Chapter 5

Microbial Metabolism

Overview of Metabolism

Metabolism is the sum of all chemical reactions within a living organism. It includes two main processes: catabolism and anabolism. These processes are fundamental to microbial life, enabling cells to extract energy, build cellular components, and maintain homeostasis.

• Catabolism: The breakdown of complex molecules into simpler ones, releasing energy and providing building blocks for anabolic reactions. Catabolic reactions are often hydrolytic (involve water) and exergonic (release energy).

• Anabolism (Biosynthesis): The synthesis of complex molecules from simpler ones, requiring energy input. Anabolic reactions often involve dehydration synthesis and are endergonic (consume energy).

ATP: The Energy Currency

Adenosine triphosphate (ATP) acts as an energy intermediary, transferring energy from catabolic to anabolic reactions. ATP is generated during catabolism and consumed during anabolism.

Basic Principles of Chemical Reactions

• Collision Theory: Chemical reactions occur when atoms, ions, or molecules collide with sufficient energy.

• Activation Energy: The minimum energy required for a reaction to occur.

• Reaction Rate: The frequency of effective collisions leading to a reaction.

Enzymes and Catalysis

Enzymes are biological catalysts that speed up chemical reactions without being consumed. They are highly specific for their substrates and are named based on the reactions they catalyze (often ending in -ase).

• Catalyst: Substance that increases reaction rate without being altered.

• Ligase: Joins two molecules together.

• Polymerase: Synthesizes polymers from monomers.

Enzyme Structure

• Apoenzyme: The protein portion of an enzyme (inactive alone).

• Cofactor: Non-protein component required for enzyme activity (can be metal ions or organic molecules).

• Coenzyme: Organic cofactor (e.g., NAD+, FAD).

• Holoenzyme: The complete, active enzyme (apoenzyme plus cofactor).

Mechanism of Enzymatic Action

1. Substrate binds to the enzyme’s active site, forming an enzyme-substrate complex.

2. The enzyme lowers the activation energy, facilitating the reaction.

3. Products are released from the enzyme.

4. The enzyme remains unchanged and can be reused.

Factors Influencing Enzyme Activity

• Temperature: Extreme temperatures can denature enzymes.

• pH: Each enzyme has an optimal pH range.

• Substrate Concentration: Increased substrate increases reaction rate until enzymes are saturated.

• Enzyme Concentration: More enzyme increases reaction rate if substrate is available.

• Inhibitors: Substances that decrease or stop enzyme activity.

Enzyme Inhibition

• Competitive Inhibition: Inhibitor competes with substrate for the active site. Can be overcome by increasing substrate concentration.

• Noncompetitive Inhibition: Inhibitor binds to an allosteric site (not the active site), changing the enzyme’s shape and function. Can be reversible or irreversible.

Ribozymes

Ribozymes are RNA molecules with catalytic activity. They bind to substrates, catalyze reactions (such as cutting and splicing RNA), and are not consumed in the process. Ribozymes play roles in RNA processing and protein synthesis.

Oxidation-Reduction (Redox) Reactions

• Oxidation: Loss of electrons (often with protons, as hydrogen atoms).

• Reduction: Gain of electrons.

• Redox Reaction: Paired oxidation and reduction reactions involving electron transfer.

• Biological oxidations are often dehydrogenations (removal of hydrogen atoms).

ATP Generation: Phosphorylation Mechanisms

• Phosphorylation: Addition of a phosphate group to a molecule.

• ATP is generated by phosphorylation of ADP with energy input.

Type	Description	Example
Substrate-level phosphorylation	Direct transfer of phosphate from a substrate to ADP	ATP production during glycolysis
Oxidative phosphorylation	ATP generated using energy from electrons moving through the electron transport chain (ETC)	ATP production during cellular respiration
Photophosphorylation	Light energy drives ATP production	ATP production during photosynthesis

Metabolic Pathways

Metabolic pathways are series of enzyme-catalyzed reactions that extract energy from nutrients, produce ATP, synthesize cellular components, and process waste products.

• Enable cells to extract and store energy in ATP.

• Build molecules needed for growth and repair.

Glycolysis

• Reactants: Glucose, 2 ATP, 2 NAD+, ADP

• Products: 2 pyruvate, net gain of 2 ATP, 2 NADH

• By-product: Water

Krebs Cycle (Citric Acid Cycle)

• Breaks down Acetyl-CoA, transferring energy to electron carriers.

• For each glucose molecule (cycle runs twice):

  • 4 CO2

  • 6 NADH

  • 2 FADH2

  • 2 ATP

Chemiosmotic Model for ATP Generation

1. Electron transport chain (ETC) uses energy from electrons to pump H+ across a membrane.

2. H+ builds up on one side, creating a proton gradient.

3. H+ flows back through ATP synthase.

4. ATP synthase uses this energy to convert ADP and phosphate into ATP.

Equation:

$\text{ADP} + \text{P}_i \xrightarrow{\text{ATP synthase}} \text{ATP}$

Aerobic vs. Anaerobic Respiration

Feature	Aerobic Respiration	Anaerobic Respiration
Oxygen Requirement	Requires O2	No O2 required
Final Electron Acceptor	O2	Sulfate, nitrate, or other inorganic molecules
ATP Yield	High	Lower
ETC Used?	Yes	Yes

Fermentation

• Breaks down organic molecules to produce a small amount of ATP without using an ETC.

• No O2 required; no Krebs cycle or ETC involved.

• Lactic Acid Fermentation: Glucose is oxidized to pyruvic acid, which is reduced by NADH to lactic acid.

• Alcohol Fermentation: Glucose is oxidized to pyruvic acid, converted to acetaldehyde and CO2, then reduced by NADH to ethanol.

Biochemical Tests for Bacterial Identification

• Fermentation Test: Detects acid production from carbohydrate or protein catabolism (e.g., Escherichia).

• Oxidase Test: Identifies bacteria with cytochrome c oxidase (e.g., Pseudomonas).

• H2S Production: Detects hydrogen sulfide production (e.g., Salmonella).

Photosynthesis

Photosynthesis synthesizes complex organic compounds from simple inorganic substances using light energy. It converts light energy to chemical energy, provides energy-rich molecules for cells, and releases O2 (in oxygenic photosynthesis).

Light-Dependent vs. Light-Independent Reactions

Feature	Light-Dependent Reactions	Light-Independent Reactions
Light Requirement	Directly require light	Do not require light directly
Main Inputs	Light, water	ATP, NADPH, CO2
Main Outputs	ATP, NADPH, O2	G3P (used to make sugars)

Metabolic Diversity Among Organisms

• Phototrophs: Use light energy to drive ATP production.

• Photoautotrophs: Use light energy and CO2 as a carbon source (e.g., plants, cyanobacteria).

• Oxygenic Photoautotrophs: Produce O2 (e.g., cyanobacteria).

• Anoxygenic Photoautotrophs: Do not produce O2.

• Photoheterotrophs: Use light for energy but require organic compounds for carbon; typically anoxygenic.

• Chemoautotrophs: Obtain energy from inorganic chemicals and use CO2 as a carbon source.

• Chemoheterotrophs: Obtain both energy and carbon from organic chemicals.

Nutritional Patterns and ATP Generation

• Organisms are categorized by their energy and carbon sources, as well as their mechanisms for carbohydrate catabolism and ATP generation.

• Major patterns include phototrophy, chemotrophy, autotrophy, and heterotrophy.

Additional info: The above notes expand on the provided learning objectives with definitions, examples, and context for each metabolic process, as would be expected in a microbiology textbook chapter.