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Chapter 5: Microbial Metabolism. Microbial Metabolism Metabolism refers to all chemical reactions that occur within a living a living organism. These chemical reactions are generally of two types:

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Chapter 5:

Microbial Metabolism

Microbial Metabolism

Metabolism refers to all chemical reactions that occur within a living a living organism.

These chemical reactions are generally of two types:

  • Catabolic: Degradative reactions that release energy by breaking down large, complex molecules into smaller ones.

Often involve hydrolysis, breaking bonds with water.

  • Anabolic: Biosynthetic reactions that build large complex molecules from simpler ones.

Require energy and often involve dehydration synthesis.

Coupling of Anabolic and Catabolic Reactions
  • Catabolic reactions provide the energy needed to drive anabolic reactions.
  • ATP stores energy from catabolic reactions and releases it to drive anabolic reactions.
  • Catabolic reactions are often coupled to ATPsynthesis:

ADP + Pi + Energy -----------> ATP

  • Anabolic reactions are often coupled to ATP hydrolysis:

ATP -----------> ADP + Pi + Energy

  • Efficiency: Only part of the energy released in catabolism is available for work, the rest is lost as heat. Energy transformations are inefficient.
  • Protein molecules that catalyze chemical reactions.
  • Enzymes are highly specific and usually catalyze only one or a few closely related reactions.


Sucrose + H2O -----------> Glucose + Fructose

(substrate) (products)

  • Enzymes are extremely efficient. Speed up reaction up to 10 billion times more than without enzyme.
  • Turnover number: Number of substrate molecules an enzyme molecule converts to product each second. Ranges from 1 to 500,000.
Enzymes (Continued)
  • The rate of a chemical reaction depends on temperature, pressure, substrate concentration, pH, and several other factors in the cell.
  • Energy of activation: The amount of energy required to trigger a chemical reaction.
  • Enzymes speed up chemical reactions by decreasing their energy of activation without increasing the temperature or pressure inside the cell.

Example: Bring reactants together, create stress on a bond, etc.

Naming Enzymes
  • Enzyme names typically end in -ase.
  • There are six classes of enzymes

1. Oxidoreductases: Catalyze oxidation-reduction reactions. Include dehydrogenases and oxidases.

2. Transferases: Transfer functional groups (amino, phosphate, etc).

3. Hydrolases: Hydrolysis, break bonds by adding water.

4. Lyases: Remove groups of atoms without hydrolysis.

5. Isomerases: Rearrange atoms within a molecule.

6. Ligases: Join two molecules, usually with energy provided by ATP hydrolysis.

Enzyme Components
  • Some enzymes consist of protein only.
  • Others have a protein portion (apoenzyme) and a nonprotein component (cofactor).

Holoenzyme = Apoenzyme + Cofactor

  • Enzyme cofactors may be a metal ion (Mg2+ , Ca2+, etc.) or an organic molecule (coenzyme). Many coenzymes are derived from vitamins.


    • NAD+: Nicotinamide adenine dinucleotide
    • NADP+: Nicotinamide adenine dinucleotide phosphate

are both cofactors derived from niacin (B vitamin).

    • Coenzyme A is derived from panthotenic acid.
Mechanism of Enzymatic Action

Surface of enzyme contains an active site that binds specifically to the substrate.

1. An enzyme-substrate complex forms.

2. Substrate molecule is transformed by:

  • Rearrangement of existing atoms
  • Breakdown of substrate molecule
  • Combination with another substrate molecule

3.Products of reaction no longer fit the active site and are released.

4. Unchanged enzyme is free to bind to more substrate molecules.

Factors Affecting Enzymatic Action

Enzymes are protein molecules and their three- dimensional shape is essential for their function. The shape of the active site must not be altered so that it can bind specifically to the substrate. Several factors can affects enzyme activity:

  • Temperature:Most enzymes have an optimaltemperature. At low temperatures most reactions proceed slowly due to slow particle movement. At very high temperatures reactions slow down because the enzyme is denatured.

Denaturation: Loss of three-dimensional protein structure. Involves breakage of H and noncovalent bonds.

Factors Affecting Enzymatic Action
  • pH: Most enzymes have an optimum pH. Above or below this value activity slows down. Extreme changes in pH cause denaturation.
  • Substrate concentration: Enzyme acts at maximum rate at high substrate concentration.

Saturation point: Substrate concentration at which enzyme is acting at maximum rate possible.

  • Inhibitors: Inhibit enzyme activity. Two types:
    • Competitive inhibitors: Bind to enzyme active site. Example: Sulfa drugs, AZT.
    • Noncompetitive inhibitors: Bind to an allostericsite.

Example: Cyanide, fluoride.

Factors Affecting Enzymatic Action
  • Feedback Inhibition: Also known as end-product inhibition.

Some allosteric inhibitors stop cell from making more of a product than it needs.

The end product of a series of reactions, inhibits the activity of an earlier enzyme.

Enzyme 1 Enzyme 2 Enzyme 3

A --------> B -------> C --------> D

Enzyme 1 is inhibited by product D.

Feedback inhibition is used to regulate ATP, amino acid, nucleotide, and vitamin synthesis by the cell.

  • Catalytic RNA molecules
  • Have active sites that bind to substrates
  • Discovered in 1982
  • Act on RNA substrates by cutting and splicing them.
Energy Production

Oxidation-Reduction or Redox Reactions: Reactions in which both oxidation and reduction occur.

Oxidation: Removal of electrons or H atoms

Addition of oxygen

Associated with loss of energy

Reduction: Gain of electrons or H atoms

Loss of oxygen

Associated with gain of energy

Examples: Aerobic respiration & photosynthesis are redox processes.

aerobic respiration is a redox reaction
Aerobic Respiration is a Redox Reaction

C6H12O6 + 6 O2 -----> 6 CO2 + 6 H2O + ATP

Glucose oxygen oxidized reduced

ATP Production

Some of the energy released in oxidation-reduction processes is trapped as ATP; the rest is lost as heat.

Phosphorylation reaction:

ADP + Energy + P ---------> ATP

There are three different mechanisms of ATP phosphorylation in living organisms:

1. Substrate-Level Phosphorylation:

  • Direct transfer of phosphate from phosphorylated compound to ADP.
  • Simple process that does not require intact membranes.
  • Generates a small amount of energy during aerobic respiration.

Two Mechanisms of ATP Synthesis:

Oxidative and Substrate Level Phosphorylation

2. Oxidative Phosphorylation:
  • Involves electron transport chain, in which electrons are transferred from organic compounds to electron carriers (NAD+ or FAD) to a final electron acceptor (O2 or other inorganic compounds).
  • Occurs on membranes (plasma membrane of procaryotes or inner mitochondrial membrane of eucaryotes).
  • ATP is generated through chemiosmosis.
  • Generates most of the ATP in aerobic respiration.

3. Photophosphorylation:

  • Occurs in photosynthetic cells only.
  • Convert solar energy into chemical energy (ATP and NADPH).
  • Also involves an electron transportchain.
Carbohydrate Catabolism
  • Most microorganisms use glucose or other carbohydrates as their primary source of energy.
  • Lipids and proteins are also used as energy sources.

Two general processes are used to obtain energy from glucose: cellular respiration and fermentation.

Carbohydrate Catabolism

I. Cellular respiration:

  • ATP generating process in which food molecules are oxidized.
  • Requires an electron transport chain.
  • Final electron acceptor is an inorganic molecule:
    • Aerobic respiration final electron acceptor is oxygen. Much more efficient process.
    • Anaerobic respiration final electron acceptor is another inorganicmolecule. Energetically inefficient process.
II. Fermentation:
  • Releases energy from sugars or other organic molecules.
  • Does not requireoxygen, but may occur in its presence.
  • Does not require an electron transport chain.
  • Final electron acceptor is organic molecule.
  • Inefficient: Produces a small amount of ATP for each molecule of food.
  • End-products are energy rich organic compounds:
    • Lactic acid
    • Alcohol
Cellular Respiration

I. Aerobic Respiration

C6H12O6 + 6 O2 -----> 6 CO2 + 6 H2O + ATP

Glucose oxygen oxidized reduced

  • Most energy efficient catabolic process.
  • Oxygen is final electron acceptor.

Aerobic Respiration occurs in three stages:

1. Glycolysis

2. Kreb’s Cycle

3. Electron Transport & Chemiosmosis

Cellular Respiration

I. Stages of Aerobic Respiration

1. Glycolysis: “Splitting of sugar”.

  • Glucose (6 C) is split and oxidized to two molecules of pyruvic acid (3C).
  • Most organisms can carry out this process.
  • Does not require oxygen.

Net yield per glucose molecule:

  • 2 ATP (substrate level phosphorylation)
  • 2 NADH
Cellular Respiration

I. Stages of Aerobic Respiration

2. Krebs Cycle (Citric Acid Cycle):

  • Before cycle can start, pyruvic acid (3C) loses one carbon (as CO2) to become acetyl CoA (2C).
  • Acetyl CoA (2C) joins oxaloacetic acid (4C) to form citric acid (6C).
  • Cycle of 8 oxidation-reduction reactions that transfer energy to electron carrier molecules (coenzymes NAD+ and FAD).
  • 2 molecules of carbon dioxide are lost during each cycle.
  • Oxaloacetic acid is regenerated in final step.

Net yield per glucose molecule:

    • 2 ATP (substrate level phosphorylation)
    • 8 NADH
    • 2 FADH2
pyruvic acid is converted to acetyl coa before the kreb s cycle starts
Pyruvic Acid is Converted to Acetyl CoA Before the Kreb’s Cycle Starts

Notice that carbon dioxide is lost.

Cellular Respiration

I. Stages of Aerobic Respiration

3. Electron Transport Chain and Chemiosmosis:

  • Electrons from NADH and FADH2 are released to chain of electron carriers.
  • Electron carriers are on cell membrane (plasma membrane of bacteria or inner mitochondrial membrane in eucaryotes).
  • Final electron acceptor is oxygen.
  • A proton gradient is generated across membrane as electrons flow down chain.
  • ATP is made by ATP synthase (chemiosmosis) as protons flow down concentration gradient.

Net ATP yield:

  • 2 FADH2 generate 2 ATPs each: 4 ATP
  • 10 NADH generate 3 ATPs each: 30 ATP
Total Yield from Aerobic Respiration of 1 Glucose molecule: 36-38 molecules of ATP

In procaryotes:

C6H12O6 + 6 O2-----> 6CO2 + 6 H2O + 38 ATP

In eucaryotes:

C6H12O6 + 6 O2 -----> 6CO2 + 6 H2O + 36 ATP

Yield is lower in eucaryotes because transport of

pyruvic acid into mitochondria requires energy.


Cellular Respiration

II. Anaerobic Respiration

  • Final electron acceptor is not oxygen.
  • Instead it is an inorganic molecule:
    • Nitrate (NO3-):Pseudomonas and Bacillus. Reduced to nitrite (NO2-):, nitrous oxide, or nitrogen gas.
    • Sulfate (SO42-):Desulfovibrio. Reduced to hydrogen sulfide (H2S).
    • Carbonate (CO32-): Reduced to methane.
  • Inefficient (2 ATPs per glucose molecule).
    • Only part of the Krebs cycle operates without oxygen.
    • Not all carriers in electron transport chain participate.
  • Anaerobes tend to grow more slowly than aerobes.
  • Releases energy from sugars or other organic molecules.
  • Does not require oxygen, but may occur in its presence.
  • Does not require Krebs cycle or an electron transport chain.
  • Final electron acceptor is organic molecule.
  • Inefficient. Produces a small amount of ATP for each molecule of food. (1 or 2 ATPs)
  • End-products may be lactic acid, alcohol, or other energy rich organic compounds.
    • Lactic Acid Fermentation: Carried out by Lactobacillus and Streptococcus. Can result in food spoilage. Used to make yogurt, sauerkraut, and pickles.
    • Alcohol Fermentation: Carried out by yeasts and bacteria.

6 CO2 + 6 H2O + Light -----> C6H12O6 + 6 O2

Light Dependent Reactions

    • Light energy is trapped by chlorophyll.
    • Water is split into oxygen and hydrogen.
    • NADP+ is reduced to NADPH.
    • ATP is made.
  • Light Independent Reactions
    • Do not require light.
    • CO2 from air is fixed and used to make sugar.
    • Sugar is synthesized, using ATP and NADPH.
Metabolic Diversity

Living organisms can be classified based on where they obtain their energy and carbon.

Energy Source

  • Phototrophs: Light is primary energy source.
  • Chemotrophs: Oxidation of chemical compounds.

Carbon Source

  • Autotrophs: Carbon dioxide.
  • Heterotrophs: Organic carbon source.
Four Groups Based on Metabolic Diversity

1. Chemoheterotrophs:

  • Energy source: Organic compounds.
  • Carbon source: Organic compounds.
    • Examples: Most bacteria, all protozoans, all fungi, and all animals.

2. Chemoautotrophs:

  • Energy source: Inorganic compounds (H2S, NH3, S, H2, Fe2+, etc.)
  • Carbon source: Carbon dioxide.
    • Examples: Iron, sulfur, hydrogen, and nitrifying bacteria.

3. Photoheterotrophs:

  • Energy source: Light.
  • Carbon source: Organic compounds.
    • Examples: Purple and green nonsulfur bacteria.

4. Photoautotrophs:

  • Energy source: Light.
  • Carbon source: Carbon dioxide.
    • Examples: Plants, algae, photosynthetic bacteria