Cell Metabolism & Energy: Catabolism, Anabolism & ATP

• Metabolism represents the sum of all chemical reactions within a cell.

Metabolism Types

• Catabolism involves the breakdown of molecules, releasing energy.
• Anabolism is the synthesis of biomolecules, requiring energy.
• Energy is vital for cell maintenance, growth, and reproduction.
• Precursor metabolites from catabolism act as building blocks for anabolic processes.

Energy and Gibbs Free Energy (ΔG)

• ΔG = ΔH - TΔS
  • ΔH (enthalpy) is the change in heat content.
  • ΔS (entropy) signifies the change in disorder.
  • T represents temperature, which affects ΔG.
• A negative ΔG indicates a spontaneous reaction (exergonic).
• A positive ΔG indicates a non-spontaneous reaction (endergonic).
• The actual ΔG is influenced by reactant/product concentrations and temperature.

ATP: The Cell's Energy Currency

• ATP (adenosine triphosphate) stores energy within its phosphate bonds.

ATP Hydrolysis

• ATP + H2O → ADP + Pi + Energy (ΔG°' = -30.5 kJ/mol)
• Energy-requiring reactions are often coupled with ATP hydrolysis to proceed.

Redox Reactions in Metabolism

• Oxidation is the loss of electrons.
• Reduction is the gain of electrons.
• Electron carriers (NAD+/NADH, FAD/FADH2) transport electrons between reactions.
• Reduction potential (E') determines the direction of electron flow in redox reactions.

Enzymes in Metabolism

• Enzymes lower activation energy, thereby increasing reaction rates.

Mechanisms of Enzymes

• Enzymes bring substrates close together.
• They orient substrates in the proper way.
• They provide a reactive site for catalysis.
• Allosteric regulation is how enzyme activity is controlled.
• Cofactors and coenzymes (e.g., NAD+, FAD) assist in enzyme function.

Chemoorganotrophy Overview

• Chemoorganotrophs get energy from the oxidation of organic molecules.
• Three major pathways transform glucose to pyruvate.
  • Embden-Meyerhof-Parnas (EMP) Pathway (Glycolysis)
  • Entner-Doudoroff (ED) Pathway
  • Pentose Phosphate (PP) Pathway

Glycolysis (EMP Pathway)

• Glycolysis occurs in the cytoplasm.
• Glycolysis can occur during aerobic and anaerobic conditions.

Steps in Glycolysis

• Investment Phase: 2 ATP are used to phosphorylate glucose.
• Payoff Phase: 4 ATP are produced via substrate-level phosphorylation, resulting in a net gain of 2 ATP, 2 NADH, and 2 pyruvate.

Key Enzymes in Glycolysis

• Pyruvate kinase catalyzes the last step.

Alternative Pathways for Glucose Catabolism

• The Entner-Doudoroff (ED) Pathway is in some bacteria (not eukaryotes)
  • Produces 1 ATP, 1 NADH, and 1 NADPH per glucose molecule.
  • Functions in sugar acid catabolism (e.g., gluconate in intestinal mucus).
• The Pentose Phosphate (PP) Pathway produces NADPH (for biosynthesis) and precursor metabolites.
  • Generates ribose-5-phosphate (for nucleotides) and aromatic amino acids.

Tricarboxylic Acid (TCA) Cycle

• The TCA cycle is found in the cytoplasm (prokaryotes) or mitochondria (eukaryotes).
• The TCA cycle generates 3 NADH, 1 FADH2, and 1 ATP (or GTP) per acetyl-CoA.
  • Precursor metabolites for biosynthesis are also generated.

Glyoxylate Bypass

• The Glyoxylate Bypass is a modification of the TCA cycle
  • It is used when carbon needs to be conserved.
  • Bypasses steps that release CO2.

Fermentation vs. Respiration

• ATP is ONLY made in fermentation via substrate-level phosphorylation.
• NADH donates electrons to an endogenous electron acceptor (like pyruvate).
• Produces diverse end products (e.g., lactic acid, ethanol) in fermentation.
• Uses the ETC to generate ATP in respiration.
• Requires a terminal electron acceptor (O2 for aerobic, nitrate/sulfate for anaerobic) in respiration.

Catabolism of Other Organic Molecules

• Lipids are broken into glycerol (→ glycolysis) and fatty acids (→ β-oxidation → TCA cycle).
• Proteins are broken into amino acids (deaminated → TCA cycle intermediates).

Electron Flow and Energy Generation

• The ETC transfers electrons stepwise, gradually releasing energy.
• Electrons move from low to high reduction potential.

ETC Components

• Initial dehydrogenase (e.g., NADH dehydrogenase)
• Mobile electron carriers (e.g., quinones)
• Terminal oxidase (e.g., cytochrome oxidase)
• Protons are pumped across the membrane, which creates the PMF.
• ATP synthase (F1FO ATPase) uses the PMF to generate ATP.

Anaerobic Respiration

• Uses alternative electron acceptors (e.g., nitrate, sulfate, fumarate).
• Example: Paracoccus denitrificans performs denitrification: 2NO3- + 10e- + 12H+ → N2 + 6H2O

Chemolithotrophy

• Uses inorganic molecules (H2, Fe2+, NH4+) as electron donors.
• Acidothiobacillus ferrooxidans oxidizes Fe2+ to generate energy.
• Nitrification (by Nitrosomonas & Nitrobacter) occurs when NH4+ → NO2- → NO3-.

Phototrophy (Photosynthesis)

• Phototrophs use light energy for ATP production.
• Oxygenic Phototrophy (Cyanobacteria, plants): Uses PSI & PSII, splitting water to produce O2.
• Anoxygenic Phototrophy (Purple & Green Bacteria): Uses H2S or organic molecules instead of water.
• Chlorophyll & Light Absorption occur when different chlorophyll types absorb different light wavelengths. Light-harvesting antennae increase photon capture.

Key Differences in Electron Flow

• Aerobic Respiration
  • Electron Source: Organic molecules (glucose)
  • Final Electron Acceptor: O2
  • ATP Generation: Oxidative phosphorylation
• Anaerobic Respiration
  • Electron Source: Organic molecules
  • Final Electron Acceptor: Nitrate, sulfate, etc.
  • ATP Generation: Oxidative phosphorylation
• Chemolithotrophy
  • Electron Source: Inorganic molecules (H2, NH4+, Fe2+)
  • Final Electron Acceptor: O2, nitrate, etc.
  • ATP Generation: Oxidative phosphorylation
• Phototrophy
  • Electron Source: Light
  • Final Electron Acceptor: NADP+ or quinones
  • ATP Generation: Photophosphorylation