Chapter 5
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Chapter 5. Microbial Metabolism. Catabolic and Anabolic Reactions. Metabolism : The sum of the chemical reactions in an organism. Catabolic and Anabolic Reactions. Catabolism : Provides energy and building blocks for anabolism.

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Chapter 5

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Chapter 5

Microbial Metabolism

Catabolic and Anabolic Reactions

  • Metabolism:

  • The sum of the chemical reactions in an organism

Catabolic and Anabolic Reactions

  • Catabolism: Provides energy and building blocks for anabolism.

  • Anabolism: Uses energy and building blocks to build large molecules

Catabolic and Anabolic Reactions

  • A metabolic pathway is a sequence of enzymatically catalyzed chemical reactions in a cell

  • Metabolic pathways are determined by enzymes

  • Enzymes are encoded by genes

Collision Theory

  • The collision theory states that chemical reactions can occur when atoms, ions, and molecules collide

  • Activation energy is needed to disrupt electronic configurations

  • Reaction rate is the frequency of collisions with enough energy to bring about a reaction.

  • Reaction rate can be increased by enzymes or by increasing temperature or pressure

Enzyme Specificity and Efficiency

  • The turnover number is generally 1 to 10,000 molecules per second

The Mechanism of Enzymatic Action

Figure 5.4a

Factors Influencing Enzyme Activity

  • Temperature

  • pH

  • Substrate concentration

  • Inhibitors

Factors Influencing Enzyme Activity

  • Temperature and pH denature proteins

Figure 5.6

Enzyme Inhibitors: Competitive Inhibition

Figure 5.7a–b

Sulfa drugs (sulfonamides) (Discovered in the 1930s) Enzyme Inhibitors: Competitive Inhibition

Sulfa drugs  

  • a) Structure: Chemically similar (chemical analogues) to the chemical PABA (para-aminobenzoic acid) which is required by microbes. It normally functions as a cofactor in the synthesis of nucleotide nitrogen bases. b) Mode of action: ‘Competitive Inhibition’Normal functioning when no sulfa drugs are present: PABA is used by bacteria to produce folic acid. Folic acid is a bacterial vitamin that is necessary for the production of nucleotides. What molecules are nucleotides made of?

When sulfa drugs are present: Competitive Inhibition

  • Since sulfa drugs are chemically similar to (analogues of) PABA, they may “trick” the enzyme into using the sulfa drug to produce folic acid instead of PABA. In effect, the sulfa drug competes with the PABA. When the enzyme is ‘tricked’, the folic acid in the bacterial cell is defective and will not produce nitrogen bases. It there is a shortage of nitrogen bases, DNA cannot be replicated, and therefore, growth stops (no binary fission). The bacterial cell has been inhibited from reproducing.

Energy Production The cell’s ‘currency’ = ATP. And I mean ALL cells.

The Generation of ATP

  • ATP is generated by the phosphorylation of ADP

3 Ways ATP is Produced in Living Cells

  • Substrate-Level Phosphorylation.

    • Occurs during glycolysis (or alternate pathway) during

      • Fermentation (in Microbes and our

  • own skeletal muscle cells and brain

  • Cells)

  • b. Respiration: Glycolysis and Krebs Cycle

  • 2. Oxidative Phosphorylation

  • Occurs during respiratory e- transport chains

  • (aerobic or anaerobic)

  • 3. Photophosphorylation.

  • Occurs during photosynthesis

  • Substrate-Level Phosphorylation

    • A chemical reaction where a phosphate group is transferred from one molecule to ADP. This requires a specific enzyme that can transfer the phosphate from this specific molecule to ADP.

    • This is how the process of FERMENTATION produces ATP.

    Oxidation-Reduction Reactions

    • Oxidation: Removal of electrons. The general process of electron donation to an electron acceptor is also referred to as oxidation even though the electron acceptor may not be oxygen.

    • Reduction: Gain of electrons

    • Redox reaction: An oxidation reaction paired with a reduction reaction


    • Light causes chlorophyll to give up electrons. The electrons go through a process similar to what happens during respiration (an electron transport chain and chemiosmosis). This process releases energy used to bond a phosphate to ADP producing ATP.

    • The ATP produced is used to produce food molecules (sugars-glucose).


    Figure 5.9

    Oxidation-Reduction Reactions

    • In biological systems, the electrons are often associated with hydrogen atoms. Biological oxidations are often dehydrogenations.

    Representative Biological Oxidation

    Figure 5.10

    Oxidative Phosphorylation

    • Energy released from transfer of electrons (oxidation) of one compound to another (reduction) is used to generate ATP in the electron transport chain

    • An electron transport chain(ETC) couples a chemical reaction between an electron donor (such as NADH) and an electron acceptor (such as O2) to the transfer of H+ ions across a membrane, through a set of mediating biochemical reactions.

    Carbohydrate Catabolism

    • The breakdown of carbohydrates to release energy

      • Glycolysis (or alternative)

      • Preparatory Step

      • Krebs cycle

      • Electron transport chain

        • Chemiosmosis

        • ADP Phosphorylation


    • The oxidation of glucose to pyruvic acid produces ATP and NADH

    Figure 5.11

    Preparatory Stage of Glycolysis

    • 2 ATP are used

    • Glucose is split to form 2 glucose-3-phosphate

    Figure 5.12, steps 1–5

    Energy-Conserving Stage of Glycolysis

    • 2 glucose-3-phosphate oxidized to 2 pyruvic acid

    • 4 ATP produced

    • 2 NADH produced

    Figure 5.12, steps 6–10


    • Glucose + 2 ATP + 2 ADP + 2 PO4– + 2 NAD+ 2 pyruvic acid + 4 ATP + 2 NADH + 2H+

    Alternatives to Glycolysis

    • Pentose phosphate pathway

      • Produces pentoses (Any of a class of monosaccharides having five carbon atoms per molecule and including ribose and several other sugars) and NADPH (used by photosynthetic organisms) and certain amino acids

      • Only net 1 ATP

      • Bacillus subtilis, E. coli

    • Entner-Doudoroff pathway

      • Produces NADPH (photosynthesis) and net 1ATP

      • Pseudomonas, Agrobacterium

    Preparatory Step Intermediate between Glycolysis and Krebs Cycle

    • Pyruvic acid (from glycolysis) is oxidized and decarboyxlated

    Figure 5.13

    The Krebs Cycle

    • Series of biochemical reactions in which the large amount of chemical energy now in actyl CoA is released step by step in a series of redox reactions

    • Oxidation of acetyl CoA produces NADH and FADH2

    The Krebs Cycle

    Figure 5.13

    The Electron Transport Chain

    • A series of carrier molecules that are, in turn, oxidized and reduced as electrons are passed down the chain

    • Energy released can be used to produce ATP by chemiosmosis

    Chemiosmotic Generation of ATP

    Figure 5.16

    An Overview of Chemiosmosis

    Figure 5.15


    Figure 5.16

    Carbohydrate Catabolism

    Carbohydrate Catabolism

    • Energy produced from Substrate-level phosphorylation only

    Carbohydrate Catabolism

    • ATP produced from complete oxidation of one glucose using aerobic respiration

    • # ATPs Eukaryote vs. Prokaryote?

    A Summary of Respiration

    • Aerobic respiration: The final electron acceptor in the electron transport chain is molecular oxygen (O2).

    • Anaerobic respiration: The final electron acceptor in the electron transport chain is not O2. Yields less energy than aerobic respiration because only part of the Krebs cycles operates under anaerobic conditions.

    Anaerobic Respiration


    • FERMENTATION Scientific definition:

      • Releases energy from oxidation of organic molecules

      • Does not require oxygen

      • Does not use the Krebs cycle or ETC

      • Uses an organic molecule as the final electron acceptor

    An Overview of Fermentation

    Figure 5.18a

    End-Products of Fermentation

    Figure 5.18b

    Types of Fermentation

    Figure 5.19

    Types of Fermentation

    Table 5.4

    Types of Fermentation

    Table 5.4

    Catabolism of Organic Food Molecules

    Figure 5.21


    Figure 4.15


    • Conversion of light energy into chemical energy (ATP) and nutrients (glucose)

    • Overall Summary Reaction?


    • Compare and Contrast

    • Oxidative Phosphorylation and Photophosphorylation.


    • Oxygenic:

    • Anoxygenic:

    A Nutritional Classification of Organisms

    Figure 5.28

    Metabolic Diversity among OrganismsSee Fig. 5.28 p. 143

    Amphibolic Pathways

    Figure 5.33

    Amphibolic Pathways

    Figure 5.33

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