Chapter Three and Four

Study Guide - Smart Notes

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Microbial Metabolism

Overview of Metabolism

Microbial metabolism encompasses all the chemical reactions that occur within a microorganism, enabling it to grow, reproduce, maintain its structures, and respond to environments. Metabolism is divided into two main processes: catabolism and anabolism.

Catabolism: The breakdown of complex molecules into simpler ones, releasing energy that is captured in the form of ATP.
Anabolism: The synthesis of complex molecules from simpler ones, requiring an input of energy, usually from ATP.

Diagram of anabolic and catabolic reactions

Key requirements for metabolism:

Water
Carbon and other nutrients
Free energy (energy available to do work)
Reducing power (source of electrons)

Metabolic Types by Energy Source

Microorganisms are classified based on their energy and carbon sources:

Chemotrophs: Obtain energy from chemicals.
Phototrophs: Obtain energy from light.
Chemoorganotrophs: Use organic chemicals as energy sources (e.g., Escherichia coli).
Chemolithotrophs: Use inorganic chemicals (e.g., Thiobacillus thiooxidans).
Phototrophs: Use light (e.g., Rhodobacter capsulatus).

Classification of energy sources in microorganisms

Redox Reactions and Energy Conservation

Reducing Power and Electron Flow

Energy generation in cells is closely tied to the transfer of electrons in oxidation-reduction (redox) reactions. These reactions involve:

Electron donor: The molecule that loses electrons (is oxidized).
Electron acceptor: The molecule that gains electrons (is reduced).

OIL RIG: Oxidation Is Loss, Reduction Is Gain (of electrons).

Redox reaction showing electron transfer from glucose to oxygen

The Redox Tower

The redox tower is a visual representation of the reduction potentials of various redox couples. The further electrons fall down the tower, the more energy is released.

Strongest electron donors are at the top (most negative E0').
Strongest electron acceptors are at the bottom (most positive E0').

The redox tower showing reduction potentials

Example reactions and their free energy changes are shown at the bottom of the tower.

Table of reduction potentials for common redox couples

Electron Carriers

Electron carriers are molecules that shuttle electrons during metabolic reactions, representing reducing power. Common carriers include:

NAD+/NADH
NADP+/NADPH
FAD/FADH2

Table of electron carriers and their properties

Precursor Metabolites

Precursor metabolites are intermediates in catabolic pathways that serve as building blocks for biosynthesis (anabolism). For example, pyruvate can be converted into amino acids such as alanine, leucine, or valine.

Table of precursor metabolites, their pathways, and biosynthetic roles

ATP Generation and Enzyme Function

Mechanisms of ATP Generation

ATP is generated in cells by three main mechanisms:

Substrate-level phosphorylation: Direct transfer of a phosphate group to ADP from a high-energy substrate.
Oxidative phosphorylation: ATP synthesis driven by the proton motive force generated by electron transport chains.
Photophosphorylation: Light energy is used to generate a proton motive force for ATP synthesis.

Role of Enzymes

Enzymes are biological catalysts that accelerate chemical reactions by lowering the activation energy. They are highly specific and typically proteins (some are RNAs).

Enzyme-substrate interaction and catalysis

Enzymes may require cofactors (inorganic ions like Mg2+, Zn2+) or coenzymes (organic molecules, often derived from vitamins) to function.

Enzyme with cofactor and substrate Table of coenzymes, their vitamin sources, and functions

Central Metabolic Pathways

Overview of Catabolism

Central metabolic pathways include glycolysis, the pentose phosphate pathway, and the tricarboxylic acid (TCA) cycle. These pathways generate ATP, reducing power, and precursor metabolites.

Overview of central metabolic pathways Diagram of glycolysis, pentose phosphate pathway, and TCA cycle

Comparison of Central Metabolic Pathways

Pathway	Characteristics
Glycolysis	2 ATP (net) by substrate-level phosphorylation, 2 NADH + 2 H+, six different precursor metabolites
Pentose phosphate cycle	NADPH + H+ (amount varies), two different precursor metabolites
Transition step	2 NADH + 2 H+, one precursor metabolite
TCA cycle	2 ATP (or GTP), 6 NADH + 6 H+, 2 FADH2, two different precursor metabolites

Table comparing central metabolic pathways

Respiration and Fermentation

Respiration involves transferring electrons from glucose to an electron transport chain, generating a proton motive force for ATP synthesis. If cells cannot respire, fermentation regenerates NAD+ by reducing pyruvate or its derivatives, allowing glycolysis to continue.

Diagram of glycolysis Diagram of fermentation

ATP Yield in Different Pathways

Metabolic Process	Uses Electron Transport Chain	Terminal Electron Acceptor	ATP by Substrate-Level Phosphorylation	ATP by Oxidative Phosphorylation	Total ATP (Theoretical Maximum)
Aerobic respiration	Yes	O2	2 in glycolysis (net), 2 in TCA cycle	34	38
Anaerobic respiration	Yes	Molecule other than O2	Varies	Varies	<38
Fermentation	No	Organic molecule	2 in glycolysis (net)	0	2

Table of ATP-generating processes

Fermentation Pathways and Products

Fermentation end products are diverse and useful for microbial identification and industrial applications. Examples include lactic acid, ethanol, butyric acid, and propionic acid.

Diagram of fermentation pathways and products

Citric Acid Cycle and Glyoxylate Cycle

Citric Acid Cycle (TCA/Krebs Cycle)

The TCA cycle oxidizes pyruvate to CO2, regenerates oxaloacetate, and provides intermediates for biosynthesis.

Diagram of the citric acid cycle

Glyoxylate Cycle

The glyoxylate cycle enables the catabolism of C2 compounds like acetate, regenerating oxaloacetate for biosynthesis.

Diagram of the glyoxylate cycle

Electron Transport Chain and Proton Motive Force

Electron Transport Chain (ETC)

The ETC is a series of protein complexes that transfer electrons from NADH and FADH2 to a terminal electron acceptor, generating a proton gradient across the membrane (proton motive force).

Diagram of the electron transport chain in eukaryotes

ATP Synthase

ATP synthase uses the proton motive force to synthesize ATP from ADP and inorganic phosphate.

Diagram of ATP synthase structure and function

Metabolic Diversity and Oxygen Relationships

Metabolic Diversity

Microorganisms display a wide range of metabolic strategies, including aerobic and anaerobic respiration, fermentation, chemolithotrophy, and phototrophy.

Diagram of metabolic diversity and electron acceptors Diagram of phototrophy and electron donors

Respiration in E. coli

Escherichia coli can perform aerobic respiration, anaerobic respiration, and fermentation, depending on environmental conditions and available electron acceptors.

Diagram of respiration and anaerobic respiration in E. coli

Anabolism: Biosynthesis of Cellular Macromolecules

CO2 and N2 Fixation

Cells require carbon and nitrogen for biosynthesis. Atmospheric CO2 and N2 must be chemically reduced for assimilation, processes that require ATP and reducing power.

CO2 fixation: Incorporation of CO2 into organic molecules (e.g., Calvin cycle).
N2 fixation: Conversion of atmospheric nitrogen to ammonia by nitrogenase.

Example equation for ATP generation by substrate-level phosphorylation:

Example equation for aerobic respiration: