Chaper 5,6, & 8

Chapter 6: Microbial Metabolism: Fueling Cell Growth

A Glimpse of History 📜

• Alcohol and CO2CO2​ are produced in grape juice as yeast cells increase in number.

• 1850s: Louis Pasteur showed that yeast were producing the alcohol.

  • Yeast cells multiplied in a clear solution of sugar, ammonia, mineral salts, and trace elements. Sugar decreased, and alcohol levels increased.

  • Pasteur could not extract the component from inside the cells that converted sugar.

• 1897: Eduard Buchner showed that crushed yeast cells could convert sugar to ethanol and was awarded the Nobel Prize in 1907.

Introduction 💡

• All cells need to:

  • Synthesize new parts such as cell walls, membranes, ribosomes, and nucleic acids.

  • Harvest energy to power reactions.

The sum of chemical reactions in a cell is called metabolism.

• Implications of microbial metabolism include:

  • Biofuels

  • Food and beverage production

  • Important models for study

  • Unique pathways are potential drug targets

• Metabolism can be expressed as:

  Metabolism=Anabolism+CatabolismMetabolism=Anabolism+Catabolism

  where:

  • Anabolism is the build up of molecules.

  • Catabolism is the breakdown of molecules.

Energy ⚡️

Energy is the capacity to do work.

• Potential Energy: Stored energy such as chemical bonds, a rock on a hill, or water behind a dam.

• Kinetic Energy: Energy of motion, such as moving water.

  The energy in the universe cannot be created or destroyed, but it can be changed from one form to another.

• Photosynthetic organisms harvest energy in sunlight:

  • This powers the synthesis of organic compounds from CO2CO2​.

  • Kinetic energy of photons converted to potential energy of chemical bonds.

• Chemoorganotrophs obtain energy from organic compounds. They depend on the activities of photosynthetic organisms or chemolithoautotrophs.

Free Energy ⚙

Free energy is energy available to do work.

• Energy is released when a chemical bond is broken.

• Exergonic reactions: Reactants have more free energy than products, and energy is released in the reaction.

• Endergonic reactions: Products have more free energy than reactants, and the reaction requires an input of energy.

• The change in free energy for a given reaction is the same regardless of the number of steps involved.

• Cells use multiple steps when degrading compounds.

• Energy released from exergonic reactions powers endergonic reactions.

Exergonic vs. Endergonic Reactions ⚖

• Exergonic Reactions

  • Energy is released.

  • Reactants have more free energy than products.

• Endergonic Reactions

  • Energy is required.

  • Products have more free energy than reactants.

Components of Metabolic Pathways

Role of Enzymes 🧪

Enzymes are biological catalysts that speed up the conversion of substrate into product by lowering activation energy.

• A specific enzyme is required for each step of a metabolic pathway.

• Without enzymes, energy-yielding reactions would occur too slowly.

Role of ATP 💰

Adenosine triphosphate (ATP) is the energy currency of the cell.

• ATP is composed of ribose, adenine, and three phosphate groups.

• Cells use energy to produce ATP by adding a phosphate group to adenosine diphosphate (ADP).

• Energy is released by removing a phosphate group from ATP to yield ADP.

Processes That Generate ATP ⚡️

• Chemoorganotrophs

  • Substrate-level phosphorylation: Energy generated in exergonic reactions.

  • Oxidative phosphorylation: Energy generated by proton motive force.

• Photosynthetic organisms

  • Photophosphorylation: Sunlight used to create proton motive force.

Energy Sources and Terminal Electron Acceptors 🔋

• Prokaryotes use diverse energy sources and terminal electron acceptors.

  • Organic and inorganic compounds are used as energy sources.

  • O2O2​ and other molecules are used as terminal electron acceptors.

• Electrons are removed through a series of oxidation-reduction reactions (redox reactions).

  • The substance that loses electrons is oxidized.

  • The substance that gains electrons is reduced.

  • An electron-proton pair, or hydrogen atom, is transferred.

  • Dehydrogenation = oxidation

  • Hydrogenation = reduction

Chemical Energy Sources and Terminal Electron Acceptors ♻

• When electrons move from a molecule with low affinity for electrons (energy source) to a molecule with high affinity for electrons (terminal electron acceptor), energy is released.

The Role of Electron Carriers 载体

• Energy is harvested in a stepwise process.

• Electrons are initially transferred to electron carriers.

• Electron carriers can be considered hydrogen carriers.

• Ultimately, electron carriers drive the synthesis of ATP or biosynthesis.

Electron Carriers 🚃

Precursor Metabolites 🧱

• E. coli can grow in glucose-salts medium.

  • Glucose is the energy source.

  • Glucose is the starting point for all cellular components, including proteins, lipids, carbohydrates, and nucleic acids.

• Some glucose molecules are completely oxidized for energy.

• Other glucose molecules are broken into smaller precursor metabolites that exit the catabolic pathway early to be used in biosynthesis.

Overview of Catabolism 🐱‍👤

• Two key sets of processes:

  • Oxidizing glucose molecules to generate ATP, reducing power (NADH, FADH2, and NADPH), and precursor metabolites accomplished in a series of reactions called the central metabolic pathways.

  • Transferring the electrons carried by NADH and FADH2 to the terminal electron acceptor, which is done by either cellular respiration or fermentation.

Overview of Catabolism 2 🐱‍👤

• Central metabolic pathways oxidize glucose to CO2CO2​.

  • This is catabolic, but precursor metabolites and reducing power can be diverted for use in biosynthesis.

  • Termed amphibolic to reflect dual role.

• Glycolysis: Splits glucose (6C) into two pyruvate molecules (3C). Generates modest ATP, reducing power, and precursors.

• Pentose phosphate pathway: Primary role is the production of precursor metabolites and NADPH.

• Tricarboxylic acid (TCA) cycle (Citric acid cycle): With transition step, oxidizes pyruvate and releases CO2CO2​. Generates reducing power, precursor metabolites, and ATP.

Overview of Catabolism 3 🐱‍👤

• Respiration (or cellular respiration) transfers electrons from glucose to the electron transport chain (ETC) to a terminal electron acceptor.

  • The electron transport chain generates proton motive force.

  • The proton motive force is harvested to make ATP by oxidative phosphorylation.

    • Aerobic respiration: O2O2​ is the terminal electron acceptor.

    • Anaerobic respiration: A molecule other than O2O2​is the terminal electron acceptor.

Overview of Catabolism 4 🐱‍👤

• Fermentation recycles electron carriers in a cell that cannot respire so that it can continue to make ATP.

  • Uses pyruvate or a derivative as a terminal electron acceptor to receive H from NADH.

  • Regenerates NAD+NAD+ so that glycolysis can continue.

  • Glycolysis provides a small amount of ATP (38 vs 2).

Enzymes 催化剂

• The active site on the surface of the enzyme binds substrate(s) weakly.

  • This causes the enzyme shape to change slightly, known as induced fit.

  • The resulting enzyme-substrate complex destabilizes existing bonds or allows new ones to form.

  • This lowers the activation energy of the reaction.

Enzymes 2 催化剂

• Enzymes are used to break large molecules into smaller ones or to build large molecules from subunits.

• Theoretically, enzyme-catalyzed reactions are reversible, but the free energy of some reactions prevents reversibility.

Cofactors 辅助因子

Some enzymes require the assistance of an attached non-protein component called a cofactor.

• Examples include magnesium, zinc, and copper.

• Coenzymes are organic cofactors that help some enzymes transfer certain molecules or electrons from one compound to another (e.g., NADH).

• Coenzymes are often derived from vitamins.

Environmental Factors That Influence Enzyme Activity 🌡

• Enzymes have a narrow range of optimal conditions, including:

  • Temperature

  • pH

  • Salt concentration

• A 10 degrees Celsius increase doubles the speed of enzymatic reaction up to the maximum. Proteins denature at higher temperatures.

Regulation of Allosteric Enzymes 调节酶

• Enzyme activity is controlled by a regulatory molecule binding to an allosteric site.

• This distorts the enzyme shape, which prevents or enhances the binding of the substrate to the active site.

• The regulatory molecule is usually the end product of a metabolic pathway, allowing for feedback inhibition.

Competitive Inhibition of Enzymes 抑制剂

• In competitive inhibition, an inhibitor binds to the active site.

  • The chemical structure of the inhibitor is usually similar to the substrate.

  • This is concentration-dependent; the inhibitor blocks the substrate.

  • An example includes sulfa drugs that block folate synthesis.

Characteristics of Enzyme Inhibitors 🧪

Microbial Metabolism: Fueling Cell Growth

🔬 A Glimpse of History

• Alcohol and CO2CO2​ are produced in grape juice as yeast cells increase in number.

• Louis Pasteur (1850s) demonstrated that yeast produce alcohol but couldn't extract the sugar-converting substance from the cells.

• Eduard Buchner (1897) showed crushed yeast cells could convert sugar to ethanol and was awarded the Nobel Prize in 1907.

⚡ Introduction to Microbial Metabolism

• All cells must:

  • Synthesize new parts (cell walls, membranes, ribosomes, nucleic acids).

  • Harvest energy to power reactions.

• Metabolism: Sum of chemical reactions in a cell.

  Metabolism = Anabolism (build up) + Catabolism (breakdown)

• Implications of microbial metabolism include:

  • Biofuels

  • Food and beverage production

  • Important models for study

  • Unique pathways are potential drug targets

🔋 Energy Concepts

• Energy: The capacity to do work.

  • Potential Energy: Stored energy (e.g., chemical bonds, a rock on a hill, water behind a dam).

  • Kinetic Energy: Energy of motion (e.g., moving water).

• Energy cannot be created or destroyed, but it can be changed from one form to another.

🔆 Energy Sources

• Photosynthetic organisms harvest energy from sunlight to synthesize organic compounds from CO2CO2​. They convert kinetic energy of photons into potential energy of chemical bonds.

• Chemoorganotrophs obtain energy from organic compounds.

  • They depend on photosynthetic organisms or chemolithoautotrophs.

📉 Free Energy

• Free energy is the energy available to do work.

• Energy is released when a chemical bond is broken.

• Exergonic reactions: Reactants have more free energy than products, releasing energy.

• Endergonic reactions: Products have more free energy than reactants, requiring energy input.

• The change in free energy for a reaction is the same regardless of the number of steps involved.

• Cells use multiple steps when degrading compounds, and energy released from exergonic reactions powers endergonic reactions.

↔ Exergonic vs. Endergonic Reactions

• ΔGΔG means change in free energy

⚙ Components of Metabolic Pathways

Role of Enzymes

• Enzymes are biological catalysts that speed up the conversion of substrate into product by lowering activation energy.

• Each step of a metabolic pathway requires a specific enzyme.

• Without enzymes, energy-yielding reactions would occur too slowly.

Role of ATP

• Adenosine triphosphate (ATP): The energy currency of the cell.

  • Composed of ribose, adenine, and three phosphate groups.

• Cells produce ATP by adding a phosphate group to adenosine diphosphate (ADP).

• Energy is released by removing a phosphate group from ATP to yield ADP.

💡 Processes That Generate ATP

🧫 Metabolic Diversity in Prokaryotes

• Prokaryotes use diverse energy sources and terminal electron acceptors.

• They utilize organic and inorganic compounds as energy sources.

• O2O2​ and other molecules serve as terminal electron acceptors.

• Electrons are removed through oxidation-reduction (redox) reactions.

  • Oxidation: Substance loses electrons.

  • Reduction: Substance gains electrons.

  • An electron-proton pair (hydrogen atom) is transferred.

    • Dehydrogenation = oxidation

    • Hydrogenation = reduction

⚡️ Chemical Energy Sources and Electron Acceptors

• Energy is released when electrons move from a molecule with low affinity for electrons (energy source) to one with high affinity (terminal electron acceptor).

🚚 Role of Electron Carriers

• Energy is harvested in a stepwise process.

• Electrons are initially transferred to electron carriers, which can be considered hydrogen carriers.

• Ultimately, these carriers drive the synthesis of ATP or biosynthesis.

载 Electron Carriers

🧱 Precursor Metabolites

• E. coli can grow in glucose-salts medium.

• Glucose serves as both an energy source and a starting point for all cellular components (proteins, lipids, carbohydrates, nucleic acids).

• Some glucose molecules are completely oxidized for energy, while others are broken into smaller precursor metabolites that exit the catabolic pathway early to be used in biosynthesis.

⚗ Overview of Catabolism

• Two key sets of processes:

  • Oxidizing glucose molecules to generate ATP, reducing power (NADH, FADH2FADH2​, and NADPH), and precursor metabolites. This occurs in the central metabolic pathways.

  • Transferring electrons carried by NADH and FADH2FADH2​to the terminal electron acceptor via cellular respiration or fermentation.

🔄 Central Metabolic Pathways

• Central metabolic pathways oxidize glucose to CO2CO2​.

• The process is catabolic, but precursor metabolites and reducing power can be diverted for use in biosynthesis. This dual role makes it amphibolic.

• Key pathways:

  • Glycolysis: Splits glucose (6C) into two pyruvate molecules (3C), generating modest ATP, reducing power, and precursors.

  • Pentose phosphate pathway: Primarily produces precursor metabolites and NADPH.

  • Tricarboxylic acid (TCA) cycle (Citric acid cycle): With a transition step, oxidizes pyruvate, releases CO2CO2​, and generates reducing power, precursor metabolites, and ATP.

呼吸 Cellular Respiration

• Respiration (cellular respiration) transfers electrons from glucose to the electron transport chain (ETC) to a terminal electron acceptor.

• The electron transport chain generates a proton motive force, which is harvested to make ATP by oxidative phosphorylation.

• Aerobic respiration: O2O2​ is the terminal electron acceptor.

• Anaerobic respiration: A molecule other than O2O2​ is the terminal electron acceptor.

🍺 Fermentation

• Fermentation recycles electron carriers in cells that cannot respire so that it can continue to make ATP.

• It uses pyruvate or a derivative as a terminal electron acceptor to receive H from NADH.

• This regenerates NAD+NAD+ so that glycolysis can continue.

• Glycolysis provides a small amount of ATP (38 vs. 2).

催 Enzymes

• The active site on the enzyme surface binds substrate(s) weakly, causing the enzyme shape to change slightly (induced fit).

• The resulting enzyme-substrate complex destabilizes existing bonds or allows new ones to form.

• This lowers the activation energy of the reaction.

• Enzymes break down large molecules or build large molecules from subunits.

• Theoretically, enzyme-catalyzed reactions are reversible, but the free energy of some reactions prevents reversibility.

辅助 Cofactors

• Some enzymes require a non-protein component called a cofactor (e.g., magnesium, zinc, copper).

• Coenzymes are organic cofactors that help enzymes transfer molecules or electrons (e.g., NADH).

  • Often derived from vitamins.

🌡 Environmental Factors Affecting Enzyme Activity

• Enzymes have a narrow range of optimal conditions (temperature, pH, salt concentration).

• A 10 degrees Celsius increase doubles the speed of enzymatic reactions up to a maximum, as proteins denature at higher temperatures.

регуляция Regulation of Allosteric Enzymes

• Enzyme activity is controlled by a regulatory molecule binding to the allosteric site.

• This distorts the enzyme shape, preventing or enhancing substrate binding to the active site.

• The regulatory molecule is usually the end product of the metabolic pathway, allowing feedback inhibition.

🚫 Competitive Inhibition of Enzymes

• In competitive inhibition, the inhibitor binds to the active site.

• The chemical structure of the inhibitor is usually similar to the substrate.

• Inhibition is concentration-dependent; the inhibitor blocks the substrate.

• An example is sulfa drugs blocking folate synthesis.

⛔ Enzyme Inhibition

• In non-competitive inhibition, the inhibitor binds to a site other than the active site.

• Allosteric inhibitors are one example, and their action is reversible.

Microbial Metabolism: Fueling Cell Growth

History of Metabolism Research 🔬

• In the 1850s, Louis Pasteur investigated alcohol production by yeast. He demonstrated that yeast cells consume sugar, leading to increased alcohol levels. However, he couldn't extract the sugar-converting substance from the cells.

• In 1897, Eduard Buchner discovered that crushed yeast cells could convert sugar to ethanol, earning him the Nobel Prize in 1907.

Fundamental Tasks of Cells ⚙

All cells must perform these tasks:

• Synthesize new cellular components like cell walls, membranes, ribosomes, and nucleic acids.

• Harvest energy to power reactions.

• Metabolism is the sum of all chemical reactions in a cell.

  Metabolism = Anabolism + Catabolism (build up) (breakdown)

• Implications of microbial metabolism include:

  • Biofuels

  • Food and beverage production

  • Important models for study

  • Unique pathways are potential drug targets

Energy Principles ⚡

• Energy is the capacity to do work.

• Forms of energy:

  • Potential energy: Stored energy (e.g., chemical bonds, a rock on a hill, water behind a dam).

  • Kinetic energy: Energy of motion (e.g., moving water).

• Energy in the universe cannot be created or destroyed but can be converted from one form to another.

Energy Acquisition ☀

• Photosynthetic organisms harvest sunlight to synthesize organic compounds from CO2CO2​, converting the kinetic energy of photons into the potential energy of chemical bonds.

• Chemoorganotrophs obtain energy from organic compounds, depending on the activities of photosynthetic organisms or chemolithoautotrophs.

Free Energy and Reactions 💥

• Free energy is the energy available to do work.

• Energy is released when a chemical bond is broken.

• Types of reactions:

  • Exergonic reactions: Reactants have more free energy than products; energy is released.

  • Endergonic reactions: Products have more free energy than reactants; energy input is required.

• The change in free energy for a reaction is the same regardless of the number of steps involved. Cells use multiple steps when degrading compounds.

• Energy released from exergonic reactions powers endergonic reactions.

Metabolic Pathways 🛤

Role of Enzymes

• Enzymes are biological catalysts that speed up the conversion of substrate into product by lowering the activation energy.

• A specific enzyme is required for each step of a metabolic pathway.

• Without enzymes, energy-yielding reactions would occur too slowly.

Role of ATP

• Adenosine triphosphate (ATP) is the energy currency of the cell.

• ATP is composed of ribose, adenine, and three phosphate groups.

• Cells produce ATP by adding a phosphate group to adenosine diphosphate (ADP).

• Energy is released by removing a phosphate group from ATP, yielding ADP.

ATP Generation ♻

Diverse Energy Sources and Terminal Electron Acceptors ⚡

• Prokaryotes use diverse energy sources (organic, inorganic compounds) and terminal electron acceptors (O2O2​, other molecules).

• Electrons are removed through oxidation-reduction (redox) reactions.

  • Oxidation: Substance loses electrons (Dehydrogenation).

  • Reduction: Substance gains electrons (Hydrogenation).

• An electron-proton pair, or hydrogen atom, is transferred.

Redox Reactions 🔄

When electrons move from a molecule with low affinity for electrons (energy source) to a molecule with high affinity for electrons (terminal electron acceptor), energy is released. This can be visualized using a redox tower.

Electron Carriers 载体

• Energy is harvested in a stepwise process.

• Electrons are initially transferred to electron carriers, which can be considered hydrogen carriers.

• Electron carriers ultimately drive the synthesis of ATP or biosynthesis.

Common Electron Carriers 🚃

Precursor Metabolites 🧱

• E. coli can grow in glucose-salts medium, where glucose is both the energy source and the starting point for all cellular components (proteins, lipids, carbohydrates, nucleic acids).

• Some glucose molecules are completely oxidized for energy.

• Other glucose molecules are broken into smaller precursor metabolites that exit the catabolic pathway early to be used in biosynthesis.

Overview of Catabolism 🔪

Two main processes:

1. Oxidizing glucose molecules to generate ATP, reducing power (NADH, FADH2, NADPH), and precursor metabolites through central metabolic pathways.

2. Transferring electrons carried by NADH and FADH2 to a terminal electron acceptor via cellular respiration or fermentation.

Central Metabolic Pathways 🛣

• Oxidize glucose to CO2CO2​.

• Catabolic but can be amphibolic, with precursor metabolites and reducing power diverted for biosynthesis.

• Include:

  • Glycolysis: Splits glucose (6C) into two pyruvate molecules (3C), generating modest ATP, reducing power, and precursors.

  • Pentose phosphate pathway: Produces precursor metabolites and NADPH.

  • Tricarboxylic acid (TCA) cycle (Citric acid cycle): With a transition step, oxidizes pyruvate, releases CO2CO2​, and generates reducing power, precursor metabolites, and ATP.

Respiration vs. Fermentation 🔄

Enzymes: Biological Catalysts 🧪

• Active site: Binds substrate(s) weakly, causing enzyme shape to change slightly (induced fit).

• The resulting enzyme-substrate complex destabilizes existing bonds or allows new ones to form.

• Enzymes lower the activation energy of a reaction.

• Enzymes can break large molecules into smaller ones or build large molecules from subunits.

• Theoretically, enzyme-catalyzed reactions are reversible, but the free energy of some reactions prevents reversibility.

Cofactors and Coenzymes 助手

• Some enzymes require a cofactor, a non-protein component (e.g., magnesium, zinc, copper).

• Coenzymes are organic cofactors that help enzymes transfer molecules or electrons (e.g., NADH), often derived from vitamins.

Environmental Factors Influencing Enzyme Activity 🌡

• Enzymes have a narrow range of optimal conditions, including:

  • Temperature

  • pH

  • Salt concentration

• A 10 degrees Celsius increase can double the speed of an enzymatic reaction up to a maximum; proteins denature at higher temperatures.

Enzyme Regulation 调节

Allosteric Enzymes

• Enzyme activity is controlled by a regulatory molecule binding to the allosteric site, which distorts the enzyme shape and prevents or enhances substrate binding to the active site.

• The regulatory molecule is often the end product of a metabolic pathway, allowing for feedback inhibition.

Competitive Inhibition

• An inhibitor binds to the active site, blocking the substrate.

• The chemical structure of the inhibitor is usually similar to the substrate.

• This inhibition is concentration-dependent.

• An example is sulfa drugs that block folate synthesis.

Non-Competitive Inhibition

• An inhibitor binds to a site other than the active site (e.g., allosteric site), causing a reversible action.

Microbial Metabolism: Fueling Cell Growth

Historical Context 🧪

• Alcohol and CO2CO2​ production in grape juice led to the study of yeast.

• Louis Pasteur showed that yeast produced alcohol but couldn't extract the sugar-converting component from the cells.

• In 1897, Eduard Buchner demonstrated that crushed yeast cells could convert sugar to ethanol, earning him the Nobel Prize in 1907.

Fundamental Tasks of Cells 🎯

• Synthesize new cellular components, including:

  • Cell walls

  • Membranes

  • Ribosomes

  • Nucleic acids

• Harvest energy to power reactions.

• Metabolism: Sum of chemical reactions in a cell.

  Implications of microbial metabolism are wide ranging, spanning from biofuel production to drug discovery, including:

  • Biofuels

  • Food and beverage production

  • Important models for study

  • Unique pathways as potential drug targets

• Metabolism is the sum of Anabolism and Catabolism

  Metabolism=Anabolism+CatabolismMetabolism=Anabolism+Catabolism

  • Anabolism refers to the build up of molecules.

  • Catabolism refers to the breakdown of molecules.

Energy Concepts ⚡️

• Energy is the capacity to do work.

• Forms of energy:

  • Potential Energy: Stored energy (e.g., chemical bonds, a rock on a hill, water behind a dam).

  • Kinetic Energy: Energy of motion (e.g., moving water).

• The energy in the universe is neither created nor destroyed but can be changed from one form to another.

• Photosynthetic organisms: Harvest energy from sunlight to power the synthesis of organic compounds from CO2CO2​. They convert the kinetic energy of photons into the potential energy of chemical bonds.

• Chemoorganotrophs: Obtain energy from organic compounds and depend on the activities of photosynthetic organisms or chemolithoautotrophs.

• Free energy is the energy available to do work.

• Energy is released when a chemical bond is broken.

• Exergonic reactions: Reactants have more free energy than products, resulting in the release of energy.

• Endergonic reactions: Products have more free energy than reactants, requiring energy input.

• The change in free energy for a reaction is the same, regardless of the number of steps involved. Cells often use multiple steps when degrading compounds.

• Energy released from exergonic reactions powers endergonic reactions.

Exergonic vs. Endergonic Reactions 📊

Metabolic Pathways and Enzymes ⚙

• Enzymes: Biological catalysts that speed up the conversion of a substrate into a product by lowering the activation energy.

• A specific enzyme is required for each step of a metabolic pathway. Without enzymes, energy-yielding reactions would occur too slowly.

• ATP (Adenosine Triphosphate): The energy currency of the cell, composed of ribose, adenine, and three phosphate groups.

• Cells produce ATP by adding a phosphate group to adenosine diphosphate (ADP). Energy is released by removing a phosphate group from ATP to yield ADP.

ATP Generation Processes 🔋

• Chemoorganotrophs:

  • Substrate-level phosphorylation: Energy generated in exergonic reactions.

  • Oxidative phosphorylation: Energy generated by proton motive force.

• Photosynthetic organisms:

  • Photophosphorylation: Sunlight used to create proton motive force.

Energy Sources and Electron Acceptors ♻

• Prokaryotes use diverse energy sources and terminal electron acceptors.

• Organic and inorganic compounds serve as energy sources.

• O2O2​ and other molecules are used as terminal electron acceptors.

• Electrons are removed through oxidation-reduction reactions (redox reactions).

• Oxidation: Substance loses electrons (Dehydrogenation).

• Reduction: Substance gains electrons (Hydrogenation).

• Energy is released when electrons move from a molecule with low affinity for electrons (energy source) to a molecule with high affinity (terminal electron acceptor).

Electron Carriers 🚚

• Energy is harvested in a stepwise process.

• Electrons are initially transferred to electron carriers (considered hydrogen carriers).

• Electron carriers ultimately drive the synthesis of ATP or are used in biosynthesis.

Common Electron Carriers

Precursor Metabolites 🌱

• E. coli can grow in glucose-salts medium, using glucose as an energy source and starting point for all cellular components (proteins, lipids, carbohydrates, nucleic acids).

• Some glucose molecules are completely oxidized for energy.

• Other glucose molecules are broken into smaller precursor metabolites that exit the catabolic pathway early to be used in biosynthesis.

Overview of Catabolism ⚙

• Two key processes:

  1. Oxidizing glucose molecules to generate ATP, reducing power (NADHNADH, FADH2FADH2​, and NADPHNADPH), and precursor metabolites via central metabolic pathways.

  2. Transferring electrons carried by NADHNADH and FADH2FADH2​ to a terminal electron acceptor through cellular respiration or fermentation.

• Central metabolic pathways oxidize glucose to CO2CO2​. These pathways are catabolic, but precursor metabolites and reducing power can be diverted for biosynthesis (amphibolic role).

• Key pathways include:

  • Glycolysis: Splits glucose (6C) into two pyruvate molecules (3C), generating modest ATP, reducing power, and precursors.

  • Pentose Phosphate Pathway: Primarily produces precursor metabolites and NADPHNADPH.

  • Tricarboxylic Acid (TCA) Cycle (Citric Acid Cycle): With a transition step, oxidizes pyruvate, releasing CO2CO2​, generating reducing power, precursor metabolites, and ATP.

Respiration vs. Fermentation 🔄

• Respiration (Cellular Respiration): Transfers electrons from glucose to the electron transport chain (ETC) to a terminal electron acceptor. The ETC generates a proton motive force, harvested to make ATP by oxidative phosphorylation.

  • Aerobic Respiration: O2O2​ is the terminal electron acceptor.

  • Anaerobic Respiration: A molecule other than O2O2​ is the terminal electron acceptor.

• Fermentation: Recycles electron carriers in cells that cannot respire, allowing continued ATP production. It uses pyruvate or a derivative as a terminal electron acceptor to receive H from NADHNADH, regenerating NAD+NAD+ so glycolysis can continue, providing a small amount of ATP. (e.g., 2 ATP via fermentation vs. 38 ATP via respiration).

Enzyme Function ⚙

• Active site: The region on an enzyme where the substrate(s) bind weakly, causing the enzyme shape to change slightly (induced fit). This enzyme-substrate complex destabilizes existing bonds or allows new ones to form, lowering the activation energy of the reaction.

• Enzymes break large molecules into smaller ones or build large molecules from subunits.

• Theoretically, enzyme-catalyzed reactions are reversible, but the free energy of some reactions prevents reversibility.

Cofactors and Coenzymes 辅助因子

• Cofactor: A non-protein component that some enzymes require for assistance (e.g., magnesium, zinc, copper).

• Coenzyme: An organic cofactor that helps some enzymes transfer molecules or electrons from one compound to another (e.g., NADHNADH). Often derived from vitamins.

Environmental Influences on Enzyme Activity 🌡

• Enzymes function within a narrow range of optimal conditions, including temperature, pH, and salt concentration.

• A 10-degree Celsius increase can double the speed of an enzymatic reaction up to a maximum point; proteins denature at higher temperatures.

Enzyme Regulation 🛑

• Allosteric Enzymes: Enzyme activity is controlled by a regulatory molecule binding to an allosteric site, distorting the enzyme shape and preventing or enhancing substrate binding to the active site. The regulatory molecule is usually the end product of the metabolic pathway, allowing feedback inhibition.

• Competitive Inhibition: An inhibitor binds to the active site, with its chemical structure usually resembling the substrate. The effect is concentration-dependent, blocking the substrate. An example is sulfa drugs that block folate synthesis.

• Non-competitive Inhibition: An inhibitor binds to a site other than the active site (e.g., allosteric inhibitors), and its action is reversible.

Microbial Metabolism

A Glimpse of History 🍇

• Alcohol and CO2 are produced in grape juice as yeast cells increase in number.

• Louis Pasteur (1850s):

  • Set out to show that yeast produces alcohol.

  • Introduced yeast cells to a clear solution of sugar, ammonia, mineral salts, and trace elements.

  • Observed yeast multiplication, sugar decrease, and alcohol increase.

  • Strongly supported his idea but couldn't extract the alcohol-producing substance from the cells.

• Eduard Buchner (1897):

  • German chemist.

  • Showed that crushed yeast cells could convert sugar to ethanol.

  • Awarded Nobel Prize in 1907.

Introduction to Microbial Metabolism 🧪

• Cells have two fundamental tasks:

  • Synthesize new parts (cell walls, membranes, ribosomes, nucleic acids).

  • Harvest energy to power reactions.

• Metabolism:

  The sum of chemical reactions in a cell.

• Implications of microbial metabolism:

  • Biofuels

  • Food and beverage production

  • Important models for study

  • Unique pathways are potential drug targets

• Metabolism Equation:

  Metabolism=Anabolism+CatabolismMetabolism=Anabolism+Catabolism

  • Anabolism: Building up

  • Catabolism: Breaking down

Energy Principles ⚡

• Energy:

  The capacity to do work.

• Types of energy:

  • Potential energy: Stored energy (e.g., chemical bonds, rock on a hill, water behind a dam).

  • Kinetic energy: Energy of motion (e.g., moving water).

• Laws of Thermodynamics:

  Energy in the universe cannot be created or destroyed, but it can be changed from one form to another.

• Photosynthetic organisms:

  • Harvest energy in sunlight.

  • Power the synthesis of organic compounds from CO2.

  • Convert kinetic energy of photons to potential energy of chemical bonds.

• Chemoorganotrophs:

  • Obtain energy from organic compounds.

  • Depend on the activities of photosynthetic organisms or chemolithoautotrophs.

• Free energy:

  Energy available to do work.

• Exergonic reactions:

  • Reactants have more free energy than products.

  • Energy is released in the reaction.

• Endergonic reactions:

  • Products have more free energy than reactants.

  • Reaction requires input of energy.

• Change in free energy for a given reaction remains the same regardless of the number of steps involved.

• Cells use multiple steps when degrading compounds.

• Energy released from exergonic reactions powers endergonic reactions.

Exergonic vs. Endergonic Reactions 📉 📈

• Exergonic Reactions: Energy is released.

• Endergonic Reactions: Energy is consumed.

Metabolic Pathways and Enzymes ⚙

• Enzymes:

  Biological catalysts that speed up the conversion of substrate into product by lowering activation energy.

• Each step of a metabolic pathway requires a specific enzyme.

• Without enzymes, energy-yielding reactions would occur too slowly.

ATP: The Energy Currency 💰

• ATP (Adenosine triphosphate):

  Energy currency of the cell.

• Composed of ribose, adenine, and three phosphate groups.

• Cells produce ATP by adding a phosphate group to adenosine diphosphate (ADP).

• Energy is released when a phosphate group is removed from ATP to yield ADP.

ATP Generation Processes 🔄

• Chemoorganotrophs:

  • Substrate-level phosphorylation: Energy generated in exergonic reactions.

  • Oxidative phosphorylation: Energy generated by proton motive force.

• Photosynthetic organisms:

  • Photophosphorylation: Sunlight used to create proton motive force.

Diversity in Energy and Electron Acceptors 🌍

• Prokaryotes use remarkably diverse energy sources and terminal electron acceptors.

• Organic and inorganic compounds serve as energy sources.

• O2 and other molecules serve as terminal electron acceptors.

• Redox reactions:

  Electrons are removed through a series of oxidation-reduction reactions.

  • Oxidation: Substance loses electrons.

  • Reduction: Substance gains electrons.

  • Electron-proton pair, or hydrogen atom, is transferred.

  • Dehydrogenation: Oxidation

  • Hydrogenation: Reduction

Chemical Energy Sources and Electron Affinity ⚛

• When electrons move from a molecule with low affinity for electrons (energy source) to a molecule with high affinity for electrons (terminal electron acceptor), energy is released.

Electron Carriers: The Stepwise Energy Harvest 🚚

• Energy is harvested in a stepwise process.

• Electrons are initially transferred to electron carriers.

• These carriers can be considered hydrogen carriers.

• Ultimately, they drive the synthesis of ATP or biosynthesis.

Electron Carriers and Their Roles 📊

Precursor Metabolites 🌱

• E. coli can grow in glucose-salts medium.

• Glucose is the energy source and the starting point for all cellular components.

  • Includes proteins, lipids, carbohydrates, and nucleic acids.

• Some glucose molecules are completely oxidized for energy.

• Other glucose molecules are broken into smaller precursor metabolites that exit the catabolic pathway early to be used in biosynthesis.

Overview of Catabolism 🔄

• Two key sets of processes:

  • Oxidizing glucose molecules to generate ATP, reducing power (NADH, FADH2, and NADPH), and precursor metabolites. This is accomplished through central metabolic pathways.

  • Transferring the electrons carried by NADH and FADH2 to the terminal electron acceptor via cellular respiration or fermentation.

Central Metabolic Pathways 🛣

• Oxidize glucose to CO2.

• Catabolic, but precursor metabolites and reducing power can be diverted for use in biosynthesis.

• Termed amphibolic to reflect their dual role.

  • Glycolysis:

    • Splits glucose (6C) into two pyruvate molecules (3C).

    • Generates modest ATP, reducing power, and precursors.

  • Pentose phosphate pathway:

    • Primary role is the production of precursor metabolites and NADPH.

  • Tricarboxylic acid (TCA) cycle (Citric acid cycle):

    • With transition step, oxidizes pyruvate and releases CO2.

    • Generates reducing power, precursor metabolites, and ATP.

Respiration 呼吸

• Respiration (or cellular respiration) transfers electrons from glucose to the electron transport chain (ETC) to a terminal electron acceptor.

• The electron transport chain generates a proton motive force.

• This force is harvested to make ATP by oxidative phosphorylation.

  • Aerobic respiration: O2 is the terminal electron acceptor.

  • Anaerobic respiration: A molecule other than O2 is the terminal electron acceptor.

Fermentation 🍺

• Fermentation recycles electron carriers in a cell that cannot respire, allowing it to continue making ATP.

• Pyruvate or a derivative is used as the terminal electron acceptor to receive H from NADH.

• Regenerates NAD+ so that glycolysis can continue.

• Glycolysis provides a small amount of ATP (38 vs. 2).

Enzymes: Biological Catalysts ⚙

• Active site: The surface of an enzyme that binds substrate(s) weakly.

• This binding causes the enzyme's shape to change slightly, known as induced fit.

• The resulting enzyme-substrate complex destabilizes existing bonds or allows new ones to form.

• This lowers the activation energy of the reaction.

• Enzymes are used to break large molecules into smaller ones or to build large molecules from subunits.

• Theoretically, enzyme-catalyzed reactions are reversible, but the free energy of some reactions prevents reversibility.

Cofactors and Coenzymes 💊

• Cofactor:

  A non-protein component required by some enzymes for assistance.

  • Examples: magnesium, zinc, copper.

• Coenzymes:

  Organic cofactors that help some enzymes transfer certain molecules or electrons from one compound to another.

  • Example: NADH

  • Often derived from vitamins.

Environmental Factors Influencing Enzyme Activity 🌡

• Enzymes have a narrow range of optimal conditions, including:

  • Temperature

  • pH

  • Salt concentration

• A 10-degree Celsius increase doubles the speed of enzymatic reactions up to the maximum point; proteins denature at higher temperatures.

Regulation of Allosteric Enzymes 🛑

• Enzyme activity is controlled by a regulatory molecule binding to an allosteric site.

• This binding distorts the enzyme's shape, either preventing or enhancing the binding of the substrate to the active site.

• The regulatory molecule is usually the end product of the metabolic pathway.

• This allows for feedback inhibition.

Competitive Inhibition of Enzymes 🚫

• In competitive inhibition, the inhibitor binds to the active site.

• The chemical structure of the inhibitor is usually similar to that of the substrate.

• This process is concentration-dependent; the inhibitor blocks the substrate.

• An example is sulfa drugs that block folate synthesis.

Characteristics of Enzyme Inhibitors 🧪

• Enzyme Inhibition:

  • Non-competitive inhibition: The inhibitor binds to a site other than the active site.

  • Allosteric inhibitors are one example; their action is reversible.

Microbial Metabolism

History of Microbial Metabolism 🔬

• In the 1850s, Louis Pasteur aimed to prove that yeastproduces alcohol.

  • He observed that yeast cells multiplied, sugar decreased, and alcohol levels increased when yeast cells were added to a solution of sugar, ammonia, mineral salts, and trace elements.

  • He was unable to extract the substance inside the cells responsible for converting sugar.

• In 1897, Eduard Buchner demonstrated that crushed yeast cells could convert sugar to ethanol, earning him the Nobel Prize in 1907.

Introduction to Metabolism 🧬

• All cells must:

  • Synthesize new parts: cell walls, membranes, ribosomes, nucleic acids

  • Harvest energy to power reactions

• Metabolism:

  Sum of chemical reactions in a cell

• Implications of microbial metabolism:

  • Biofuels

  • Food and beverage production

  • Important models for study

  • Unique pathways are potential drug targets

• Metabolism = Anabolism + Catabolism

  • Anabolism = build up

  • Catabolism = breakdown

Energy Principles ⚡️

• Energy:

  The capacity to do work

• Types of energy:

  • Potential: stored energy (chemical bonds, rock on a hill, water behind a dam)

  • Kinetic: energy of motion (moving water)

• Energy Transformation: Energy in the universe cannot be created or destroyed, but it can be changed from one form to another.

• Photosynthetic organisms harvest energy from sunlight and convert the kinetic energy of photons into the potential energy of chemical bonds. They use this energy to synthesize organic compounds from CO2.

• Chemoorganotrophs obtain energy from organic compounds, depending on the activities of photosynthetic organisms or chemolithoautotrophs.

• Free energy:

  Energy available to do work

  • Energy is released when a chemical bond is broken.

• Exergonic reactions:

  Reactants have more free energy than products; energy is released in the reaction.

• Endergonic reactions:

  Products have more free energy than reactants; the reaction requires an input of energy.

• The change in free energy for a given reaction is the same regardless of the number of steps involved.

• Cells use multiple steps when degrading compounds.

• Energy released from exergonic reactions powers endergonic reactions.

Metabolic Pathways ⚙

• Enzymes:

  Biological catalysts that speed up the conversion of a substrate into a product by lowering the activation energy.

• Each step of a metabolic pathway requires a specific enzyme.

• Without enzymes, energy-yielding reactions would occur too slowly.

• ATP (Adenosine Triphosphate):

  The energy currency of the cell, composed of ribose, adenine, and three phosphate groups.

  • Cells produce ATP by adding a phosphate group to adenosine diphosphate (ADP).

  • Energy is released by removing a phosphate group from ATP to yield ADP.

ATP Generation 🔋

• Chemoorganotrophs

  • Substrate-level phosphorylation: Energy generated in exergonic reactions

  • Oxidative phosphorylation: Energy generated by proton motive force

• Photosynthetic organisms

  • Photophosphorylation: Sunlight used to create proton motive force

Energy Sources and Redox Reactions ⚡️

• Prokaryotes use diverse energy sources and terminal electron acceptors.

  • Organic and inorganic compounds are used as energy sources.

  • O2 and other molecules are used as terminal electron acceptors.

• Electrons are removed through a series of oxidation-reduction reactions (redox reactions).

  • Oxidation: Substance loses electrons.

  • Reduction: Substance gains electrons.

  • An electron-proton pair, or hydrogen atom, is transferred.

    • Dehydrogenation = oxidation

    • Hydrogenation = reduction

• Energy Release: When electrons move from a molecule with low affinity for electrons (energy source) to a molecule with high affinity for electrons (terminal electron acceptor), energy is released.

Electron Carriers 载体

• Energy is harvested in a stepwise process.

• Electrons are initially transferred to electron carriers, which can be considered hydrogen carriers.

• Electron carriers ultimately drive the synthesis of ATP or biosynthesis.

Common Electron Carriers

Precursor Metabolites 🌱

• E. coli can grow in glucose-salts medium.

  • Glucose is the energy source.

  • Glucose is the starting point for all cellular components, including proteins, lipids, carbohydrates, and nucleic acids.

• Some glucose molecules are completely oxidized for energy.

• Other glucose molecules are broken into smaller precursor metabolites that exit the catabolic pathway early to be used in biosynthesis.

Catabolism Overview 🔪

• Two key processes:

  1. Oxidizing glucose molecules to generate ATP, reducing power (NADH, FADH2, and NADPH), and precursor metabolites.

     • Accomplished in central metabolic pathways.

  2. Transferring electrons carried by NADH and FADH2 to the terminal electron acceptor.

     • Done by cellular respiration or fermentation.

Central Metabolic Pathways 🚦

• Central metabolic pathways oxidize glucose to CO2.

• Catabolic, but precursor metabolites and reducing power can be diverted for biosynthesis (amphibolic).

• Glycolysis:

  Splits glucose (6C) into two pyruvate molecules (3C).

  • Generates modest ATP, reducing power, and precursors.

• Pentose phosphate pathway:

  Primarily produces precursor metabolites and NADPH.

• Tricarboxylic acid (TCA) cycle (Citric acid cycle):

  With a transition step, it oxidizes pyruvate and releases CO2.

  • Generates reducing power, precursor metabolites, and ATP.

Respiration and Fermentation ♻

• Respiration (cellular respiration):

  Transfers electrons from glucose to an electron transport chain (ETC) to a terminal electron acceptor.

  • The electron transport chain generates a proton motive force, which is harvested to make ATP by oxidative phosphorylation.

    • Aerobic respiration: O2 is the terminal electron acceptor.

    • Anaerobic respiration: A molecule other than O2 serves as the terminal electron acceptor.

• Fermentation:

  Recycles electron carriers in a cell that cannot respire so that it can continue to make ATP.

  • Uses pyruvate or a derivative as the terminal electron acceptor to receive H from NADH.

  • Regenerates NAD+ so that glycolysis can continue.

  • Glycolysis provides a small amount of ATP (38 vs. 2).

Enzymes Explained 催化剂

• Active site:

  The region on the surface of an enzyme that binds substrate(s) weakly.

  • This binding causes the enzyme's shape to change slightly (induced fit).

  • The resulting enzyme-substrate complex destabilizes existing bonds or allows new ones to form.

  • Lowers the activation energy of the reaction.

• Enzymes are used to break large molecules into smaller ones or to build large molecules from their subunits.

• Theoretically, enzyme-catalyzed reactions are reversible, but the free energy of some reactions prevents reversibility.

• Cofactor:

  A non-protein component that assists some enzymes. * Examples: magnesium, zinc, copper

  • Coenzymes:

    Organic cofactors that help some enzymes transfer certain molecules or electrons from one compound to another. Example: NADH Often derived from vitamins

Environmental Factors Affecting Enzyme Activity 🌡

• Enzymes have a narrow range of optimal conditions.

  • Temperature, pH, and salt concentration.

  • A 10-degree Celsius increase doubles the speed of an enzymatic reaction up to its maximum.

  • Proteins denature at higher temperatures.

Enzyme Regulation ⚙

• Allosteric enzymes:

  Enzyme activity is controlled by a regulatory molecule binding to an allosteric site.

  • This binding distorts the enzyme's shape, preventing or enhancing the binding of the substrate to the active site.

  • The regulatory molecule is often the end product of a metabolic pathway, allowing for feedback inhibition.

Enzyme Inhibition 🚫

• Competitive Inhibition:

  The inhibitor binds to the active site.

  • The chemical structure of the inhibitor is usually similar to that of the substrate.

  • The effect is concentration-dependent; the inhibitor blocks the substrate.

  • Example: sulfa drugs that block folate synthesis.

• Non-competitive Inhibition:

  The inhibitor binds to a site other than the active site. * Allosteric inhibitors are one example; their action is reversible.

Microbial Metabolism: Fueling Cell Growth

A Glimpse of History 📜

• Alcohol and CO2 are produced in grape juice as yeast cells increase in number.

• Louis Pasteur (1850s) aimed to demonstrate that yeast produces alcohol but couldn't extract the sugar-converting substance from the cells.

• Eduard Buchner (1897) demonstrated that crushed yeast cells could convert sugar to ethanol and was awarded the Nobel Prize in 1907.

Introduction 🚀

• All cells must:

  • Synthesize new parts (cell walls, membranes, ribosomes, nucleic acids).

  • Harvest energy to power reactions.

• Metabolism:

  Sum of chemical reactions in a cell.

• Implications of microbial metabolism:

  • Biofuels

  • Food and beverage production

  • Important models for study

  • Unique pathways are potential drug targets

• Metabolism = Anabolism (build up) + Catabolism(breakdown)

Energy Fundamentals 💡

• Energy:

  The capacity to do work.

• Forms of energy:

  • Potential energy: Stored energy (e.g., chemical bonds, a rock on a hill, water behind a dam).

  • Kinetic energy: Energy of motion (e.g., moving water).

• Energy in the universe:

  Cannot be created or destroyed, but it can be changed from one form to another.

• Photosynthetic organisms harvest energy from sunlight. They power the synthesis of organic compounds from CO2, converting kinetic energy of photons to potential energy of chemical bonds.

• Chemoorganotrophs obtain energy from organic compounds, depending on the activities of photosynthetic organisms or chemolithoautotrophs.

Free Energy and Reactions ⚡

• Free energy:

  Energy available to do work.

• Energy is released when a chemical bond is broken.

• Exergonic reactions:

  Reactants have more free energy than products; energy is released.

• Endergonic reactions:

  Products have more free energy than reactants; reaction requires energy input.

• The change in free energy for a given reaction remains the same regardless of the number of steps involved. Cells use multiple steps when degrading compounds.

• Energy released from exergonic reactions powers endergonic reactions.

Metabolic Pathways and Enzymes ⚙

• Enzymes:

  Biological catalysts that speed up the conversion of substrate into product by lowering activation energy.

• A specific enzyme is required for each step of a metabolic pathway. Without enzymes, energy-yielding reactions would occur too slowly.

• ATP (Adenosine Triphosphate):

  The energy currency of the cell, composed of ribose, adenine, and three phosphate groups.

• Cells use energy to produce ATP by adding a phosphate group to adenosine diphosphate (ADP). Energy is released by removing a phosphate group from ATP to yield ADP.

ATP Generation Processes 🔋

Metabolic Diversity in Prokaryotes 🦠

• Prokaryotes utilize diverse energy sources and terminal electron acceptors.

• Energy sources: Organic and inorganic compounds.

• Terminal electron acceptors: O2 and other molecules.

• Redox reactions: Electrons are removed through a series of oxidation-reduction reactions.

  • Oxidation: Substance loses electrons.

  • Reduction: Substance gains electrons.

  • Dehydrogenation = oxidation

  • Hydrogenation = reduction

• Electron-proton pairs, or hydrogen atoms, are transferred.

Redox Tower and Electron Carriers 🗼

• When electrons move from a molecule with low affinity for electrons (energy source) to a molecule with high affinity for electrons (terminal electron acceptor), energy is released.

• Energy is harvested in a stepwise process, with electrons initially transferred to electron carriers (which can be considered hydrogen carriers).

• These carriers ultimately drive the synthesis of ATP or biosynthesis.

Electron Carriers Table 📝

Precursor Metabolites 🌱

• E. coli can grow in glucose-salts medium, where glucose serves as both an energy source and a starting point for all cellular components (proteins, lipids, carbohydrates, nucleic acids).

• Some glucose molecules are completely oxidized for energy, while others are broken down into smaller precursor metabolites that exit the catabolic pathway early for use in biosynthesis.

Catabolism Overview 🔄

• Two key processes:

  1. Oxidizing glucose molecules to generate ATP, reducing power (NADH, FADH2, and NADPH), and precursor metabolites through central metabolic pathways.

  2. Transferring electrons carried by NADH and FADH2 to a terminal electron acceptor via cellular respiration or fermentation.

Central Metabolic Pathways 🛣

• Central metabolic pathways oxidize glucose to CO2. They are catabolic, but precursor metabolites and reducing power can be diverted for use in biosynthesis (amphibolic role).

Respiration vs. Fermentation ♻

• Respiration (Cellular Respiration): Transfers electrons from glucose to the electron transport chain (ETC), then to a terminal electron acceptor. The ETC generates a proton motive force, which is harvested to make ATP by oxidative phosphorylation.

  • Aerobic respiration: O2 is the terminal electron acceptor.

  • Anaerobic respiration: A molecule other than O2 is the terminal electron acceptor.

• Fermentation: Recycles electron carriers in cells that cannot respire, allowing them to continue making ATP. It uses pyruvate or a derivative as the terminal electron acceptor to receive H from NADH, regenerating NAD+ so that glycolysis can continue. Glycolysis provides a small amount of ATP (e.g., 2 ATP vs. 38 in respiration).

Enzymes in Detail 🔬

• The active site on the enzyme surface binds substrate(s) weakly, causing a slight change in enzyme shape (induced fit).

• The resulting enzyme-substrate complex destabilizes existing bonds or allows new ones to form, lowering the activation energy of the reaction.

• Enzymes can break large molecules into smaller ones or build large molecules from subunits.

• Theoretically, enzyme-catalyzed reactions are reversible, but the free energy of some reactions prevents reversibility.

Cofactors and Coenzymes 🧪

• Cofactor:

  A non-protein component that some enzymes require for assistance (e.g., magnesium, zinc, copper).

• Coenzymes:

  Organic cofactors that help some enzymes transfer molecules or electrons from one compound to another (e.g., NADH). Often derived from vitamins.

Environmental Influences on Enzyme Activity 🌡

• Enzymes have a narrow range of optimal conditions (temperature, pH, salt concentration).

• A 10-degree Celsius increase can double the speed of an enzymatic reaction up to a maximum, but proteins denature at higher temperatures.

Enzyme Regulation 🚦

• Allosteric Enzymes: Enzyme activity is controlled by a regulatory molecule binding to an allosteric site, distorting the enzyme's shape and either preventing or enhancing the binding of the substrate to the active site. The regulatory molecule is usually the end product of the metabolic pathway, allowing for feedback inhibition.

• Competitive Inhibition: An inhibitor binds to the active site. The chemical structure of the inhibitor is usually similar to the substrate, and the inhibition is concentration-dependent. An example is sulfa drugs blocking folate synthesis.

Enzyme Inhibition Types 🚫

A Glimpse of History 🍇

• Alcohol and CO2CO2​ are produced in grape juice as yeast cells increase in number.

• Louis Pasteur (1850s) demonstrated that yeast produces alcohol.

  • He showed that yeast cells multiply when added to a clear solution of sugar, ammonia, mineral salts, and trace elements, leading to a decrease in sugar and an increase in alcohol levels.

  • However, Pasteur couldn't extract the substance from the cells responsible for converting sugar.

• Eduard Buchner (1897) showed that crushed yeast cells could convert sugar to ethanol and was awarded the Nobel Prize in 1907.

Introduction 🤔

• All cells must:

  • Synthesize new parts (cell walls, membranes, ribosomes, nucleic acids).

  • Harvest energy to power reactions.

• Metabolism: The sum of chemical reactions in a cell.

  Metabolism = Anabolism + Catabolism

  • Anabolism refers to building up.

  • Catabolism refers to breaking down.

• Implications of microbial metabolism:

  • Biofuels

  • Food and beverage production

  • Important models for study

  • Unique pathways are potential drug targets

Energy ⚡️

• Energy: The capacity to do work.

  • Potential energy: Stored energy (e.g., chemical bonds, a rock on a hill, water behind a dam).

  • Kinetic energy: Energy of motion (e.g., moving water).

• The energy in the universe cannot be created or destroyed, but it can be changed from one form to another.

• Photosynthetic organisms harvest energy from sunlight.

  • Powers synthesis of organic compounds from CO2CO2​.

  • Converts kinetic energy of photons to potential energy of chemical bonds.

• Chemoorganotrophs obtain energy from organic compounds.

  • Depend on activities of photosynthetic organisms or chemolithoautotrophs.

• Free energy is energy available to do work.

  • Energy is released when a chemical bond is broken.

  • Exergonic reactions: Reactants have more free energy than products; energy is released.

  • Endergonic reactions: Products have more free energy than reactants; the reaction requires energy input.

  • The change in free energy for a reaction is the same regardless of the number of steps involved.

  • Cells use multiple steps when degrading compounds.

  • Energy released from exergonic reactions powers endergonic reactions.

Components of Metabolic Pathways ⚙

Role of Enzymes

• Enzymes are biological catalysts that speed up the conversion of substrate into product by lowering the activation energy.

• Each step of a metabolic pathway requires a specific enzyme.

• Without enzymes, energy-yielding reactions would occur too slowly.

Role of ATP

• Adenosine triphosphate (ATP) is the energy currency of the cell.

  • Composed of ribose, adenine, and three phosphate groups.

  • Cells produce ATP by adding a phosphate group to adenosine diphosphate (ADP).

  • Energy is released by removing a phosphate group from ATP to yield ADP.

Processes That Generate ATP

• Chemoorganotrophs:

  • Substrate-level phosphorylation: Energy is generated in exergonic reactions.

  • Oxidative phosphorylation: Energy is generated by proton motive force.

• Photosynthetic organisms:

  • Photophosphorylation: Sunlight is used to create proton motive force.

Chemical Energy Sources and Terminal Electron Acceptors 🧪

• Prokaryotes use diverse energy sources and terminal electron acceptors.

  • Organic and inorganic compounds are used as energy sources.

  • O2O2​ and other molecules are used as terminal electron acceptors.

• Electrons are removed through a series of oxidation-reduction reactions (redox reactions).

  • Oxidation: Substance loses electrons.

  • Reduction: Substance gains electrons.

  • An electron-proton pair (hydrogen atom) is transferred.

    • Dehydrogenation = oxidation

    • Hydrogenation = reduction

• When electrons move from a molecule with low affinity for electrons (energy source) to a molecule with high affinity for electrons (terminal electron acceptor), energy is released.

The Role of Electron Carriers 载体

• Energy is harvested in a stepwise process.

• Electrons are initially transferred to electron carriers, which can be considered hydrogen carriers.

• Ultimately, electron carriers drive the synthesis of ATP or biosynthesis.

Electron Carriers 🚃

Precursor Metabolites 🧱

• E. coli can grow in glucose-salts medium.

  • Glucose is the energy source and the starting point for all cellular components (proteins, lipids, carbohydrates, nucleic acids).

  • Some glucose molecules are completely oxidized for energy.

  • Other glucose molecules are broken into smaller precursor metabolites that exit the catabolic pathway early to be used in biosynthesis.

Overview of Catabolism 🔄

• Two key sets of processes:

  • Oxidizing glucose molecules to generate ATP, reducing power (NADH, FADH2, and NADPH), and precursor metabolites; accomplished in central metabolic pathways.

  • Transferring electrons carried by NADH and FADH2 to the terminal electron acceptor, which is done by either cellular respiration or fermentation.

• Central metabolic pathways oxidize glucose to CO2CO2​.

  • Catabolic, but precursor metabolites and reducing power can be diverted for biosynthesis.

  • Termed amphibolic to reflect the dual role.

• Glycolysis: Splits glucose (6C) into two pyruvate molecules (3C).

  • Generates modest ATP, reducing power, and precursors.

• Pentose phosphate pathway: Primary role is the production of precursor metabolites and NADPH.

• Tricarboxylic acid (TCA) cycle (Citric acid cycle): With a transition step, oxidizes pyruvate and releases CO2CO2​.

  • Generates reducing power, precursor metabolites, and ATP.

Respiration vs. Fermentation 💨

• Respiration (or cellular respiration): Transfers electrons from glucose to the electron transport chain (ETC) to the terminal electron acceptor.

  • The electron transport chain generates a proton motive force.

  • This force is harvested to make ATP by oxidative phosphorylation.

    • Aerobic respiration: O2O2​ is the terminal electron acceptor.

    • Anaerobic respiration: A molecule other than O2O2​is the terminal electron acceptor.

• Fermentation: Recycles electron carriers in a cell that cannot respire, allowing it to continue making ATP.

  • Uses pyruvate or a derivative as the terminal electron acceptor to receive H from NADH.

  • Regenerates NAD+NAD+ so that glycolysis can continue.

  • Glycolysis provides a small amount of ATP (2 ATP) compared to respiration (38 ATP).

Enzymes 催化剂

• The active site on the surface of the enzyme binds substrate(s) weakly.

  • This binding causes the enzyme's shape to change slightly, called induced fit.

  • The resulting enzyme-substrate complex destabilizes existing bonds or allows new ones to form.

  • Lowers the activation energy of the reaction.

• Enzymes break large molecules into smaller ones or build large molecules from subunits.

• Theoretically, enzyme-catalyzed reactions are reversible, but the free energy of some reactions prevents reversibility.

Cofactors 助手

• Some enzymes require a non-protein component called a cofactor for assistance (e.g., magnesium, zinc, copper).

• Coenzymes are organic cofactors that help enzymes transfer molecules or electrons (e.g., NADH).

  • Often derived from vitamins.

Environmental Factors That Influence Enzyme Activity 🌡

• Enzymes have a narrow range of optimal conditions, including temperature, pH, and salt concentration.

• A 10∘C10∘C increase can double the speed of an enzymatic reaction, up to a maximum, after which proteins denature at higher temperatures.

Regulation of Allosteric Enzymes 调节酶

• Enzyme activity is controlled by a regulatory molecule binding to the allosteric site.

  • This binding distorts the enzyme's shape, preventing or enhancing the binding of the substrate to the active site.

  • The regulatory molecule is usually the end product of a metabolic pathway, allowing for feedback inhibition.

Competitive Inhibition of Enzymes 抑制剂

• In competitive inhibition, the inhibitor binds to the active site.

  • The chemical structure of the inhibitor is usually similar to that of the substrate.

  • The inhibition is concentration-dependent; the inhibitor blocks the substrate.

  • An example is sulfa drugs that block folate synthesis.

Characteristics of Enzyme Inhibitors 🚧

• In non-competitive inhibition, the inhibitor binds to a site other than the active site.

  • Allosteric inhibitors are an example, and their action is often reversible.

  • Some non-competitive inhibitors are not reversible.# Metabolic Pathways and Energy Production

Enzyme Inhibition 🚫

Irreversible Non-Competitive Inhibition

• Mercury oxidizes the SH groups of the amino acid cysteine, converting it to cystine.

• Cystine cannot form important disulfide bonds (SS).

• The enzyme changes shape and becomes nonfunctional.

Types of Enzyme Inhibition

Central Metabolic Pathways ⚙

Glycolysis

• Converts 1 glucose molecule to 2 pyruvate molecules.

• Net yield: 2 ATP, 2 NADH

• Investment phase:

  • 2 ATP consumed

  • 2 phosphate groups added

  • Glucose split into two 3-carbon molecules

• Pay-off phase:

  • 3-carbon molecules converted to pyruvate

  • Generates 4 ATP, 2 NADH

  • Net ATP production: 4 ATP - 2 ATP = 2 ATP

Pentose Phosphate Pathway

• Breaks down glucose.

• Important in biosynthesis for precursor metabolites:

  • Ribose 5-phosphate

  • Erythrose 4-phosphate

• Also generates a variable amount of NADPH.

• Product glyceraldehyde-3-phosphate can enter glycolysis.

Transition Step (Pyruvate Oxidation)

• CO2CO2​ is removed from pyruvate.

• Electrons are transferred, reducing it to a 2-carbon acetyl group joined to coenzyme A to form acetyl-CoA.

• Links previous pathways to the TCA cycle.

Tricarboxylic Acid (TCA) Cycle (Citric Acid Cycle)

• Completes the oxidation of glucose.

• Produces:

  • 4 CO2CO2​

  • 2 ATP

  • 6 NADH

  • 2 FADH2FADH2​

• Produces precursor metabolites.

Cellular Respiration ⚡

Oxidative Phosphorylation

• Uses reducing power (NADH, FADH2FADH2​) generated by glycolysis, transition step, and TCA cycle to synthesize ATP.

• Two processes involved:

  • Electron transport chain: Uses reducing power of NADH, FADH2FADH2​ to generate proton motive force.

  • ATP synthase: Uses energy of proton motive force to generate ATP.

• Process proposed by Peter Mitchell in 1961.

• He received a Nobel Prize in 1978 for what is now called the chemiosmotic theory.

Electron Transport Chain (ETC)

• Series of membrane-embedded electron carriers.

• Accepts electrons from NADH, FADH2FADH2​.

• Energy released as electrons are passed from one carrier to the next.

• Energy pumps protons across the membrane:

  • Prokaryotes: Cytoplasmic membrane

  • Eukaryotes: Inner mitochondrial membrane

• Creates electrochemical gradient called proton motive force.

Components of an Electron Transport Chain (ETC)

• Most carriers are grouped into large protein complexes that function as proton pumps.

• Others move electrons from one complex to the next.

• Quinones: Lipid-soluble, move freely in the membrane, and can transfer electrons between complexes.

• Cytochromes: Proteins contain heme, a molecule with an iron atom at the center; several types can be used to distinguish bacteria.

• Flavoproteins: Proteins to which a flavin group is attached; FAD and other flavins are synthesized from riboflavin.

General Mechanisms of Proton Pumps

• Some carriers accept only hydrogen atoms (proton-electron pairs), others only electrons.

• Spatial arrangement in the membrane shuttles protons to the outside of the membrane.

• The net effect is the movement of protons across the membrane, establishing a concentration gradient driven by energy released during electron transfer.

Electron Transport Chain Variations

• Mitochondria ETC

• Prokaryotes: Tremendous variation, even single species can have several alternate carriers.

Anaerobic Respiration in E. coli

• Harvests less energy than aerobic respiration.

• Lower electron affinities of terminal electron acceptors.

• Some components are different.

• Can synthesize terminal oxidoreductase that uses nitrateas a terminal electron acceptor.

• Produces nitrite.

• E. coli converts to less toxic ammonia; others convert to N2ON2​O (nitrous oxide) or N2N2​.

• Sulfate-reducers use sulfate (SO4SO4​) as a terminal electron acceptor and produce hydrogen sulfide as an end product.

ATP Synthase

• Energy is required to establish the gradient; energy is released when the gradient is removed or reduced.

• ATP synthase allows protons to flow down the gradient in a controlled manner and uses the energy to add a phosphate group to ADP.

• 1 ATP is formed from the entry of approximately 3 protons.

Theoretical ATP Yield of Oxidative Phosphorylation in Prokaryotes

• Glycolysis: 2 NADH yields 6 ATP

• Transition step: 2 NADH yields 6 ATP

• TCA Cycle: Total maximum oxidative phosphorylation yield = 34 ATP

ATP Yield of Aerobic Respiration in Prokaryotes

• Substrate-level phosphorylation:

  • 2 ATP (from glycolysis; net gain)

  • 2 ATP (from the TCA cycle)

  • 4 ATP (total)

• Oxidative phosphorylation:

  • 6 ATP (from reducing power gained in glycolysis)

  • 6 ATP (from reducing power gained in the transition step)

  • 22 ATP (from reducing power gained in the TCA cycle)

  • 34 ATP (total)

• Total ATP gain (theoretical maximum) = 38

Fermentation 🍺

• Used when respiration is not an option.

• E. coli is a facultative anaerobe and can undergo aerobic respiration, anaerobic respiration, and fermentation.

• Streptococcus pneumoniae lacks an electron transport chain, making fermentation the only option.

• ATP-generating reactions are only those of glycolysis.

• Regenerates NAD+NAD+.

Fermentation End Products

• Varied end products are helpful in identification and are commercially useful.

  • Lactic Acid

  • Ethanol

  • Butyric acid

  • Propionic Acid

  • Mixed Acids

  • 2,3-Butanediol

Catabolism of Organic Compounds Other Than Glucose 🍎

• Microbes can use a variety of compounds.

• Secrete enzymes, transport subunits into the cell, and degrade them further to appropriate precursor metabolites.

• Polysaccharides and disaccharides are broken down by amylases, cellulases, and disaccharides.

  • Glucose enters glycolysis directly; other monosaccharides are converted to precursor metabolites.

• Lipids are broken down by lipases.

  • Glycerol is converted to dihydroxyacetone phosphate, which enters glycolysis.

  • Fatty acids are degraded by ββ-oxidation to enter the TCA cycle.

• Proteins are broken down by proteases.

  • The amino group is deaminated; carbon skeletons are converted into precursor metabolites.

Chemolithotrophs ⛰

• Prokaryotes are unique in their ability to use reduced inorganic compounds as energy sources.

• Waste products of one organism may serve as an energy source for another.

• Hydrogen sulfide (H2SH2​S) and ammonia (NH3NH3​) are produced by anaerobic respiration when inorganic molecules (sulfate, nitrate) serve as terminal electron acceptors.

• Used as energy sources for sulfur bacteria and nitrifying bacteria.

Groups of Chemolithotrophs

• Hydrogen bacteria: Oxidize hydrogen gas.

• Sulfur bacteria: Oxidize hydrogen sulfide.

• Iron bacteria: Oxidize reduced forms of iron.

• Nitrifying bacteria: Include two groups:

  • One oxidizes ammonia, forming nitrite.

  • Another oxidizes nitrite, producing nitrate.

Chemolithotrophy Process

• Chemolithotrophs extract electrons from inorganic energy sources.

• Pass electrons to an electron transport chain that generates a proton motive force.

• The energy of the gradient is used to make ATP.

• Chemolithotrophs generally thrive in specific environments where reduced inorganic compounds are found.

• Thermophilic chemolithotrophs grow near hydrothermal vents of the deep ocean and obtain energy from reduced inorganic compounds from the vents.

• Many chemolithotrophs incorporate CO2CO2​ into an organic form.

Photosynthesis ☀

Photosynthesis: Harvest the energy of light power for the synthesis of organic compounds from CO2CO2​

• Plants, algae, and several groups of bacteria perform photosynthesis.

• General reaction: CO2+H2X→(CH2O)+H2O+XCO2​+H2​X→(CH2​O)+H2​O+X

  • Where X indicates an element such as oxygen or sulfur.

• In cyanobacteria and photosynthetic eukaryotic cells, the X is an atom of oxygen.

  • Referred to as oxygenic because O2O2​ is produced.

• Purple and green bacteria use a molecule such as H2SH2​Sinstead of water.

  • The process is anoxygenic.

Photosynthetic Components

• Photosynthetic organisms contain pigments to capture light energy; colors are due to reflected wavelengths.

• Chlorophylls: Found in plants, algae, and cyanobacteria.

• Accessory pigments: Absorb at additional wavelengths.

• Pigments are located in photosystems, protein complexes within membranes.

• In eukaryotic organisms, photosystems are in chloroplasts.

Photosynthetic Processes

• Considered in two stages:

  • The first stage, the light-dependent reactions, captures radiant energy and uses it to generate the following compounds needed to synthesize organic compounds from CO2CO2​:

    • ATP

    • Reducing power (NADPH or NADH)

Photosystems

• Reaction-center pigments donate excited electrons to the electron transport chain.

• The energy of the electrons is used to pump protons across the membrane to generate a proton motive force.

• ATP synthase uses that energy to synthesize ATP.

• The process is called photophosphorylation to reflect its dependence on radiant energy.

Light-Dependent Reactions

• Cyanobacteria, plants, and algae have two types of photosystems (photosystem I and photosystem II).

• Work together to raise the energy of electrons stripped from water.

• Both photosystems use chlorophyll a as a reaction-center pigment.

Metabolism

Enzyme Inhibition 🚫

Competitive Inhibition

Inhibitor binds to the active site, preventing substrate access.

• Example: Sulfa drugs as antibacterial medications.

Non-Competitive Inhibition (Reversible)

Inhibitor alters the enzyme's shape, hindering substrate binding.

• Regulatory molecules control allosteric enzymes through this method.

Non-Competitive Inhibition (Irreversible)

Inhibitor permanently changes the enzyme's shape, rendering it non-functional.

• Example: Enzyme poisons like mercury in antimicrobial compounds. Mercury oxidizes SH groups of cysteine, converting it to cystine which disrupts disulfide bonds and enzyme function.

Central Metabolic Pathways 🛤

Glycolysis

• Converts 1 glucose into 2 pyruvate molecules.

• Net yield: 2 ATP, 2 NADH

  • Investment phase: 2 ATP consumed, 2 phosphate groups added, glucose splits into two 3-carbon molecules.

  • Pay-off phase: 3-carbon molecules convert to pyruvate, generating 4 ATP and 2 NADH.

    • $4 ATP - 2 ATP = 2 ATP$

Pentose Phosphate Pathway

• Breaks down glucose

• Important in biosynthesis for precursor metabolites: Ribose 5-phosphate, erythrose 4-phosphate

• Generates variable amounts of NADPH

• Product glyceraldehyde-3-phosphate can enter glycolysis

Transition Step (Pyruvate Oxidation)

• $CO_2$ is removed from pyruvate

• Electrons are transferred, reducing it to a 2-carbon acetyl group

• Acetyl group joins with coenzyme A to form acetyl-CoA

• Links glycolysis to the TCA cycle.

Tricarboxylic Acid (TCA) Cycle (Citric Acid Cycle)

• Completes oxidation of glucose

• Produces:

  • 4 $CO_2$

  • 2 ATP

  • 6 NADH

  • 2 $FADH_2$

• Generates precursor metabolites

Cellular Respiration 🧮

Oxidative Phosphorylation

• Uses reducing power (NADH, $FADH_2$) from glycolysis, transition step, and TCA cycle to synthesize ATP.

• Involves two processes:

  • Electron Transport Chain (ETC): Uses reducing power of NADH and $FADH_2$ to generate proton motive force.

  • ATP Synthase: Uses energy of proton motive force to generate ATP.

• Chemiosmotic Theory: Process proposed by Peter Mitchell, who received a Nobel Prize in 1978 for this theory.

Electron Transport Chain (ETC) ⚡

Generating a Proton Motive Force

• Electron transport chain (ETC): Series of membrane-embedded electron carriers

  • Accepts electrons from NADH, $FADH_2$.

  • Energy is released as electrons are passed from one carrier to the next.

  • Energy pumps protons across the membrane.

    • Prokaryotes: cytoplasmic membrane

    • Eukaryotes: inner mitochondrial membrane

  • Creates electrochemical gradient called proton motive force.

Components of ETC

General Mechanisms of Proton Pumps

• Some carriers accept only hydrogen atoms (proton-electron pairs), while others accept only electrons.

• Spatial arrangement in the membrane shuttles protons to the outside of the membrane.

• Net effect: Movement of protons across the membrane, establishing a concentration gradient.

• Driven by energy released during electron transfer.

ETC in Mitochondria and Prokaryotes

• Mitochondria have a specific ETC arrangement.

• Prokaryotes show tremendous variation; a single species can have several alternate carriers.

Anaerobic Respiration in E. coli 🦠

• Harvests less energy than aerobic respiration due to lower electron affinities of terminal electron acceptors.

• Some components differ.

• E. coli can synthesize terminal oxidoreductase using nitrate as a terminal electron acceptor, producing nitrite.

  • E. coli converts nitrite to less toxic ammonia, or to nitrous oxide ($N_2O$) or $N_2$.

• Sulfate-reducers use sulfate ($SO_4$) as a terminal electron acceptor, producing hydrogen sulfide as an end product.

ATP Synthase ⚙

Using Proton Motive Force to Synthesize ATP

• Energy is required to establish the gradient; energy is released when the gradient is reduced.

• ATP synthase allows protons to flow down the gradient in a controlled manner.

• Uses energy to add a phosphate group to ADP.

• Approximately 3 protons entering result in 1 ATP being formed.

Theoretical ATP Yield of Oxidative Phosphorylation in Prokaryotes

• Glycolysis: 2 NADH yields 6 ATP

• Transition step: 2 NADH yields 6 ATP

• TCA Cycle: Total maximum oxidative phosphorylation yield = 34 ATP

ATP Yield of Aerobic Respiration in Prokaryotes

Fermentation 🍷

• Used when respiration is not an option.

• E. coli is a facultative anaerobe, capable of aerobic respiration, anaerobic respiration, and fermentation.

• Streptococcus pneumoniae lacks an electron transport chain, so fermentation is the only option.

• ATP-generating reactions are only those of glycolysis.

• Regenerates $NAD^+$.

• End products are varied, which is helpful in identification and has commercial uses:

  • Lactic Acid

  • Ethanol

  • Butyric acid

  • Propionic Acid

  • Mixed Acids

  • 2,3-Butanediol

Catabolism of Organic Compounds Other than Glucose 🍎

• Microbes can use a variety of compounds.

• Secrete enzymes, transport subunits into the cell, and degrade further to appropriate precursor metabolites.

• Polysaccharides and disaccharides are broken down by amylases, cellulases, and disaccharides.

  • Glucose enters glycolysis directly; other monosaccharides are converted to precursor metabolites.

• Lipids are broken down by lipases.

  • Glycerol is converted to dihydroxyacetone phosphate and enters glycolysis.

  • Fatty acids are degraded by beta-oxidation to enter the TCA cycle.

• Proteins are broken down by proteases.

  • Amino groups are deaminated; carbon skeletons are converted into precursor metabolites.

Chemolithotrophs 🪨

• Prokaryotes uniquely use reduced inorganic compounds as energy sources.

• Waste products of one organism can serve as an energy source for another.

• Examples:

  • Hydrogen sulfide ($H_2S$) and ammonia ($NH_3$) are produced by anaerobic respiration when inorganic molecules (sulfate, nitrate) serve as terminal electron acceptors.

  • These are used as energy sources for sulfur bacteria and nitrifying bacteria.

Groups of Chemolithotrophs

• Hydrogen bacteria: Oxidize hydrogen gas.

• Sulfur bacteria: Oxidize hydrogen sulfide.

• Iron bacteria: Oxidize reduced forms of iron.

• Nitrifying bacteria:

  • One group oxidizes ammonia forming nitrite.

  • Another oxidizes nitrite producing nitrate.

Chemolithotroph Characteristics

• Extract electrons from inorganic energy sources.

• Pass electrons to an electron transport chain that generates a proton motive force.

• Energy of the gradient is used to make ATP.

• Thrive in specific environments where reduced inorganic compounds are found.

  • Thermophilic chemolithotrophs grow near hydrothermal vents in the deep ocean, obtaining energy from reduced inorganic compounds.

• Many incorporate $CO_2$ into an organic form.

Photosynthesis ☀

• Harvesting light energy to synthesize organic compounds from $CO_2$.

• Plants, algae, and several groups of bacteria perform photosynthesis.

• General reaction:

  • $CO_2 + H_2X \rightarrow (CH_2O) + H_2O + X_2$

    • Where X indicates an element such as oxygen or sulfur

• In cyanobacteria and photosynthetic eukaryotic cells, X is an atom of oxygen, and the process is oxygenic because $O_2$ is produced.

• Purple and green bacteria use a molecule such as $H_2S$ instead of water; the process is anoxygenic.

Photosynthetic Organisms

• Contain pigments to capture light energy; colors are due to reflected wavelengths.

• Chlorophylls: Found in plants, algae, and cyanobacteria.

• Accessory pigments: Absorb at additional wavelengths.

• Pigments are located in photosystems, which are protein complexes within membranes.

• In eukaryotic organisms, photosystems are in chloroplasts.

Photosynthetic Processes

• Divided into two stages:

  • Light-dependent reactions: Capture radiant energy and use it to generate ATP and reducing power (NADPH or NADH), which are needed to synthesize organic compounds from $CO_2$.

Photosystems

• Reaction-center pigments donate excited electrons to the electron transport chain.

• The energy of the electrons is used to pump protons across the membrane to generate a proton motive force.

• ATP synthase uses that energy to synthesize ATP.

• The process is called photophosphorylation to reflect its dependence on radiant energy.

Light-Dependent Reactions in Cyanobacteria and Photosynthetic Eukaryotic Cells

• Cyanobacteria, plants, and algae have two types of photosystems (photosystem I and photosystem II).

• Work together to raise the energy of electrons stripped from water.

• Both photosystems use chlorophyll a as a reaction-center pigment.

Electron Transport Chain ⚙

Overview

• The electron transport chain involves the spatial arrangement of molecules within a membrane.

• It shuttles protons to the outside of the membrane.

• The net effect is the movement of protons across the membrane, establishing a concentration gradient.

• This process is driven by the energy released during electron transfer.

Prokaryotic Variations

Prokaryotes exhibit tremendous variation in their electron transport chains compared to mitochondria. Even a single species can have several alternate carriers.

Anaerobic Respiration in E. coli

• Anaerobic respiration harvests less energy than aerobic respiration.

• It uses terminal electron acceptors with lower electron affinities.

• Some components of the electron transport chain are different.

• E. coli can synthesize a terminal oxidoreductase that uses nitrate as the terminal electron acceptor, producing nitrite.

  • Nitrite is converted to less toxic ammonia.

  • Other bacteria convert it to N2O (nitrous oxide) or N2.

• Sulfate-reducers use sulfate (SO4) as the terminal electron acceptor, producing hydrogen sulfide as the end product.

ATP Synthase and Proton Motive Force 🔋

ATP Synthase Mechanism

• Energy is required to establish the proton gradient.

• Energy is released when the gradient is reduced.

• ATP synthase allows protons to flow down the gradient in a controlled manner.

• This energy is used to add a phosphate group to ADP, forming ATP.

• Approximately 3 protons are needed for the formation of 1 ATP.

Theoretical ATP Yield in Prokaryotes

ATP Yield of Aerobic Respiration in Prokaryotes

Fermentation 🍷

When Respiration Isn't an Option

• Fermentation is used when respiration is not an option.

• E. coli is a facultative anaerobe, capable of:

  • Aerobic respiration

  • Anaerobic respiration

  • Fermentation

• Streptococcus pneumoniae lacks an electron transport chain, making fermentation its only option.

• ATP-generating reactions are only those of glycolysis.

• Fermentation regenerates NAD+.

Fermentation End Products

Fermentation end products vary and are helpful for identification purposes and are commercially useful. These include:

• Lactic Acid

• Ethanol

• Butyric acid

• Propionic Acid

• Mixed Acids

• 2,3-Butanediol

Catabolism of Non-Glucose Organic Compounds 🍎

Utilizing a Variety of Compounds

• Microbes can use a variety of organic compounds.

• They secrete enzymes and transport subunits into the cell.

• These are further degraded into appropriate precursor metabolites.

Breakdown Processes

• Polysaccharides and disaccharides: Broken down by amylases, cellulases, and disaccharidases.

  • Glucose enters glycolysis directly.

  • Other monosaccharides are converted to precursor metabolites.

• Lipids: Broken down by lipases.

  • Glycerol is converted to dihydroxyacetone phosphate and enters glycolysis.

  • Fatty acids are degraded by beta-oxidation to enter the TCA cycle.

• Proteins: Broken down by proteases.

  • Amino group is deaminated.

  • Carbon skeletons are converted into precursor metabolites.

Chemolithotrophs 🪨

Unique Prokaryotic Ability

Prokaryotes uniquely use reduced inorganic compounds as energy sources.

• Waste products of one organism can be an energy source for another.

• Examples include hydrogen sulfide (H2S) and ammonia (NH3), which are produced by anaerobic respiration when inorganic molecules (sulfate, nitrate) serve as terminal electron acceptors.

• These are used as energy sources for sulfur bacteria and nitrifying bacteria.

Groups of Chemolithotrophs

• Hydrogen bacteria: Oxidize hydrogen gas.

• Sulfur bacteria: Oxidize hydrogen sulfide.

• Iron bacteria: Oxidize reduced forms of iron.

• Nitrifying bacteria:

  • One group oxidizes ammonia forming nitrite.

  • Another oxidizes nitrite producing nitrate.

Chemolithotrophic Electron Extraction

• Chemolithotrophs extract electrons from inorganic energy sources.

• Electrons are passed to an electron transport chain, generating a proton motive force.

• The energy of the gradient is used to make ATP.

• They thrive in specific environments where reduced inorganic compounds are found.

• Thermophilic chemolithotrophs grow near hydrothermal vents of the deep ocean and obtain energy from reduced inorganic compounds from the vents.

• Many chemolithotrophs incorporate CO2 into an organic form.

Photosynthesis ☀

Harnessing Light Energy

Photosynthesis: The process of harvesting the energy of light to synthesize organic compounds from CO2.

• Performed by plants, algae, and several groups of bacteria.

• General reaction:

  CO2+HX→(CH2O)+X2CO2​+HX→(CH2​O)+X2​

  Where X indicates an element such as oxygen or sulfur.

• In cyanobacteria and photosynthetic eukaryotic cells, X is an atom of oxygen, and the process is oxygenic because O2 is produced.

• Purple and green bacteria use a molecule such as H2S instead of water, making the process anoxygenic.

Photosynthetic Pigments

• Photosynthetic organisms contain pigments to capture light energy.

  • Colors are due to reflected wavelengths.

• Chlorophylls are used by plants, algae, and cyanobacteria.

• Accessory pigments absorb at additional wavelengths.

• Pigments are located in photosystems, which are protein complexes within membranes.

• In eukaryotic organisms, photosystems are in chloroplasts.

Two Stages of Photosynthesis

1. Light-dependent reactions: Capture radiant energy and use it to generate compounds needed to synthesize organic compounds from CO2:

   • ATP

   • Reducing power (NADPH or NADH)