Microbial Metabolism: Study Notes for Chapter 5

Microbial Metabolism

Overview of Metabolism

Metabolism encompasses all controlled biochemical reactions that occur within a cell. These reactions are essential for maintaining life, providing energy, and synthesizing necessary cellular components.

• Catabolism: The breakdown of complex molecules into simpler ones, releasing energy (exergonic reactions).

• Anabolism: The synthesis of complex molecules from simpler precursors, requiring energy input (endergonic reactions).

• Energy Storage: Energy released from catabolic reactions is stored in the form of adenosine triphosphate (ATP).

• Precursor Metabolites: Small molecules generated by catabolism, used as building blocks in anabolic reactions.

Oxidation-Reduction (Redox) Reactions

Redox reactions involve the transfer of electrons from an electron donor to an electron acceptor. These reactions are fundamental to energy production in cells.

• Oxidation: Loss of electrons (often as hydrogen atoms).

• Reduction: Gain of electrons.

• Electron Carriers: Molecules that transport electrons during metabolic reactions. The three main carriers are:

  • NAD+ / NADH (Nicotinamide adenine dinucleotide)

  • NADP+ / NADPH (Nicotinamide adenine dinucleotide phosphate)

  • FAD / FADH2 (Flavine adenine dinucleotide)

ATP Production and Phosphorylation

ATP is generated by adding a phosphate group to ADP, a process called phosphorylation. There are three main types of phosphorylation in metabolism:

• Substrate-level phosphorylation: Direct transfer of a phosphate group from a substrate to ADP. Occurs in glycolysis and the Krebs cycle.

• Oxidative phosphorylation: Uses energy from redox reactions in the electron transport chain (ETC) to add phosphate to ADP. Involves ATP synthase and a proton gradient.

• Photophosphorylation: Utilizes light energy to phosphorylate ADP (mainly in photosynthetic organisms).

Proteins and Enzymes

Proteins serve various functions, including catalyzing metabolic reactions as enzymes. They are sensitive to environmental conditions such as pH, temperature, and ionic concentration.

• Amino Acids: Monomers of proteins, linked by peptide bonds.

• Protein Structure: Determined by the sequence and properties of amino acid side groups.

• Enzymes: Biological catalysts, mostly proteins, that lower activation energy and speed up reactions.

• Cofactors: Non-protein components required by some enzymes for activity.

• Active Site: Region on the enzyme where the substrate binds and the reaction occurs.

• Induced-fit Model: The enzyme changes shape slightly to fit the substrate more closely upon binding.

Enzyme Activity and Regulation

Enzyme activity is influenced by several factors, and enzymes can be regulated or inhibited by various mechanisms.

• Factors Affecting Activity: Temperature, pH, ionic concentration, enzyme and substrate concentrations, and presence of inhibitors.

• Denaturation: Extreme changes in temperature, pH, or ionic concentration can irreversibly inactivate enzymes.

• Enzyme Inhibitors:

  • Competitive Inhibitors: Resemble the substrate and compete for binding at the active site.

  • Noncompetitive Inhibitors: Bind to an allosteric site, changing the enzyme's shape and reducing activity.

• Examples: Many drugs act as enzyme inhibitors (e.g., penicillin, aspirin, Lipitor).

Carbohydrate Catabolism

Most organisms use carbohydrates, especially glucose, as their primary energy source. Glucose catabolism occurs via two main pathways: cellular respiration and fermentation.

• Cellular Respiration: Complete breakdown of glucose to CO2 and H2O through glycolysis, the Krebs cycle, and the electron transport chain.

• Fermentation: Partial oxidation of glucose, resulting in organic end products such as lactate or ethanol. Used when cells lack an ETC or oxygen.

Glycolysis

Glycolysis is the first step in glucose catabolism, occurring in the cytoplasm of nearly all cells.

• Glucose (6C) is split into two pyruvate (3C) molecules.

• Net gain: 2 ATP (via substrate-level phosphorylation), 2 NADH, and 2 pyruvic acid.

• Some electrons are transferred to the ETC for further ATP production.

Cellular Respiration

Cellular respiration involves the complete oxidation of pyruvate to CO2 and H2O, producing ATP through a series of redox reactions.

1. Conversion of Pyruvate to Acetyl-CoA: Pyruvate dehydrogenase converts pyruvate to acetyl-CoA, producing CO2 and NADH.

2. Krebs Cycle: Occurs in the cytosol (prokaryotes) or mitochondrial matrix (eukaryotes). Acetyl-CoA is oxidized, generating ATP, NADH, FADH2, and CO2.

3. Electron Transport Chain (ETC): NADH and FADH2 donate electrons to the ETC, which uses the energy to pump protons and create a gradient for ATP synthesis.

Electron Transport Chain (ETC) and Oxidative Phosphorylation

• Located in the inner mitochondrial membrane (eukaryotes) or cytoplasmic membrane (prokaryotes).

• Electrons are passed through a series of carriers, including cytochromes.

• Proton gradient (proton motive force) is established across the membrane.

• ATP synthase uses the energy from the proton gradient to phosphorylate ADP to ATP.

• Final Electron Acceptor:

  • O2 in aerobic respiration.

  • Other molecules (e.g., SO42-, NO3-, CO32-) in anaerobic respiration.

ATP Yield from Aerobic Respiration

• In prokaryotes, approximately 38 ATP molecules are produced per glucose molecule (includes glycolysis, pyruvate to acetyl-CoA, Krebs cycle, and ETC).

Fermentation

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

• Less efficient than respiration; produces fewer ATP molecules.

• End products (e.g., lactic acid, ethanol, acetate) are often waste to the cell but useful in industry (e.g., yogurt, alcohol, vinegar).

• Fermentation does not use the ETC; an organic molecule serves as the final electron acceptor.

Comparison of Metabolic Pathways

Pathway	Final Electron Acceptor	ATP Yield (per glucose)	End Products
Aerobic Respiration	O2	~38 (prokaryotes)	CO2, H2O
Anaerobic Respiration	Inorganic molecules (e.g., NO3-, SO42-)	Varies (<38)	CO2, reduced inorganic compounds
Fermentation	Organic molecules	2	Lactic acid, ethanol, acetate, etc.

Integration and Regulation of Metabolism

Cells regulate metabolism by controlling the expression of genes encoding metabolic enzymes and by feedback mechanisms.

• Catabolic Enzymes: Synthesized only when the substrate is available.

• Anabolic Enzymes: Synthesis ceases if the end product is available in the environment.

• Amphibolic Reactions: Pathways that function in both catabolism and anabolism.

Key Terms and Definitions

• Metabolism: All chemical reactions in a cell.

• Catabolism: Breakdown of molecules to release energy.

• Anabolism: Synthesis of complex molecules from simpler ones.

• Redox Reaction: Coupled oxidation and reduction reactions.

• ATP: Main energy currency of the cell.

• Enzyme: Protein catalyst that speeds up chemical reactions.

• Substrate: Molecule upon which an enzyme acts.

• Activation Energy: Energy required to initiate a reaction.

• Active Site: Region of enzyme where substrate binds.

• Allosteric Site: Site on enzyme where a molecule can bind and change enzyme activity.

• Competitive Inhibitor: Molecule that competes with substrate for active site.

• Noncompetitive Inhibitor: Molecule that binds elsewhere on enzyme, altering its function.

• Ribozyme: RNA molecule with catalytic activity.

• Cellular Respiration: Process of producing ATP by oxidizing organic molecules.

• Fermentation: Anaerobic process that regenerates NAD+ and produces organic end products.

• Glycolysis: First step in glucose catabolism, splitting glucose into pyruvate.

• Krebs Cycle: Series of reactions that oxidize acetyl-CoA to CO2.

• Electron Transport Chain: Series of electron carriers that generate a proton gradient for ATP synthesis.

• Chemiosmosis: Movement of protons across a membrane to drive ATP synthesis.

• Beta-oxidation: Catabolism of fatty acids to acetyl-CoA.

• Deamination: Removal of amino group from amino acids during protein catabolism.

Notable Scientific Contribution

• Peter Mitchell: Proposed the chemiosmotic theory, explaining how ATP is generated by a proton gradient across membranes during oxidative phosphorylation.

Example: Commercial Products from Fermentation

• Lactic Acid: Used in yogurt and cheese production.

• Ethanol: Used in alcoholic beverages and biofuel.

• Acetate: Used in vinegar production.

Sample Equations

• ATP Hydrolysis: $\mathrm{ATP} \rightarrow \mathrm{ADP} + \mathrm{P_i} + \text{energy}$

• General Redox Reaction: $\text{AH}_2 + \text{B} \rightarrow \text{A} + \text{BH}_2$

• Glycolysis Net Reaction: $\mathrm{Glucose} + 2\,\mathrm{NAD}^+ + 2\,\mathrm{ADP} + 2\,\mathrm{P_i} \rightarrow 2\,\mathrm{Pyruvate} + 2\,\mathrm{NADH} + 2\,\mathrm{ATP} + 2\,\mathrm{H}_2\mathrm{O}$

Additional info: Some details, such as the exact ATP yield in eukaryotes (typically 36 ATP per glucose), were not specified in the original notes but are standard in academic context.