Microbial Metabolism: Chapter 8

• Chapter 8 covers introduction to microbial metabolism

Microbial Growth

• Microbial growth depends on available resources/energy and suitable environmental conditions
• Assessment includes mechanics of microbial growth
• Chemoheterotrophs like E. coli require a source of energy, carbon, hydrogen, oxygen, nitrogen, and phosphorus, with approximately 5000 compounds and 4000 proteins

Metabolism Overview

• Metabolism is the sum of all chemical and physical workings of a cell
• It involves two types of chemical reactions called catabolism and anabolism

Catabolism

• Catabolism involves degradative reactions
• Breaks down larger molecules into smaller molecules
• Releases energy in the process

Anabolism

• Anabolism involves biosynthesis reactions
• Forms larger macromolecules from smaller molecules
• Requires energy input

Life's Work and Energy

• Life necessitates work in the form of chemical synthesis, transport processes, and mechanical actions like cell motility
• Energy is defined as the capacity to do work

Thermodynamics

• Thermodynamics is fundamentally the study of energy transformations

Laws of Thermodynamics

• The First Law of Thermodynamics states energy can neither be created nor destroyed, only redistributed within or between systems
• The Second Law of Thermodynamics addresses entropy (disorder) in a system
• Physical and chemical processes proceed in a way that increases the disorder of the universe to the maximum extent possible

Cellular Bioenergetics and ATP

• ATP is a central molecule in cellular energetics
• Anabolic processes require ATP
• Catabolic processes release energy
• Exergonic reactions increase entropy, indicated by a negative change in Gibbs free energy (-ΔG)

Role of ATP in Metabolism

• ATP's exergonic breakdown is coupled with endergonic reactions to make them more thermodynamically favorable
• The hydrolysis of ATP to ADP + Pi releases energy: ATP + H2O → ADP + Pi + H+; ΔG°' = -7.3 kcal/mol

Metabolic Pathways and ATP

• Aerobic respiration, anaerobic respiration, and fermentation are metabolic pathways starting with glucose
• ATP is the "energy currency" which drives chemical, transport, and mechanical work via anabolism

Enzyme Structure and Classification

• Enzymes increase a reaction's rate without being permanently altered
• They have high specificity for the reaction they catalyze and the molecules they act on
• Substrates are reacting molecules, and products are the substances formed by the reaction
• Some enzymes consist solely of one or more polypeptides, while others are composed of polypeptides and nonprotein components
• The reaction scheme for this is E + S → ES → E + P, where E is enzyme, S is substrate, ES is enzyme-substrate complex, and P is product

Enzyme Types

• Simple enzymes consist of protein alone
• Conjugated enzymes (holoenzymes) contain protein and nonprotein molecules
• Apoenzyme is the protein portion of a conjugated enzyme
• Cofactors are the nonprotein portion, comprised of inorganic elements (metal ions) or organic molecules (coenzymes)

Enzyme Mechanisms

• Enzymes lower the activation energy (Ea), speeding up reactions
• Enzymes lower Ea by increasing substrate concentrations at the active site and orienting substrates to form transition-state complexes
• The induced fit model explains enzyme-substrate interaction

Enzyme Interactions

• Enzymes lower Ea by increasing substrate concentrations at the active site and orienting substrates to form transition-state complexes
• The induced fit model explains enzyme-substrate interaction

Redox Reactions

• Redox reactions are fundamental in metabolism because they involve oxidation-reduction reactions with electron transfers
• Electron carriers transfer electrons from an electron donor to an electron acceptor

Electron Transfer

• Electron transfer can result in energy release, which is then conserved and used to form ATP
• The more electrons a molecule has, the more energy-rich it is

Covalent Bonds

• Shared electrons in covalent bonds are rearranged during chemical reactions
• Electrons lose potential energy as they move closer to electronegative atoms

Redox Potential

• The greater the difference between the redox potential (E0) of the donor and acceptor, the more negative the Gibbs free energy change (ΔG°') is
• Negative Gibbs free energy indicates a spontaneous reaction

Role of Coenzymes

• Coenzymes like NAD, FAD, and coenzyme A repeatedly accept and release electrons, facilitating redox energy transfer
• These compounds act as electron carriers in the respiratory chain

ATP Synthesis

• ATP is synthesized through three mechanisms: substrate-level phosphorylation, oxidative phosphorylation, and photophosphorylation

Mechanisms of ATP Synthesis

• Substrate-level phosphorylation transfers a phosphate group from a phosphorylated compound to ADP
• Oxidative phosphorylation is a series of redox reactions in the respiratory pathway
• Photophosphorylation occurs in photosynthetic organisms and utilizes sunlight

Bioenergetics Pathways

• Bioenergetics is the study of cellular energy release mechanisms
• Primary catabolism of fuels such as glucose proceeds through glycolysis, the Krebs cycle, and the respiratory chain

Metabolic Strategies

• Nutrient processing involves three catabolic pathways that convert glucose to CO2 and releases energy: aerobic respiration, anaerobic respiration, and fermentation

ATP in different modes

• Aerobic respiration uses glycolysis, the Krebs cycle, and a respiratory chain, with molecular oxygen as the final electron acceptor
• Anaerobic respiration is similar to aerobic respiration but molecular oxygen is not the final electron acceptor
• Fermentation uses glycolysis, with organic compounds as the final electron acceptors, and yields less ATP

Glycolysis and Pyruvate

• Glycolysis, which takes place in both eukaryotic and prokaryotic cells yields pyruvic acid
• Pyruvic acid is further processed depending on available metabolic strategies

Fate of Pyruvate

• Pyruvate, generated from glycolysis, can undergo various pathways including synthesis of amino acids, sugars, and fat metabolites within anabolic pathways
• Pyruvate can also be used during the respiration stage
• Also Pyruvate can be used in fermentation

Amphibolic Pathways

• Amphibolic pathways integrate catabolism and anabolism for efficient metabolism
• For example, the Krebs cycle serves both energy production and biosynthesis

Fermentation Specifics

• Fermentation is the incomplete oxidation of glucose or other carbohydrates in the absence of oxygen, using organic compounds as terminal electron acceptors and yields a small amount of ATP
• Key processes include ethyl alcohol production by yeasts and the formation of acids and gas by bacteria on pyruvic acid

Alcoholic and Acidic Fermentation

• Yeasts conduct fermentation to give an alcohol
• Homolactic bacteria and human muscle also carry out fermentation

Krebs Cycle

• The Krebs cycle takes place in the mitochondrial matrix of eukaryotes and the cytoplasm of prokaryotes

Electron Transport and Phosphorylation

• Final electron processing and a major ATP generator
• Carriers receive electrons from reduced carriers (NADH and FADH2)
• ETS shuttles electrons down the chain, where ATP synthase complexes capture released energy to produce ATP via oxidative phosphorylation

Chemiosmosis

• Chemiosmosis is when electron transport (ETS) proteins transport protons (H+) across a membrane, creating a proton gradient that drives ATP synthesis via ATP synthase
• Three protons are needed for each ATP