Microbial Metabolism: Study Notes for Chapter 8

Microbial Metabolism

Introduction to Metabolism

Metabolism encompasses the sum of all chemical reactions that occur within a cell. These reactions are responsible for both the buildup and breakdown of nutrients, providing energy and creating substances essential for life.

• Metabolic pathways are sequences of chemical reactions, each catalyzed by a specific enzyme.

• Enzymes and ATP (adenosine triphosphate) are crucial for metabolic processes.

Catabolism and Anabolism

Metabolism is divided into two complementary processes: catabolism and anabolism. Both are necessary for maintaining cellular energy balance.

• Catabolism: The breakdown of large molecules into smaller ones, releasing energy. Example: Glycolysis (breaking down glucose).

• Anabolism: The synthesis of complex molecules from simpler ones, requiring energy. Example: Protein synthesis from amino acids.

• Catabolic pathways are generally hydrolytic (use water), exergonic (release energy), and exothermic (release heat).

• Anabolic pathways are generally dehydration synthesis reactions (release water), endergonic (consume energy), and endothermic (absorb heat).

Energy Flow: About 40% of the energy stored in nutrient molecules is captured as ATP; the rest is lost as heat.

ATP: The Energy Currency

ATP (Adenosine Triphosphate) is the primary energy carrier in cells. It stores energy in high-energy phosphate bonds, which can be released to drive cellular work.

• ATP is regenerated from ADP (adenosine diphosphate) and inorganic phosphate ($Pi$) through phosphorylation.

• The ATP-ADP cycle allows cells to efficiently store and use energy.

Equation:

• $\text{ADP} + \text{Pi} + \text{Energy} \rightarrow \text{ATP}$

Types of Phosphorylation

ATP is generated by three main types of phosphorylation:

• Substrate-level phosphorylation: Direct transfer of a phosphate group from a substrate to ADP.

• Oxidative phosphorylation: Energy from electron transport chain is used to add $Pi$ to ADP (involves chemiosmosis).

• Photophosphorylation: Light energy is used to generate ATP in photosynthetic cells.

Classification of Organisms by Energy and Carbon Source

Microorganisms are classified based on their energy and carbon sources:

Classification	Energy Source	Carbon Source	Examples
Photoautotrophs	Light	CO2	Plants, algae, cyanobacteria
Chemoautotrophs	Chemicals	CO2	Nitrifying bacteria
Photoheterotrophs	Light	Organic compounds	Purple non-sulfur bacteria
Chemoheterotrophs	Chemicals	Organic compounds	Most animals, fungi, protozoa, bacteria

Oxidation-Reduction (Redox) Reactions

Cells extract energy from nutrients via oxidation-reduction reactions (redox), where electrons are transferred from one molecule to another.

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

• Reduction: Gain of electrons.

• Electron carriers such as NAD+, NADP+, and FAD shuttle electrons in metabolic pathways.

Equation:

• $\text{NAD}^+ + 2e^- + 2H^+ \rightarrow \text{NADH} + H^+$

Enzymes: Biological Catalysts

Enzymes are proteins that speed up chemical reactions by lowering activation energy, without being consumed in the process.

• Each enzyme is specific to a substrate and reaction.

• Enzymes can be regulated by environmental factors (temperature, pH, substrate concentration) and inhibitors.

• Some enzymes require cofactors (inorganic ions) or coenzymes (organic molecules, often derived from vitamins) for activity.

Enzyme Inhibition

• Competitive inhibitors: Bind to the active site, blocking substrate access.

• Non-competitive (allosteric) inhibitors: Bind elsewhere, altering enzyme shape and function.

• Feedback inhibition: End-product of a pathway inhibits an earlier enzyme, regulating pathway activity.

Carbohydrate Catabolism

Microbes obtain energy by breaking down carbohydrates, primarily glucose, through respiration and fermentation.

• Respiration: Complete oxidation of glucose, yielding high ATP (aerobic or anaerobic).

• Fermentation: Partial breakdown of glucose, yielding less ATP.

Glycolysis

• Occurs in the cytoplasm; does not require oxygen.

• Converts glucose to pyruvate, producing ATP and NADH.

• Pathways: Embden-Meyerhof-Parnas (EMP), Pentose Phosphate Pathway (PPP), Entner-Doudoroff (ED).

EMP Pathway Equation:

• $\text{Glucose} + 2\text{ATP} + 2\text{NAD}^+ \rightarrow 2\text{Pyruvate} + 2\text{NADH} + 4\text{ATP}$

Krebs Cycle (Citric Acid Cycle)

• Occurs in cytoplasm (prokaryotes) or mitochondria (eukaryotes).

• Oxidizes acetyl-CoA to CO2, generating NADH, FADH2, and ATP.

• Amphibolic: provides intermediates for biosynthesis.

Electron Transport Chain (ETC) and Chemiosmosis

• Located in plasma membrane (prokaryotes) or inner mitochondrial membrane (eukaryotes).

• Electrons from NADH and FADH2 pass through carrier proteins, pumping protons to create a gradient.

• ATP synthase uses proton motive force to generate ATP (oxidative phosphorylation).

Fermentation

• Occurs in cytoplasm; does not require oxygen.

• ATP produced only during glycolysis.

• End-products (e.g., lactic acid, ethanol) are useful for identifying bacteria.

Lipid and Protein Catabolism

• Lipases hydrolyze fats into glycerol and fatty acids, which enter the Krebs cycle.

• Proteases and peptidases break down proteins into amino acids, which are deaminated and enter metabolic pathways.

Photosynthesis

Photosynthesis is an anabolic process converting light energy into chemical energy, producing glucose from CO2 and H2O.

• Light-dependent reactions generate ATP and NADPH.

• Light-independent reactions (Calvin-Benson cycle) fix CO2 into sugars.

Equation:

• $6\text{CO}_2 + 6\text{H}_2\text{O} + \text{light energy} \rightarrow \text{C}_6\text{H}_{12}\text{O}_6 + 6\text{O}_2$

Summary Table: Respiration vs. Fermentation

Process	ATP Yield	Final Electron Acceptor	Pathways Used
Respiration (Aerobic)	High (36-38 ATP)	O2	Glycolysis, Krebs, ETC
Respiration (Anaerobic)	Lower	Nitrate, sulfate, etc.	Glycolysis, partial Krebs, ETC
Fermentation	Low (2 ATP)	Organic molecule	Glycolysis only

Additional info: These notes expand on fragmented points and diagrams, providing full academic context and definitions for all major concepts in microbial metabolism.