Microbial Metabolism: Structured Study Notes for Microbiology Students

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Microbial Metabolism

Overview of Metabolism

Metabolism encompasses all controlled biochemical reactions within a microbe, serving the ultimate function of reproducing the organism. It is divided into two major classes: catabolism and anabolism. These processes are interconnected and essential for cellular function, growth, and reproduction.

Diagram of catabolic and anabolic reactions in a cell

Catabolism: Breakdown of larger molecules into smaller products; releases energy (exergonic).
Anabolism: Synthesis of larger molecules from smaller products; requires energy (endergonic).
ATP: Energy is stored in adenosine triphosphate (ATP), which is used to drive anabolic reactions.
Precursor Metabolites: Small molecules generated by catabolism, used in anabolic pathways.

Eight Elementary Statements Guiding Metabolic Processes

Every cell acquires nutrients.
Metabolism requires energy from light or catabolism of nutrients.
Energy is stored in ATP.
Cells catabolize nutrients to form precursor metabolites.
Precursor metabolites, energy from ATP, and enzymes are used in anabolic reactions.
Enzymes plus ATP form macromolecules.
Cells grow by assembling macromolecules.
Cells reproduce once they have doubled in size.

Catabolism vs. Anabolism

Catabolic and anabolic pathways are distinguished by their direction and energy flow. Catabolic reactions are exergonic, releasing energy, while anabolic reactions are endergonic, requiring energy input.

Catabolic Pathways: Use NAD+ as an electron collector for ATP production.
Anabolic Pathways: Use NADP+ as an electron donor to power biosynthesis.

Oxidation and Reduction Reactions

Oxidation-reduction (redox) reactions involve the transfer of electrons from an electron donor to an electron acceptor. These reactions always occur simultaneously and are fundamental to energy production in cells.

Electron Carriers: NAD+, NADP+, and FAD are key carriers.
Redox Reactions: Essential for cellular respiration and fermentation.

Oxidation-reduction reaction diagram

ATP Production and Energy Storage

Organisms release energy from nutrients and store it in high-energy phosphate bonds of ATP. ATP is produced by phosphorylation, which involves adding inorganic phosphate to ADP. There are three main types of phosphorylation:

Substrate-level phosphorylation
Oxidative phosphorylation
Photophosphorylation

The Roles of Enzymes in Metabolism

Enzyme Structure and Function

Enzymes are organic catalysts that increase the likelihood of biochemical reactions. They are classified based on their mode of action into six categories: hydrolases, isomerases, ligases/polymerases, lyases, oxidoreductases, and transferases.

Apoenzyme: Protein portion, inactive without cofactors.
Cofactors: Nonprotein components (inorganic ions or coenzymes).
Holoenzyme: Active enzyme formed by binding apoenzyme and cofactors.
Ribozymes: RNA molecules with catalytic activity.

Structure of a protein holoenzyme

Enzyme Activity and Regulation

Enzyme activity is influenced by several factors, including temperature, pH, enzyme and substrate concentrations, and the presence of inhibitors. Enzymes lower the activation energy required for reactions, thereby increasing reaction rates.

Activation Energy: Enzymes reduce the energy barrier for reactions.
Induced Fit: Substrate binding induces a change in the enzyme's active site for optimal fit.

Effect of enzymes on activation energy Enzyme fitted to substrate (induced fit model) Process of enzymatic activity

Factors Affecting Enzyme Activity

Enzyme activity is sensitive to environmental conditions. Optimal temperature and pH are required for maximal activity, and substrate concentration affects the rate until saturation is reached.

Temperature: High or low temperatures can denature enzymes.
pH: Extreme pH values can alter enzyme structure and function.
Substrate Concentration: Increased substrate increases activity until saturation.

Effects of temperature, pH, and substrate concentration on enzyme activity Denaturation of protein enzymes

Enzyme Regulation: Activators and Inhibitors

Enzymes can be regulated by activators and inhibitors. Activators bind to allosteric sites, making the active site functional. Inhibitors block enzyme activity and can be competitive or noncompetitive. Feedback inhibition is a common regulatory mechanism.

Allosteric Activation: Cofactor binds to a site other than the active site, activating the enzyme.
Competitive Inhibition: Inhibitor competes with substrate for the active site.
Noncompetitive Inhibition: Inhibitor binds to an allosteric site, altering enzyme function.
Feedback Inhibition: End product inhibits the first committed enzyme in a pathway.

Allosteric activation of enzymes Competitive inhibition of enzyme activity Noncompetitive inhibition at an allosteric site Feedback inhibition diagram

Carbohydrate Catabolism

Glucose Catabolism: Cellular Respiration and Fermentation

Glucose is the primary carbohydrate used by cells for energy. It is catabolized by cellular respiration and fermentation. Cellular respiration involves complete oxidation of glucose, while fermentation is a partial oxidation process.

Cellular Respiration: Pyruvate is converted to acetyl-CoA, enters the citric acid cycle, and electrons are transferred via the electron transport chain (ETC).
Fermentation: Pyruvate is converted to various end products (lactate, ethanol, etc.), regenerating NAD+.

Summary of glucose catabolism

Glycolysis

Glycolysis occurs in the cytoplasm and involves splitting a six-carbon glucose into two three-carbon pyruvic acid molecules. It consists of three stages: energy-investment, lysis, and energy-conserving.

Net Gain: 2 ATP, 2 NADH, and 2 pyruvic acid molecules.
Substrate-level Phosphorylation: Direct transfer of phosphate between substrates.

Glycolysis pathway (EMP) Example of substrate-level phosphorylation

Cellular Respiration: Stages and Key Reactions

Cellular respiration consists of three stages: synthesis of acetyl-CoA, Krebs cycle, and electron transport chain. Each stage is essential for complete oxidation of glucose and maximal ATP production.

Synthesis of Acetyl-CoA: Pyruvic acid is converted to acetyl-CoA, CO2, and NADH.
Krebs Cycle: Acetyl-CoA enters the cycle, producing ATP, NADH, FADH2, and CO2.
Electron Transport Chain: Electrons are passed through carrier molecules, creating a proton gradient for ATP synthesis.

Synthesis of acetyl-CoA Citric acid cycle (Krebs cycle) Electron transport chain arrangement

Chemiosmosis and ATP Synthesis

ATP is generated by chemiosmosis, where protons flow down their electrochemical gradient through ATP synthase, phosphorylating ADP to ATP. This process is called oxidative phosphorylation.

Metabolic Diversity: Alternative Pathways

Some bacteria use alternative pathways for glucose catabolism:

Entner-Doudoroff (ED) Pathway: Produces 1 ATP, 1 NADH, and 1 NADPH.
Pentose Phosphate Pathway: Produces precursor metabolites and NADPH; used for biosynthesis of nucleotides, steroids, and fatty acids.

Fermentation

Fermentation provides an alternative method for regenerating NAD+ when cellular respiration is not possible. It results in partial oxidation of sugars and produces various end products depending on the organism.

Examples of fermentation pathways Fermentation products and organisms

Other Catabolic Pathways

Lipid Catabolism

Lipids are broken down by lipases into glycerol and fatty acids. Glycerol enters glycolysis, while fatty acids undergo beta-oxidation to form acetyl-CoA, which enters the citric acid cycle.

Catabolism of a triglyceride molecule Lipid catabolism pathways

Protein Catabolism

Proteins are degraded by proteases into amino acids, which are deaminated and converted into metabolites that enter the citric acid cycle. Waste products include ammonia and urea.

Protein catabolism pathway

Other Anabolic Pathways

Anabolic Reactions and Amphibolic Pathways

Anabolic reactions synthesize complex molecules using energy from ATP and precursor metabolites. Many anabolic pathways are the reverse of catabolic pathways and are termed amphibolic.

Gluconeogenesis and Biosynthesis

Gluconeogenesis is the synthesis of glucose from non-carbohydrate precursors. It is essential for biosynthesis of complex carbohydrates, polysaccharides, and peptidoglycan.

Role of gluconeogenesis in biosynthesis

Biosynthesis of Lipids, Amino Acids, and Nucleotides

Lipids: Synthesized from acetyl-CoA and glycerol.
Amino Acids: Formed by amination (adding NH3) or transamination (transferring amine group).
Nucleotides: Synthesized from ribose 5-phosphate, ATP, and purine/pyrimidine bases.

Biosynthesis of a triglyceride fat Synthesis of amino acids via amination and transamination Biosynthesis of nucleotides

Integration and Regulation of Metabolic Function

Regulation of Metabolism

Cells regulate metabolism by controlling gene expression and metabolic activity. Enzymes are synthesized only when substrates are available, and feedback inhibition prevents wasteful use of resources. Eukaryotic cells compartmentalize metabolic pathways within organelles.

Control of Gene Expression: Regulates amount and timing of enzyme production.
Control of Metabolic Expression: Regulates activity of enzymes once produced.

Integration of cellular metabolism

Goals of Cellular Metabolism

Energy Production: Catabolism of organic molecules to produce ATP.
Biosynthesis: Anabolism to build complex structures for cell division and function.
Homeostasis and Adaptation: Maintaining internal stability and adapting to environmental changes.
Waste Removal: Recycling or breaking down unnecessary components.
Regulation and Signaling: Modulating cellular signaling and enzymatic activity for metabolic health.

Additional info: Amphibolic pathways are those that can function in both catabolic and anabolic directions, depending on cellular needs. Feedback inhibition is a key regulatory mechanism in metabolic pathways, ensuring efficient use of resources.