PowerPoint 4 - Microbial Metabolism

Page 1: Introduction

• College Physics Chapter: Microbial Metabolism

• Presentation modified for BIO 275 (CVCC)

• Licensed under Creative Commons

• Access resources: OpenStax Microbiology

Page 2: Metabolic Diversity of Prokaryotes

• Prokaryotes display significant metabolic diversity which impacts life forms.

  • Acidic Mine Drainage:

    • Result of mining processes introducing oxygen and water to sulfide-oxidizing bacteria.

    • Leads to sulfuric acid production, harming aquatic life.

  • Nitrogen-Fixing Bacteria:

    • Found in root nodules of plants, converting atmospheric nitrogen into ammonia.

    • Provides usable nitrogen for plants.

Page 3: Understanding Metabolism

• Metabolism: Collection of biochemical reactions in living organisms.

  • Anabolic Reactions: Require energy to construct larger molecules (endergonic).

  • Catabolic Reactions: Release energy by breaking down larger molecules (exergonic).

  • Both pathways are essential for energy balance within cells.

Page 4: Classification of Organisms by Energy Source

• Organisms categorized by energy acquisition:

  • Autotrophs (Producers):

    • Convert inorganic CO2 into organic compounds (carbohydrates, lipids).

    • Examples: Plants, algae, cyanobacteria (photoautotrophs).

  • Heterotrophs (Consumers):

    • Depend on organic compounds for nutrients (animals, fungi, protozoans).

  • Decomposers: A type of heterotroph.

Page 5: Sources of Energy in Organisms

• Electrons as Energy Carriers:

  • Energy derived from electron transfer; sources vary among organisms.

  • Phototrophs: Obtain energy from light.

  • Chemotrophs: Gain energy from breaking chemical bonds, often in organic compounds.

Page 6: Classifying Chemotrophs

• Chemotrophs divided into two groups:

  • Organotrophs: Derive energy from organic compounds (e.g., humans, fungi).

  • Lithotrophs: Obtain energy from inorganic compounds (e.g., some prokaryotes).

Page 7: Energy Source Classification

• Chemoheterotrophs:

  • Use organic molecules for both electron and carbon sources.

  • Energy Source / Carbon Source:

    • Chemotrophs:

      • Chemoautotrophs (Chemical, Inorganic) - various bacteria.

      • Chemoheterotrophs (Chemical, Organic) - animals, most fungi, most bacteria.

    • Phototrophs:

      • Photoautotrophs (Light, Inorganic) - plants, algae.

      • Photoheterotrophs (Light, Organic) - certain bacteria.

Page 8: Oxidation-Reduction Reactions

• Electron Transfer:

  • Oxidation: Molecules lose electrons (oxidized).

  • Reduction: Molecules gain electrons (reduced).

  • Allows for energy transfer in smaller packets, preventing energy bursts in cells.

Page 9: Redox Reactions Summary

• Mnemonic to remember: LEO GER.

  • Lose Electrons = Oxidized; Gain Electrons = Reduced.

  • Oxidation and reduction occur simultaneously (redox reactions).

Page 10: Mechanisms of Oxidation-Reduction

• Molecule can be oxidized by:

  • Losing an electron, losing a hydrogen atom, or gaining an oxygen atom.

• Molecule can be reduced by:

  • Gaining an electron or gaining a hydrogen atom.

• Dehydrogenation Reactions: Loss of hydrogen atoms in oxidation.

Page 11: Energy Carriers in Cells

• Mobile Electron Carriers:

  • Electrons carried by unique molecules, often vitamin B derivatives.

  • Facilitate easy transfer and recycling in metabolic processes.

Page 12: Key Electron Carriers

• Important electron carriers include:

  • Nicotinamide adenine dinucleotide (NAD+ / NADH).

  • Flavin adenine dinucleotide (FAD / FADH2).

  • Nicotinamide adenine dinucleotide phosphate (NADP+ / NADPH).

Page 13: Adenosine Triphosphate (ATP) Structure

• ATP Composition:

  • Nitrogenous adenine base, ribose sugar, three phosphate groups (high-energy bonds).

  • ATP functions as the primary energy currency of the cell.

Page 14: Phosphorylation Process

• ATP Formation:

  • AMP + inorganic phosphate → ADP + inorganic phosphate → ATP.

  • Involves phosphorylation reactions requiring energy.

Page 15: Dephosphorylation Reactions

• Energy Release:

  • High-energy phosphate bonds broken in ADP or ATP release energy.

  • Products of reactions: inorganic phosphate (Pi) or pyrophosphate (PPi).

Page 16: ATP in Cellular Work

• Cellular Functions:

  • Energy from ATP hydrolysis drives metabolic work including anabolic pathways.

  • ATP is regenerated through phosphorylation using chemical or sunlight energy.

Page 17: Coupled Reactions in Metabolism

• Coupled Exergonic and Endergonic Reactions:

  • Endergonic ATP phosphorylation is coupled with exergonic catabolism.

  • Helps conserve energy through recycling.

Page 18: Role of Enzymes in Reactions

• Enzymes as Catalysts:

  • Enzymes lower activation energy for reactions, necessary for spontaneous occurrence.

  • Enzymatic activity speeds up both endergonic and exergonic reactions.

Page 19: Impact of Enzymes on Activation Energy

• Illustration of Activation Energy:

  • Enzymes facilitate lowering activation energy for both reaction types.

  • Critical for efficient metabolic processes.

Page 20: Enzyme Structure and Specificity

• Nature of Enzymes:

  • Usually protein molecules with specific 3D shapes for substrate binding.

  • Substrates bind at the active site to form an enzyme-substrate complex.

Page 21: Induced-Fit Model in Enzyme Function

• Complex Formation:

  • Substrates bind to the active site, forming temporary complexes.

  • Induced-fit model suggests substrate stretching to weaken bonds, speeding reactions.

Page 22: Induced Fit Mechanism

• Active site undergoes conformational change upon substrate binding, enhancing reaction speed.

Page 23: Naming Enzymes

• Common Naming Convention:

  • Enzymes typically end in “-ase” and are often named based on substrates or actions.

  • Examples: Ligase, Transferase, Lipase, Dehydrogenase.

Page 24: Factors Affecting Enzyme Activity

• Denaturation Impacts:

  • Temperature changes, pH shifts, and exposure to chemicals can affect activity.

  • Each enzyme has an optimal range for effectiveness.

Page 25: Enzymatic Function and Helper Molecules

• Helper Molecules:

  • Some enzymes require non-protein helpers (cofactors/coenzymes) for functionality.

  • These can alter the active site shape for better substrate affinity.

Page 26: Cofactors and Coenzymes

• Types:

  • Cofactors: Inorganic ions (e.g., Fe²⁺, Mg²⁺).

  • Coenzymes: Organic molecules (e.g., vitamins) that assist enzymes.

Page 27: Holoenzymes and Apoenzymes

• Enzyme Activation:

  • Binding of coenzymes or cofactors forms active holoenzyme from inactive apoenzyme.

Page 28: Enzyme Regulation Mechanisms

• Competitive Inhibitors:

  • Compete with substrates at the active site, blocking binding.

  • Reversible inhibitors can be overcome by increasing substrate concentration.

  • Example: Sulfa drugs inhibit bacterial folic acid biosynthesis.

Page 29: Non-Competitive Inhibition**

• Allosteric Inhibitors: bind to different sites, altering enzyme shape and reducing substrate affinity.

• Activators: enhance substrate binding at allosteric sites.

Page 30: Summary of Enzyme Activity Regulation

• Enzymes regulated by either competitive (active site) or noncompetitive (allosteric site) inhibitors.

Page 31: Metabolic Pathways Overview

• Sequential Reactions:

  • Each reaction requires a specific enzyme; if any are missing, the pathway halts.

  • Metabolic pathways consist of sequential catalyzed reactions.

Page 32: Feedback Inhibition in Metabolic Pathways

• Product Regulation:

  • The endpoint product can act as an inhibitor in early pathway steps, preventing resource wastage.

Page 33: Allosteric Mechanisms in Feedback Inhibition

• Binding of inhibitors or activators to allosteric sites affects enzymatic activity in feedback mechanisms.

Page 34: Glycolysis Overview

• Universal Process:

  • Nearly all organisms undergo glycolysis in either prokaryotic or eukaryotic cells.

  • Conversion of glucose into pyruvate with some ATP produced.

Page 35: Phases of Glycolysis

• Energy Investment Phase:

  • 2 ATP used to convert glucose into two phosphorylated G3P molecules.

• Energy Payoff Phase: Extracts energy by oxidizing G3P to pyruvate, yielding ATP and NADH.

Page 36: Glycolysis Pathway Summary

• Investment phase yields two G3P and payoff phase results in four ATP and two NADH.

• Net gain of 2 ATP from glycolysis.

Page 37: Energy Investment Pathway Details

• Begins with glucose, ends with two G3P, requires 2 ATP input.

Page 38: Energy Payoff Pathway Overview

• Follows energy investment, produces NADH and ATP, ending in pyruvate.

Page 39: Substrate-Level Phosphorylation

• ATP formation occurs through substrate-level phosphorylation during glycolysis.

Page 40: Glycolysis Summary

• Key outcomes of glycolysis summarized, detailing net products produced.

Page 41: Alternative Glycolytic Pathway: ED Pathway

• Entner-Doudoroff (ED) Pathway:

  • Used by some prokaryotes like Pseudomonas aeruginosa, producing less ATP than EMP pathway.

Page 42: Other Glycolytic Pathways

• Pentose Phosphate Pathway (PPP):

  • Used for synthesizing nucleic acids/proteins in all cell types.

Page 43: Pyruvate Oxidation Overview

• Pyruvate converted into acetyl-CoA for incorporation into Krebs cycle.

  • Decarboxylation: one carbon released, electron transfer to NAD+ forms NADH.

Page 44: Acetyl-CoA Formation

• Acetyl group attached to coenzyme A, producing two acetyl-CoA molecules from glycolysis.

Page 45: Krebs Cycle Initiation

• Acetyl-CoA enters the Krebs cycle (TCA), occurring in cytoplasm (prokaryotes) or mitochondria (eukaryotes).

Page 46: Purpose of the Krebs Cycle

• Continue capturing energy from glucose breakdown via redox reactions producing NADH and FADH2.

Page 47: Krebs Cycle Outputs

• Each complete cycle yields products including CO2, ATP/GTP, NADH, FADH2 and plays a role in biosynthesis.

Page 48: Overview of the Krebs Cycle

• Detailed outputs per turn, highlighting significance for energy storage.

Page 49: Biosynthesis from Krebs Cycle Intermediates

• Krebs cycle intermediates serve as building blocks for essential macromolecules.

Page 50: ATP Production via Oxidative Phosphorylation

• Final electron acceptors in the process lead to substantial ATP generation through electron transport system.

Page 51: Electron Transport System Function

• A series of reactions transferring electrons through membrane-bound carriers, pumping protons across membranes.

Page 52: Types of Electron Carriers

• Various classes of electron carriers function within electron transport systems, facilitating energy transfer.

Page 53: Proton Storage During Electron Transport

• Proton gradients form across membranes during electron transfer, crucial for ATP synthesis.

Page 54: Final Electron Acceptor Types

• Aerobic Respiration: Uses oxygen.

• Anaerobic Respiration: May use molecules like nitrates or sulfates, depending on organism type.

Page 55: Establishing Proton Gradients

• Accumulation of protons on one side of the membrane creates an electrochemical gradient.

Page 56: Contribution of Dr. Peter Mitchell

• Nobel laureate recognized for the chemiosmotic model demonstrating ATP synthesis through proton gradients.

Page 57: Mechanism of ATP Synthase

• ATP synthase utilizes proton gradients to synthesize ATP utilizing chemiosmosis.

Page 58: ATP Synthase Functionality

• ATP synthase acts as a generator, converting proton gradient energy into usable ATP.

Page 59: ATP Synthase Structure

• Overview of ATP synthase as integrated into prokaryotic membranes and its mechanism of action.

Page 60: Bacterial Electron Transport Chain Overview

• Describes how H+ ions are pumped and their role in ATP generation through oxidative phosphorylation.

Page 61: ATP Yield Variability

• Theoretical maximum ATP yield in aerobic respiration; actual yield varies by species.

Page 62: Summary of Aerobic Respiration Stages

• Gains from glycolysis, transition reaction, and Krebs cycle leading to ATP generation tally.

Page 63: Limitations to Aerobic Respiration

• Factors limiting respiration include absence of final electron acceptors and genetic constraints on enzyme production.

Page 64: Purpose of Fermentation

• Fermentation regenerates NAD+ necessary for glycolysis amid low oxygen availability.

Page 65: Human Applications of Fermentation

• Used in food production and diagnostics, with implications for health and industry.

Page 66: Lactic Acid Fermentation Process

• Lactic acid produced in human muscles under oxygen depletion and in fermentation processes.

Page 67: Types of Lactic Acid Fermentation

• Distinctions between homolactic and heterolactic fermentation with examples of bacteria involved.

Page 68: Human Role of Lactic Acid Bacteria

• Importance of lactic acid bacteria in human microbiota for digestion and health.

Page 69: Alcohol Fermentation Overview

• Chemical reactions involved in ethanol production noted for food and beverage industries.

Page 70: Common Fermentation Pathways

• Summary of various fermentation pathways and associated products with microbial examples.

Page 71: Analytical Profile Index Test Utilization

• Use of API strips for identification of bacterial species based on metabolic product tests.

Page 72: Photosynthesis Phases

• Overview of the photosynthesis process: light-dependent vs. light-independent reactions.

Page 73: Photosynthesis Summary

• Captures light energy conversion into chemical energy during the initial phases.

Page 74: Photosystem Structures

• Distinction between prokaryotic and eukaryotic photosynthesis structures and functions.

Page 75: Photosystem Functions

• Description of photosystems in chloroplasts and their role in photosynthetic processes.

Page 76: Photosynthetic Pigments

• Various pigments involved in light absorption during photosynthesis and their significance.

Page 77: Photosystem Electron Transfer

• Mechanism of energy transfer within photosystems leading to ATP and NADPH production.

Page 78: Photophosphorylation Process

• Summary of how proton gradients form and ATP is generated during photosynthesis.

Page 79: Noncyclic Photophosphorylation

• Describes electron flow paths and processes involved in ATP and NADPH production in plants.

Page 80: Electron Replacement During Photosynthesis

• Water as the electron donor in oxygenic photosynthesis; alternatives in anaerobic bacteria.

Page 81: Types of Photosystems

• Difference between photosystem types: PSI and PSII with their respective functions outlined.

Page 82: Oxygenic vs. Anoxygenic Photosynthesis

• Comparison of oxygen-producing and non-oxygen-producing photosynthetic organisms.

Page 83: Calvin Cycle Overview

• Calvin cycle’s role in fixing carbon into stable forms using ATP and NADPH.

Page 84: Carbon Fixation Steps

• Detailed functions of rubisco during carbon fixation and subsequent ATP/NADPH consumption.

Page 85: Summary of the Calvin-Benson Cycle

• Comprehensive outline of ATP, NADPH usage and product formation within the cycle.

Page 86: Regeneration of RuBP

• Regeneration of RuBP to maintain continual carbon fixation, requiring ATP usage.

Page 87: Biogeochemical Cycles

• Brief overview of cycles recycling inorganic matter in nature.

Page 88: Carbon Cycle Summary

• Carbon cycling through living organisms, emphasizing the impact of prokaryotes and methane.

Page 89: Nitrogen Cycle Overview

• Summary of nitrogen fixation processes and their necessity for plant growth.

Page 90: Nitrogen Cycle Processes

• Explanation of ammonification, nitrification, and their significance in soil health.

Page 91: Denitrification Process Overview

• Nitrate reduction done by soil bacteria, emphasizing the environmental implications.

Page 92: Sulfur Cycle Summary

• Overview of sulfur cycling, illustrating its importance for organisms.