Microbial Genetics, Ecology, and Immunity Fundamentals

Posted on Oct 28, 2025 in Biology

Chapter 13 – Bacterial Genome Replication and Expression

Discovery of Genetic Material

• Griffith’s experiment: Showed that non-virulent bacteria could transform into virulent forms by taking up DNA from dead virulent cells. Proved DNA is the genetic material.
• Hershey and Chase Experiment: Used radioactive labeling (P for DNA, S for protein) to show that only DNA enters bacterial cells during phage infection. Proved DNA is the genetic material.

Nucleic Acid Structure

• Structure of DNA: Double helix of two antiparallel strands; nucleotides (A-T, G-C), sugar-phosphate backbone.
• Structure of RNA: Single-stranded, ribose sugar, uracil replaces thymine.

DNA Replication

• Semi-conservative replication: Each new DNA molecule has one old strand and one newly synthesized strand.
• Proteins in DNA replication:
  • Helicase: Unwinds DNA.
  • Primase: Synthesizes RNA primers.
  • DNA polymerase III: Main replication enzyme.
  • DNA polymerase I: Replaces RNA primers.
  • Ligase: Joins Okazaki fragments.
  • SSBs (Single-strand binding proteins): Stabilize single strands.
• Replication initiation: Begins at the origin of replication (OriC), involves DnaA (initiator), helicase, and primase forming a replisome. The replication fork is where DNA is unwound and copied.
• Proofreading: DNA polymerase III checks and corrects errors during replication.

Gene Expression and the Genetic Code

• Operon: Cluster of genes transcribed together under one promoter.
• Polycistronic: mRNA encoding multiple proteins (common in prokaryotes).
• Transcription initiation: Sigma factor guides RNA polymerase to the promoter.
• Elongation: RNA polymerase synthesizes the RNA strand.
• Termination: Rho-dependent or rho-independent mechanisms stop transcription.
• Codon: Triplet of nucleotides coding for an amino acid.
• Start codon: AUG
• Stop codons: UAA, UAG, UGA
• Sense codon: Encodes amino acids.
• Code degeneracy: Multiple codons can code for the same amino acid.
• Translation: Ribosome assembles on mRNA, tRNA brings amino acids, peptide bonds form, protein elongates and is released at the stop codon.

Chapter 14 – Regulation of Cellular Processes

• Constitutive gene: Always expressed.
• Gene regulation in bacteria: Via repressors, activators, operons, riboswitches.
• Negative control: Repressor blocks transcription.
• Positive control: Activator enhances transcription.
• Lac operon: Includes lacZ, lacY, lacA. Induced by lactose presence, repressed by glucose (catabolite repression). Controlled by the lac repressor and CAP-cAMP.
• Riboswitch: Regulatory RNA segment that binds a metabolite and alters gene expression.
• Sigma factors: Direct RNA polymerase to specific promoters; control global transcription responses.
• Chemotaxis: Driven by methyl-accepting chemotaxis proteins (MCPs), guides movement toward or away from stimuli.
• CRISPR-Cas: Bacterial immune system for targeting and cutting foreign DNA.

Chapter 15 – Eukaryotic and Archaeal Genome Replication and Expression

Eukaryotic DNA Replication

• Initiation: Multiple origins; uses ORC, helicase, DNA polymerases.
• DNA polymerase types:
  • α: Adds RNA primers.
  • δ/ε: Lagging/leading strand synthesis.
• End replication problem: Lagging strand can’t fully replicate ends — solved by telomerase adding telomeres.

Archaeal Replication

• Archaeal replication: Single origin like bacteria but machinery resembles eukaryotes.

Eukaryotic Transcription

• Initiation: Initiated by RNA polymerase II, uses transcription factors.
• Includes post-transcriptional modifications (5′ cap, poly-A tail, splicing).
• Monocistronic: One mRNA codes for one protein (eukaryotic genes).
• Introns/Exons: Exons code for proteins; introns are removed.
• Eukaryotic vs. bacterial transcription: Eukaryotes use more complex machinery and processing.

Archaeal Transcription and Regulation

• Archaeal transcription: Similar to eukaryotes but less complex.
• Regulation points: Transcription, translation, post-translational modifications.

Chapter 16 – Mechanisms of Genetic Variation

Mutation and Repair

• Mutation: Permanent DNA change.
• Types: Point, insertion, deletion, frameshift.
• Causes: Errors in replication, radiation, chemicals.
• Thymine dimers: UV-induced DNA lesions that distort the helix.
• Terminology:
  • Wild type: Normal.
  • Forward mutation: WT → mutant.
  • Reversion: Mutant → WT.
• Mutation effects:
  • Silent: No amino acid change.
  • Missense: One amino acid changed.
  • Nonsense: Introduces a stop codon.
  • Frameshift: Changes the reading frame.
• Replica plating: Detects mutants by growing colonies under different conditions.
• DNA methylation: Regulates gene expression and mismatch repair.
• Excision repair: Damaged DNA is removed and replaced.

Horizontal Gene Transfer (HGT)

• Horizontal gene transfer: Movement of genes between organisms.
• Homologous recombination: Exchange between similar sequences.
• Site-specific recombination: Occurs at specific sites.
• Conjugation: Plasmid transfer via a pilus.
• Transformation: Uptake of free DNA.
• Transduction: Transfer via bacteriophages.

Chapter 26 – Microbial Ecology

• Microbial ecology: Study of interactions among microorganisms and their environment.
• Habitat vs. Niche:
  • Habitat: Physical location.
  • Niche: Role or function in an ecosystem.
• Microenvironment: Immediate, small-scale environment around a microbe; changes rapidly.
• Biofilms: Microbial communities attached to surfaces in a self-produced matrix.
• Benefits (of biofilms): Protection, nutrient access, gene exchange.
• Quorum sensing: Cell-density-dependent communication for coordinated behavior.
• Guild: Group of microbes with similar metabolism.
• Functional redundancy: Different organisms perform the same function; increases ecosystem stability.

Chapter 27 – Microbial Interactions

Types of Symbiosis

• Mutualism: Both benefit (e.g., termites and gut protozoa).
• Cooperation: Optional, both benefit.
• Commensalism: One benefits, the other is unaffected.
• Predation: One kills the other (e.g., Bdellovibrio).
• Parasitism: One benefits at the other’s expense.
• Ammensalism: One harmed, the other unaffected (e.g., antibiotic production).
• Competition: Both harmed due to limited resources.

Host and Community Structures

• Consortia: Stable microbial communities, often in aquatic environments.
• Microbiota: Collection of all microbes living in or on a host.
• Normal flora: Microbes commonly found in healthy individuals.

Chapter 28 – Biogeochemical Cycling

• Biogeochemical cycles: Recycling of elements (C, N, S, P, etc.) by microbes.

Major Cycles

• Carbon cycle:
  • Photosynthesis: Fixes CO₂.
  • Respiration/Fermentation: Releases CO₂.
  • Methanogenesis: Anaerobic CO₂ reduction to CH₄ (methane).
• Nitrogen cycle:
  • Nitrogen fixation: N₂ → NH₃ (e.g., Rhizobium).
  • Nitrification: NH₃ → NO₂⁻ → NO₃⁻.
  • Denitrification: NO₃⁻ → N₂ (loss of N to atmosphere).
  • Ammonification: Organic N → NH₃.
• Sulfur cycle:
  • Assimilatory reduction: S → organic compounds.
  • Dissimilatory reduction: S used as terminal electron acceptor.
• Phosphorus cycle: No gaseous form; microbes solubilize phosphate.
• Iron cycle: Microbial redox reactions affect Fe availability.

Chapter 29 – Microorganisms in Terrestrial Environments

Soil Structure and Interactions

• Soil horizons:
  • O: Organic material.
  • A: Topsoil, high microbial activity.
  • B: Subsoil.
  • C: Bedrock.
• Rhizosphere: Soil region around plant roots with high microbial activity.
• Mycorrhizae: Fungi-plant root symbiosis for nutrient exchange.
• Endophytes: Microbes living within plant tissues.

Key Soil Microbes

• Actinobacteria: Abundant in soil, produce antibiotics.
• Soil microbe functions: Decomposition, nutrient cycling, promoting plant growth.

Chapter 30 – Microorganisms in Marine and Freshwater Ecosystems

Marine Environments

• Oligotrophic: Low nutrient levels; microbes adapt to survive.
• Key Organisms: Pelagibacter (most abundant ocean bacterium), Prochlorococcus (abundant photosynthetic cyanobacterium).
• Ocean zones:
  • Epipelagic: Sunlit, most microbial activity.
  • Bathypelagic/Abyssal/Hadal: Deep, dark, pressure-adapted microbes.

Freshwater Ecosystems

• Lentic: Still water (lakes).
• Lotic: Flowing water (rivers).
• Stratification: Layering of water; affects oxygen and microbial distribution.
• Eutrophication: Nutrient over-enrichment leading to algal blooms and oxygen depletion.
• Microbial loop: Recycling of carbon and nutrients through microbial interactions.

Chapter 31 – Water Pollution and Water Purification

Pollution and Indicators

• Water pollution sources: Domestic sewage, industrial waste, agricultural runoff.
• Biochemical Oxygen Demand (BOD): Oxygen used by microbes to decompose organic matter.
• Indicator organisms: Coliforms (e.g., E. coli) signal fecal contamination.

Water Treatment Processes

• Water purification steps: Sedimentation → Coagulation → Filtration → Disinfection (chlorine/UV).
• Wastewater treatment:
  • Primary: Physical removal (screens, sedimentation).
  • Secondary: Biological treatment (activated sludge, trickling filter).
  • Tertiary: Chemical/advanced filtration.
• Sludge digestion: Anaerobic microbes break down organic matter, produce methane.

Chapter 32 – Microbial Diseases

Pathogenesis and Virulence

• Pathogen: Microorganism that causes disease.
• Virulence factors: Traits that enhance a pathogen’s ability to cause disease (Adherence factors, toxins, immune evasion).
• Infectious dose (ID50): Number of microbes needed to cause infection in 50% of hosts.

Disease Characteristics

• Signs vs. Symptoms:
  • Signs: Observable (fever, rash).
  • Symptoms: Felt by the patient (pain, fatigue).
• Types of disease: Acute (rapid onset), Chronic (long-term), Latent (dormant then reactivates).

Transmission and Epidemiology

• Transmission routes: Direct contact, airborne, vehicle, vector-borne.
• Epidemiology terms:
  • Endemic: Constant presence.
  • Epidemic: Sudden rise.
  • Pandemic: Global spread.

Chapter 33 – Immunology

Innate Immunity (Non-Specific)

• First line of defense: Physical (skin, mucous membranes), chemical (pH, enzymes), and biological barriers (normal flora).
• Cell types:
  • Neutrophils: First responders, phagocytic.
  • Macrophages: Phagocytosis and antigen presentation.
  • Dendritic cells: Bridge innate and adaptive immunity; present antigens to T cells.
  • Natural killer (NK) cells: Destroy infected or cancerous cells.
• Recognition: Pattern recognition receptors (PRRs) recognize PAMPs (Pathogen-Associated Molecular Patterns), including Toll-like receptors (TLRs).
• Inflammatory response: Redness, heat, swelling, pain. Mediated by cytokines, histamines.
• Complement system: Cascade of proteins leading to opsonization, inflammation, and lysis of microbes.

Adaptive Immunity (Specific)

• Humoral immunity (B cells): B cells produce antibodies (IgG, IgA, IgM, IgE, IgD). Plasma cells secrete antibodies. Memory B cells provide long-term immunity.
• Cell-mediated immunity (T cells):
  • Helper T cells (CD4⁺): Activate B cells and macrophages.
  • Cytotoxic T cells (CD8⁺): Kill infected cells.
  • Regulatory T cells: Suppress immune responses to avoid autoimmunity.
• Antigen presentation:
  • MHC I: On all nucleated cells; presents to CD8⁺ T cells.
  • MHC II: On APCs; presents to CD4⁺ T cells.
• Immune Response Timing:
  • Primary: First exposure; slower, IgM predominant.
  • Secondary: Faster, stronger; IgG predominant (due to memory cells).
• Immunological memory: Basis of vaccination; involves memory B and T cells.

Vaccination and Disorders

• Vaccination types: Live attenuated, Inactivated, Subunit, Toxoid, mRNA vaccines.
• Immune Disorders:
  • Hypersensitivities: Allergies, autoimmune disorders.
  • Immunodeficiencies: Congenital (e.g., SCID) or acquired (e.g., HIV/AIDS).
  • Autoimmunity: Immune system attacks self (e.g., lupus, rheumatoid arthritis).