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Microbiology: A Systems Approach, 2nd ed. Chapter 8: Microbial Metabolism- the Chemical Crossroads of Life 8.4 Biosynthesis and the Crossing Pathways of Metabolism ... – PowerPoint PPT presentation

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Title: Microbiology: A Systems Approach, 2nd ed.


1
Microbiology A Systems Approach, 2nd ed.
  • Chapter 8 Microbial Metabolism- the Chemical
    Crossroads of Life

2
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

3
Figure 8.1
4
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

5
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6
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

7
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)

8
Figure 8.3
9
Figure 8.2
10
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11
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

12
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

13
Figure 8.4
14
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

15
Classification of Enzyme Functions
  • Site of action
  • Type of action
  • Substrate

16
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

17
Figure 8.5
18
Synthesis and Hydrolysis Reactions
Figure 8.7
19
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

20
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

21
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

22
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

23
Figure 8.8
24
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

25
Control of Enzyme Activity
  • Direct control of enzyme activity (constitutive
    enzymes)
  • Regulation of enzyme synthesis (regulated enzymes)

26
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

27
Figure 8.9
28
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

29
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.

30
Figure 8.6
31
Figure 8.10
32
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

33
Figure 8.11
34
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

35
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

36
Figure 8.12
37
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

38
Figure 8.13
39
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

40
Figure 8.14
41
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

42
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.

43
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.

44
Figure 8.15
45
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

46
Figure 8.16
47
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

48
Figure 8.17
49
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

50
Insight 8.3
51
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

52
Figure 8.18
53
Figure 8.19
54
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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56
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

57
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

58
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

59
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

60
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

61
Alcoholic Fermentation Products
  • Occurs in yeast or bacterial species that have
    metabolic pathways for converting pyruvic acid to
    ethanol
  • Products ethanol and CO2

62
Figure 8.20
63
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

64
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

65
Figure 8.21
66
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

67
Figure 8.22
68
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

69
Figure 8.23
70
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

71
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

72
8.5 It All Starts with the Sun
  • Photosynthesis
  • Proceeds in two phases
  • Light-dependent reactions
  • Light-independent reactions

73
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

74
Figure 8.24
75
Figure 8.25
76
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

77
Figure 8.26
78
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
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