Microbial Metabolism

Overview of Metabolism

Metabolism encompasses all chemical reactions in a cell, including those that break down substances to release energy (catabolism) and those that use energy to build new molecules (anabolism). These reactions are essential for microbial survival, growth, and reproduction.

• Catabolic pathways: Break down molecules, releasing energy (hydrolytic, exergonic reactions). Example: Breakdown of sugars into CO2 and H2O.

• Anabolic pathways: Use energy and small molecules to build larger molecules (dehydration synthesis, endergonic reactions).

• Amphibolic pathways: Function in both catabolism and anabolism, providing flexibility in metabolism.

Catabolic and anabolic reactions are often coupled—energy released from catabolism powers anabolism, maintaining cellular energy balance.

Adenosine Triphosphate (ATP)

• ATP is the main energy currency of the cell, composed of adenine, ribose, and three phosphate groups.

• ATP is generated by catabolic reactions and used to drive anabolic reactions.

• When ATP loses its terminal phosphate (dephosphorylation), it becomes ADP (adenosine diphosphate).

Example: A cell breaks down a polysaccharide (catabolism) to produce ATP, which is then used to build a polypeptide (anabolism).

Enzymes and Catalysis

Enzyme Structure and Function

Enzymes are protein catalysts that speed up chemical reactions without being consumed. They lower the activation energy required for reactions and are highly specific for their substrates.

• Enzyme names typically end in -ase.

• The substrate is the molecule acted upon by the enzyme.

• The active site is where the substrate binds; the induced fit model describes how enzymes and substrates adjust their shapes for optimal interaction.

• Enzyme-substrate complex formation stabilizes the transition state, facilitating the reaction.

Factors Affecting Enzyme Activity

• Temperature: Low temperatures slow activity; high temperatures can denature enzymes, making them nonfunctional.

• pH: Each enzyme has an optimal pH; deviations can alter structure and reduce activity or cause denaturation.

• Substrate concentration: Enzyme activity increases with substrate concentration until saturation is reached.

• Cofactors: Nonprotein components (e.g., metal ions like Fe2+, Zn2+, Mg2+, Ca2+) or organic molecules (coenzymes) required for enzyme function.

• Inhibitors:

  • Competitive inhibitors: Compete with substrate for the active site.

  • Noncompetitive inhibitors: Bind elsewhere on the enzyme, altering its function.

• Feedback inhibition: End products inhibit earlier steps in a pathway, preventing overproduction.

Denaturation: Loss of enzyme structure (and function) due to extreme temperature or pH; may be reversible or irreversible.

Enzyme Forms

• Apoenzyme: Inactive enzyme without its cofactor.

• Holoenzyme: Active enzyme with its cofactor.

Common coenzymes (electron carriers): NAD+, FAD.

Redox Reactions and Energy Production

Oxidation-Reduction (Redox) Reactions

Redox reactions involve the transfer of electrons between molecules. They are central to energy extraction in cells.

• Oxidation: Loss of electrons.

• Reduction: Gain of electrons.

Remember: OIL RIG—Oxidation Is Loss, Reduction Is Gain.

Redox reactions are always paired; one molecule is oxidized while another is reduced. Electron carriers like NAD+ and FAD shuttle electrons between reactions.

ATP Generation Mechanisms

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

• Oxidative phosphorylation: ATP is produced using energy from a proton gradient generated by the electron transport chain (ETC).

• Photophosphorylation: ATP is generated using light energy (photosynthesis).

Carbohydrate Catabolism

Cellular Respiration Pathways

Cells extract energy from carbohydrates via cellular respiration, which includes glycolysis, the intermediate step, Krebs cycle, and the electron transport chain.

• Glycolysis: Splits glucose (6C) into two pyruvic acid (3C) molecules. Net gain: 2 ATP, 2 NADH.

• Intermediate step: Pyruvic acid is decarboxylated to acetyl-CoA, producing NADH and CO2.

• Krebs cycle (Citric Acid Cycle): Acetyl-CoA is oxidized, generating 2 ATP (or GTP), 6 NADH, 2 FADH2, and 4 CO2 per glucose.

• Electron Transport Chain (ETC): NADH and FADH2 donate electrons, creating a proton gradient used by ATP synthase to produce ATP. Oxygen is the final electron acceptor in aerobic respiration.

Summary Table: ATP and Electron Carrier Production

Additional info: In eukaryotes, total ATP yield per glucose is typically 30–32; older sources may state 36.

Alternative Carbohydrate Pathways

• Pentose Phosphate Pathway: Converts pentoses to glycolytic intermediates; produces NADPH for biosynthesis.

• Entner-Doudoroff Pathway: Alternative to glycolysis in some Gram-negative bacteria; yields 1 ATP and NADPH per glucose.

Fermentation

Fermentation allows ATP production via glycolysis when the ETC is unavailable. Its main role is to regenerate NAD+ from NADH.

• Homolactic fermentation: Pyruvic acid → lactic acid (e.g., Lactobacillus, human muscle cells).

• Heterolactic fermentation: Pyruvic acid → lactic acid, ethanol, CO2, and other acids (e.g., Lactobacillus, Leuconostoc).

• Alcohol fermentation: Pyruvic acid → ethanol + CO2 (e.g., Saccharomyces cerevisiae).

• Mixed acid fermentation: Produces various acids and gases (e.g., enteric bacteria).

• Butanediol fermentation: Produces neutral end products like butanediol.

Catabolism of Other Macromolecules

Lipid Catabolism

• Lipases break down lipids into glycerol and fatty acids.

• Glycerol enters glycolysis as DHAP; fatty acids undergo beta-oxidation to acetyl-CoA for the Krebs cycle.

Protein Catabolism

• Proteases and peptidases break proteins into amino acids.

• Amino acids are deaminated and enter the Krebs cycle or are recycled for biosynthesis.

Nucleic Acid Catabolism

• Nucleases break down DNA/RNA into nucleotides, which are usually salvaged rather than used for energy.

Anabolic Pathways and Biosynthesis

• Biosynthesis: Building biological molecules (anabolism); requires ATP and reducing power (e.g., NADPH).

• Gluconeogenesis: Synthesis of glucose from non-sugar precursors.

• Glycogenesis: Formation of glycogen from glucose-6-phosphate.

• Lipid biosynthesis: Glycerol from DHAP; fatty acids from acetyl-CoA.

• Amino acid biosynthesis: Nonessential amino acids made by amination; essential amino acids must be acquired from the environment.

• Nucleotide biosynthesis: Purines (adenine, guanine) and pyrimidines (uracil, thymine, cytosine) are essential for nucleic acids and ATP.

Microbial Nutrition and Classification

Carbon and Energy Sources

• Autotrophs: Use inorganic carbon (CO2) for biosynthesis via carbon fixation.

• Heterotrophs: Require organic carbon sources.

• Phototrophs: Obtain energy from light.

• Chemotrophs: Obtain energy from chemical compounds.

• Lithotrophs: Use inorganic molecules for reducing power.

• Organotrophs: Use organic molecules for reducing power.

Biochemical Tests for Microbial Identification

Common Biochemical Tests

Other tests include amino acid catabolism (e.g., phenylalanine deaminase, ornithine decarboxylase, sulfur reduction).

Comparisons and Key Concepts

Substrate-Level vs. Oxidative Phosphorylation

Obligate vs. Facultative Anaerobes

Key Equations and Concepts

• ATP hydrolysis:

• Redox reactions:

• Glycolysis summary:

• Krebs cycle (per glucose):

Electron Transport Chain (ETC) and Chemiosmosis

• NADH and FADH2 donate electrons to the ETC.

• Electron transfer pumps H+ ions across the membrane, creating a proton gradient.

• Protons flow back through ATP synthase, driving ATP production (chemiosmosis).

• Oxygen (aerobic) or other inorganic molecules (anaerobic) serve as final electron acceptors.

• Location: Plasma membrane (prokaryotes), inner mitochondrial membrane (eukaryotes).

Summary Points

• Metabolism includes all chemical reactions in a cell.

• Catabolic reactions provide energy and building blocks for anabolic reactions.

• ATP is the universal energy currency.

• Enzymes are essential for metabolic reactions and are regulated by various factors.

• Redox reactions and electron carriers are central to energy extraction.

• Microbes use diverse metabolic pathways, which can be used for identification in the lab.