Microbiology: A Systems Approach, 2nd ed.

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Microbiology A Systems Approach, 2nd ed.

• Chapter 8 Microbial Metabolism- the Chemical
  Crossroads of Life

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8.1 The Metabolism of Microbes

• Metabolism All chemical reactions and physical
  workings of the cell
• Anabolism also called biosynthesis- any process
  that results in synthesis of cell molecules and
  structures (usually requires energy input)
• Catabolism the breakdown of bonds of larger
  molecules into smaller molecules (often release
  energy)
• Functions of metabolism
• Assembles smaller molecules into larger
  macromolecules needed for the cell
• Degrades macromolecules into smaller molecules
  and yields energy
• Energy is conserved in the form of ATP or heat

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Figure 8.1
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Enzymes

• Catalyze the chemical reactions of life
• Enzymes an example of catalysts, chemicals that
  increase the rate of a chemical reaction without
  becoming part of the products or being consumed
  in the reaction

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How do Enzymes Work?

• Energy of activation the amount of energy which
  must be overcome for a reaction to proceed. Can
  be achieved by
• Increasing thermal energy to increase molecular
  velocity
• Increasing the concentration of reactants to
  increase the rate of molecular collisions
• Adding a catalyst
• An enzyme promotes a reaction by serving as a
  physical site upon which the reactant molecules
  (substrates) can be positioned for various
  interactions

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Enzyme Structure

• Most- protein
• Can be classified as simple or conjugated
• Simple enzymes consist of protein alone
• Conjugated enzymes contain protein and
  non-protein molecules
• A conjugated enzyme (haloenzyme) is a combination
  of a protein (now called the apoenzyme) and one
  or more cofactors
• Cofactors are either organic molecules
  (coenzymes) or inorganic elements (metal ions)

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Figure 8.3
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Figure 8.2
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Apoenzymes Specificity and the Active Site

• Exhibits levels of molecular complexity called
  the primary, secondary, tertiary, and quaternary
  organization
• The actual site where the substrate binds is a
  crevice or groove called the active site or
  catalytic site

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Enzyme-Substrate Interactions

• For a reaction to take place, a temporary
  enzyme-substrate union must occur at the active
  site. (Called an enzyme-substrate complex.)
• Lock-and-key fit
• The bonds are weak and easily reversible

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Figure 8.4
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Cofactors Supporting the Work of Enzymes

• Metallic cofactors
• Include Fe, Cu, Mg, Mn, Zn, Co, Se
• Metals activate enzymes, help bring the active
  site and substrate close together, and
  participate directly in chemical reactions with
  the enzyme-substrate complex
• Coenzymes
• Organic compounds that work in conjunction with
  an apoenzyme to perform a necessary alteration of
  a substrate
• Removes a chemical group from one substrate
  molecule and adds it to another substrate
• Vitamins one of the most important components
  of coenzymes

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Classification of Enzyme Functions

• Site of action
• Type of action
• Substrate

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Location and Regularity of Enzyme Action

• Either inside or outside of the cell
• Exoenzymes break down molecules outside of the
  cell
• Endoenzymes break down molecules inside of the
  cell

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Figure 8.5
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Synthesis and Hydrolysis Reactions
Figure 8.7
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Transfer Reactions by Enzymes

• Oxidation-reduction reactions
• A compound loses electrons (oxidized)
• A compound receives electrons (reduced)
• Common in the cell
• Important components- oxidoreductases
• Other enzymes that play a role in necessary
  molecular conversions by directing the transfer
  of functional groups
• Aminotransferases
• Phosphotransferases
• Methyltranferases
• Decarboxylases

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The Role of Microbial Enzymes in Disease

• Many pathogens secrete unique exoenzymes
• Help them avoid host defenses or promote
  multiplication in tissues
• These exoenzymes are called virulence factors or
  toxins

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The Sensitivity of Enzymes to Their Environment

• Enzyme activity is highly influenced by the
  cells environment
• Enzymes generally operate only under the natural
  temperature, pH, and osmotic pressure of an
  organisms habitat
• When enzymes are subjected to changes in normal
  conditions, they become chemically unstable
  (labile)
• Denaturation the weak bonds that maintain the
  native shape of the apoenzyme are broken

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Regulation of Enzymatic Activity and Metabolic
Pathways

• Metabolic Pathways
• Metabolic reactions usually occur in a
  multiseries step or pathway
• Each step is catalyzed by an enzyme
• Every pathway has one or more enzyme pacemakers
  that set the rate of a pathways progression

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Figure 8.8
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Rate of Enzyme Production

• Enzymes are not all produced in the cell in equal
  amounts or at equal rates
• Constitutive enzymes production is continuous
  and in relatively constant amounts
• Regulated enzymes production is either induced
  or repressed in response to a change in
  concentration of the substrate

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Control of Enzyme Activity

• Direct control of enzyme activity (constitutive
  enzymes)
• Regulation of enzyme synthesis (regulated enzymes)

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Direct Controls on the Action of Enzymes

• Competitive inhibition The cell supplies a
  molecule that resembles the enzymes normal
  substrate, which then occupies and blocks the
  enzymes active site
• Noncompetitive inhibition The enzyme has two
  binding sites- the active site and the regulatory
  site a regulator molecule binds to the
  regulatory site providing a negative feedback
  mechanism

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Figure 8.9
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Controls on Enzyme Synthesis

• Enzymes eventually must be replaced
• Enzyme repression stops further synthesis of an
  enzyme somewhere along its pathway
• Enzyme induction The inverse of enzyme
  repression

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Regulated Enzymes

• Inducible enzymes- break down complex substrates
  into simpler products eg. lactose to glucose
  enzymes are only synthesized (induced) when
  excess substrate is present. Otherwise the
  enzymes are not synthesized.
• Repressible enzymes- synthesize products such as
  tryptophan when the product is not available in
  nutrient sources. Presence of excess product
  represses enzyme production.

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Figure 8.6
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Figure 8.10
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8.2 The Pursuit and Utilization of Energy

• Energy in Cells
• Exergonic reaction a reaction that releases
  energy as it goes forward
• Endergonic reaction a reaction that is driven
  forward with the addition of energy

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Figure 8.11
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A Closer Look at Biological Oxidation and
Reduction

• Biological systems often extract energy through
  redox reactions
• Redox reactions always occur in pairs
• An electron donor and electron acceptor
• Redox pair
• Electron donor (reduced) electron acceptor
  (oxidized) ? Electron donor (oxidized)
  electron acceptor (reduced)
• This process leaves the previously reduced
  compound with less energy than the now oxidized
  one
• The energy in the electron acceptor can be
  captured to phosphorylate to ADP or some other
  compound, storing the energy in a high-energy
  molecule like ATP

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Electron Carriers Molecular Shuttles

• Electron carriers repeatedly accept and release
  electrons and hydrogens
• Facilitate the transfer of redox energy
• Most carriers are coenzymes that transfer both
  electrons and hydrogens
• Some transfer electrns only
• Most common carrier- NAD

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Figure 8.12
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Adenosine Triphosphate Metabolic Money

• ATP
• Can be earned, banked, saved, spent, and
  exchanged
• A temporary energy repository
• The Molecular Structure of ATP
• Three-part molecule
• Nitrogen base (adenine)
• 5-carbon sugar (ribose)
• Chain of three phosphate groups
• The high energy originates in the orientation of
  the phosphate groups
• Breaking the bonds between two successive
  phosphates of ATP yields ADP
• ADP can then be converted to AMP

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Figure 8.13
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The Metabolic Role of ATP

• Primary energy currency of the cell
• When used in a chemical reaction, must be
  replaced
• Ongoing cycle
• Adding a phosphate to ADP replenishes ATP but it
  requires an input of energy
• In heterotrophs, this energy comes from certain
  steps of catabolic pathways
• Some ATP molecules are formed through
  substrate-level phosphorylation
• ATP is formed by a transfer of a phosphate group
  from a phosphorylated compound (substrate)
  directly to ADP

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Figure 8.14
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Phosphorylation

• Oxidative phosphorylation
• Series of redox reactions occurring during the
  final phase of the respiratory pathway
• Photophosphorylation
• ATP is formed through a series of sunlight-driven
  reactions in phototrophic organisms

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8.3 The Pathways

• Pathway- a series of biochemical reactions
• Metabolism uses enzymes to catalyze reactions
  that break down (catabolize) organic molecules to
  materials (precursor molecules) that cells can
  then use to build (anabolize) larger, more
  complex molecules that are particularly suited to
  them.
• Reducing power and energy are needed in large
  quantities for the anabolic parts of metabolism
  they are produced during the catabolic part of
  metabolism.

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Catabolism Getting Materials and Energy

• Frequently the nutrient needed is glucose
• Most common pathway to break down glucose is
  glycolysis
• Three major pathways
• Respiration series of reactions that convert
  glucose to CO2 and allows the cell to recover
  significant amounts of energy
• Fermentation when facultative and aerotolerant
  anaerobes use only the glycolysis scheme to
  incompletely oxidize glucose
• Aerobic respiration When oxygen is used as the
  final electron acceptor at the end of the
  respiration scheme to produce H2O.
• Anaerobic respiration Does not use molecular
  oxygen as the final electron acceptor, but uses
  nitrogen or compounds of nitrogen or sulfur or
  compounds of sulfur, or other inorganic
  substances and the final electron acceptor.

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Figure 8.15
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Aerobic Respiration

• Series of enzyme-catalyzed reactions
• Electrons are transferred from fuel molecules to
  oxygen as a final electron acceptor
• Principal energy-yielding scheme for aerobic
  heterotrophs
• Provides both ATP and metabolic intermediates for
  many other pathways in the cell
• Glucose is the starting compound
• Glycolysis enzymatically converts glucose through
  several steps into pyruvic acid

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Figure 8.16
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Pyruvic Acid- A Central Metabolite

• Pyruvic acid from glycolysis serves an important
  position in several pathways
• Different organisms handle it in different ways
• In strictly aerobic organisms and some anaerobes,
  pyruvic acid enters the Krebs cycle

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Figure 8.17
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The Krebs Cycle A Carbon and Energy Wheel

• Pyruvic acid is energy-rich, but its hydrogens
  need to be transferred to oxygen
• Takes place in the cytoplasm of bacteria and in
  the mitochondrial matrix in eukaryotes
• Produces reduced coenzymes NADH and FADH2, 2 ATPs
  for each glucose molecule

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Insight 8.3
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The Respiratory Chain Electron Transport and
Oxidative Phosphorylation

• The final processing mill for electrons and
  hydrogen ions
• The major generator of ATP
• A chain of special redox carriers that receives
  electrons from reduced carriers (NADH and FADH2)
  and passes them in a sequential and orderly
  fashion from one redox molecule to the next

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Figure 8.18
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Figure 8.19
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Potential Yield of ATPs from Oxidative
Phosphorylation

• Five NADHs (four from Krebs cycle and one from
  glycolysis) can be used to synthesize
• 3 ATPs per electron pair from NADH
• 15 ATPs for ETS (5 X 3 per electron pair)
• 15 X 2 30 ATPs per glucose
• The single FADH produced during the Krebs cycle
  results in
• 2 ATPs per electron pair
• 2 X 2 4 ATPs per glucose

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Summary of Aerobic Respiration

• The total possible yield of ATP is 40
• 4 from glycolysis
• 2 from the Krebs cycle
• 34 from electron transport
• But 2 ATPs are expended in early glycolysis, so a
  maximum yield of 38 ATPs for prokaryotes
• 6 CO2 molecules are generated during the Krebs
  cycle
• 6 O2 molecules are consumed during electron
  transport
• 6 H2O molecules are produced in electron
  transport and 2 in glycolysis but 2 are used in
  Krebs cycle for a net number of 6

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The Terminal Step

• Oxygen accepts the electrons
• Catalyzed by cytochrome aa3 (cytochrome oxidase)
• 2 H 2 e- 1/2O2 ? H2O
• Most eukaryotic aerobes have a fully functioning
  cytochrome system
• Bacteria exhibit wide-ranging variations which
  can be used to differentiate among certain genera
  of bacteria

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Anaerobic Respiration

• Functions like the aerobic cytochrome system
  except it utilizes atoms or oxygen-containing
  ions rather than free oxygen as the final
  electron acceptor
• The nitrate and nitrite reduction systems are
  best known, using the enzyme nitrate reductase
• Denitrification when enzymes can further reduce
  nitrite to nitric oxide, nitrous oxide, and
  nitrogen gas- important in recycling nitrogen in
  the biosphere

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Fermentation

• The incomplete oxidation of glucose or other
  carbohydrates in the absence of oxygen
• Uses organic compounds as the terminal electron
  acceptors and yields a small amount of ATP
• Many bacteria can grow as fast using fermentation
  as they would in the presence of oxygen
• This is made possible by an increase in the rate
  of glycolysis
• Permits independence from molecular oxygen

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Products of Fermentation in Microorganisms

• Products of Fermentation in Microorganisms
• Alcoholic beverages
• Organic acids
• Dairy products
• Vitamins, antibiotics, and even hormones
• Two general categories
• Alcoholic fermentation
• Acidic fermentation

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Alcoholic Fermentation Products

• Occurs in yeast or bacterial species that have
  metabolic pathways for converting pyruvic acid to
  ethanol
• Products ethanol and CO2

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Figure 8.20
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Acidic Fermentation Products

• Extremely varied pathways
• Lactic acid bacteria ferment pyruvate and reduce
  it to lactic acid
• Heterolactic fermentation- when glucose is
  fermented to a mixture of lactic acid, acetic
  acid, and carbon dioxide
• Mixed acid fermentation- produces a combination
  of acetic, lactic, succinic, and formic acids and
  lowers the pH of a medium to about 4.0

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Catabolism of Noncarboyhdrate Compounds

• Polysaccharides can easily be broken down into
  their component sugars which can enter glycolysis
• Microbes can break down lipids and proteins to
  produce precursor metabolites and energy
• Lipases break apart fats into fatty acids and
  glycerol
• The glycerol is then converted to DHAP
• DHAP can enter step 4 of glycolysis
• The fatty acid component goes through beta
  oxidation
• Can yield a large amount of energy (oxidation of
  a 6-carbon fatty acid yields 50 ATPs)
• Proteases break proteins down to their amino acid
  components
• Amino groups are then removed by deamination
• Results in a carbon compound which can be
  converted to one of several intermediates of
  either glycolysis or the Krebs cycle

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Figure 8.21
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8.4 Biosynthesis and the Crossing Pathways of
Metabolism

• The Frugality of the Cell- Waste Not, Want Not
• Most catabolic pathways contain strategic
  molecular intermediates (metabolites) that can be
  diverted into anabolic pathways
• Amphibolism the property of a system to
  integrate catabolic and anabolic pathways to
  improve cell efficiency
• Principal sites of amphibolic interaction occur
  during glycolysis and the Krebs cycle

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Figure 8.22
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Amphibolic Sources of Cellular Building Blocks

• Glyceraldehyde-3-phosphate can be diverted away
  from glycolysis and converted into precursors for
  amino acid, carbohydrate, and triglyceride
  synthesis
• Pyruvate also provides intermediates for amino
  acids and can serve as the starting point in
  glucose synthesis from metabolic intermediates
  (gluconeogenesis)
• The acetyl group that starts the Krebs cycle can
  be fed into a number of synthetic pathways
• Fats can be degraded to acetyl through beta
  oxidation
• Two metabolites of carbohydrate catabolism that
  the Krebs cycle produces are essential
  intermediates in the synthesis of amino acids
• Oxaloacetic acid
• ?-ketoglutaric acid
• Occurs through amination
• Amino acids and carbohydrates can be interchanged
  through transanimation

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Figure 8.23
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Anabolism Formation of Macromolecules

• Monosaccharides, amino acids, fatty acids,
  nitrogen bases, and vitamins come from two
  possible sources
• Enter the cell from outside as nutrients
• Can be synthesized through various cellular
  pathways
• Carbohydrate Biosynthesis
• Several alternative pathways
• Amino Acids, Protein Synthesis, and Nucleic Acid
  Synthesis
• Some organisms can synthesize all 20 amino acids
• Other organisms (especially animals) must acquire
  the essential ones from their diets

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Assembly of the Cell

• When anabolism produces enough macromolecules to
  serve two cells
• When DNA replication produces duplicate copies of
  the cells genetic material
• Then the cell undergoes binary fission

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8.5 It All Starts with the Sun

• Photosynthesis
• Proceeds in two phases
• Light-dependent reactions
• Light-independent reactions

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Light-Dependent Reactions

• Solar energy delivered in discrete energy packets
  called photons
• Light strikes photosynthetic pigments
• Some wavelengths are absorbed
• Some pass through
• Some are reflected
• Light is absorbed through photosynthetic pigments
• Chlorophylls (green)
• Carotenoids (yellow, orange, or red)
• Phycobilinss (red or blue-green)
• Bacterial chlorophylls
• Contain a photocenter- a magnesium atom held in
  the center of a complex ringed molecule called a
  porphyrin
• Harvest the energy of photons and converts it to
  electron energy
• Accessory photosynthetic pigments trap light
  energy and shuttle it to chlorophyll

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Figure 8.24
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Figure 8.25
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Light-Independent Reactions

• Occur in the chloroplast stroma or the cytoplasm
  of cyanobacteria
• Use energy produced by the light phase to
  synthesize glucose by means of the Calvin cycle

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Figure 8.26
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Other Mechanisms of Photosynthesis

• Oxygenic (oxygen-releasing) photosynthesis that
  occurs in plants, algae, and cyanobacteria the
  dominant type of photosynthesis on earth
• Other photosynthesizers such as green and purple
  bacteria
• Possess bacteriochlorophyll
• More versatile in capturing light
• Only have a cyclic photosystem I
• These bacteria use H2, H2S, or elemental sulfur
  rather than H2O as a source of electrons and
  reducing power
• They are anoxygenic (non-oxygen-producing) many
  are strict anaerobes