Microbial Metabolism: Foundations and Pathways

CH 5: Microbial Metabolism

Introduction to Microbial Metabolism

Microbial metabolism encompasses all the chemical reactions that occur within a microorganism, enabling it to grow, reproduce, and respond to its environment. These reactions are essential for converting nutrients from the environment into energy and cellular components.

• Growth Medium: Provides essential nutrients (e.g., carbon, nitrogen, minerals) for microbial growth, such as Escherichia coli cultures.

• Metabolic Reactions: The sum of all chemical processes, including catabolism (breakdown of molecules) and anabolism (synthesis of molecules).

• Key Question: What fuels microbial growth? The answer lies in metabolic reactions that extract and store energy.

Learning Objectives

• Define metabolism and distinguish between catabolism and anabolism.

• Describe the role of ATP as an energy intermediary.

• Explain oxidation-reduction (redox) reactions.

• Identify and provide examples of three types of phosphorylation reactions that generate ATP.

• Explain the function of metabolic pathways.

• Describe glycolysis and its chemical reactions.

• Identify the functions of the pentose phosphate and Entner-Doudoroff pathways.

• List the products of the Krebs cycle.

• Describe the chemiosmotic model for ATP generation.

• Compare aerobic and anaerobic respiration.

• Describe fermentation and its products.

• Compare cyclic and noncyclic photophosphorylation.

• Compare light-dependent and light-independent reactions of photosynthesis.

• Compare oxidative phosphorylation and photophosphorylation.

• Summarize energy production in cells.

• Categorize nutritional patterns among organisms based on carbon source and ATP generation mechanisms.

Metabolism

Definition and Organization

Metabolism is the sum total of all chemical reactions in a cell. These reactions are enzyme-catalyzed and organized into regulated pathways, where the product of one reaction becomes the substrate for the next.

• Catabolic Reactions: Energy-releasing (exergonic); break down complex molecules into simpler ones.

• Anabolic Reactions: Energy-requiring (endergonic); build complex molecules from simpler ones.

• Pathway Example: A →(Enzyme 1)→ B →(Enzyme 2)→ C →(Enzyme 3)→ D (Product)

ATP: The Energy Currency

Structure and Function

Adenosine triphosphate (ATP) is the primary energy carrier in cells, performing much of the cellular "work." It consists of adenine, ribose, and three phosphate groups.

• ATP Hydrolysis: Releases energy (catabolic process).

• ATP Formation: Requires energy input (anabolic process).

Chemical Reactions Involving ATP/ADP:

• Hydrolysis (energy-releasing): $\mathrm{ATP} + \mathrm{H}_2\mathrm{O} \rightarrow \mathrm{ADP} + \mathrm{P}_i + \mathrm{H}^+$

• Formation (energy-requiring): $\mathrm{ADP} + \mathrm{P}_i + \mathrm{H}^+ \rightarrow \mathrm{ATP} + \mathrm{H}_2\mathrm{O}$

Role of ATP: Couples catabolic and anabolic reactions, storing energy from catabolism and providing it for cellular work.

Catabolism vs. Anabolism

Key Differences

• Catabolism: Breaks down macromolecules (e.g., carbohydrates, lipids, proteins) into simpler molecules, releasing energy.

• Anabolism: Builds up macromolecules from simpler molecules, consuming energy.

Example: Glycolysis (catabolic) breaks down glucose to pyruvate, while protein synthesis (anabolic) assembles amino acids into proteins.

Redox Reactions in Metabolism

Oxidation-Reduction (Redox) Reactions

Redox reactions involve the transfer of electrons between molecules, fundamental to energy extraction in cells.

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

• Reduction: Gain of electrons.

• Electron Carriers: Molecules like NAD+ and FAD capture and transfer electrons.

Example Equations:

• $\mathrm{NAD}^+ + 2\mathrm{H} \rightarrow \mathrm{NADH} + \mathrm{H}^+$

• $\mathrm{FAD} + 2\mathrm{H} \rightarrow \mathrm{FADH}_2$

ATP Generation Mechanisms

Phosphorylation Types

• Substrate-Level Phosphorylation: Direct transfer of a phosphate group to ADP from a phosphorylated intermediate. Occurs in glycolysis and fermentation.

• Oxidative Phosphorylation: Involves the electron transport chain and chemiosmosis, using a proton gradient to drive ATP synthesis. Occurs in respiration.

• Photophosphorylation: Light-driven ATP synthesis in photosynthetic organisms.

Carbohydrate Catabolism

Overview

Microorganisms primarily oxidize carbohydrates (e.g., glucose) for energy, using two main processes:

• Respiration: Complete oxidation of glucose via glycolysis, Krebs cycle, and electron transport chain. Can be aerobic (O2 as terminal electron acceptor) or anaerobic (other acceptors).

• Fermentation: Incomplete oxidation of glucose, yielding organic acids or alcohols as end products.

Glycolysis (Embden-Meyerhof Pathway)

Glycolysis is the oxidation of glucose to pyruvate, generating ATP and NADH.

• Phases: Energy investment and energy harvest.

• Net Gain: 2 ATP (substrate-level phosphorylation), 2 NADH, 2 pyruvate per glucose.

• Anaerobic Process: Does not require oxygen.

Alternative Pathways

• Pentose Phosphate Pathway: Generates NADPH and pentoses for biosynthesis.

• Entner-Doudoroff Pathway: Found in some Gram-negative bacteria; yields ATP and NADPH.

Krebs Cycle (Citric Acid Cycle)

Completes the oxidation of glucose derivatives, producing NADH, FADH2, and ATP.

• Acetyl-CoA Formation: Pyruvate is converted to acetyl-CoA, releasing CO2 and generating NADH.

• Cycle Outputs (per glucose): 6 NADH, 2 FADH2, 2 ATP, 4 CO2.

Electron Transport Chain (ETC) and Chemiosmosis

The ETC transfers electrons from NADH and FADH2 to a terminal electron acceptor, generating a proton gradient used to synthesize ATP via ATP synthase (chemiosmosis).

• Components: Flavoproteins, cytochromes, ubiquinones.

• Proton Motive Force: Electrochemical gradient of protons across the membrane.

• ATP Yield: Up to 38 ATP per glucose in aerobic respiration.

Aerobic vs. Anaerobic Respiration

• Aerobic: O2 is the final electron acceptor; higher ATP yield.

• Anaerobic: Other inorganic molecules (e.g., NO3-, SO42-) serve as acceptors; lower ATP yield.

Fermentation

Process and Products

Fermentation is an anaerobic process that recycles NADH by transferring electrons to organic molecules, producing acids or alcohols.

• Lactic Acid Fermentation: Pyruvate is reduced to lactic acid (e.g., Lactobacillus).

• Alcoholic Fermentation: Pyruvate is converted to ethanol and CO2 (e.g., yeasts).

Photosynthesis

Overview

Photosynthetic microbes convert light energy into chemical energy, using it to fix CO2 into organic compounds.

• Oxygenic Photosynthesis: Uses H2O as electron donor, producing O2 (e.g., cyanobacteria, algae, plants).

• Anoxygenic Photosynthesis: Uses other electron donors (e.g., H2S); does not produce O2 (e.g., purple and green sulfur bacteria).

Light-Dependent and Light-Independent Reactions

• Light-Dependent Reactions: Capture light energy to produce ATP and NADPH.

• Light-Independent Reactions (Calvin Cycle): Use ATP and NADPH to fix CO2 into sugars.

Photophosphorylation

• Cyclic Photophosphorylation: Electrons cycle within photosystem I, generating ATP only.

• Noncyclic Photophosphorylation: Electrons flow from water through photosystems II and I to NADP+, producing ATP, NADPH, and O2.

Classification of Microbial Metabolic Types

Based on Energy and Carbon Sources

Energy Source	Carbon Source	Type
Chemical (organic/inorganic)	CO2	Chemoautotroph
Chemical (organic/inorganic)	Organic compounds	Chemoheterotroph
Light	CO2	Photoautotroph
Light	Organic compounds	Photoheterotroph

Summary Table: ATP Production Pathways

Process	Electron Donor	Terminal Electron Acceptor	ATP Generation	Products
Fermentation	Organic molecule (e.g., glucose)	Organic molecule (internal)	Substrate-level phosphorylation	Acids, alcohols, CO2
Cellular Respiration (Aerobic)	Organic or inorganic	O2	Oxidative phosphorylation	CO2, H2O, ATP
Cellular Respiration (Anaerobic)	Organic or inorganic	NO3-, SO42-, etc.	Oxidative phosphorylation	CO2, reduced acceptors, ATP
Photosynthesis	H2O (oxygenic) or H2S (anoxygenic)	NADP+	Photophosphorylation	O2 (oxygenic), sugars, ATP, NADPH

Summary

• Metabolism includes all enzyme-catalyzed reactions, both exergonic (catabolic) and endergonic (anabolic).

• Redox reactions and electron carriers (NAD+, FAD) are central to energy extraction.

• ATP is generated by substrate-level, oxidative, and photophosphorylation.

• Glycolysis, Krebs cycle, and electron transport chain are key pathways in respiration.

• Fermentation and photosynthesis provide alternative energy-generating strategies.

• Microbes are classified by their energy and carbon sources, reflecting metabolic diversity.