Microbial Metabolism

MIC 101

Energy and ATP

A. Metabolism

  • Defined as chemical processes carried out by living organisms
  • Two types of reactions:
    1. Catabolism
      • Complex molecules breakdown into smaller molecules + energy
    2. Anabolism (Biosynthesis)
      • Small molecules + energy used to build complex molecules

B. Adenosine Triphosphate (ATP)

  • Major energy carrier of the cell
  • Functions:
    1. Stores energy in phosphate bonds
      • Reaction: ATP<br/>ightarrowADP+Pi+extEnergyATP <br /> ightarrow ADP + Pi + ext{Energy}
    2. Often referred to as the “energy currency” of the cell, used for metabolic processes requiring energy
    3. E. coli contains 5 million ATP molecules but spends 2.5 million ATP molecules per second!

C. Making ATP

  • ATP generated from ADP and inorganic phosphate (Pi) via:
    1. Substrate-level phosphorylation
      • Phosphate added from another organic molecule
    2. Oxidative phosphorylation
      • Energy released by electron transport used to generate ATP
    3. Photophosphorylation
      • Light energy used to produce ATP
  • General reaction formula:
    ADP+Pi+extEnergy<br/>ightarrowATPADP + Pi + ext{Energy} <br /> ightarrow ATP
  • Constant cycling between ATP and ADP + Pi:
    ADP+Pi+extEnergy<br/>ightleftharpoonsATPADP + Pi + ext{Energy} <br /> ightleftharpoons ATP

D. Oxidation and Reduction (Redox Reactions)

  1. Oxidation: Removal of electrons from a molecule (energy release).
  2. Reduction: Addition of electrons to a molecule (energy storage).
  3. These reactions are coupled: when one molecule loses electrons, the electrons are transferred to another molecule.

Enzymes

A. Enzymes

  • Protein catalysts that speed up reactions without being consumed.

B. Substrate Specificity

  • Enzymes interact with specific substrates to catalyze biochemical reactions.
  • Active site of enzymes designed for binding specific substrates.

C. Lowering Activation Energy

  • Enzymes catalyze reactions by lowering activation energy.
  • Activation Energy: The minimum energy needed to initiate a chemical reaction.

D. Cofactors

  • Inorganic ions (e.g., Mg++) or coenzymes that increase enzyme activity.
  • Examples of coenzymes:
    • Nicotinamide adenine dinucleotide (NAD+).

E. Factors Affecting Enzyme Activity

  • 1. Temperature: Enzyme activity can increase with temperature to an optimal point but may decrease beyond that due to denaturation.
  • 2. pH: Each enzyme has an optimal pH range.
  • 3. Concentrations: Levels of enzyme, substrate, and reactants affect activity.

F. Inhibition of Enzyme Activity

  • Competitive Inhibition: Inhibitor mimics the substrate and occupies the active site.
  • Non-Competitive Inhibition: Inhibitor binds to an allosteric site, changing the enzyme's shape and activity.
  • Example: Feedback inhibition where a product inhibits the enzyme that catalyzes its formation.

Carbohydrate Metabolism

A. Definition

  • The breakdown of carbohydrate molecules to produce energy.
  • Glucose is the most common carbohydrate and central to metabolic processes.

B. Types of Carbohydrate Metabolism

  • 1. Fermentation
  • 2. Cellular Respiration
  • Both processes share glycolysis.

Glycolysis

A. Definition

  • Refers to the breakdown of glucose to pyruvate.

B. Steps of Glycolysis

  1. Two phosphates are added to glucose from ATP, activating glucose and raising its energy level.
  2. The sugar molecule is split into two molecules.
  3. NAD+ is converted to NADH by accepting electrons from the sugar molecule (providing reducing power).
  4. ATP is generated by substrate-level phosphorylation.

C. Summary equation of glycolysis:
C<em>6H</em>12O<em>6+2ADP+2Pi+2NAD+ightarrow2C</em>3H<em>4O</em>3+2ATP+2NADH+2H++2H2OC<em>6H</em>{12}O<em>6 + 2 ADP + 2 Pi + 2 NAD^+ ightarrow 2 C</em>3H<em>4O</em>3 + 2 ATP + 2 NADH + 2 H^+ + 2 H_2O

Cellular Respiration

A. General Overview

  • Cellular respiration includes three linked processes:
    1. Krebs Cycle
    2. Electron Transport Chain (ETC)
    3. Chemiosmosis

B. Krebs Cycle

  • Pyruvate is fully broken down to release carbon dioxide (CO2).
  • Generates reducing power in electron carrier molecules:
    • 3 NADH and 1 FADH2 produced.
  • Produces ATP by substrate-level phosphorylation (1 ATP per pyruvate).

C. Electron Transport Chain

  • Captures electrons from electron carrier molecules.
  • Generates ATP via oxidative phosphorylation.
  • Oxygen (O2) acts as the final electron acceptor, forming water (H2O).
  • Four types of electron carriers:
    • 1. Flavoproteins (e.g., FMN)
    • 2. Metal-containing proteins (e.g., iron-sulfur proteins)
    • 3. Ubiquinones
    • 4. Cytochromes

D. Proton Gradient and Chemiosmosis

  • Energy from electron transport synthesizes a proton gradient.
  • Process of using the H+ gradient to synthesize ATP: chemiosmosis.
  • ATP synthase utilizes energy from H+ ions moving down their concentration gradient to produce ATP through oxidative phosphorylation.

E. Total ATP Yield from Aerobic Respiration

  • Total production: 38 ATP
    • Glycolysis: 2 ATP net (4 produced, but 2 utilized for initiation).
    • Krebs Cycle: 2 ATP produced.
    • Electron Transport Chain/Chemiosmosis: 34 ATP produced.

F. Anaerobic Respiration

  • Any respiration type where the final electron acceptor is not O2.
  • Examples include nitrate reduced to nitrite in E. coli.

Fermentation

A. Definition and Overview

  • A special type of anaerobic respiration where an organic molecule serves as the final electron acceptor.
  • Produces energy but in lesser amounts than aerobic respiration.
  • Does not require oxygen and does not involve Krebs Cycle or Electron Transport Chain.

B. Types of Fermentation

  • 1. Lactic Acid Fermentation
  • 2. Ethanol Fermentation
  • 3. Butyric Acid Fermentation
  • 4. 2,3-butanediol Fermentation
    • Intermediate: acetoin (detected via Voges-Proskauer test).
  • 5. Mixed Acid Fermentation
    • Detected via methyl red test.

Other Metabolic Processes

A. Protein Catabolism

  1. Proteases are enzymes that digest proteins into amino acids.
  2. Amino acids undergo deamination and subsequently enter the Krebs Cycle.

B. Lipid Metabolism

  1. Lipases are enzymes that breakdown fats into fatty acids and glycerol.
  2. Beta-Oxidation: Breakdown of fatty acids into two-carbon segments (acetyl CoA) that enter the Krebs Cycle.

C. Anabolic Pathways

  1. Many anabolic pathways are actually amphibolic; they can proceed in either direction (catabolic or anabolic) depending on metabolic needs.
  2. These pathways include the production of most metabolites.

D. Photosynthesis

  1. Net Reaction:
    6CO<em>2+6H</em>2O+extlight<br/>ightarrowC<em>6H</em>12O<em>6+6O</em>26 CO<em>2 + 6 H</em>2O + ext{light} <br /> ightarrow C<em>6H</em>{12}O<em>6 + 6 O</em>2
  2. Composed of two parts:
    a. Light-dependent reactions:
    - Chlorophyll absorbs light energy (exciting electrons).
    - Generates ATP (photophosphorylation).
    - Creates reducing power (NADPH).
    b. Light-independent reactions:
    - Utilize CO2 to synthesize glucose.