabolism is produced Carbon dioxide is a waste product 2

3 Note that photosynthetic organisms (whether microbes or plants) do consume chemical energy in much the same way as heterochemotrophs. They just make it for themselves first. (i.e., they metabolize glucose by glycolysis, etc. to make ATP and synthesize other organic macromolecules) Metabolic Pathways Chemical transformations like photosynthesis & glycolysis occur in a series of chemical reactions Such a chain of reactions is called a metabolic pathway A B C D E A is the initial substrate; B,C,D are intermediates; and E is the final product Enzymes Proteins (usually) that catalyze reactions Enzyme catalysts: Are themselves unchanged by the reaction Speed up reactions (tremendously) Lower activation energy Are exquisitely specific Activity can be regulated Often named by substrate + ase For example, Proteases break down proteins; Lipases degrade lipid Enzyme catalysis: Activation Energy Exergonic / exothermic reactions are, in theory, spontaneous as the products of such reactions are at a lower energy state than the original reactant(s) However, the rate at which many such reactions occur spontaneously is SLOW One way to increase reaction rates is to increase the temperature Not an option for living things (not viable at higher temps) Another way? Activation Energy! How do enzymes activation energy? Precise 3-D conformation (shape) Active site Location where enzyme binds its substrate Substrate(s) bind in a way that resembles the transition state (a kind of halfway point in the reaction) Analogies: Rock resting in a depression at the top of a hill Charcoal waiting to be lit Activation energy as a hurdle over which molecules must be raised to get a reaction started 3

4 Specificity An exact match of the shape of the active site with its substrate is critical Each enzyme catalyzes only one type of reaction, often only on one particular substrate (with single atom changes, or changes in chiralty, often ruining the fit) Often, an additional chemical is needed at the active site to make the substrate fit, or to aid catalysis: coenzymes & cofactors Coenzymes & Cofactors Coenzyme: A nonprotein organic molecule Many are synthesized from vitamins Often this is the reason why a certain nutrient is essential Niacin is used to make NAD nicotinamide adenine dinucleotide Critical reagent for energy production by aerobic respiration Cofactor Inorganic, often a metal ion (Mg, Zn, etc.) Factors affecting enzyme activity NOTE: While the shapes of these curves will recur, various species of bacteria will have peaks at a variety of temperatures and ph s Inhibition of enzyme activity Sometimes, it is important to reduce catalytic activity When a better substrate is available When enough product has been made Competitive inhibition: A molecule similar enough to the enzyme s true substrate that it can bind to the active site, but the enzyme doesn t affect it The true substrate can t get in the site is occupied The enzyme s activity stops / slows 4

5 Competitive Inhibition Noncompetitive (allosteric) Inhibition A molecule binds to the enzyme outside of the active site Allosteric site This binding alters the enzyme s shape so that the active site no longer functions Feedback inhibition often is allosteric When enough of the enzyme s product is present, the product binds to an allosteric site and slows / stops production of any more Noncompetitive / Allosteric Inhibition Inhibition & Drugs/Toxins Many drugs and poisons act by disrupting vital enzyme activity. Such inhibition can be temporary, depending on how long the drug/toxin stays around (reversible inhibitors) or permanent (irreversible inhibitors) e.g., lead, mercury Our study of bacterial metabolism will focus on energy acquisition: What is food for bacteria? The various biochemical pathways available for catabolism of glucose The impact of these metabolic pathways on cell growth The role of oxygen The conversion of the chemical energy of food into the chemical energy of ATP The end products of metabolism In lab, you will learn how unknown bacterial isolates can be identified on the basis of what they can eat, how they eat it, and what trash they leave behind when they re done. 5

6 BCP-carbohydrate broths: Lab 13 Eating is all about taking the energy stored in the chemical bonds of food, and transferring that energy to a form directly usable by the cell. + for sugar fermentation + for H 2 gas production + for sugar fermentation -- for sugar fermentation In metabolism, the energy carrier is often electrons, moving through redox reactions. Redox reactions Oxidation & reduction reactions are always coupled so we call them redox In redox reactions, Electrons are transferred from one atom/molecule to another Simultaneously 2 reactions: red/ox: electron gain/electron loss The electrons carry energy (so redox reactions are energy transfers) In a chain of reactions, the electrons must have a final resting place (a terminal electron acceptor). Often, this is oxygen. Reduction: net charge is reduced (made more negative) because electrons are gained Energy is gained (reduced compound has more energy) Often, hydrogen is gained, oxygen is lost For example, think: Hydrocarbons. Totally reduced Saturated with hydrogen No oxygen Lots of energy stored Propane Electrons are lost Energy is lost Oxidation: Often, the electrons are transferred to oxygen Oxygen is NOT the only electron acceptor around There must always be an electron acceptor and an electron donor in redox reactions (coupled) If it has hydrogens, it likely can be oxidized as an energy source (food) by some type of bacteria! For example, think: Hydrocarbons burning The molecule gains oxygen/loses hydrogen (yielding CO 2 & H 2 O) Energy is released (heat) Oxygen is the electron acceptor Propane 6

7 Redox terms Electron donor = reducing agent The atom or molecule that is oxidized It causes something else to be reduced (hence the name reducing agent) Electron donor Electron acceptor = oxidizing agent The atom or molecule that is reduced It causes something else to be oxidized (oxidizing agent) Electron acceptor Electron Carriers in metabolism Electron carriers NAD+ & FAD NAD (nicotinamide adenine dinucleotide) Derived from vitamin niacin FAD (flavin adenine dinucleotide) Derived from vitamin riboflavin Both carriers cycle between oxidized (NAD+, FAD) and reduced states (NADH, FADH 2 ) ATP: Adenosine triphosphate is a nucleotide (yes, the same one that goes into DNA!) Has 3 phosphate groups attached (tri-) The distal, third phosphate group can be hydrolyzed to release a significant amount of energy: ATP ADP + P i + energy Where ADP = adenosine diphosphate P i = inorganic phosphate (PO 4 3- ) Release of the next phosphate group also releases a lot of energy (ADP AMP + P i + energy) This process is not used as much by living things One reason why so much energy is released by hydrolysis of the 2 nd and 3 rd phosphate groups: Electrostatic repulsion Each phosphate group is negatively charged; binding them together takes a lot of energy {The first phosphate, attached to the adenosine, can also be cleaved off but the energy release is not impressive: no repulsion from other phosphates!} 7

8 ATP as global energy currency ATP ADP + P i + energy The energy of ATP hydrolysis can be captured to perform the work of the cell ATP is like money that can buy almost any energy-requiring activity This reaction is reversible i.e., an input of energy (such as the energy derived from glucose) can be used to make ATP from ADP & Pi Phosphorylation of ADP to make ATP is a key feature of metabolism Relevant reading in Black s Microbiology: (pages from 6 th edition) Ch. 5: p ;

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