Microbial Metabolism: Study Guide and Key Concepts

Microbial Metabolism

Overview of Metabolism

Metabolism encompasses all chemical reactions occurring within a living organism. These reactions are essential for maintaining life, providing energy, and synthesizing necessary cellular components.

• Catabolism: Breakdown of complex molecules into simpler ones, releasing energy.

• Anabolism: Synthesis of complex molecules from simpler ones, requiring energy input.

• The energy released from catabolic reactions is used to drive anabolic reactions.

• Energy is primarily stored and transferred in the form of ATP (adenosine triphosphate).

Enzymes

Structure and Function

Enzymes are biological catalysts that accelerate chemical reactions by lowering the activation energy required. They are crucial for metabolic processes.

• Enzymes are generally globular proteins with specific three-dimensional shapes.

• They are highly efficient and function under mild cellular conditions.

• Enzymes exhibit specificity due to their unique active sites.

• After catalysis, enzymes are recovered unchanged.

Naming and Classification

• Enzyme names typically end with -ase (e.g., sucrase, lipase).

• There are six major classes of enzymes, categorized by the reactions they catalyze.

Enzyme Components

• Most enzymes are holoenzymes, consisting of:

  • Apoenzyme: The protein portion.

  • Cofactor: The nonprotein component, which may be a metal ion (e.g., Fe, Mg, Zn) or a complex organic molecule called a coenzyme (e.g., NAD+, FAD, coenzyme A).

Factors Influencing Enzyme Activity

• Temperature: High temperatures can denature enzymes; low temperatures slow reaction rates.

• pH: Each enzyme has an optimum pH for maximal activity.

• Substrate Concentration: Activity increases with substrate concentration until enzymes are saturated.

• Inhibitors:

  • Competitive inhibitors compete with the substrate for the active site.

  • Noncompetitive inhibitors bind elsewhere, altering enzyme function.

Regulation of Enzyme Activity

• Feedback inhibition: The end-product of a metabolic pathway inhibits an early enzyme in the pathway, preventing overproduction.

Ribozymes

• Ribozymes are RNA molecules with catalytic activity, especially in protein synthesis.

Energy Production

Oxidation-Reduction (Redox) Reactions

Redox reactions are central to energy production in cells, involving the transfer of electrons between molecules.

• Oxidation: Loss of electrons (often with protons, H+).

• Reduction: Gain of electrons.

• Redox reactions are coupled; when one molecule is oxidized, another is reduced.

• NAD+ is reduced to NADH during these reactions.

• Glucose is a reduced molecule; its oxidation releases energy.

ATP Generation

• Energy from metabolic reactions is used to form ATP from ADP and inorganic phosphate (Pi).

• Phosphorylation: Addition of a phosphate group to a molecule.

• Substrate-level phosphorylation: Direct transfer of a high-energy phosphate to ADP.

• Oxidative phosphorylation: Energy from electron transport is used to generate ATP.

• Photophosphorylation: Light energy is used to generate ATP in photosynthetic organisms.

Metabolic Pathways of Energy Production

Carbohydrate Catabolism

Carbohydrates are the primary energy source for most cells. Their catabolism occurs via several pathways:

• Respiration: Complete breakdown of sugars to CO2 and H2O.

• Fermentation: Partial breakdown of sugars, producing organic end-products.

Glycolysis

• Main pathway for glucose oxidation; end-product is pyruvic acid.

• Net yield per glucose: 2 ATP and 2 NADH.

Alternative Pathways

• Pentose phosphate pathway: Oxidizes five-carbon sugars; yields 1 ATP and 12 NADPH per glucose.

• Entner-Doudoroff pathway: Yields 1 ATP and 2 NADPH per glucose.

Cellular Respiration

• Organic molecules are oxidized; energy is generated via the electron transport chain (ETC).

• Aerobic respiration: O2 is the final electron acceptor.

• Anaerobic respiration: Final electron acceptor is an inorganic molecule other than O2 (e.g., NO3-, SO42-, CO32-).

• Pyruvic acid is decarboxylated to acetyl-CoA, which enters the Krebs cycle.

• Each glucose yields 6 NADH, 2 FADH2, and 2 ATP in the Krebs cycle; 6 CO2 are released.

• NADH and FADH2 donate electrons to the ETC, which includes flavoproteins, cytochromes, and ubiquinones.

• Proton motive force generated by proton pumping drives ATP synthesis via ATP synthase.

• Location of ETC: Inner mitochondrial membrane (eukaryotes), plasma membrane (prokaryotes).

• Total ATP yield per glucose: 38 (prokaryotes), 36 (eukaryotes) in aerobic respiration.

• Anaerobic respiration yields less ATP due to incomplete Krebs cycle operation.

Fermentation

• Releases energy from organic molecules without O2.

• Yields 2 ATP per glucose via substrate-level phosphorylation.

• Electrons from substrate reduce NAD+.

• Final electron acceptor is an organic molecule from within the cell.

• Lactic acid fermentation: Pyruvic acid is reduced to lactic acid.

• Alcohol fermentation: Acetaldehyde is reduced to ethanol.

• Heterolactic fermenters: Produce lactic acid and ethanol via the pentose phosphate pathway.

Lipid and Protein Catabolism

• Lipases hydrolyze lipids into glycerol and fatty acids.

• Fatty acids are catabolized by beta-oxidation.

• Catabolic products enter glycolysis and the Krebs cycle.

• Amino acids are converted (via transamination, decarboxylation, desulfurization) to intermediates for the Krebs cycle.

Biochemical Tests and Bacterial Identification

• Bacteria and yeast can be identified by their enzyme activities.

• Fermentation tests detect acid and gas production from carbohydrate fermentation.

Photosynthesis

Light-Dependent Reactions (Photophosphorylation)

• Photosynthesis converts light energy into chemical energy for carbon fixation.

• Chlorophyll a is used by green plants, algae, and cyanobacteria.

• Electrons from chlorophyll pass through an ETC, generating ATP by chemiosmosis.

• Photosystems are pigment complexes in thylakoid membranes.

• Cyclic photophosphorylation: Electrons return to chlorophyll.

• Noncyclic photophosphorylation: Electrons reduce NADP+; electrons from H2O or H2S replenish chlorophyll.

• O2 is produced when H2O is oxidized; S0 granules are produced when H2S is oxidized.

Light-Independent Reactions (Calvin-Benson Cycle)

• CO2 is fixed into sugars via the Calvin-Benson cycle.

Summary of Energy Production Mechanisms

• Phototrophs convert sunlight to chemical energy; chemotrophs use chemical energy.

• Energy is derived from electron transfer in redox reactions.

• Cells require an electron donor, electron carriers, and a final electron acceptor for energy production.

Metabolic Diversity Among Organisms

• Photoautotrophs: Use light for energy and CO2 for carbon (e.g., cyanobacteria).

• Oxygenic phototrophs: Produce O2 (e.g., cyanobacteria).

• Anoxygenic phototrophs: Do not produce O2 (e.g., green and purple bacteria).

• Photoheterotrophs: Use light for energy and organic compounds for carbon and electrons.

• Chemoautotrophs: Use inorganic compounds for energy and CO2 for carbon.

• Chemoheterotrophs: Use organic molecules for both energy and carbon.

Metabolic Pathways of Energy Use

Polysaccharide Biosynthesis

• Glycogen is synthesized from ADP-glucose (ADPG).

• UDP-N-acetylglucosamine (UDPNAc) is the precursor for peptidoglycan biosynthesis.

Lipid Biosynthesis

• Lipids are synthesized from fatty acids and glycerol.

• Glycerol is derived from dihydroxyacetone phosphate; fatty acids are built from acetyl-CoA.

Amino Acid and Protein Biosynthesis

• Amino acids are essential for protein synthesis.

• They are synthesized from intermediates of carbohydrate metabolism, especially the Krebs cycle.

Purine and Pyrimidine Biosynthesis

• Nucleotide sugars are derived from the pentose phosphate or Entner-Doudoroff pathways.

• Purine and pyrimidine backbones are formed from carbon and nitrogen atoms of certain amino acids.

Integration of Metabolism

• Anabolic and catabolic reactions are interconnected via common intermediates.

• Such interconnected pathways are called amphibolic pathways.

Key Equations

• ATP Formation:

  • $\mathrm{ADP} + \mathrm{P_i} \rightarrow \mathrm{ATP}$

• General Redox Reaction:

  • $\mathrm{AH}_2 + \mathrm{B} \rightarrow \mathrm{A} + \mathrm{BH}_2$

• Glycolysis (Net Reaction):

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

Table: Types of Metabolism and Their Characteristics

Type	Energy Source	Carbon Source	Examples
Photoautotroph	Light	CO2	Cyanobacteria, plants
Photoheterotroph	Light	Organic compounds	Green non-sulfur bacteria
Chemoautotroph	Inorganic compounds	CO2	Nitrifying bacteria
Chemoheterotroph	Organic compounds	Organic compounds	Most bacteria, animals, fungi

Example: Escherichia coli is a chemoheterotroph, using glucose as both its energy and carbon source.

Additional info: Some details, such as the specific numbers of ATP produced in various pathways, were expanded for clarity and completeness.