Microbial Metabolism, Nutrition, Growth, and Genetics: Structured Study Notes

Microbial Metabolism

Metabolism, Anabolism, and Catabolism

Metabolism refers to all chemical reactions within a cell, divided into two main types: anabolism and catabolism.

• Anabolism: The synthesis of complex molecules from simpler ones; requires energy (endergonic).

• Catabolism: The breakdown of complex molecules into simpler ones; releases energy (exergonic).

• Metabolism: The sum of all anabolic and catabolic reactions.

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

Oxidation and Reduction Reactions

Oxidation-reduction (redox) reactions are essential for energy transfer in cells.

• Oxidation: Loss of electrons (or hydrogen atoms).

• Reduction: Gain of electrons (or hydrogen atoms).

• Redox Pair: One molecule is oxidized, another is reduced.

• Example: NAD+ is reduced to NADH during glycolysis.

ATP Phosphorylation Types

ATP is generated by three main phosphorylation mechanisms:

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

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

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

Enzyme Types, Activities, and Examples

Enzymes are classified based on their activities:

Type	Activity	Example
Oxidoreductases	Oxidation-reduction reactions	Lactate dehydrogenase
Transferases	Transfer functional groups	Hexokinase
Hydrolases	Hydrolysis reactions	Protease
Lyases	Break bonds without water	Aldolase
Isomerases	Isomerization	Phosphoglucoisomerase
Ligases	Join molecules using ATP	DNA ligase

Holoenzyme Components; Protein vs. RNA Enzymes

A holoenzyme is a complete, active enzyme consisting of:

• Apoenzyme: Protein portion.

• Cofactor: Non-protein component (metal ion or coenzyme).

• Coenzyme: Organic molecule (often derived from vitamins).

• Active site: Region where substrate binds.

• Substrate: Molecule acted upon by enzyme.

• Protein enzymes: Most cellular enzymes.

• RNA enzymes (ribozymes): Catalyze RNA splicing.

Activation Energy and Enzyme Activity

Enzymes lower activation energy, facilitating reactions.

• Activation energy: Minimum energy required for a reaction.

• Enzyme: Biological catalyst.

• Role: Enzymes speed up reactions by stabilizing transition states.

Factors Affecting Enzyme Activity

Enzyme activity is influenced by environmental and chemical factors:

• Temperature: High temperatures denature enzymes; optimal range varies.

• pH: Extreme pH alters enzyme structure.

• Substrate concentration: Higher concentration increases activity up to saturation.

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

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

Aerobic Glucose Catabolism Stages

Glucose catabolism involves three main stages:

• Glycolysis: Substrate: glucose; Products: pyruvate, ATP, NADH; Net ATP: 2.

• Krebs cycle: Substrate: acetyl-CoA; Products: CO2, ATP, NADH, FADH2; Net ATP: 2.

• Electron transport chain: Substrate: NADH, FADH2; Products: ATP, H2O; Net ATP: ~34.

Roles of Acetyl-CoA, Krebs Cycle, and ETC

• Acetyl-CoA: Entry molecule for Krebs cycle.

• Krebs cycle: Oxidizes acetyl-CoA, produces electron carriers.

• Electron transport chain: Uses electrons to generate ATP via oxidative phosphorylation.

Aerobic vs. Anaerobic Respiration

• Aerobic: Uses O2 as final electron acceptor; produces more ATP.

• Anaerobic: Uses other molecules (e.g., nitrate, sulfate); less ATP produced.

Electron Carrier Classes

• Flavoproteins

• Ubiquinones (Coenzyme Q)

• Cytochromes

• Iron-sulfur proteins

Photosynthesis: Chemical and Structural Components

Photosynthesis converts light energy to chemical energy.

• Prokaryotes: Thylakoid membranes, pigments (e.g., bacteriochlorophyll).

• Eukaryotes: Chloroplasts, chlorophyll.

Photosystems I and II

• Photosystem I: Absorbs longer wavelengths; produces NADPH.

• Photosystem II: Absorbs shorter wavelengths; splits water, produces ATP.

Cyclic vs. Noncyclic Phosphorylation

• Cyclic: Electrons cycle back to photosystem I; only ATP produced.

• Noncyclic: Electrons flow from water to NADP+; produces ATP and NADPH.

Light-dependent vs. Light-independent Reactions

• Light-dependent: Require light; produce ATP and NADPH.

• Light-independent: Use ATP and NADPH to fix CO2 (Calvin-Benson cycle).

Calvin-Benson Cycle: Reactants and Products

• Reactants: CO2, ATP, NADPH.

• Products: Glucose (or other carbohydrates).

Microbial Nutrition and Growth

Roles of Elements and Vitamins in Microbial Growth

• Carbon: Backbone of organic molecules.

• Hydrogen: Maintains pH, forms organic compounds.

• Oxygen: Terminal electron acceptor, component of water.

• Nitrogen: Amino acids, nucleic acids.

• Trace elements: Enzyme cofactors (e.g., Fe, Zn).

• Vitamins: Coenzymes (e.g., NAD, FAD).

Categories of Organisms by Carbon and Energy Sources

Category	Carbon Source	Energy Source
Photoautotroph	CO2	Light
Chemoautotroph	CO2	Chemicals
Photoheterotroph	Organic compounds	Light
Chemoheterotroph	Organic compounds	Chemicals

Oxygen Requirements: Types of Microbes

• Aerobes: Require oxygen.

• Anaerobes: Cannot tolerate oxygen.

• Aerotolerant anaerobes: Do not use oxygen but tolerate it.

• Facultative anaerobes: Can grow with or without oxygen.

Toxic Forms of Oxygen and Protection Mechanisms

• Singlet oxygen: Highly reactive; protected by carotenoids.

• Superoxide radical: Detoxified by superoxide dismutase.

• Peroxide anion: Detoxified by catalase or peroxidase.

• Hydroxyl radical: Most reactive; no specific enzyme defense.

Nitrogen Fixation

• Definition: Conversion of atmospheric N2 to ammonia.

• Importance: Essential for biosynthesis of amino acids and nucleotides.

Environmental Limits on Microbial Growth

• Temperature: Psychrophiles, mesophiles, thermophiles.

• pH: Acidophiles, neutrophiles, alkaliphiles.

• Osmotic pressure: Halophiles tolerate high salt.

• Hydrostatic pressure: Barophiles thrive under pressure.

Quorum Sensing and Biofilm Formation

• Quorum sensing: Cell-to-cell communication via signaling molecules.

• Biofilm: Structured microbial community; increases resistance.

Microbial Isolation Methods

• Streak plate method: Dilutes cells on agar for single colonies.

• Pour plate method: Dilutes cells in liquid agar.

Types of Culture Media

Type	Description
Defined	Exact chemical composition known
Complex	Contains extracts; composition varies
Selective	Favors growth of specific microbes
Differential	Distinguishes microbes by reactions
Anaerobic	Supports anaerobes
Transport	Preserves samples during transport

Enrichment Culture

• Definition: Enhances growth of less abundant microbes.

• Application: Used to isolate rare organisms.

Preservation Methods

• Refrigeration: Short-term storage.

• Deep-freezing: Long-term storage at -50°C to -95°C.

• Lyophilization: Freeze-drying for long-term preservation.

Binary Fission and Generation Time

• Binary fission: Asexual reproduction; cell divides into two.

• Generation time: Time for population to double.

Logarithmic Growth and Bacterial Growth Curve

• Logarithmic growth: Population doubles each generation.

• Bacterial growth curve: Four phases: lag, log, stationary, death.

Growth Curve Phases:

• Lag phase: Adaptation, no growth.

• Log phase: Rapid, exponential growth.

• Stationary phase: Nutrient depletion, growth equals death.

• Death phase: Cells die faster than they divide.

Measuring Bacterial Reproduction

• Direct methods: Plate counts, microscopy.

• Indirect methods: Turbidity, metabolic activity.

Microbial Genetics

Genomes of Prokaryotes vs. Eukaryotes

• Prokaryotes: Single, circular chromosome; plasmids.

• Eukaryotes: Multiple, linear chromosomes; organelle DNA.

DNA Structure

• Double helix: Two antiparallel strands.

• Nucleotides: Deoxyribose, phosphate, nitrogenous base (A, T, G, C).

Prokaryotic Chromosomes and Plasmids

• Chromosome: Circular, located in nucleoid.

• Plasmids: Small, circular DNA; carry non-essential genes (e.g., antibiotic resistance).

DNA Replication: Semiconservative Process

• Each new DNA: One old strand, one new strand.

• Complementarity: Ensures accuracy (A-T, G-C pairing).

Leading vs. Lagging Strand Synthesis:

• Leading strand: Synthesized continuously.

• Lagging strand: Synthesized in Okazaki fragments.

Genotype and Phenotype

• Genotype: Genetic makeup.

• Phenotype: Observable traits; determined by genotype.

Central Dogma of Genetics

• DNA → RNA → Protein

• Roles: DNA stores information; RNA transmits; proteins execute functions.

RNA Transcription Steps

• Initiation: RNA polymerase binds promoter.

• Elongation: RNA synthesized 5' to 3'.

• Termination: RNA polymerase reaches terminator or Rho factor.

Genetic Code: Codons and Amino Acids

• Codon: Three-nucleotide sequence; specifies amino acid.

• Relationship: 64 codons, 20 amino acids.

Polypeptide Synthesis: Roles of RNA

• mRNA: Carries genetic code.

• tRNA: Brings amino acids.

• rRNA: Forms ribosome structure.

Microbial Genetics Regulation and Mutation

Operon Model of Transcriptional Control

• Operon: Cluster of genes under single promoter.

• Regulation: Controlled by operator, repressor, and activator proteins.

Inducible vs. Repressible Operons

• Inducible: Activated by substrate (e.g., lac operon).

• Repressible: Inactivated by product (e.g., trp operon).

Genetic Control by RNA Molecules

• microRNA: Regulates gene expression post-transcriptionally.

• siRNA: Silences genes by degrading mRNA.

• Riboswitches: mRNA regions that bind metabolites to regulate translation.

Mutation Types and Effects

• Mutation: Change in DNA sequence.

• Point mutation: Single nucleotide change.

• Types: Substitution, insertion, deletion.

• Effects: Silent, missense, nonsense mutations.

Mutagenesis: Radiation and Chemicals

• Radiation: UV causes pyrimidine dimers; X-rays cause breaks.

• Chemical mutagens: Nucleotide analogs, alkylating agents, deaminating agents.

DNA Repair Mechanisms

• Base-excision repair: Removes damaged bases.

• Light repair: Photolyase fixes pyrimidine dimers.

• Nucleotide-excision repair: Removes damaged DNA segments.

• Mismatch repair: Corrects replication errors.

• Error-prone repair (SOS response): Last-resort repair; may introduce mutations.

Genetic Recombination and Horizontal Gene Transfer

• Genetic recombination: Exchange of DNA between molecules.

• Horizontal gene transfer: Transfer of genes between organisms.

Bacterial Conjugation: F Factor, F+ and Hfr Cells

• F factor: Fertility plasmid enabling conjugation.

• F+ cells: Have F factor; can donate DNA.

• Hfr cells: F factor integrated into chromosome; transfer chromosomal genes.

Gene Transfer Mechanisms

• Crossing over: Exchange of DNA segments.

• Transformation: Uptake of naked DNA.

• Transduction: DNA transfer via bacteriophage.

• Conjugation: DNA transfer via cell-to-cell contact.

Transposons: Structure and Action

• Simple transposons: Contain only transposase gene.

• Complex transposons: Carry additional genes (e.g., antibiotic resistance).

• Transposition: Movement of transposon within genome; can disrupt genes.