Biol 20: Chapter 8

Microbial Metabolism Notes

Introduction to Metabolism

  • Metabolism: Involves two main processes, catabolism and anabolism.

  • Catabolism: Breakdown of complex molecules into simpler ones, releasing energy.

  • Anabolism: Building up of complex molecules from simpler ones, requiring energy.

  • Together, these processes are referred to as metabolic reactions.

Metabolic Diversity in Prokaryotes

  • Prokaryotes exhibit a wide range of metabolic pathways, which affect other life forms significantly.

  • Acid Mine Drainage: A major environmental issue caused by sulfide-oxidizing bacteria during mining, leading to the production of sulfuric acid.

    • Resulting low pH can be harmful to aquatic life.

  • Root Nodules: Found in legumes, host bacteria capable of fixing atmospheric nitrogen, creating usable nitrogen sources for plants.

Catabolism vs. Anabolism

  • Catabolism:

    • Breaks down polymers into monomers.

    • Example: Respiration: releases energy from the breakdown of larger molecules.

  • Anabolism:

    • Forms larger molecules from smaller ones.

    • Requires energy from catabolic reactions.

Carbon Sources in Organisms

  • Autotrophs: Self-feeders that convert inorganic CO₂ into organic carbon (food).

  • Heterotrophs: Depend on organic compounds for nutrition; cannot synthesize their food.

Energy Sources in Organisms

  • Organisms categorized based on their energy sources:

    • Phototrophs: Use light energy.

    • Chemotrophs: Obtain energy from chemical compounds.

    • Organotrophs: Derived from organic molecules.

    • Lithotrophs: Get energy from inorganic molecules.

Enzymes: Biological Catalysts

  • Enzymes: Proteins that increase the rate of chemical reactions by lowering activation energy.

    • Highly specific for their substrates.

    • Reactions may be exergonic (releasing energy) or endergonic (requiring energy).

Types of Reactions

  • Exergonic Reactions: Generate energy, do not require additional input of energy beyond activation.

  • Endergonic Reactions: Absorb energy and require energy input exceeding their activation energy.

  • Coupling: Endergonic reactions are often coupled with exergonic reactions to make them energetically favorable.

ATP and Energy Transfer

  • ATP (Adenosine Triphosphate): Key energy carrier in cells, releases energy through dephosphorylation (removal of a phosphate group).

  • Phosphorylation: Addition of a phosphate group to ADP to regenerate ATP.

Enzyme Structure and Function

  • Enzymes consist of:

    • Apoenzyme: Protein part of the enzyme.

    • Cofactor: Inorganic part, needed for enzyme activity.

    • Coenzyme: Organic part that assists in the enzyme's function.

    • Together, they form a Holoenzyme, which is the active form necessary for catalysis.

Enzyme Activity Regulation

  • Induced Fit Model: Describes how enzyme binds to substrate, changing shape to form an enzyme-substrate complex.

  • Inhibition:

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

    • Noncompetitive Inhibition: Inhibitor binds to an allosteric site, altering enzyme shape and function.

Allosteric Regulation

  • Allosteric Inhibitors: Decrease enzyme activity upon binding to an allosteric site.

  • Allosteric Activators: Increase enzyme activity, facilitating a more efficient metabolic pathway.

Feedback Inhibition

  • A regulatory mechanism whereby the end product of a metabolic pathway inhibits an earlier step in the pathway, maintaining homeostasis within cells.

Conclusion

  • Summary of catabolism, anabolism, enzymatic function, and regulation provides a foundation for understanding microbial metabolism and its significance in broader biological contexts.

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Respiration Overview

  • Definition: Respiration is a biochemical process where energy is extracted from glucose.

Main Types of Respiration

  • Aerobic Respiration

    • Requires oxygen.

    • Preferred by most organisms for greater energy yield.

  • Anaerobic Respiration (Fermentation)

    • Occurs without oxygen.

    • Produces less energy compared to aerobic respiration.

Terminology Based on Oxygen Requirements

  • Obligate Aerobes: Must have oxygen to survive.

  • Obligate Anaerobes: Cannot survive in oxygen.

  • Facultative Anaerobes: Can survive with or without oxygen.

  • Aerotolerant Anaerobes: Do not use oxygen but can tolerate its presence.

  • Microaerophiles: Require low levels of oxygen.

Steps of Aerobic Respiration

  1. Glycolysis

    • Location: Cytoplasm (occurs in both prokaryotes and eukaryotes).

    • Breakdown of glucose (6 carbon) into 2 pyruvate molecules (3 carbon).

    • ATP Produced: Net gain of 2 ATP (4 ATP produced, 2 ATP consumed).

    • Phosphorylation Mechanism: Substrate-level phosphorylation (using phosphates from substrates).

  2. Krebs Cycle (Citric Acid Cycle)

    • Location: Mitochondrial matrix in eukaryotes.

    • Pyruvate is converted to Acetyl CoA before entering the Krebs Cycle.

    • ATP Produced: 2 ATP (1 from each pyruvate entering separately).

    • Byproducts: Carbon dioxide and electron carriers (NADH and FADH₂).

  3. Electron Transport Chain (ETC)

    • Location: Inner mitochondrial membrane in eukaryotes; plasma membrane in prokaryotes.

    • Uses oxygen as the final electron acceptor, forming water.

    • ATP Produced: 32-34 ATP through oxidative phosphorylation via ATP synthase.

    • Overall ATP yield from aerobic respiration: 36-38 ATP.

Anaerobic Respiration (Fermentation)

  • Definition: Processes that occur in the absence of oxygen.

  • Common Features:

    • Glycolysis occurs (producing 2 ATP).

    • No further ATP produced via Krebs Cycle or ETC.

  • Types of Fermentation:

    • Alcoholic Fermentation:

      • Pyruvate → Acetaldehyde → Ethanol.

      • Example organisms: Yeast.

    • Lactic Acid Fermentation:

      • Pyruvate → Lactic Acid.

      • Example organisms: Muscle cells in humans, some bacteria.

Summary of Energy Production

  • Aerobic Respiration: 36-38 ATP

  • Anaerobic Respiration: 2 ATP (limited by glycolysis)

Efficiency Comparison

  • Aerobic respiration is more efficient than anaerobic processes due to the higher ATP yield.

  • Facultative anaerobes can switch between aerobic respiration and fermentation based on oxygen availability.

Conclusion

  • Respiration is essential for energy production in living organisms.

  • Understanding both aerobic and anaerobic pathways highlights the metabolic flexibility of various organisms.

  • Next topic: Photosynthesis, which is an anabolic process where glucose is synthesized.

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Photosynthesis Overview

  • Photosynthesis is an anabolic metabolic process where sunlight is the ultimate source of energy used by organisms to manufacture their own food.

  • Organisms that capture sunlight to create food are called autotrophs or more specifically photoautotrophs (photo = light, auto = self).

Key Concepts

  • Autotrophs:

    • Organisms that can use carbon dioxide from the air as a carbon source.

    • Example: Plants that perform photosynthesis.

  • Photosynthesis:

    • Process by which plants convert light energy (sunlight) into chemical energy (sugars/glucose).

    • Essential for providing food for nearly all other lifeforms on Earth.

Stages of Photosynthesis

1. Light-Dependent Reactions (Light Reactions)

  • Occur in the grana within the chloroplasts (structures containing thylakoids where chlorophyll is located).

  • Key Events:

    • Light energy is converted into chemical bond energy in ATP molecules.

    • Water is oxidized (7; split) to release oxygen, which is a byproduct of this reaction.

    • Chlorophyll absorbs sunlight and gets excited, releasing electrons in a complex process known as photophosphorylation.

    • Photophosphorylation: Light energy is used to add phosphate to ADP, forming ATP.

  • Major products: Oxygen, ATP, and NADPH (which carries electrons/hydrogens for later stages).

2. Light-Independent Reactions (Dark Reactions or Calvin Cycle)

  • Occur in the stroma of the chloroplasts (the jelly-like substance surrounding the thylakoids).

  • Key Events:

    • ATP and NADPH produced in light reactions are used to convert carbon dioxide into sugars (glucose).

    • Carbon dioxide is "fixed" or reduced to form organic products such as glucose.

  • Major outcome: Production of glucose and other forms of sugars.

Chloroplast Structure

  • Contains thylakoids (stacks called granum) and stroma (fluid surrounding thylakoids).

  • Photosynthesis in eukaryotes occurs specifically in chloroplasts, where multiple reactions are compartmentalized for efficiency.

Types of Photosynthesis

Oxygenic Photosynthesis

  • Process where light energy is utilized with the production of glucose, oxygen, and water.

  • Occurs in plants and some bacteria (primarily cyanobacteria).

Anoxygenic Photosynthesis

  • Similar to oxygenic but does not produce oxygen as a byproduct.

  • Uses alternative electron donors like hydrogen sulfide or other compounds, resulting in different products (e.g., carbohydrates, sulfur, methane).

Summary

  • Photosynthesis is crucial for life on Earth, serving as the foundational energy source through autotrophic organisms, primarily plants.

  • Understanding the stages of photosynthesis (light-dependent and light-independent) and their products is essential for comprehending how energy flows through an ecosystem.