Mikrobiologi Umum 2011

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    Metabolism of Bacteria

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    Why do we must know the metabolism of

    bacteria ?Because we want to know how to inhibit or stopbacteria

    growth and want to control their metabolism to prolong

    shelf-lifeof food products.

    What is Metabolism?

    The Greek metabole, meaning change

    It is the totality of an organism's chemical processes to

    maintain life.

    - Catabolism

    - Anabolism

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    What are nutrients that bacteria want?

    C Sugar, Lipid Energy, Biosynthesis

    N Protein Biosynthesis

    O Air Energy

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    Biochemical Components of Cells Water: 80 % of wet weight

    Dry weight

    Protein 40-70 %

    Nucleic acid 13-34%

    Lipid 10-15 %

    Also monomers, intermediates and

    inorganic ions

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    Microorganisms require about ten elements in large

    quantities, because they are used to construct

    carbohydrates, lipids, proteins, and nucleic acids.

    Several other elements are needed in very small

    amounts and are parts of enzymes and cofactors.

    Concepts:

    Nutrientrequirements

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    Macronutrients Cells make proteins, nucleic acids and

    lipids

    Macronutrients

    macromolecules, metabolism

    C, H, O, N, S, P, K, Mg, Fe

    Sources

    Organic compounds

    Inorganic salts

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    Micronutrients and growth

    factors Micronutrients: Metals and metalloids

    Elements needed in trace quantities

    Generally not necessary to add to medium Deficiencies can arise when medium constituents

    are very pure

    Growth factors: organic requirements

    Vitamins, amino acids, purines, pyrimidines,

    acetate

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    micronutrients: required in lesser,

    sometimes trace

    amounts

    not every element is

    required by all cells

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    growth factors:organic compounds required in small amountsnot every growth factor is required by all cells

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    A. Basic Concepts Definitions

    Metabolism: The processes of catabolism and

    anabolism Catabolism: The processes by which a living

    organism obtains its energy and raw materialsfrom nutrients

    Anabolism: The processes by which energyand raw materials are used to buildmacromolecules and cellular structures(biosynthesis)

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    Overview of cell metabolism

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    Breakdown

    Proteins to Amino Acids, Starch to Glucose

    SynthesisAmino Acids to Proteins, Glucose to Starch

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    Bacterial Metabolism

    Exoenzymes: Bacteria cannot transport

    large polymers into the cell. They must

    break them down into basic subunits fortransport into the cell. Bacteria therefore

    elaborate extracellular enzymes for the

    degradation of carbohydrates to sugars

    (carbohydrases), proteins to amino acids

    (proteases), and lipids to fatty acids

    (Lipases).

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    After Sugars are made or obtained, they are

    the energy source of life.

    Breakdown of sugar(catabolism) different

    ways:

    Aerobic respiration Anaerobic respiration

    Fermentation

    Energy Generating Patterns

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    Aerobic respiration

    Glucose is a hexose, monosaccharide, C6H12O6 It is systematically broken down through

    three related pathways to Carbon dioxide

    (CO2) and Water (H2O) Process:

    1. Glycolysis (in cytoplasm)

    2. Kreb Cycle (in mitochondria)

    3. Electron transport chain

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    Glycolysis: Several glycolytic pathways

    The most common one:

    glucose----->pyruvic acid + 2 NADH + 2ATP

    Fi 8 Gl l ti P th

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    Section 8 1: Glycolysis

    Figure 8.3 Glycolytic Pathway

    From McKee and McKee, Biochemistry, 5th Edition, 2011 Oxford University Press

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    Glycolysis

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    Glycolytic Pathways

    4 major glycolytic pathways found in differentbacteria:

    Embden-Meyerhoff-Parnas pathway

    Classic glycolysis

    Found in almost all organisms Hexose monophosphate pathway

    Also found in most organisms

    Responsible for synthesis of pentose sugars used in

    nucleotide synthesis

    Entner-Doudoroff pathway

    Found in Pseudomonasand related genera

    Phosphoketolase pathway

    Found in Bifidobacteriumand Leuconostoc

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    cyclic pathwayPyruvic acid is first acted on by an NZ and a coenzyme (COA).

    The end product is Acetyl-Coa and a CO2molecule.

    Remember this occurs twice for each glucose molecule. (One

    glucose is split into two pyruvic acid molecules.)

    TCA

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    TCA

    Cycle

    (Krebs)

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    Return to Krebs and show how it works with electron

    transport chain. Note how glycolysis and Krebs are

    working together. Note that each produces reduced

    carriers that need to be processed.

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    Carbohydrates,

    fats, and

    proteins can all

    be catabolized

    through the

    same pathways.

    Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsFig. 9.19

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    Lipid Metabolism Lipids are essential to the structure and function of membranes

    Lipids also function as energy reserves, which can be mobilized assources of carbon

    90% of this lipid is triacyglycerol

    triacyglycerol lipase glycerol + 3 fatty acids

    The major fatty acid metabolism is -oxidation

    Lipids are catabolized to Glyerol and Fatty acids

    Glycerol easily enters glycolysis and Krebs just like pyruvate

    Fatty acids are chopped into 2 or 3 acid fragments that are

    broken downt to carbondioxide

    Even nucleic acidsOH SO MUCH MORE!!! Take

    biochem.

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    Lipid Metabolism

    -oxidation of fatty acid

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    Lipid Metabolism

    Glycerol Metabolism

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    Other fuels

    Proteins: digested to amino acids Amino acids are :

    deaminated : amino group removed, the

    reulting acid can be further metabolized,more ATP

    decarboxylated: carboxyl group removed,

    the end products then enter glycolysis orKrebs to make ATP

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    Nitrogen Metabolism

    Nitrogenis an essential element ofbiological molecules, such as amino acids,

    nucleotides, proteins, and DNA

    Bacteria vary widely in their ability toutilize various sources of nitrogen for

    synthesis of proteins

    G l i f it t b li

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    General view of nitrogen metabolism

    i id d d i

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    Amino acid degradation

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    Pathways Involved in Nitrogen Utilization

    1. Protein Digestionby proteinase and peptidase

    2. Oxidative Deamination

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    3. Reductive Deamination

    4. Decarboxylation

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    5. Transamination Reactions

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    Anaerobic respiration

    Final electron acceptor : never be O2

    Sulfate reducer: final electron acceptor is sodium

    sulfate (Na2 SO4)

    Methane reducer: final electron acceptor is CO2

    Nitrate reducer : final electroon acceptor is

    sodium nitrate (NaNO3)

    O2/H2O coupling is the most oxidizing, more energy

    in aerobic respiration.

    Therefore, anaerobic is less energy efficient.

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    Chemoautotroph:

    Nitrifying bacteria

    2 NH4++ 3 O2 2 NO2- + 2 H2O + 4 H++ 132

    Kcal

    Bacteria Electron

    donor

    Electron

    acceptor

    Products

    Alcaligens and

    Pseudomonas sp.H2 O2 H2O

    Nitrobacter NO2- O2 NO3

    -, H2O

    Nitrosomonas NH4+ O2 NO2- , H2ODesulfovibrio H2 SO4 2- H2O. H2SThiobacillus denitrificans S0. H2S NO3

    - SO4 2- , N2

    Thiobacillus ferrooxidans Fe2+ O2 Fe3+ , H2O

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    C. Fermentation

    Features of fermentation pathways Pyruvic acid is reduced to form reduced

    organic acids or alcohols.

    The final electron acceptor is a reducedderivative of pyruvic acid

    NADH is oxidized to form NAD: Essentialfor continued operation of the glycolytic

    pathways.

    O2is not required.

    No additional ATP are made.

    Gasses (CO2and/or H2) may be released

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    Fermentation Glycosis:

    Glucose ----->2 Pyruvate + 2ATP + 2NADH

    Fermentation pathwaysa. Homolactic acid F.

    P.A -----> Lactic Acid

    eg. Streptococci, Lactobacilli

    b.Alcoholic F.

    P.A -----> Ethyl alcohol

    eg. yeast

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    Some organisms (facultative anaerobes),

    including yeast and many bacteria, can survive

    using either fermentation or respiration. For facultative anaerobes,

    pyruvate is a fork in the

    metabolic road that leads

    to two alternative routes.

    Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsFig. 9.18

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    Re Dox Reactions

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    Re-Dox Reactions

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    Central

    Metabolism

    Fermentation Products

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    Fermentation Products

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    Nutrition

    Table 27.1

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    Alternative energy generating

    patterns(3)

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    Alternative energy generating

    patterns(4)

    Energy/carbon classes of organisms

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    Energy/carbon classes of organisms

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    Overview of Metabolism

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    Overview of Metabolism

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    Electron Transport Chain

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    p

    Electron Flow

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    Electron Flow

    and Energy

    Trapping

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    Microbiology chapters 7 - 8 part 2

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    gy p p

    Glycolysis: Anaerobic, no oxygen required,

    linear NZ pathway Begins with ______

    End products _________

    How much ATP? _______

    How many carrier molecules? ____

    Name the carrier molecule. ____

    Where in the cell? _______

    What happens after if the organism

    Is an aerobe? _____

    Facultative? ______ Strict anaerobe? ______

    Aerobe deprived of oxygen? ____

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    ATPAdenosine triphosphate, universal cellular energy

    Cyclically made and energy is stored and then broken down and the

    energy is released

    Microbiology chapters 7 8 part 2

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    Microbiology chapters 7 - 8 part 2

    Note: ATP is a ribonucleotide, it has ribose, a nitogenous base

    (adenine), and phosphate. The high energy bond of the terminalof the three phosphates is the one cyclically broken and

    regenerated.

    Sugars like glucose can be broken down in a catabolic pathwaycontrolled by many cellular enzymes. Some of the energy

    released by the breaking of covalent bonds is harvested and

    stored in the energy bonds of ATP.

    Most any biomolecule can be used for energy; we will focus on

    the catabolism of glucose (a monosaccharide) and later show

    how the others are involved (lipids, AA, etc)

    Microbiology chapters 7 - 8 part 2

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    gy p p

    This is a cyclic pathway

    Pyruvic acid is first acted on by an NZ and a coenzyme (COA).

    The end product is Acetyl-Coa and a CO2molecule.

    Remember this occurs twice for each glucose molecule. (One

    glucose is split into two pyruvic acid molecules.)

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    Krebs cycle (TCA, Citric acid cycle) Aerobic stage, Occurs in the

    fluid of the Matrix

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    This is a cyclic pathway Pyruvic acid is

    first acted on by an NZ and a coenzyme

    (COA). The end product is Acetyl-Coa

    and a CO2molecule.

    Remember this occurs twice for each

    glucose molecule. (One glucose is splitinto two pyruvic acid molecules.)

    Return to Krebs and show how it works with electron transport

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    Return to Krebs and show how it works with electron transport

    chain. Note how glycolysis and Krebs are working together. Note

    that each produces reduced carriers that need to be processed.

    The electrons are passed down the chain and end up being added to

    Th H d i (H+) i d t ( t ) d

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    oxygen. The Hydrogen ion (H+) is pumped out (proton pump) and

    flows back in at special sites to be added to the Oxygen and electron

    to form Water. Energy is conserved (harvested; stored) in the bonds

    of ATP

    Theory of Chemiosmosis: Proton pump, increased H+ ion

    concentration flo thro gh ATP s nthase related channel energ

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    concentration, flow through ATP synthase related channel, energy

    is harvested in high energy bonds of ATP. Enough to generate 34

    more ATP.

    Carbohydrate Metabolism

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    Carbohydrate Metabolism

    2. EntnerDoudoroff (ED) pathway

    Carbohydrate Metabolism

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    Carbohydrate Metabolism

    3. Pentose phosphate (PP) pathway

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    Formation of intermediates of the EmbdenMeyerhofParnas

    (EMP) and EntnerDoudoroff (ED) pathway from carbohydrates

    other than glucose

    Table 1:Distribution of EmbdenMeyerhofParnas

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    y(EMP), EntnerDoudoroff (ED), and pentose phosphate(PP) pathway in bacteria

    Organism EMP ED PP

    Pseudomonas aeruginosa - +i -

    Enterococcus faecalis + +i +

    (Streptococcus)

    Salmonella typhimurium + +i +Bacillus subtilis + - -

    Escherichia coli + +i +

    Yersinia pseudotuberculosis + +i -

    Remark: + = Present;

    = not present.

    i = inducible