Microbiology Chapter 4

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  1. Define: Activation energy
    the energy required to bring the substrate of an enzyme to the reactive state
  2. Define: Adenosine triphosphate (ATP)
    a nucleotide that is the primary form in which chemical energy is conserved and utilized in cells
  3. Define: Anabolic reactions (Anabolism)
    the sum total of all biosynthetic reactions in the cell
  4. Define: Anaerobic respiration
    a form of respiration in which oxygen is absent and alternative electron acceptors are reduced
  5. Define: ATPase (ATP synthase)
    a multiprotein enzyme complex embedded in the cytoplasmic membrane that catalyzes the synthesis of ATP coupled to dissipation of the proton motive force
  6. Define: Autotroph
    an organism capable of biosynthesizing all cell material from CO2 as the sole carbon source
  7. Define: Catabolic reactions (Catabolism)
    biochemical reactions leading to energy conservation (usually as ATP) by the cell
  8. Define: Catalyst
    a substance that accelerates a chemical reaction but is not consumed in the reaction
  9. Define: Chemolithotroph
    an organism that can grow with inorganic compounds as electron donors in energy metabolism
  10. Define: Chemoorganotroph
    an organism that obtains its energy from the oxidation of organic compounds
  11. Define: Citric acid cycle
    a cyclical series of reactions resulting in the conversion of acetate to two molecules of CO2
  12. Define: Coenzyme
    a small and loosely bound nonprotein molecule that participates in a reaction as part of an enzyme
  13. Define: Electron acceptor
    a substance that can accept electrons from an electron donor, becoming reduced in the process
  14. Define: Electron donor
    a substance that can donate electrons to an electron acceptor, becoming oxidized in the process
  15. Define: Endergonic
    requires energy
  16. Define: Enzyme
    a protein that can speed up (catalyze) a specific chemical reaction
  17. Define: Exergonic
    releases energy
  18. Define: Fermentation
    anaerobic catabolism in which an organic compound is both an electron donor and an electron acceptor and ATP is produced by substrate-level phosphorylation
  19. Define: Free energy (G)
    energy available to do work; G0′ is free energy under standard conditions
  20. Define: Glycolysis
    a biochemical pathway in which glucose is fermented, yielding ATP and various fermentation products; also called the Embden–Meyerhof–Parnas pathway
  21. Define: Glyoxylate cycle
    a modification of the citric acid cycle in which isocitrate is cleaved to form succinate and glyoxylate during growth on two-carbon electron donors such as acetate
  22. Define: Heterotroph
    an organism that uses organic compounds as a carbon source
  23. Define: Nitrogenase
    the enzyme complex required to reduce N2 to NH3 in biological nitrogen fixation.
  24. Define: Nitrogen fixation
    the reduction of N2 to NH3 by the enzyme nitrogenase
  25. Define: Oxidative phosphorylation
    the production of ATP from a proton motive force formed by electron transport of electrons from organic or inorganic electron donors
  26. Define: Pentose phosphate pathway
    a series of reactions in which pentoses are catabolized to generate precursors for nucleotide biosynthesis or to synthesize glucose
  27. Define: Photophosphorylation
    the production of ATP from a proton motive force formed from light-driven electron transport
  28. Define: Phototrophs
    organisms that use light as their source of energy
  29. Define: Proton motive force (pmf)
    a source of energy resulting from the separation of protons from hydroxyl ions across the cytoplasmic membrane, generating a membrane potential
  30. Define: Reduction potential (E0′)
    the inherent tendency, measured in volts under standard conditions, of a compound to donate electrons
  31. Define: Respiration
    the process in which a compound is oxidized with O2 (or an O2 substitute) as the terminal electron acceptor, usually accompanied by ATP production by oxidative phosphorylation
  32. Define: Substrate-level phosphorylation
    the production of ATP by the direct transfer of an energy-rich phosphate molecule from a phosphorylated organic compound to ADP
  33. Describe Metabolism
    Before a cell can replicate, a variety of chemical reactions must take place. Collectively, these reactions are termed Metabolism. Metabolism, therefore, is the sum of all the chemical reactions in a cell.
  34. Which are the two forms in which metabolic reactions can occur?
    Metabolic reactions are either energy releasing (exergonic), called catabolic reactions, or energy requiring (endergonic), called anabolic reactions.
  35. What elements make up the bulk of a cell's dry weight
    Hydrogen (H), oxygen (O), carbon (C), nitrogen (N), phosphorus (P), sulfur (S) make up close to 95% of our a cell's dry weight. Also K, Mg, Ca, Na, Cl are all necessary elements
  36. Define organotrophs
    Prokaryotes that require an organic compound as their source of carbon
  37. Describe autotrophs
    Prokaryotes that are able to use CO2 as their sole source of carbon are termed autotrophs (lithotrophs)
  38. What two forms does Nitrogen present itself as?
    Nitrogen, the second most abundant element, comes in two forms; organic and inorganic. The bulk of Nitrogen is in the inorganic form as ammonia (NH3), nitrate (NO3-), or nitrogen gas (N2).
  39. Differentiate between Obligate Aerobes and Obligate Anaerobes
    • Obligate Aerobes can only extract energy from compounds in the presence of oxygen
    • Obligate Anaerobes can only extract energy in the absence of oxygen
  40. Differentiate between Facultative Anaerobes & Facultative Aerobes
    Facultative anaerobes & Facultative aerobes can extract energy in the presence or absence of oxygen. But, Facultative aerobes grow better in presence of O2, whereas Facultative anaerobes grow no better in presence of oxygen.
  41. What are the two forms of energy sources used by bacteria
    • Light - phototrophs:
    • - Photoorganotrophs (photoheterotrophs): organic compound as Carbon (C) source
    • - Photolithotropes (photoautotrophs): CO2 as C source

    • Chemicals (chemotrophs):
    • - Chemoorganotrophs: organic chemicals for E & C source
    • - Chemolithotrophs: Inorganic chemicals for E & CO2 for C
  42. How is energy measured in biological systems?
    In biological systems, energy is measured in units of kilojoules (kJ) also use kilocalories (kcal)
  43. What must an organism be able to do with energy, regardless of how it receives it?
    Regardless of how an organism gets its energy, it must be able conserve that energy in chemical bonds (high energy) like ATP
  44. Define Free Energy
    Free energy (G): energy released that is available to do work (named G after Gibb’s)
  45. How is the change of free energy expressed
    • The change in free energy during a reaction is expressed as ∆Go´ (std. conditions, pH = 7)
    • ∆ should be read as the “change in
    • 0´: Zero and prime mean that the free energy value was obtained under standard condition at pH= 7:
  46. What does it mean if ∆Go´ is negative?
    If the ∆Go´ of a reaction is negative, the reaction will proceed with the release of free energy (under standard conditions), energy that the cell may be able to conserve as ATP. Such reactions are termed as exergonic

    A + B -> C + D + energy (under standard conditions)
  47. What does it mean if ∆Go´ is positive?
    if ∆Go´ is positive, the reaction requires energy to proceed. These reactions are called endergonic

    Energy + A + B -> C + D (under standard conditions)
  48. How is the change in free energy calculated
    • Using free energies of formation, it is possible to calculate the change (standard) in free energy of a reaction:
    • For the reaction A + B -> C + D, ∆Go´ is calculated by subtracting the sum of the free energies of formation of the reactants (in this case A & B) from that of the products (C & D)

    • ∆Go´ = [G(C) + Gf (D)] – [G(A) + Gf (B)]
    • ∆Go´ = Σ G(products) – Σ G(reactants)
  49. Can a free-energy calculation tell you anything about the rate of a reaction?
    A free-energy calculation tells us only whether energy is released or required in direction written as it goes to equilibrium; it says nothing about the rate of the reaction
  50. What is activation energy?
    • The breaking of bonds requires energy, and this energy is referred to as activation energy
    • Requires around 20-30 kcal which cannot be supplied by free energy of motion as physiological temperatures
  51. Describe what a catalyst is
    A catalyst is a substance that lowers the activation energy of a reaction, thereby increasing the rate of reaction (lowers it to amount that might be provided by free energy of motion)
  52. Are catalysts consumed by a reaction?
    Catalysts facilitate reactions but are not consumed or transformed by the reaction
  53. Do catalysts affect the equilibrium of a reaction?
    Catalysts do not affect the energetics or the equilibrium of a reaction; catalysts affect only the speed at which reactions proceed
  54. Which direction is favored for spontaneous reactions? Do they always go fast?
    • Thermodynamically favored reactions that should go in the direction of product formation (∆G= - )
    • do not necessarily go fast.
  55. How is velocity (speed) or a reaction determined?
    Velocity (speed) of a reaction is determined by energy of activation. At high temperatures, reactions will go fast, but this is not feasible in living cells
  56. Contrast what Free Energy and Activation Energy determine
    Free energy determines direction for reactions as they proceed to equilibrium, while the speed at which those reactions occur is determined by activation energy that in cells is lowered by enzymes that result in increased reaction velocity.
  57. What are biological catalysts called?
    The catalysts of biological systems are proteins called enzymes
  58. T or F: Enzymes are highly specific

    Enzymes are highly specific, catalyzing only a single type or class of reaction
  59. Describe the enzyme substrate complex, and how it forms
    In enzyme catalyzed reactions, the enzyme (E) temporarily combines with the reactant or “substrate”(S) forming an enzyme-substrate complex (E-S)

    When E forms complex with S, certain bonds in the substrate [S] are weakened, more easily broken, and new bonds are more likely to form. Thus, not as much activation energy is needed for the reaction to proceed at significant rates.

    E + S → [ES] → [E-P] → E + P
  60. What bonds are associated with enzyme-subsrtate bonding?
    The substrate binds to the enzymes active site with weak bonds: hydrogen bonds, ionic bonds, hydrophobic interactions, van der Waals forces
  61. Contrast Lock and Key with Induced Fit
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  62. How fast is an enzymes catalytic power
    Enzymes display enormous catalytic power, accelerating reactions rates between 108 to 1020 times faster than uncatalyzed reactions. This is far faster than any synthetic catalysts
  63. What does an enzyme's specificity ensure?
    In enzyme-catalyzed reactions, the specificity of the enzyme’s active site ensures that none of the substrate is diverted to nonproductive side-reactions. No wasteful by products are formed
  64. What are the two nonprotein groups that enzymes may contain? Give an example of each
    Many enzymes contain small nonprotein molecules that participate in catalysis but are not themselves substrates. Can be divided into two groups:

    • 1. Prosthetic Groups:  bind very tightly to their enzymes, usually covalently and permanently; The heme group present in cytochromes is an example of a prosthetic group
    • 2. Coenzymes: are loosely bound to enzymes, and a single coenzyme molecule may associate with a number of different enzymes; Most coenzymes are derivatives of vitamins, and NAD+/NADH, a derivative of the vitamin niacin, is a good example.
  65. Differentiate between an energy diagram for an Exergonic and Endergonic reaction
    In Biological Systems these are coupled; thus, energy not released as heat or heat required is instead provided by ΔG – reaction (breaking of high energy bond)

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  66. Imagine the energy diagram for a catalyst
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  67. Differentiate between Oxidation and Reduction
    • Oxidation involves the removal of an electron(s) from a substance
    • Reduction is defined as the addition of an electron(s)
  68. What do Oxidation-Reduction reactions involve?
    Oxidation-Reduction reactions involve electrons being donated by an electron donor and being accepted by an electron acceptor.
  69. Describe half-reactions
    1/2 reaction implies that, for any oxidation reaction to occur, a reduction reaction is also necessary

    • Hydrogen gas can be oxidized to release electrons and hydrogen ions:
    • H2 → 2 e- + 2 H+
    • This is the oxidation half of the reaction

    • ½ O2 + 2 e- → O-2
    • This is the reduction half of the reaction
  70. Describe how Hoxidation may be coupled
    H2 oxidation can be coupled to the reduction of many substances including O2 in a second reaction (Overall: ½ O2 + 2e- + 2H+ → 2H+ + O-2).

    2H+ and O-2 is water and 2 e- + 2 H+ is H2

    • Thus putting the two half-reactions together yields the following overall balanced reaction:
    • H2 + 1/2 O2 → H2O
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  71. In circumstances such as H2 oxidation, how are the oxidized and reduced substances referred to?
    In these types of reactions, we refer to the substance oxidized, in this case H2, as the electron donor (reducing agent), and the substance reduced, in this case O2, as the electron acceptor (oxidizing agent)
  72. How is a Redox couple conventionally written?
    • By convention, in writing a redox couple, the oxidized form of the couple is always placed on the left, before the forward slash, followed by the reduced form after the forward slash.
    • "Oxidized/Reduced"
  73. In reactions between two redox couples, which substance is the reduced and which is oxidized?
    • In reactions between two redox couples, the reduced substance of the couple whose E0′ is more negative donates electrons to the oxidized substance of the couple whose E0′ is more positive.
    • Reduced has > (-)E0′
    • Oxidized has > (+)E0′
  74. Describe Reduction Potential
    • Substances differ in their tendency to be electron donors or electron acceptors. This tendency is expressed as their reduction potential (Eo´, standard conditions), which is measured in volts (V) in reference to that of a standard substance, H2
    • By convention, reduction potentials are given for half reactions written as reductions, with reactions at pH 7 because the cytoplasm of most cells is neutral (or nearly so)
  75. Detail how H2 oxidation coupled to O2 reduction would look
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  76. T or F: Most molecules can either be electron donors or electron acceptors

    Most molecules can either be electron donors or electron acceptors, depending on the substances with which they react
  77. What can the atom on each side of the arrow in half reactions be thought of as?
    The same atom on each side of the arrow in the half reactions can be thought of as representing a redox couple: 2H+/H2 or 1/2 O2/H2O

    *Remember that the reduced substance of a redox couple whose reduction potential is more negative donates electrons to the oxidized substance of a redox couple whose potential is more positive
  78. What is the Reduction Tower?
    • The tower represents a range of reduction potentials for redox couples from the most negative at the top to the most positive at the bottom
    • The reduced substance in the redox pair at the top of the tower has the greatest tendency to donate electrons, whereas the oxidized substance in the couple at the bottom has the greatest tendency to accept electrons
    • As electrons from donors at the top of the tower fall, they can be “caught” by acceptors at various levels below.
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  79. How is the difference in potential between two substances in the Reduction Tower expressed?
    The difference in potential between two substances is expressed as ∆Eo´
  80. The farther the electrons drop from a donor before they are caught by an ____, the greater the amount of _______; that is, ____ is proportional to _____
    The farther the electrons drop from a donor before they are caught by an acceptor, the greater the amount of energy released; that is, ∆Eo´ is proportional to ∆Go´

    *Look at redox tower: Greatest drop is from CO2/Glucose (-0.43) pair to O2/H2O pair (+0.82)
  81. What are the two rules when writing a Redox Couple (describe)
    • 1. When writing a redox couple, the reduced member (on right) of the redox pair that is more negative, donates electrons to the oxidized member (on left) of the redox pair that is more positive
    • 2. The greater the difference in redox potential ∆Eo´ between the redox pair that serves as the electron donor and the pair that serves as the acceptor, the greater amount of energy available in the oxidation-reduction reaction
  82. What are the two rules when writing a Redox Couple (pictures from slides)
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  83. Name a very common redox reaction mediator
    • Redox reactions in microbial cells are typically mediated by one or more small molecules. A very common carrier is the coenzyme nicotinamide adenine dinucleotide (NAD+), and it's reduced form is NADH.
    • NAD+ is an electron plus proton carrier, transporting 2 e- and 2 H+ at the same time.
  84. Show how NADH is a good electron donor (picture)
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  85. Shows an example of electron shuttling by NAD+/NADH (picture)
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  86. NADH is a very good ____, while NAD_ is a rather weak ____
    NADH is a good electron donor while NAD+ is a rather weak electron acceptor
  87. How may Phosphate be bonded to organic compounds?
    Phosphate can be bonded to organic compounds by either ester or anhydride bonds
  88. How is the chemical energy released in redox reactions conserved by living organisms?
    In living organisms, chemical energy released in redox reactions is conserved primarily in phosphorylated compounds
  89. The most important energy-rich phosphate compound in cells is _____
    The most important energy-rich phosphate compound in cells is adenosine triphosphate (ATP)
  90. What does ATP consist of?
    ATP consists of the ribonucleoside adenosine to which three phosphate molecules are bonded in series
  91. What are some examples of energy storage polymers?
    Examples of energy storage polymers in prokaryotes include glycogen, poly-β-hydroxybutyrate and other polyhydroxyalkanoates, and elemental sulfur, stored from the oxidation of H2S by sulfur chemolithotrophs
  92. What are the major reserve materials for Eukaryotes?
    In eukaryotic microorganisms, starch (polyglucose) and simple fats are the major reserve materials
  93. What are two major strategies for energy conservation in chemoorganotrophs?
    Fermentation and respiration are two major strategies for energy conservation in chemoorganotrophs
  94. Contrast Fermentation and respiration
    • Fermentation is a form of anaerobic catabolism in which an organic compound is both an electron donor and an electron acceptor. 
    • Respiration is the form of aerobic or anaerobic catabolism in which an elec- tron donor is oxidized with O2 or an O2 substitute as the terminal electron acceptor.
  95. Describe Glycolysis
    The glycolytic pathway is used to break glucose down to pyruvate and is a widespread mechanism for energy conservation by fermentative anaerobes. The pathway releases only a small amount of ATP and generates fermentation products (ethanol, lactic acid, and so on) characteristic of the organism. For each glucose fermented by yeast in glycolysis, 2 ATP are produced.
  96. What is a nearly universal pathway for catabolism of glucose? What is it also called?
    A nearly universal pathway for the catabolism of glucose is glycolysis, which breaks down glucose into pyruvate. Glycolysis is also called the Embden–Meyerhof–Parnas pathway (EM Pathway)
  97. How is ATP Synthesized in Fermentation? What is this in contrast with?
    • In fermentation, ATP is synthesized by substrate-level phosphorylation. In this process, ATP is synthesized directly from energy-rich intermediates during steps in the catabolism of the fermentable substrate.
    • This is in contrast to oxidative phosphorylation, which occurs in respiration; ATP is synthesized here at the expense of the proton motive force
  98. What are the stages of Fermentation?
    The fermentation of glucose through the glycolytic pathway can be divided into three stages, each requiring several independent enzymatic reactions.

    • Stage I: comprises “preparatory” reactions; these are not redox reactions and do not release energy but instead form a key intermediate of the pathway
    • Stage II: redox reactions occur, energy is conserved, and two molecules of pyruvate are formed
    • Stage III: redox balance is achieved and fermentation products are formed
  99. When does the first redox reaction in Glycolysis occur?
    The first redox reaction of glycolysis occurs in Stage II during the oxidation of glyceraldehyde 3-phosphate to 1,3-bisphosphoglyceric acid
  100. During Stages I and II of glycolysis, ____ ATP molecules are consumed and ____ ATP molecules are synthesized. Thus, the net energy yield in glycolysis is _____ molecules of ATP per molecule of glucose fermented.
    During Stages I and II of glycolysis, two ATP molecules are consumed and four ATP molecules are synthesized (Figure 3.14). Thus, the net energy yield in glycolysis is two molecules of ATP per molecule of glucose fermented.
  101. Oxidation using O2 as the terminal electron acceptor is called ________; oxidation using other acceptors under anoxic conditions is called _______
    Oxidation using O2 as the terminal electron acceptor is called aerobic respiration; oxidation using other acceptors under anoxic conditions is called anaerobic respiration
  102. Where does Electron Transport occur, and what types of enzymes does it include?
    Electron transport occurs in the membrane, and several types of oxidation–reduction enzymes participate in electron transport. These include NADH dehydrogenases, flavoproteins, iron–sulfur proteins, and cytochromes. Also participating are nonprotein electron carriers called quinones.
  103. How are Electron Transport carriers arranged in the membrane?
    The carriers are arranged in the membrane in order of increasingly more positive reduction potential, with NADH dehydrogenase first and the cytochromes last
  104. The cytochromes are proteins that contain _______. 
    The cytochromes are proteins that contain heme prosthetic groups
  105. What are Quinones? Are the firmly locked in the membrane?
    Quinones are hydrophobic molecules that lack a protein component. Because they are small and hydrophobic, quinones are free to move about within the membrane.
  106. How does H+ become extruded to the outer surface of the cell membrane during electron transport? What does this result in?
    • (1) NADH
    • (2) the dissociation of H2O into H+ and OH- in the cytoplasm.

    The extrusion of H+ to the environment results in the accumulation of OH- on the inside of the membrane.
  107. What does the separation of H+ and OH- from the two sides of the membrane result in? What is this called?
    • As a result of the separation of H+ and OH-, the two sides of the membrane differ in both charge and pH; this forms an electrochemical potential across the membrane.
    • This potential, along with the difference in pH across the membrane, is called the proton motive force (pmf)
  108. What are the three features that are characteristic of all electron transport chains regardless of which specific carriers they contain?
    • (1) The carriers are arranged in order of increasingly more positive E0′
    • (2) There is an alternation of electron-only and electron-plus-proton carriers in the chain
    • (3) The net result is reduction of a terminal electron acceptor and generation of a proton motive force.
  109. How does the PMF drive ATP synthesis?
    In analogy to how dissipation of the pmf applies torque that rotates the bacterial flagellum, the pmf also creates torque in a large membrane protein complex that makes ATP. This complex is called ATP synthase, or ATPase for short.
  110. What does ATPase consist of?
    • ATPases consist of two components, a multiprotein complex called F1 that sticks into the cytoplasm and carries out ATP synthesis, and a membrane-integrated component called Fo that carries out the ion-translocating function
    • F1 and Fo are actually two rotary motors.
  111. How much ATP is consumed by ATPase?
    Quantitative measures of the number of H+ consumed by ATPase per ATP produced yield a number between 3 and 4.
  112. T or F: ATPase is reversible

    ATPase is reversible; The net result in this case is generation of instead of dissipation of the proton motive force
  113. What is the Citric Acid Cycle (CAC)?
    The pathway by which pyruvate is oxidized to CO2 is called the citric acid cycle
  114. For each pyruvate molecule oxidized through the citric acid cycle, ____ CO2 molecules are produced
    For each pyruvate molecule oxidized through the citric acid cycle, three CO2 molecules are produced
  115. How does the ATP production of fermentation compare to aerobic respiration?
    Whereas only 2 ATP are produced per glucose fermented in alcoholic or lactic acid fermentations, a total of 38 ATP can be made by aerobically respiring the same glucose molecule to CO2 + H2O
  116. What two major roles does the CAC play? Can the same be said about the glycolytic pathway?
    • The citric acid cycle plays two major roles in the cell; energy conservation and biosynthesis.
    • Much the same can be said about the glycolytic pathway, as certain intermediates from this pathway can be drawn off for biosynthetic needs as well
  117. Describe the glyoxylate cycle
    When a substrate such as acetate is used as an electron donor instead of oxaloacetate, a variation on the citric acid cycle called the glyoxylate cycle is employed, so named because the C2 compound glyoxylate is a key intermediate.
  118. What are some examples of electron acceptors used in anaerobic respiration?
    • Nitrate (NO3-, reduced to nitrite, NO2-, by Escherichia coli or to N2 by Pseudomonas species)
    • Ferric iron (Fe3+, reduced to Fe2+ by Geobacter species)
    • Sulfate (SO42-, reduced to hydrogen sulfide, H2S, by Desulfovibrio species)
    • Carbonate (CO32−, reduced to methane, CH4, by methanogens or to acetate by acetogens)
    • Even certain organic compounds, such as the citric acid cycle intermediate fumarate.
  119. What can be made through biosynthesis? What are they collectively know as?
    • the building blocks of the four classes of macromolecules; sugars (polysaccharides), amino acids (proteins), nucleotides (nucleic acids), and fatty acids (lipids)
    • Collectively, these biosyntheses are that part of metabolism called anabolism
  120. What does lower temperatures promote as it pertains to lipid synthesis?
    Growth at low temperatures promotes the biosynthesis of shorter-chain fatty acids whereas growth at higher temperatures promotes longer-chain fatty acids
  121. Describe the two broad phases of metabolism
    • 1. Catabolism (fueling): Phase 1
    • -Degradative metabolism, exergonic, oxidative, ∆G = (-), “spontaneous”

    • 2. Anabolism: Phases (Subdivisions) 2-4 below
    • -Biosynthetic metabolism, endergonic, reductive, ∆G = (+)

    • Subdivisions:
    • 1. Fueling
    • 2. Biosynthesis
    • 3. Polymerization
    • 4. Assembly
  122. What does Phase I Fueling (Catabolism) provide the cell?
    Provides 3 things for the cell:

    • 1. Energy (from oxidation of energy source in a complete oxidation-reduction reaction)
    • 2. “C” skeletons: 12 intermediates (3 central pathways: EM, Krebb’s, Pentose)
    • 3. Reducing Power: ex NADH + H+
  123. The pathways of catabolism have an overall ∆G that is _____ and are ______
    The pathways of catabolism have an overall ∆G that is negative and are spontaneous
  124. Describe what Phase II Biosynthesis uses
    Biosynthesis uses the products of catabolism and involves those reactions which use the “C” skeletons to make subunits of the macromolecules

    • These are 12 key precursor metabolites that produce the correct numbered “C” skeletons for biosynthesis of the subunits:
    • -20 Amino Acids
    • -4 Ribonucleotides
    • -4 Deoxyribonucleotides
    • -Monosaccharides, N-Acetylglucosamine, N-Acetylmuramic acid, Fatty acids & Glycerol
  125. Describe what Phase II Biosynthesis produces
    Biosynthetic Reactions produce the building blocks of polymerization reactions; they also produce cofactors and related compounds including signaling molecules called Alarmones.
  126. How are the multiple biosynthetic reactions grouped?
    The hundreds of biosynthetic reactions are grouped into functional units called Biosynthetic Pathways each consisting of from one to a dozen sequential reactions that produce one or more building blocks
  127. How can Biosynthetic Pathways be differentiated?
    Biosynthetic pathways may be linear, branched, or in some cases, interconnected; each pathway is controlled en bloc
  128. What does Phase III Polymerization consist of? Where does it occur?
    Polymerization Reactions consist of the directed, sequential linkage of activated (next slide) molecules into long (sometime branched) chains (polymers).

    Polymerization of building blocks into proteins, RNA, DNA and glycogen occur inside the cell, whereas the final steps of their assembly into lipopolysaccharide, capsule, and murein occur outside the cell membrane (translocases)

    • Amino acid → polypeptides
    • Nucleotides → nucleic acids (RNA or DNA)
    • Monosaccharides → polysaccharides
    • Fatty Acids + Glycerol + Phosphate → phospholipids
  129. What are all macromolecules formed from?
    All the macromolecules are formed from the building blocks that include 20 amino acids, 8 nucleotides, numerous sugars, and fatty acids
  130. How can a reaction such as "Amino Acid1 + Amino Acid2  → Dipeptide"...occur?
    The reaction is not thermodynamically spontaneous in the direction written, and thus violates 2nd law. Instead it is spontaneous for Dipeptide breakdown. For the reaction to occur as written, Amino Acids need to be Activated...

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  131. What do Phase IV, Assembly Reactions, involve?
    Assembly Reactions involve the chemical modification of macromolecules, their transport to prespecified locations in the cell, and their association to form cellular structures: Envelope, appendages, nucleoid, polysomes, inclusions, and enzyme complexes.

    In some cases, other macromolecules must aid in the process (Directed Assembly)

  132. In living organisms, chemical energy released in redox reactions is usually conserved in the form of ______.
    In living organisms, chemical energy released in redox reactions is usually conserved in the form of high-energy phosphate bonds

    • *These compounds function as the energy source to drive energy-requiring reactions in the cell
  133. How are phosphate groups attached during the formation of high-energy phosphate bonds?
    Phosphate groups are attached via oxygen atoms by ester or anhydride bonds

    • Anhydride: high energy
    • Note: Not all phosphate bonds are high-energy bonds
  134. What are the two methods of ATP Synthesis?
    • Substrate Level Phosphorylation (SLP): Direct synthesis of ATP or other high energy phosphate in a direct chemical (metabolic) reaction
    • Oxidative Phosphorylation (OP): Electron transport mediated synthesis of ATP. Mechanism involves Mitchell’s chemiosmosis and generation of proton motive force

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  135. Briefly describe the Electron Transport Chain
    The presence of a series of membrane associated electron carriers arranged in order of increasingly more positive Eo

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Microbiology Chapter 4
Microbiology Chapter 4
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