Metabolism in Microorganisms

Overview of Metabolism

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

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

• Anabolic pathways: Build complex molecules from simpler ones, requiring energy (dehydration synthesis, endergonic reactions).

• Amphibolic pathways: Function in both catabolic and anabolic processes.

Catabolic and anabolic reactions are often coupled, with energy released from catabolism fueling anabolism. This balance maintains cellular energy homeostasis.

Adenosine Triphosphate (ATP)

• ATP: The primary energy currency of the cell, composed of adenine, ribose, and three phosphate groups.

• ADP (Adenosine Diphosphate): Formed when ATP loses a phosphate group via dephosphorylation.

• Catabolic reactions generate ATP, which is then used to power anabolic reactions and other cellular work.

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 accelerate chemical reactions by lowering activation energy. They are not consumed or permanently altered during the reaction.

• Active site: Region where the substrate binds.

• Substrate: The molecule upon which an enzyme acts.

• Enzyme-substrate complex: Temporary association that facilitates the reaction.

• Induced fit model: Enzyme and substrate both change shape slightly to optimize binding and catalysis.

Factors Affecting Enzyme Activity

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

• pH: Each enzyme has an optimal pH; deviations can disrupt hydrogen and ionic bonds, altering enzyme structure and function.

• 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 coenzymes (e.g., NAD+, FAD) required for enzyme activity.

• Inhibitors:

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

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

• Feedback inhibition: End product of a pathway inhibits an early enzyme, regulating pathway activity.

Enzyme Regulation and Specificity

• Enzymes are highly specific for their substrates due to the unique structure of their active sites.

• Enzyme activity can be regulated by feedback inhibition, ensuring efficient use of resources.

Redox Reactions and Energy Transfer

Oxidation-Reduction (Redox) Reactions

Redox reactions involve the transfer of electrons between molecules, essential for extracting energy from nutrients.

• Oxidation: Loss of electrons.

• Reduction: Gain of electrons.

• Redox pair: Oxidation and reduction always occur together.

• Oxidizing agent: Accepts electrons.

• Reducing agent: Donates electrons.

• Common coenzymes acting as electron carriers: NAD+, FAD.

Mnemonic: OIL RIG (Oxidation Is Loss, Reduction Is Gain of electrons).

ATP Generation Mechanisms

Phosphorylation Methods

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

• Oxidative phosphorylation: ATP generated using energy from electron transport chains powered by redox reactions. Occurs in aerobic and anaerobic respiration.

• Photophosphorylation: ATP generated using light energy in photosynthetic organisms.

Carbohydrate Catabolism

Cellular Respiration Pathways

Cellular respiration is a series of redox reactions that extract energy from nutrients and store it in ATP. It includes glycolysis, the intermediate step, the Krebs cycle, and the electron transport chain (ETC).

• Glycolysis: Occurs in the cytoplasm; splits glucose into two pyruvate molecules, producing 2 ATP (net) and 2 NADH.

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

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

• Electron Transport Chain: Electrons from NADH and FADH2 are transferred through membrane proteins, creating a proton gradient used by ATP synthase to generate ATP. Oxygen is the final electron acceptor in aerobic respiration.

Alternative Pathways

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

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

Fermentation

Fermentation allows ATP production via glycolysis when the ETC is unavailable. NADH transfers electrons to organic molecules, regenerating NAD+ for glycolysis.

• Homolactic fermentation: Pyruvate reduced to lactic acid; 2 ATP produced. Used by Lactobacillus, Streptococcus, and human muscle cells.

• Heterolactic fermentation: Produces lactic acid, ethanol, CO2, and other acids; 1 ATP produced.

• Alcohol fermentation: Pyruvate converted to ethanol and CO2; used by Saccharomyces cerevisiae (yeast).

• Mixed acid fermentation: Produces various acids and gases; characteristic of enteric bacteria.

• Butanediol fermentation: Produces neutral end products like butanediol and ethanol.

Catabolism of Other Macromolecules

Lipid Catabolism

• Lipases: Break down lipids into glycerol and fatty acids.

• Glycerol enters glycolysis as dihydroxyacetone phosphate (DHAP).

• Fatty acids undergo beta-oxidation to form acetyl-CoA, entering the Krebs cycle.

Protein Catabolism

• Proteases and peptidases: Break proteins into peptides and amino acids.

• Amino acids can be deaminated and catabolized in the Krebs cycle or recycled for biosynthesis.

Nucleic Acid Catabolism

• Nucleases: Break down DNA and RNA into nucleotides.

• Nucleotides are usually salvaged rather than used for energy.

Anabolic Pathways and Biosynthesis

Biosynthesis of Macromolecules

• Gluconeogenesis: Synthesis of glucose from non-carbohydrate 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 synthesized for nucleic acids and ATP.

Microbial Nutrition and Classification

Carbon and Energy Sources

• Autotrophs: Use inorganic carbon (CO2) to build organic molecules via carbon fixation.

• Heterotrophs: Require organic carbon sources.

• Phototrophs: Use light energy to make ATP.

• Chemotrophs: Use chemical energy from nutrients.

• Lithotrophs: Obtain reducing power from inorganic sources.

• Organotrophs: Obtain reducing power from organic sources.

Biochemical Tests for Microbial Identification

Metabolic Profiling

Microbes can be identified by their unique metabolic capabilities using various biochemical tests.

Other Tests

• Amino acid catabolism tests: Detect deaminases and decarboxylases (e.g., phenylalanine deaminase, ornithine decarboxylase, sulfur reduction).

• Fermentation tests: Use media with carbohydrates, pH indicators, and Durham tubes to detect acid/gas production.

• MRVP test: Differentiates between mixed acid and butanediol fermentation.

Summary Table: ATP Production Pathways

Key Equations

• ATP Hydrolysis:

• General Redox Reaction:

• Glycolysis (overall):

• Electron Transport Chain (aerobic):

Additional info:

• In eukaryotes, the electron transport chain is located in the inner mitochondrial membrane; in prokaryotes, it is in the plasma membrane.

• Obligate anaerobes cannot tolerate oxygen, while facultative anaerobes can grow with or without oxygen.

• Most ATP in aerobic respiration is produced by oxidative phosphorylation via the electron transport chain.

• Enzyme denaturation is often irreversible at high temperatures or extreme pH.