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  1. An Overview of Metabolism
    1. Metabolism (the total of all chemical reactions occurring in a cell) can be divided into two major parts: catabolism and anabolism
      1. Catabolism-the breakdown of larger, more complex molecules into smaller, simpler ones, during which energy is released, trapped, and made available for work
      2. Anabolism-the synthesis of complex molecules from simpler ones during which energy is added as input
      3. Chemolithotrophy and photosynthesis are included as energy-yielding catabolic processes, even though they do not involve degradation of complex molecules
    2. Chemotrophic microorganisms not only vary in terms of their energy source, but also in terms of their electron acceptors
      1. If an organic energy source is oxidized and degraded without the use of an exogenous electron acceptor, the process is called fermentation
      2. If the energy source is oxidized and degraded with the use of an exogenous electron acceptor, the process is called respiration; in aerobic respiration the final electron acceptor is oxygen, whereas in anaerobic respiration the final electron acceptor is a molecule other than oxygen
    3. For chemoorganoheterotrophic organisms, catabolism is often a three stage process during which nutrients are fed into common degradative pathways; these common pathways function both catabolically and anabolically and are said to be amphibolic
  2. The Breakdown of Glucose to Pyruvate
    1. The glycolytic pathway
      1. Also known as the Embden-Meyerhof pathway, it is the most common pathway and is found in all major groups of microorganisms
      2. It functions in the presence or absence of oxygen and is divided into two parts:
        1. The 6-carbon sugar stage glucose is phosphorylated twice to yield fructose 1,6-bisphosphate; this requires the expenditure of two molecules of ATP
        2. The 3-carbon sugar stage cleaves fructose 1,6-bisphosphate into two 3-carbon molecules, which are each processed to pyruvate; two molecules of ATP are produced by substrate-level phosphorylation from each of the 3-carbon molecules for a net yield of two molecules of ATP; 2 molecules of NADH are also produced per glucose molecule
    2. The pentose phosphate pathway
      1. Also known as the hexose monophosphate pathway, this pathway uses a different set of reactions to produce a variety of 3-, 4-, 5-, 6-, and 7-carbon sugar phosphates
      2. Has several catabolic and anabolic functions
        1. Production of NADPH, which serves as a source of electrons for biosynthetic processes
        2. A source of four and five carbon skeletons that can be used for the synthesis of amino acids, nucleic acids, and other macromolecules
        3. The complete catabolism of hexoses and pentoses, yielding ATP and NADH (made by converting NADPH to NADH)
    3. The Entner-Doudoroff pathway
      1. This pathway links reactions of the pentose phosphate pathway and the glycolytic pathway with unique reactions
      2. This pathway produces ATP, NADPH, and NADH
  3. Fermentations
    1. Fermentation-a process in which an organism oxidizes the NADH produced by one of the pathways above by using pyruvate or one of its derivatives as an electron and hydrogen acceptor; thus the process involves the use of an endogenous electron acceptor
    2. Many different types of fermentations are known
      1. Alcoholic fermentations produce ethanol and CO2
      2. Lactic acid fermentations produce lactic acid (lactate)
        1. Homolactic fermenters reduce almost all pyruvate to lactate
        2. Heterolactic fermenters form substantial amounts of products other than lactate
      3. Formic acid fermentation produces either mixed acids or butanediol
    3. Microorganisms can ferment substances other than sugars (e.g., amino acids)
  4. The Tricarboxylic Acid Cycle
    1. Pyruvate can be degraded to carbon dioxide by the tricarboxylic acid (TCA) cycle after first being converted to acetyl CoA; this reaction is accompanied by the loss of one carbon atom as carbon dioxide
    2. Acetyl-CoA reacts with oxaloacetate (a 4-carbon molecule) to produce a 6-carbon molecule, which is subsequently broken down to two molecules of carbon dioxide, regenerating the oxaloacetate; during this process, the following occurs:
      1. ATP is produced by substrate-level phosphorylation
      2. Three molecules of NADH and one molecule of FADH2 are produced
    3. Even those organisms that lack the complete TCA cycle usually have most of the cycle enzymes because one of the TCA cycleís major functions is to provide carbon skeletons for use in biosynthesis
  5. Electron Transport and Oxidative Phosphorylation
    1. The Electron Transport Chain
      1. The mitochondrial electron transport chain uses a series of electron carriers to transfer electrons from NADH and FADH2 to O2
        1. Electron carriers are located within the inner membrane of the mitochondrion
        2. During oxidative phosphorylation, three ATP molecules may be synthesized when a pair of electrons passes from NADH to O2; two ATP molecules may be synthesized when electrons from FADH2 pass to O2
      2. Although they operate according to the same fundamental principles, bacterial electron transport chains usually differ in structure: they may be branched, be composed of different electron carriers, or may be shorter than mitochondrial electron transport chains; bacterial electron transport chains are located in the plasma membrane
    2. Oxidative Phosphorylation
      1. The chemiosmotic hypothesis of oxidative phosphorylation postulates that the energy released during electron transport is used to establish a protonmotive force (potential energy due to the difference in proton concentration and charge on either side of the membrane), which can be used to drive ATP synthesis, flagellar rotation, and transport of molecules across the membrane
      2. ATP synthesis is catalyzed by the ATP synthase complex, which is thought to behave like a small rotary motor
      3. Inhibitors of ATP synthesis fall into two main categories:
        1. Blockers that inhibit the flow of electrons through the system
        2. Uncouplers that allow electron flow, but disconnect it from oxidative phosphorylation
    3. The Yield of ATP in Glycolysis and Aerobic Respiration
      1. The yield of ATP by glycolysis during fermentation is 2 ATP
      2. Aerobic respiration yields between 2 and 38 ATP molecules per glucose molecule, depending on the precise nature of the electron transport system
      3. The Pasteur effect is a regulatory phenomenon by which organisms lower their rate of sugar catabolism when conditions cause a shift from fermentation to aerobic respiration; this occurs because aerobic respiration is more efficient and generates greater energy per glucose molecule
  6. Anaerobic Respiration
    1. Uses molecules other than oxygen as terminal electron acceptors; the most commonly used alternative electron acceptors are nitrate, sulfate, and CO2
    2. Dissimilatory nitrate reduction occurs when nitrate is used as the terminal electron acceptor; if the nitrate is reduced to nitrogen gas, the process is called denitrification
    3. Anaerobic respiration is not as efficient in ATP synthesis as aerobic respiration because the alternative electron acceptors do not have as positive a reduction potential as O2; despite this, anaerobic respiration is useful because it is more efficient than fermentation
  7. Catabolism of Carbohydrates and Intracellular Reserve Polymers
    1. Carbohydrates
      1. Most monosaccharides feed easily into the glycolytic pathway
      2. Disaccharides are cleaved into monosaccharides either by hydrolysis or phosphorolysis
      3. Polysaccharides are cleaved into smaller molecules either by hydrolysis or phosphorolysis; many, however, are not easily degraded (e.g., cellulose, agar)
      4. Microorganisms are also capable of degrading xenobiotic molecules (foreign substances not formed by natural biosynthetic processes) such as pesticides
    2. Reserve polymers-when exogenous nutrients are absent, microorganisms catabolize internal stores of glycogen, starch, etc.
  8. Lipid Catabolism
    1. Triglycerides are common energy sources; they are hydrolyzed to glycerol and fatty acids
    2. Fatty acids are catalyzed by the b-oxidation pathway, which produces acetyl-CoA, NADH, and FADH2; NADH and FADH2 can be oxidized by an electron transport chain to produce ATP
  9. Protein and Amino Acid Catabolism
    1. Proteins are degraded by proteases to their component amino acids
    2. Amino acids are first deaminated and then the remaining carbon skeletons are converted to pyruvate, acetyl-CoA, or a TCA-cycle intermediate
  10. Oxidation of Inorganic Molecules
    1. Chemolithotrophy-a metabolic process that uses inorganic molecules as a source of energy; the energy source is oxidized; the electron acceptor is usually O2, but sulfate and nitrate are also used; the most common electron donors (energy sources) are hydrogen, reduced nitrogen compounds, reduced sulfur compounds, and ferrous iron (Fe2+)
    2. Chemolithotrophs are usually autotrophs; they use the Calvin Cycle to fix carbon dioxide
  11. Photosynthesis
    1. During photosynthesis, energy from light is trapped and used to produce ATP and NADPH (light reactions), which are used to reduce carbon dioxide to form carbohydrates (dark reactions)
    2. The light reactions of eucaryotes and cyanobacteria
      1. Chlorophyll molecules and a variety of accessory pigments are used to form antennas; the antennas trap photons and transfer them to a reaction-center chlorophyll; this special chlorophyll is directly involved in photosynthetic electron transport
      2. Eucaryotes and cyanobacteria have two photosystems; in each, electrons from the light energized reaction-center chlorophyll are transferred to the associated electron transport chain
        1. Photosystem I can carry out cyclic photophosphorylation, producing ATP
        2. Photosystems I and II, working together, can carry out noncyclic photophosphorylation, producing ATP and NADPH; the electrons for noncyclic photophosphorylation are obtained from water, which is oxidized to O2 (oxygenic photosynthesis)
      3. Photosynthetic electron transport takes place in membranes
    3. The light reactions of green and purple bacteria
      1. Green and purple bacteria carry out anoxygenic photosynthesis (they do not use water as a source of electrons, so do not produce O2), and they have different photosynthetic pigments called bacteriochlorophylls
      2. Many of the differences in the light reactions of the green and purple bacteria are due to the fact that they only have a single photosystem
      3. Green and purple bacteria are usually autotrophs that used NADH or NADPH for carbon dioxide fixation; three methods for making NADH are known:
        1. Reduction of NAD+ directly by hydrogen gas
        2. Reverse electron flow
        3. A simplified form of noncyclic electron flow

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