Ch 5 Microbial Metabolism: Study Guide and Key Concepts

Ch 5 - Microbial Metabolism

Metabolism, Anabolism, and Catabolism

Metabolism encompasses all chemical reactions within a cell, divided into two main processes: anabolism and catabolism.

• Metabolism: The sum of all biochemical reactions in an organism, including both energy-releasing and energy-consuming processes.

• Anabolism: Biosynthetic reactions that build complex molecules from simpler ones, requiring energy input (endergonic).

• Catabolism: Degradative reactions that break down complex molecules into simpler ones, releasing energy (exergonic).

• Example: Glycolysis is a catabolic pathway; protein synthesis is anabolic.

Oxidation and Reduction Reactions

Oxidation-reduction (redox) reactions are central to energy transfer in cells.

• Oxidation: Loss of electrons from a molecule.

• Reduction: Gain of electrons by a molecule.

• Redox Pair: Oxidation and reduction always occur together.

• Example: NAD+ is reduced to NADH during glycolysis.

ATP Phosphorylation Mechanisms

Cells generate ATP through three main phosphorylation methods:

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

• Oxidative phosphorylation: ATP synthesis powered by electron transport and chemiosmosis.

• Photophosphorylation: ATP generation using light energy in photosynthetic organisms.

Types of Enzymes

Enzymes are classified based on the reactions they catalyze.

Enzyme Class	Activity	Example
Oxidoreductases	Oxidation-reduction reactions	Lactate dehydrogenase
Transferases	Transfer of functional groups	Hexokinase
Hydrolases	Hydrolysis reactions	Lipase
Lyases	Removal of groups without hydrolysis	Aldolase
Isomerases	Isomerization	Phosphoglucose isomerase
Ligases	Joining of molecules using ATP	DNA ligase

Enzyme Structure and Function

Enzymes are biological catalysts with specific structures and components.

• Holoenzyme: Complete, active enzyme with its cofactor.

• Apoenzyme: Protein portion of an enzyme, inactive without cofactor.

• Cofactor: Non-protein component (metal ion or organic molecule) required for enzyme activity.

• Coenzyme: Organic cofactor, often derived from vitamins (e.g., NAD+).

• Active site: Region on enzyme where substrate binds.

• Substrate: Molecule upon which an enzyme acts.

• Protein vs. RNA enzymes: Most enzymes are proteins; some RNA molecules (ribozymes) also have catalytic activity.

Enzyme Activity and Regulation

Enzyme activity is influenced by several factors:

• Temperature: Each enzyme has an optimal temperature; high or low temperatures can denature or inactivate enzymes.

• pH: Enzymes have optimal pH ranges; deviations can alter enzyme structure and function.

• Substrate concentration: Increased substrate increases reaction rate until saturation is reached.

• Competitive inhibition: Inhibitor competes with substrate for active site.

• Noncompetitive inhibition: Inhibitor binds to allosteric site, changing enzyme shape and reducing activity.

Aerobic Glucose Catabolism

Glucose catabolism in the presence of oxygen occurs in three main stages:

• Glycolysis: Converts glucose to pyruvate, producing ATP and NADH.

• Citric Acid Cycle (Krebs Cycle): Oxidizes acetyl-CoA to CO2, generating NADH, FADH2, and ATP.

• Electron Transport Chain (ETC): Transfers electrons from NADH/FADH2 to oxygen, producing ATP via oxidative phosphorylation.

• Net energy yield: Up to 38 ATP per glucose in prokaryotes.

Roles of Acetyl-CoA, Citric Acid Cycle, and Electron Transport

These components are central to carbohydrate catabolism:

• Acetyl-CoA: Formed from pyruvate; enters the citric acid cycle.

• Citric Acid Cycle: Completes oxidation of glucose derivatives, producing electron carriers.

• Electron Transport: Uses electrons from NADH/FADH2 to generate ATP.

Aerobic vs. Anaerobic Respiration

Electron transport differs based on the final electron acceptor:

• Aerobic respiration: Oxygen is the final electron acceptor, forming water.

• Anaerobic respiration: Inorganic molecules other than oxygen (e.g., nitrate, sulfate) serve as final electron acceptors.

Chemiosmosis and Oxidative Phosphorylation

Chemiosmosis is the process by which ATP is synthesized using the energy of a proton gradient across a membrane.

• Protons are pumped across the membrane by the ETC, creating a proton motive force.

• ATP synthase uses this gradient to convert ADP to ATP.

• Equation:

$\text{ADP} + \text{P}_i + \text{energy} \rightarrow \text{ATP}$

Metabolic Diversity in Bacteria

Bacteria exhibit a wide range of metabolic capabilities:

• Obligate aerobes: Require oxygen for respiration.

• Obligate anaerobes: Cannot tolerate oxygen; use alternative electron acceptors.

• Facultative anaerobes: Can switch between aerobic and anaerobic metabolism.

• Photoautotrophs: Use light energy and CO2 as a carbon source.

• Chemolithotrophs: Obtain energy from inorganic compounds.

Fermentation

Fermentation is an anaerobic process that allows ATP production without an electron transport chain.

• Definition: Partial oxidation of sugar to release energy using an organic molecule as the final electron acceptor.

• Contrast with respiration: Fermentation yields less ATP and does not use an ETC.

• Examples of end-products: Lactic acid, ethanol, and propionic acid.

• Identification: Fermentation end-products are used in biochemical tests to identify bacteria.

Biochemical Tests for Bacterial Identification

Biochemical tests detect metabolic enzymes and products to differentiate bacterial species.

• Examples: Catalase test, oxidase test, fermentation of specific sugars.

• Results help identify unknown bacteria in clinical and environmental samples.

Lipid and Protein Catabolism

Microbes can catabolize lipids and proteins for energy and metabolites.

• Lipid catabolism: Lipases hydrolyze triglycerides to glycerol and fatty acids; fatty acids enter β-oxidation to form acetyl-CoA.

• Protein catabolism: Proteases break proteins into amino acids; deamination removes amino groups, allowing entry into central metabolic pathways.

Photosynthesis

Photosynthesis is the process by which light energy is converted to chemical energy.

• Definition: Conversion of light energy, CO2, and water into organic compounds and oxygen (in oxygenic photosynthesis).

Light-Dependent and Light-Independent Reactions

Photosynthesis consists of two main stages:

• Light-dependent reactions: Capture light energy to produce ATP and NADPH.

• Light-independent reactions (Calvin-Benson cycle): Use ATP and NADPH to fix CO2 into organic molecules.

Calvin-Benson Cycle

The Calvin-Benson cycle is the main pathway for carbon fixation in photosynthetic organisms.

• Reactants: CO2, ATP, NADPH.

• Products: Glyceraldehyde-3-phosphate (G3P), which can be used to form glucose and other carbohydrates.

Amphibolic Reactions

Amphibolic reactions function in both catabolic and anabolic pathways.

• Definition: Metabolic pathways that can be used for both breakdown and synthesis of molecules.

• Example: The citric acid cycle provides intermediates for both energy production and biosynthesis.

Biosynthesis of Macromolecules

Cells synthesize essential macromolecules through anabolic pathways:

• Carbohydrates: Synthesized from intermediates like G3P and fructose-6-phosphate.

• Lipids: Formed from acetyl-CoA and glycerol-3-phosphate.

• Amino acids: Synthesized from intermediates of glycolysis and the citric acid cycle.

• Nucleotides: Built from ribose-5-phosphate, amino acids, and other precursors.

Interrelationships Between Catabolism and Anabolism

Catabolic and anabolic pathways are interconnected through shared intermediates and energy transfer.

• ATP produced by catabolism powers anabolic reactions.

• Many intermediates serve as precursors for biosynthesis.

Regulation of Metabolic Activity

Cells regulate metabolism to conserve energy and resources.

• Enzyme regulation: Allosteric regulation, feedback inhibition, and covalent modification.

• Gene expression: Synthesis of enzymes is controlled at the transcriptional and translational levels.