Microbial Metabolism: Enzymes, Metabolic Pathways, and Energy Production

Microbial Metabolism

Enzymes

Enzymes are biological catalysts that accelerate chemical reactions in microbial cells by lowering the activation energy required for the reaction to proceed.

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

• Substrates: The specific reactants that enzymes act upon, converting them into 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).

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

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

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

Enzymatic Activity

• Influencing Factors:

  • Temperature

  • pH

  • Enzyme and substrate concentrations

  • Presence of inhibitors or activators

• Enzymatic Regulation:

  • Activators: Often bind to allosteric sites, changing the enzyme's three-dimensional shape and increasing activity.

  • Inhibitors:

    • Competitive Inhibitors: Bind to the active site, blocking substrate binding. Can be outcompeted by high substrate concentrations.

    • Noncompetitive Inhibitors: Bind to an allosteric site, altering enzyme shape and function regardless of substrate concentration.

  • 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, always occurring simultaneously as oxidation (loss of electrons) and reduction (gain of electrons).

Electron Carriers

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

• NAD+/NADH

• NADP+/NADPH

• FAD/FADH2

These carriers participate in redox reactions and are essential for the electron transport chain.

Glucose Catabolism

Glucose catabolism is the process by which cells extract energy from glucose through a series of metabolic pathways.

Glycolysis

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

• Three Stages:

  • Investment

  • Lysis

  • Energy Conservation

• Key Points to Know:

  • What enters glycolysis (glucose)

  • What is produced (pyruvate, ATP, NADH)

  • Number of ATP produced per glucose molecule

  • 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

Respiration

Respiration is a series of metabolic processes that extract energy from organic molecules, typically using oxygen as the final electron acceptor.

• Three Stages:

  • Production of acetyl-CoA

  • Krebs cycle (Citric Acid Cycle)

  • Electron transport chain

• Krebs Cycle:

  • Know what enters (acetyl-CoA)

  • Know what exits (CO2, NADH, FADH2, ATP)

Electron Transport Chain (ETC)

• Occurs in the membrane (mitochondrial cristae in eukaryotes)

• Uses electrons from NADH and FADH2 to pump H+ ions across the membrane

• Hydrogen ions return via ATP synthase, generating ATP (chemiosmosis)

• Oxidative phosphorylation of ADP

• Aerobic respiration uses oxygen as the terminal electron acceptor

Anabolic Pathways and Biosynthesis

Many intermediates from catabolic pathways serve as precursors for biosynthetic (anabolic) reactions.

• Precursors Used to Synthesize:

  • Amino acids

  • Nucleotides

  • Fatty acids

  • Porphyrins

Amino Acid Synthesis and Catabolism

• Synthesis: Involves amination and transamination reactions.

• Catabolism: Involves protease-mediated deamination, allowing entry into the Krebs cycle.

Lipid Catabolism

• Hydrolysis: Lipase enzymes remove the glycerol group from triglycerides.

• Glycerol can be phosphorylated and enter glycolysis.

• Beta Oxidation: Fatty acids are broken down, reducing NAD+ to NADH and FAD to FADH2. Acetyl groups are formed and combined with Coenzyme A to form acetyl-CoA, which enters the Krebs cycle.

Reversibility and Amphipathic Nature

• Many metabolic reactions are reversible, allowing cells to adapt to changing conditions.

• Some molecules are amphipathic, containing both hydrophilic and hydrophobic regions.

Summary Table: Key Metabolic Pathways

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

Key Equations

• General Redox Reaction: $\text{A}_{\text{red}} + \text{B}_{\text{ox}} \rightarrow \text{A}_{\text{ox}} + \text{B}_{\text{red}}$

• ATP Formation (Substrate-Level Phosphorylation): $\text{ADP} + \text{P}_i \rightarrow \text{ATP}$

• Overall Glycolysis Reaction: $\text{Glucose} + 2\ \text{NAD}^+ + 2\ \text{ADP} + 2\ \text{P}_i \rightarrow 2\ \text{Pyruvate} + 2\ \text{NADH} + 2\ \text{ATP} + 2\ \text{H}_2\text{O}$

Example: During lactic acid fermentation, Lactobacillus species convert pyruvate to lactic acid, regenerating NAD+ for glycolysis.