Microbial Metabolism

Catabolism and Anabolism

Microbial metabolism encompasses all chemical reactions within a microorganism, divided into two main processes: catabolism and anabolism.

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

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

• Example: Glycolysis is a catabolic pathway; protein synthesis is anabolic.

ATP and Phosphorylation

ATP (adenosine triphosphate) is the primary energy currency in cells. Phosphorylation is the process of adding a phosphate group to a molecule, often to ADP to form ATP.

• Three types of ATP phosphorylation:

  • Substrate-level phosphorylation: Direct transfer of a phosphate group to ADP from a substrate.

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

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

• Equation:

Oxidation and Reduction

Oxidation-reduction (redox) reactions are central to energy production in cells.

• Oxidation: Loss of electrons.

• Reduction: Gain of electrons.

• Electron Transport Chain (ETC): Series of proteins that transfer electrons, releasing energy to form ATP.

Enzyme Structure and Function

Enzymes are biological catalysts that speed up chemical reactions.

• Active site: Region where substrate binds.

• Substrate: The molecule upon which an enzyme acts.

• Specificity: Each enzyme acts on a specific substrate.

• Cofactor: Non-protein component required for enzyme activity (e.g., metal ions).

• Coenzyme: Organic cofactor (e.g., NAD+, FAD).

Enzyme Activity Regulation

• Activation energy: Minimum energy required to start a reaction; enzymes lower this barrier.

• Factors affecting activity: Temperature, pH, substrate concentration, enzyme concentration.

• Inhibition:

  • Competitive inhibition: Inhibitor binds active site, blocking substrate.

  • Noncompetitive inhibition: Inhibitor binds elsewhere, altering enzyme shape.

Carbohydrate Metabolism

Carbohydrate metabolism includes glycolysis, Krebs cycle, and electron transport chain.

• Glycolysis: Glucose is broken down into pyruvate, producing ATP and NADH.

• Krebs Cycle: Pyruvate is further oxidized, generating NADH, FADH2, and ATP.

• Electron Transport Chain: Electrons from NADH and FADH2 are transferred to oxygen, producing ATP.

Fermentation and Respiration

• Aerobic respiration: Uses oxygen as final electron acceptor; produces more ATP.

• Anaerobic respiration: Uses other molecules as final electron acceptor.

• Fermentation: Incomplete oxidation of glucose; produces less ATP and end products like lactic acid or ethanol.

Photosynthesis

• 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.

• Equation:

Amphibolic Pathways

Amphibolic pathways function in both catabolism and anabolism, providing intermediates for biosynthesis and energy production.

Microbial Nutrition and Growth

Nutritional Factors

• Major elements: Carbon, nitrogen, oxygen, hydrogen, phosphorus, sulfur.

• Trace elements: Required in small amounts (e.g., iron, zinc).

• Growth factors: Organic compounds required for growth (e.g., vitamins, amino acids).

Oxygen Requirements

• Obligate aerobes: Require oxygen.

• Obligate anaerobes: Cannot tolerate oxygen.

• Facultative anaerobes: Can grow with or without oxygen.

• Microaerophiles: Require low oxygen levels.

• Aerotolerant anaerobes: Do not use oxygen but tolerate its presence.

Carbon and Energy Sources

• Phototrophs: Use light as energy source.

• Chemotrophs: Use chemicals as energy source.

• Autotrophs: Use CO2 as carbon source.

• Heterotrophs: Use organic compounds as carbon source.

Environmental Factors Affecting Growth

• Temperature: Psychrophiles (cold), mesophiles (moderate), thermophiles (hot).

• pH: Acidophiles (acidic), neutrophiles (neutral), alkaliphiles (basic).

• Osmotic pressure: Halophiles (salt-loving), osmophiles (sugar-loving).

Microbial Growth Curve

• Lag phase: Adaptation, no division.

• Log phase: Exponential growth.

• Stationary phase: Growth rate equals death rate.

• Death phase: Decline in viable cells.

Measuring Microbial Growth

• Direct methods: Plate counts, membrane filtration, microscopic count.

• Indirect methods: Turbidity (cloudiness), metabolic activity.

Culturing Microorganisms

• Pure culture: Population of cells from a single cell.

• Streak plate and pour plate methods: Techniques to isolate pure cultures.

• Media types:

  • Selective media: Inhibits unwanted microbes.

  • Differential media: Distinguishes between organisms.

  • Complex media: Contains unknown exact composition.

Microbial Genetics

Genetic Material

• Gene: Segment of DNA coding for a protein.

• Genome: Complete set of genetic material.

• Chromosome: DNA molecule containing genes.

• Plasmid: Small, circular DNA in bacteria.

DNA Structure and Replication

• Nucleotide: Building block of DNA (phosphate, deoxyribose, nitrogenous base).

• DNA replication: Semi-conservative process; enzymes involved include DNA polymerase, ligase, helicase, primase.

• Diagram: (Students should be able to draw and label the process.)

Gene Expression

• Transcription: DNA to mRNA.

• Translation: mRNA to protein.

• Codon: Three-nucleotide sequence on mRNA coding for an amino acid.

• Anticodon: Complementary sequence on tRNA.

• Start codon: AUG (methionine).

• Stop codons: UAA, UAG, UGA.

• Ribosome: Site of protein synthesis.

Genetic Code and Mutations

• Genetic code: Universal, redundant, unambiguous.

• Mutation: Change in DNA sequence; can be substitution, insertion, deletion.

• Mutagen: Agent causing mutations (e.g., chemicals, radiation).

• Genotype vs. phenotype: Genotype is genetic makeup; phenotype is observable traits.

Gene Transfer in Bacteria

• Transformation: Uptake of naked DNA from environment.

• Conjugation: Transfer of DNA via direct contact (often plasmids).

• Transduction: Transfer of DNA by bacteriophages.

• F plasmid: Fertility plasmid involved in conjugation.

• R plasmid: Carries antibiotic resistance genes.

Biotechnology

Genetic Engineering and Recombinant DNA

• Biotechnology: Use of living organisms to make products.

• Genetic engineering: Manipulation of genes for practical purposes.

• Recombinant DNA technology: Combining DNA from different sources.

• Plasmids: Useful as vectors for gene cloning.

Restriction Enzymes and DNA Ligase

• Restriction enzyme: Cuts DNA at specific sequences.

• DNA ligase: Joins DNA fragments.

• Vector: DNA molecule used to transfer genetic material (e.g., plasmid, virus).

PCR and DNA Fingerprinting

• PCR (Polymerase Chain Reaction): Amplifies DNA sequences rapidly.

• DNA fingerprinting: Identifies individuals based on unique DNA patterns; uses techniques like RFLP, Southern blot, or PCR.

Genomics and Bioinformatics

• Genomics: Study of whole genomes.

• Bioinformatics: Use of computational tools to analyze genetic data.

CRISPR-Cas System

• CRISPR-Cas: Adaptive immune system in bacteria/archaea; used for gene editing.

• Application: Can be engineered to target and modify specific genes in various organisms.