Microbial Metabolism: Study Notes

Microbial Metabolism

Basic Chemical Reactions Underlying Metabolism

Metabolism encompasses all the biochemical reactions occurring within a microorganism. These reactions are organized into pathways that either break down molecules to release energy or build complex molecules using energy.

• Catabolism: The breakdown of nutrient molecules, releasing energy (exergonic). This energy is stored in ATP molecules.

• Anabolism: The synthesis of macromolecules, requiring energy input (endergonic), typically using ATP.

• Pathways: Series of enzyme-catalyzed reactions assembling or disassembling molecules.

• Precursor Metabolites: Small molecules produced by catabolism, used as building blocks in anabolism.

Example: The breakdown of glucose (catabolism) provides both energy and precursor metabolites for the synthesis of amino acids (anabolism).

Oxidation and Reduction Reactions

Redox reactions are central to metabolism, involving the transfer of electrons between molecules.

• Oxidation: Loss of electrons (may involve loss of hydrogen atoms).

• Reduction: Gain of electrons (becomes more negatively charged).

• Dehydrogenation: Redox reaction involving the removal of hydrogen atoms.

• Electron Carriers: NAD+, NADP+, and FAD are common carriers, shuttling electrons in metabolic pathways.

Equation:

$\text{AH}_2 + \text{B} \rightarrow \text{A} + \text{BH}_2$

(A is oxidized, B is reduced)

ATP Production and Energy Storage

ATP (adenosine triphosphate) is the primary energy currency in cells, produced by phosphorylation processes.

• Substrate-level phosphorylation: Direct transfer of phosphate from an organic molecule to ADP.

• Oxidative phosphorylation: Uses energy from electron transport to add inorganic phosphate to ADP.

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

Equation:

$\text{ADP} + \text{P}_i \rightarrow \text{ATP}$

The Roles of Enzymes in Metabolism

Enzymes are biological catalysts that speed up metabolic reactions without being consumed.

• Enzyme Structure: May be a simple protein or require cofactors (inorganic ions or organic coenzymes).

• Apoenzyme: Protein portion of an enzyme.

• Cofactor: Nonprotein component (e.g., metal ions, vitamins).

• Holoenzyme: Complete, active enzyme with its cofactors.

• Ribozymes: RNA molecules with catalytic activity, especially in RNA processing.

• Enzyme Specificity: Determined by the shape of the active site and substrate.

• Denaturation: Loss of enzyme structure and function due to temperature or pH changes.

• Enzyme Regulation: Includes allosteric activation/inhibition, competitive inhibition, and feedback inhibition.

Enzyme Classes:

• Hydrolases: Catalyze hydrolysis reactions.

• Lyases: Split molecules without water.

• Isomerases: Rearrange atoms within a molecule.

• Ligases/Polymerases: Join molecules together.

• Oxidoreductases: Catalyze redox reactions.

• Transferases: Transfer functional groups between molecules.

Carbohydrate Catabolism

Carbohydrates are a major energy source, catabolized by glycolysis, cellular respiration, or fermentation.

Glycolysis

• Occurs in the cytoplasm; splits glucose into two pyruvate molecules.

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

• Three stages: energy-investment, lysis, energy-conserving.

Equation:

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

Cellular Respiration

• Complete oxidation of pyruvate to CO2 and H2O, producing large amounts of ATP.

• Three stages: Synthesis of acetyl-CoA, Krebs cycle, Electron transport chain (ETC).

Synthesis of Acetyl-CoA

• Pyruvate is decarboxylated and joined to coenzyme A.

• Products (per glucose): 2 acetyl-CoA, 2 CO2, 2 NADH.

Krebs Cycle (Citric Acid Cycle)

• Acetyl-CoA enters a cycle of eight enzymatic steps.

• Products (per glucose): 2 ATP, 6 NADH, 2 FADH2, 4 CO2.

• Types of reactions: anabolism, isomerization, redox, decarboxylation, substrate-level phosphorylation, hydrolysis.

Electron Transport Chain (ETC) and Chemiosmosis

• Electrons from NADH and FADH2 are transferred through a series of carriers (flavoproteins, ubiquinones, metal-containing proteins, cytochromes).

• Energy from electron transfer pumps protons across the membrane, creating a proton gradient (proton motive force).

• ATP synthase uses this gradient to synthesize ATP (chemiosmosis).

• Final electron acceptor: O2 (aerobic), or other inorganic molecules (anaerobic).

• Theoretical yield: up to 38 ATP per glucose (prokaryotes).

Equation:

$\text{NADH} + \text{H}^+ + 1/2\ \text{O}_2 \rightarrow \text{NAD}^+ + \text{H}_2\text{O}$

Metabolic Diversity

• Pentose Phosphate Pathway: Alternative to glycolysis; produces NADPH and precursor metabolites for biosynthesis.

• Entner-Doudoroff Pathway: Used by some bacteria; yields NADPH and unique metabolites.

Fermentation

• Partial oxidation of sugar without an external electron acceptor.

• Regenerates NAD+ for glycolysis.

• Common products: lactic acid, ethanol.

• Fermentation products are used in microbial identification and industry.

Other Catabolic Pathways

Lipid Catabolism

• Lipases hydrolyze fats into glycerol and fatty acids.

• Glycerol enters glycolysis as DHAP.

• Fatty acids undergo beta-oxidation to form acetyl-CoA, NADH, and FADH2.

Protein Catabolism

• Proteases digest proteins into amino acids outside the cell.

• Amino acids are deaminated and converted into Krebs cycle intermediates.

Photosynthesis

Photosynthesis is the process by which light energy is converted into chemical energy, producing organic molecules.

• Light-dependent reactions: Capture light energy to produce ATP and NADPH.

• Light-independent reactions (Calvin cycle): Use ATP and NADPH to fix CO2 into organic molecules.

Other Anabolic Pathways

Anabolic reactions build complex molecules from simpler ones, requiring energy and precursor metabolites.

Carbohydrate Biosynthesis

• Gluconeogenesis: Synthesis of glucose from non-carbohydrate precursors (e.g., amino acids, glycerol).

• Shares several steps with glycolysis (amphibolic), but includes unique reactions.

Lipid Biosynthesis

• Triglycerides are synthesized from glycerol and fatty acids (reverse of catabolism).

• Steroids and carotenoids are synthesized via complex pathways from sugar and amino acid metabolites.

Amino Acid Biosynthesis

• Precursor metabolites from glycolysis, Krebs cycle, and pentose phosphate pathway are used.

• Amination: Addition of an amine group from ammonia.

• Transamination: Transfer of an amine group from one amino acid to another, using pyridoxal phosphate as a coenzyme.

• Essential amino acids must be acquired from the environment if not synthesized.

Nucleotide Biosynthesis

• Ribose and deoxyribose from ribose 5-phosphate (pentose phosphate pathway).

• Phosphate from ATP.

• Pyrimidines and purines from amino acids (glutamine, aspartic acid), ribose 5-phosphate, and folic acid.

Integration and Regulation of Metabolic Functions

Metabolic pathways are tightly regulated to ensure efficient use of resources and energy.

• Amphibolic pathways: Can function in both catabolism and anabolism as needed.

• Regulation mechanisms:

  • Control of gene expression (enzyme production).

  • Control of metabolic expression (activity of existing enzymes).

  • Feedback inhibition, substrate availability, compartmentalization, and use of different coenzymes for anabolic/catabolic reactions.

Example: Cells produce catabolic enzymes only when substrates are present, and stop producing anabolic enzymes when end products are abundant.

Summary Table: Key Metabolic Pathways and Their Features

Pathway	Main Function	Key Products	ATP Yield (per glucose)
Glycolysis	Glucose breakdown to pyruvate	2 ATP, 2 NADH, 2 pyruvate	2
Krebs Cycle	Oxidation of acetyl-CoA	2 ATP, 6 NADH, 2 FADH2, 4 CO2	2
Electron Transport Chain	Electron transfer, ATP synthesis	H2O, ATP	~34
Fermentation	Regenerate NAD+	Lactic acid, ethanol, other products	0 (beyond glycolysis)
Pentose Phosphate Pathway	Produce NADPH, precursors	NADPH, ribose-5-phosphate	Variable, less than glycolysis

Additional info: These notes expand on the original outline by providing definitions, equations, and examples for each major metabolic process, as well as a summary table for quick comparison.