Microbial Metabolism: Enzymes, Catabolism, and Energy Pathways

Microbial Metabolism

Enzymes

Enzymes are biological catalysts that accelerate chemical reactions in microbial cells by lowering the activation energy required. They are essential for metabolic processes.

• Organic Catalysts: Most enzymes are proteins, but some are RNA molecules called ribozymes.

• Substrates: The specific reactants that enzymes act upon to produce products.

• Cofactors and Coenzymes:

  • Cofactor: Nonprotein component, often an inorganic ion (e.g., Mg2+, Fe2+).

  • Coenzyme: Organic molecule, often derived from vitamins (e.g., NAD+, FAD).

  • Apoenzyme: The protein portion of an enzyme, inactive without its cofactor.

  • Holoenzyme: The complete, active enzyme with its cofactor/coenzyme.

• Induced Fit: Substrate binding may cause a conformational change in the enzyme, enhancing catalysis.

Enzymatic Activity

• Influenced by:

  • Temperature

  • pH

  • Enzyme and substrate concentrations

  • Inhibitors (reduce activity)

  • Activators (increase activity)

• Enzymatic Regulation:

  • Allosteric Regulation: Activators or inhibitors bind to sites other than the active site, changing enzyme shape and function.

  • Inhibitors:

    • Competitive Inhibitors: Bind to the active site, blocking substrate access.

    • Noncompetitive Inhibitors: Bind to an allosteric site, altering enzyme activity without blocking the active site.

  • Feedback Inhibition: The end product of a metabolic pathway inhibits an earlier step, regulating pathway activity.

Metabolism

Metabolism encompasses all chemical reactions in a cell, divided into two main types: anabolism and catabolism.

• Anabolism: Biosynthetic reactions that build complex molecules from simpler ones; typically endergonic (require energy).

• Catabolism: Degradative reactions that break down complex molecules into simpler ones; typically exergonic (release energy).

• Redox Reactions: Involve the transfer of electrons between molecules; oxidation (loss of electrons) and reduction (gain of electrons) always occur together.

Electron Carriers

Electron carriers are molecules that transport electrons during cellular respiration and fermentation.

• NAD+/NADH

• NADP+/NADPH

• FAD/FADH2

These carriers participate in redox reactions, shuttling electrons to the electron transport chain.

Glucose Catabolism

Glucose catabolism is the process by which cells extract energy from glucose. It includes glycolysis, fermentation, and respiration.

Glycolysis

• Substrate-Level Phosphorylation: Direct transfer of a phosphate group to ADP to form ATP.

• Three Stages:

  • Investment (uses ATP)

  • Lysis (splitting of glucose)

  • Energy Conservation (produces ATP and NADH)

• Key Points to Know:

  • What enters glycolysis (glucose)

  • What is produced (pyruvate, ATP, NADH)

  • Number of ATP per glucose (net gain: 2 ATP)

  • Fate of pyruvate/pyruvic acid

Fermentation

Fermentation allows cells to regenerate NAD+ from NADH in the absence of oxygen, enabling glycolysis to continue.

• Restores Redox Balance: Converts pyruvic acid into various end products.

• Common End Products:

  • Lactic acid

  • Ethanol

  • CO2

  • Other acids or alcohols (depending on organism)

Respiration

Respiration is a series of metabolic pathways that extract energy from glucose using an electron transport chain, producing more ATP than fermentation.

• Three Stages:

  • Production of acetyl-CoA (from pyruvate)

  • Krebs cycle (citric acid cycle)

  • Electron transport chain (ETC)

• Krebs Cycle:

  • Input: Acetyl-CoA

  • Outputs: NADH, FADH2, CO2, ATP (per glucose molecule)

Electron Transport Chain (ETC)

The ETC is a series of protein complexes in the membrane that transfer electrons from NADH and FADH2 to oxygen (in aerobic respiration), generating a proton gradient used to produce ATP.

• Location: Cell membrane in prokaryotes; mitochondrial cristae in eukaryotes.

• Function: Uses energy from electrons to pump H+ ions across the membrane, creating a proton motive force.

• ATP Synthesis: Protons flow back through ATP synthase, driving oxidative phosphorylation of ADP to ATP.

• Terminal Electron Acceptor: Oxygen in aerobic respiration; other molecules in anaerobic respiration.

Biosynthesis and Catabolism of Other Molecules

Intermediates from central metabolic pathways are used to synthesize amino acids, nucleotides, fatty acids, and porphyrins.

• Amino Acid Synthesis and Catabolism:

  • Synthesis: Involves amination and transamination reactions.

  • Catabolism: Involves protease activity and deamination; products can enter the Krebs cycle.

• Lipid Catabolism:

  • Hydrolysis: Lipases remove the glycerol group from triglycerides.

  • Glycerol: Can be phosphorylated and enter glycolysis.

  • Beta Oxidation: Fatty acids are broken down into acetyl-CoA, producing NADH and FADH2 for the ETC.

Reversibility and Amphipathic Nature

Many metabolic reactions are reversible, allowing cells to adapt to changing conditions. Amphipathic molecules have both hydrophilic and hydrophobic regions, important in membrane structure and function.

Summary Table: Key Metabolic Pathways

Pathway	Main Substrate	Main Products	ATP Yield (per glucose)	Electron Carriers Produced
Glycolysis	Glucose	Pyruvate, ATP, NADH	2 (net)	2 NADH
Krebs Cycle	Acetyl-CoA	CO2, ATP, NADH, FADH2	2	6 NADH, 2 FADH2
Electron Transport Chain	NADH, FADH2	ATP, H2O (aerobic)	~34	—
Fermentation	Pyruvate	Lactic acid, ethanol, CO2	0 (beyond glycolysis)	Regenerates NAD+

Key Equations

• General Redox Reaction: $\text{Oxidized molecule} + \text{e}^- \rightarrow \text{Reduced molecule}$

• ATP Synthesis (Oxidative Phosphorylation): $\text{ADP} + \text{P}_i \rightarrow \text{ATP}$

Example: During glycolysis, glucose is oxidized to pyruvate, producing ATP and NADH. In the absence of oxygen, fermentation regenerates NAD+ by reducing pyruvate to lactic acid or ethanol.