Microbial Metabolism: Structured Study Notes for Microbiology Students

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Microbial Metabolism

Overview of Metabolism

Metabolism encompasses all chemical reactions occurring within a living organism, divided into two main categories: catabolism and anabolism. These processes are essential for cellular function, growth, and energy management.

Catabolism: The breakdown of complex organic molecules into simpler ones, typically via hydrolysis. Catabolic reactions release energy, which is used to fuel anabolic processes.
Anabolism: The synthesis of complex molecules from simpler ones, usually via dehydration synthesis. Anabolic reactions require energy, often supplied by ATP.
Metabolic Pathways: Sequences of enzymatically catalyzed reactions, where the product of one reaction serves as the substrate for the next.

Hydrolysis of covalent bonds in catabolism Catabolic and anabolic pathways linked by energy Dehydration synthesis in anabolism

ATP: The Energy Currency

ATP (adenosine triphosphate) is the primary molecule for energy transfer in cells. It couples catabolic and anabolic reactions, storing energy released from catabolism and providing energy for anabolism.

ATP Hydrolysis: The hydrolysis of ATP's terminal phosphate group releases energy for cellular work.
Role in Metabolism: Catabolic reactions generate ATP, which is then used in anabolic reactions.

Role of ATP in coupling anabolic and catabolic reactions Catabolic and anabolic pathways linked by energy Energy released when ATP is hydrolyzed

Enzymes and Metabolic Pathways

Enzymes are biological catalysts that speed up chemical reactions without being consumed. They are highly specific, acting on particular substrates, and are encoded by genes.

Enzyme Structure: Enzymes consist of an apoenzyme (protein portion) and may require a cofactor (inorganic ion) or coenzyme (organic molecule, e.g., NAD+, FAD).
Enzyme Function: Enzymes lower the activation energy required for reactions, increasing reaction rates.
Enzyme Specificity: Each enzyme acts on a specific substrate due to the unique shape of its active site.

Metabolic pathway catalyzed by enzymes Collision theory requirements Activation energy with and without enzyme Enzyme catalyzed vs normal reaction Enzyme function cycle Enzyme and substrate binding Active site and substrate specificity

Enzyme Classification and Naming

Enzymes are classified based on the type of reaction they catalyze. Their names typically end in "-ase."

Oxidoreductases: Catalyze oxidation-reduction reactions (e.g., lactate dehydrogenase).
Ligases: Join two molecules using energy (e.g., DNA ligase).
Hydrolases: Catalyze hydrolysis reactions (e.g., sucrase).

Table of enzyme classes and examples

Factors Influencing Enzyme Activity

Enzyme activity is affected by temperature, pH, substrate concentration, and inhibitors.

Temperature: Enzymes have an optimal temperature; activity decreases below or above this point due to denaturation.
pH: Each enzyme has an optimal pH; extreme pH values can denature the enzyme.
Inhibitors: Competitive inhibitors bind to the active site, while noncompetitive inhibitors bind elsewhere, altering the enzyme's shape.

Active vs denatured protein Enzyme activity vs temperature Enzyme activity vs pH Competitive and noncompetitive inhibition Competitive inhibitor binding

Enzyme Inhibition and Regulation

Competitive Inhibition: Inhibitor competes with substrate for the active site.
Noncompetitive (Allosteric) Inhibition: Inhibitor binds to a regulatory site, changing the enzyme's shape and function.
Feedback Inhibition: End-product of a pathway inhibits an earlier enzyme, regulating the pathway's output.

Competitive and noncompetitive inhibition Sulfa drug and PABA structures Sulfa drugs inhibit folate synthesis Folate biosynthesis pathway Feedback inhibition in metabolic pathway

Oxidation-Reduction (Redox) Reactions

Redox reactions are fundamental to energy production in cells.

Oxidation: Loss of electrons or hydrogen atoms.
Reduction: Gain of electrons or hydrogen atoms.
Redox Pair: One molecule is oxidized while another is reduced.

Oxidation-reduction reaction Biological oxidation example NAD+ and NADH structure

Electron Carriers

NAD+ and FAD: Coenzymes that shuttle electrons during metabolic reactions, especially in cellular respiration.

Carbohydrate Catabolism: Pathways and Energy Production

Cells catabolize carbohydrates via three main pathways: aerobic respiration, anaerobic respiration, and fermentation.

Aerobic Respiration: Requires oxygen; yields the most ATP per glucose molecule.
Anaerobic Respiration: Uses inorganic molecules (e.g., nitrate, sulfate) as final electron acceptors; yields less ATP.
Fermentation: Uses organic molecules as final electron acceptors; yields the least ATP and produces diverse end products (e.g., lactic acid, ethanol).

Overview of aerobic, anaerobic, and fermentation pathways Glucose structure

Steps of Aerobic Respiration

Glycolysis: Oxidation of glucose to pyruvic acid; produces ATP and NADH.
Krebs Cycle: Oxidation of acetyl CoA; produces CO2, ATP, NADH, and FADH2.
Oxidative Phosphorylation: Electron transport chain (ETC) and chemiosmosis; generates most ATP.

Krebs cycle overview Electron transport chain and chemiosmosis Electron transport chain system Chemiosmosis and ATP synthesis Electron transport chain flow Cell respiration formula Respiration vs fermentation pathways Flow of electrons and ATP production

Aerobic vs. Anaerobic Respiration

Aerobic: Oxygen is the final electron acceptor; yields 36-38 ATP per glucose.
Anaerobic: Inorganic molecules (e.g., nitrate, sulfate) are final electron acceptors; yields 1-2 ATP per glucose.
Growth Rate: Anaerobes typically grow slower than aerobes due to lower energy yield.

Anaerobic respiration with nitrate as electron acceptor

Fermentation

Fermentation is an anaerobic process that does not use the Krebs cycle or ETC. It yields low ATP and produces various end products, such as lactic acid and ethanol.

Final Electron Acceptor: Organic molecule.
Energy Yield: 2 ATP per glucose.
Examples: Lactic acid fermentation (muscle cells, bacteria), alcoholic fermentation (yeast).

Fermentation pathway and products Sugar + yeast = alcohol and CO2

Summary Table: Metabolic Pathways

Pathway	Final Electron Acceptor	ATP Yield	Key Products
Aerobic Respiration	O2	36-38	CO2, H2O, ATP
Anaerobic Respiration	Inorganic (NO3-, SO42-)	1-2	ATP, variable products
Fermentation	Organic molecule	2	Lactic acid, ethanol, CO2

Key Terms and Concepts

Metabolism: Sum of all chemical reactions in a cell.
Catabolism: Breakdown of molecules; releases energy.
Anabolism: Synthesis of molecules; requires energy.
Enzyme: Protein catalyst; specific for substrate.
ATP: Energy currency of the cell.
Redox Reaction: Paired oxidation and reduction.
Electron Carrier: Molecule (e.g., NAD+, FAD) that transfers electrons.
Fermentation: Anaerobic process yielding diverse products.

Equations and Formulas

ATP Hydrolysis:
Cellular Respiration:

Example: Sulfa Drugs as Competitive Inhibitors

Sulfa drugs inhibit bacterial folate synthesis by competing with PABA for the active site of DHPS, an enzyme not present in humans. This selective inhibition is a key mechanism in antimicrobial therapy. Sulfa drug and PABA structures Sulfa drugs inhibit folate synthesis Folate biosynthesis pathway

Example: Lactic Acid and Ethanol Fermentation

Lactic Acid Fermentation: Pyruvic acid is reduced to lactic acid; occurs in muscle cells and certain bacteria.
Alcoholic Fermentation: Pyruvic acid is converted to ethanol and CO2; occurs in yeast.

Sugar + yeast = alcohol and CO2

Additional info:

Metabolic regulation is crucial for cellular efficiency and survival.
Enzyme activity can be modulated by genetic and environmental factors.
Fermentation is important in food production and biotechnology.