5.2_Bacterial Metabolism

Anabolism

Two Major Components of Metabolism:

• Biosynthetic Reactions

• Energy-requiring metabolic reactions that build complex molecules (e.g., proteins, nucleic acids) from simpler compounds.

• Synthesis of complex molecules from simpler ones

• Requires energy input

Examples:

• Carbon fixation (CO₂ → glucose or acetyl-CoA)

• Amino acid synthesis

• Nucleotide synthesis

Purpose:

• Cell growth

• Repair

• Biomolecule production

Anaerobic Respiration

• Respiration that uses terminal electron acceptors other than oxygen (e.g., nitrate, sulfate, fumarate).

• Electron acceptors: o Nitrate o Sulfate o Fumarate

• Lower ATP yield than aerobic respiration

Assimilatory Reduction

The reduction of inorganic compounds (e.g., nitrate or sulfate) for incorporation into cellular biomass rather than for energy production.

Autotroph

• An organism that uses carbon dioxide (CO₂) as its primary carbon source.

• use CO₂ as their sole or primary carbon source, reducing it into organic compounds via carbon fixation pathways.

• They require: • An energy source • A source of reducing power

• Carbon source: CO₂

• Examples: ▪ Cyanobacteria ▪ Nitrifying bacteria ▪ Sulfur-oxidizing bacteria

Biogeochemical Cycle

The circulation of chemical elements (e.g., carbon, nitrogen, sulfur) between biological, geological, and chemical components of Earth.

Calvin–Benson–Bassham (Calvin) Cycle

• A carbon fixation pathway that incorporates CO₂ into organic carbon using ATP and NADPH; common in plants and cyanobacteria.

• The most widespread carbon fixation pathway

• Used by: o Cyanobacteria o Algae o Plants o Some chemoautotrophic bacteria

• Operates under aerobic conditions

• Requires: o ATP o NADPH

• Produces triose phosphates, which feed into biosynthesis

• Key Enzyme: RuBisCO

Carbon Fixation

• The conversion of inorganic carbon (CO₂) into organic compounds by living organisms.

• is the process by which inorganic carbon (CO₂) is converted into organic molecules that can be used to build cellular components such as carbohydrates, lipids, proteins, and nucleic acids.

Catabolism

Two Major Components of Metabolism:

• Energy-Yielding Reactions

• Metabolic reactions that break down complex molecules to release energy.

• supports anabolism.

• Breakdown of chemical compounds

• Releases energy (often stored as ATP, NADH, FADH₂)

Examples:

• Glucose oxidation

• Sulfur oxidation

• Hydrogen oxidation

• Ammonia oxidation

Purpose:

• Provide energy for cellular work

• Generate precursor molecules for biosynthesis

Chemolithoautotroph

• An organism that obtains energy from the oxidation of inorganic compounds and carbon from CO₂.

• are invisible primary producers and are as important as the photoautotrophs.

• Energy from oxidation of inorganic chemicals

• Carbon source: CO₂

• Examples: • Nitrosomonas (ammonia oxidizer) • Thiobacillus (sulfur oxidizer)

Chemoorganotroph

An organism that obtains energy and electrons from organic compounds.

Denitrification

An anaerobic process in which nitrate (NO₃⁻) is reduced to gaseous nitrogen (N₂ or N₂O).

Dissimilatory Sulfate Reduction

An anaerobic respiratory process in which sulfate (SO₄²⁻) is reduced to hydrogen sulfide (H₂S) for energy conservation.

Electron Acceptor

A molecule that receives electrons during a redox reaction (e.g., O₂, NO₃⁻, SO₄²⁻).

Electron Donor

A molecule that supplies electrons during a redox reaction (e.g., organic compounds, H₂, H₂S).

Fermentation

• An anaerobic metabolic process where organic molecules act as both electron donors and electron acceptors, yielding limited ATP.

• No external electron acceptor

• Organic molecule serves as final electron acceptor

• Produces acids, alcohols, gases

• Examples: • Lactic acid fermentation • Alcoholic fermentation • Mixed-acid fermentation

Glycolysis

• A central metabolic pathway that converts glucose into pyruvate, producing ATP and NADH.

• Glucose → pyruvate

• Produces: o ATP o NADH • Occurs in nearly all heterotrophic microbes

Heterotroph

• An organism that relies on organic compounds as its carbon source.

• Carbon source: organic compounds

• use pre-formed organic compounds as their carbon source.

• Examples: ▪ Escherichia coli ▪ Fungi ▪ Most pathogens ▪ Decomposer microbes in soil and water

Heterocyst

A specialized, thick-walled cell in some cyanobacteria that provides an oxygen-free environment for nitrogen fixation.

Mixotroph

An organism capable of switching between autotrophic and heterotrophic metabolism depending on environmental conditions.

Nitrogenase

A multi-enzyme complex that catalyzes the reduction of atmospheric nitrogen (N₂) to ammonia (NH₃).

Nitrogen Fixation

The biological conversion of atmospheric nitrogen gas (N₂) into ammonia (NH₃).

Nitrification

A two-step aerobic process in which ammonia is oxidized to nitrite and then to nitrate by chemolithoautotrophic bacteria.

Photoautotroph

• An organism that uses light as an energy source and CO₂ as a carbon source.

• Energy from light

• Carbon source: CO₂

• Examples: ▪ Cyanobacteria ▪ Purple sulfur bacteria

• Carbon fixation pathway: o Calvin–Benson–Bassham cycle (most common)

Redox Reaction

A chemical reaction involving the transfer of electrons between molecules (reduction and oxidation).

Reverse (Reductive) TCA Cycle

• A carbon fixation pathway in which CO₂ is reduced to organic molecules by running the TCA cycle in reverse.

• Essentially the TCA cycle run in reverse

• Found in: o Green sulfur bacteria o Some ε-proteobacteria o Deep-sea or microaerophilic microbes

• Fixes CO₂ to form: o Acetyl-CoA o Pyruvate

• More energy-efficient than the Calvin cycle

• Requires specific enzymes to bypass irreversible TCA steps

• Typically found in: o Anaerobic o Low-oxygen environments

• Reflects ancient metabolic origins

• This pathway is related to early Earth conditions (low oxygen).

RuBisCO

• Ribulose-1,5-bisphosphate carboxylase/oxygenase,

• the key enzyme that catalyzes CO₂ fixation in the Calvin cycle.

• Inefficient and prone to oxygen interference

• Key Enzyme of Calvin–Benson–Bassham (CBB) Cycle

• is a critical enzyme in photosynthesis that catalyzes the first major step of carbon fixation—converting atmospheric into organic energy-rich molecules.

• It is considered the most abundant protein on Earth, found in plants, algae, and many bacteria.

Sulfur Cycle

The movement and transformation of sulfur between inorganic and organic forms mediated largely by microorganisms.

Sulfur Oxidation

The oxidation of reduced sulfur compounds (e.g., H₂S, S⁰) to sulfate (SO₄²⁻), often coupled to energy generation.

Tricarboxylic Acid (TCA) Cycle

• A central metabolic pathway that oxidizes acetyl-CoA to CO₂ while generating reducing equivalents for respiration.

• Oxidizes acetyl-CoA → CO₂

• Produces: o NADH o FADH₂ o Precursors for amino acid biosynthesis

• Central hub of metabolism

• In many microbes, the ____ is amphibolic (both catabolic and anabolic).

Wood–Ljungdahl Pathway (Acetyl-CoA Pathway)

• An anaerobic carbon fixation pathway that reduces CO₂ directly to acetyl-CoA, used by acetogens and methanogens.

• One of the simplest and most ancient carbon fixation pathways

• Used by: o Acetogenic bacteria o Methanogenic archaea

• Two branches: 1. Methyl branch (CO₂ → methyl group) 2. Carbonyl branch (CO₂ → CO)

• Combines methyl and carbonyl groups to form acetyl-CoA

• Important in: o Anaerobic sediments o Animal digestive systems

• Thought to resemble some of the earliest metabolic pathways on Earth

Microbial metabolism

refers to the complete set of chemical reactions that occur within microbial cells that allow them to:

• Obtain energy

• Build cellular components

• Maintain cell structure and function

• Grow and reproduce

• Interact with and modify their environment

underpins life on Earth and drives major element cycles (C, N, S, P).

extraordinary metabolic diversity

Unlike plants and animals, microbes display ______, allowing them to survive in environments ranging from oxygen-rich soils to deep-sea hydrothermal vents, acid mine drainage, and animal guts.

energy input

Anabolism Requires ____

nitrate (nitrifiers)

Examples of Unusual Microbial Metabolisms:

• Oxidation of ammonia →

hydrogen sulfide

Examples of Unusual Microbial Metabolisms:

• Reduction of sulfate →

NH₃

Examples of Unusual Microbial Metabolisms:

• Fixation of nitrogen gas (N₂ →

Chemotrophs

Energy from chemical compounds

Organotrophs

electrons from organic compounds

Lithotrophs

electrons from inorganic compounds (e.g., H₂, H₂S, NH₃)

Carbon cycle

• Carbon fixation

• Respiration

• Decomposition

Nitrogen cycle

• Nitrogen fixation

• Nitrification

• Denitrification

Sulfur cycle

• Sulfate reduction

• Sulfur oxidation

CO₂

is abundant but chemically stable and biologically unusable without fixation

base of food webs

Fixed carbon forms the ____

ATP & NADPH

Calvin–Benson–Bassham (CBB) Cycle requires:

triose phosphates

Calvin–Benson–Bassham (CBB) Cycle produces ___, which feed into biosynthesis

Carboxylation

Three Main Phases of Calvin–Benson–Bassham (CBB) Cycle:

• ___-CO₂ fixation

Reduction

Three Main Phases of Calvin–Benson–Bassham (CBB) Cycle:

• ___-conversion to G3P

Regeneration of RuBP

Three Main Phases of Calvin–Benson–Bassham (CBB) Cycle:

• *third phase*

Acetyl-CoA & Pyruvate

Reverse (Reductive) Tricarboxylic Acid (rTCA) Cycle Fixes CO₂ to form:

1. Methyl branch (CO₂ → methyl group)

2. Carbonyl branch (CO₂ → CO)

Two branches of Wood–Ljungdahl Pathway (Acetyl-CoA Pathway):

acetyl-CoA

Wood–Ljungdahl Pathway (Acetyl-CoA Pathway) Combines methyl and carbonyl groups to form ___

methyl and carbonyl groups

Wood–Ljungdahl Pathway (Acetyl-CoA Pathway) Combines ______to form acetyl-CoA

3-Hydroxypropionate Cycle

• Found in some green non-sulfur bacteria

• Fixes CO₂ into organic acids

3-Hydroxypropionate/4-Hydroxybutyrate Cycle

• Found mainly in archaea

• Adapted to:

  • High temperature

  • Extreme environments

Sugars (glucose, lactose) • Organic acids (acetate, lactate) • Amino acids • Lipids • Complex polymers (cellulose, lignin)

Examples of organic carbon sources:

central metabolism

Heterotrophic metabolism centers on a small number of core metabolic pathways, often called ____

ATP & NADH

Glycolysis (Embden–Meyerhof–Parnas Pathway) Produces:

Entner–Doudoroff pathway

• common in Gram-negative bacteria

• is an alternative metabolic route to glycolysis used by many prokaryotes to catabolize glucose into pyruvate.

• It yields less energy than standard glycolysis (net 1 ATP per glucose), but requires fewer enzymes, making it efficient for specific bacteria like Pseudomonas.

NADH, FADH₂, and Precursors for amino acid biosynthesis

Tricarboxylic Acid (TCA) Cycle produces:

Aerobic respiration

• Final electron acceptor: O₂

• High ATP yield

Nitrate, Sulfate, and Fumarate

Electron acceptors for Anaerobic respiration:

acids, alcohols, gases

Fermentation produces:

• Decompose organic matter

• Recycle carbon back to CO₂

• Form the base of microbial food webs

• Critical in soil, gut, and aquatic ecosystems

Ecological Role of Heterotrophs

• Ammonia (NH₃) • Nitrite (NO₂⁻) • Hydrogen sulfide (H₂S) • Elemental sulfur • Ferrous iron (Fe²⁺)

Common inorganic energy sources:

energy-intensive

Autotrophs face several constraints:

• CO₂ fixation is ____

oxygen-sensitive

Autotrophs face several constraints:

• Enzymes may be ___

Decomposers, consumers

Ecological role of Heterotrophs

Primary producers

Ecological role of Autotrophs

Soils

Linking Carbon Metabolism to Ecosystems:

• Autotrophs introduce new organic carbon

• Heterotrophs decompose plant and microbial biomass

Oceans

Linking Carbon Metabolism to Ecosystems:

• Cyanobacteria and chemoautotrophs dominate primary production

Extreme environments

Linking Carbon Metabolism to Ecosystems:

• Autotrophic microbes often form the base of food chains