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Chapter 19 and 27 - Coggle Diagram

- - - - Cell wall: peptidoglycan in bacteria; other polymers in archaea
      - Capsules/slime layers: adhesion, protection
      - Fimbriae: attachment
      - Pili: DNA transfer (conjugation)
      - Endospores: survival under harsh conditions
  - - - Transformation: uptake of environmental DNA
      - Transduction: phage-mediated DNA transfer
      - Conjugation: pilus-mediated DNA transfer (F plasmid, Hfr cells)
  - - - Filaments (e.g., Anabaena heterocysts for nitrogen fixation)
      - Biofilms: protection, nutrient/waste transport, intercellular signaling
  - - - Bacteria: diverse nutritional/metabolic modes, pathogens and beneficial species
      - Archaea: unique traits; some extremophiles
        
        Extreme halophiles → high salinity
        
        Extreme thermophiles → high temperature
        
        Methanogens → anaerobic, methane production
      - TACK Supergroup: Thaumarchaeota, Aigarchaeota, Crenarchaeota, Korarchaeota
        
        Lokiarchaeotes → possible sister group to eukaryotes
  - - - Decomposers recycle C, N, other elements
      - Cyanobacteria/autotrophs fix CO₂ → sugars & O₂
      - Nitrogen-fixing prokaryotes → usable N for plants
    - - Mutualism: flashlight fish + bioluminescent bacteria
      - Commensalism: skin bacteria benefit, humans unaffected
      - Parasitism/Pathogens: harm host
    - - Hydrothermal vent communities rely on chemoautotrophic bacteria
  - - - Gut microbiota: digestion, vitamin production, intestinal development
      - Food industry: cheese, yogurt, fermented foods, beverages
      - Biotechnology:
        
        E. coli for gene cloning
        
        Pyrococcus DNA polymerase for PCR
        
        CRISPR-Cas9 for genome editing
      - Bioremediation: oil spills, sewage treatment, radioactive cleanup
      - Bioplastics & biofuels: PHA production, ethanol from biomass
    - - Cause ~50% of human diseases (tuberculosis, diarrhea, Lyme disease)
      - Toxins:
        
        Exotoxins → secreted, cause disease even if bacteria gone (e.g., cholera, botulism)
        
        Endotoxins → released when bacteria die (e.g., Salmonella typhi)
      - Horizontal gene transfer spreads virulence → harmless bacteria → pathogens (e.g., E. coli O157:H7)
    - - Rapid evolution + HGT → multidrug-resistant strains (MRSA, XDR-TB)
      - Discovery of new antibiotics (malacidins, teixobactin) using metagenomics
- - - - DNA viruses often use host DNA polymerases.
      - RNA viruses use viral RNA polymerases because host cells cannot copy RNA from RNA.
  - - - Phage DNA hijacks host, produces progeny, host lyses, releasing hundreds of new phages.
    - - Host survives and reproduces normally.
      - Prophage DNA can later switch to the lytic cycle (triggered by stress or chemicals).
      - Example: Lambda phage (λ)
- - - - Stores snippets of viral DNA.
      - Produces guide RNAs and Cas proteins to recognize and cut phage DNA during future infections.
- - - - Viruses often have envelopes derived from host membranes.
      - Envelopes have glycoproteins that bind host receptors.
      - Envelope acquisition can occur from plasma membrane, Golgi, or nuclear envelope.
      - Viral exit often occurs via budding, which may not kill the host cell.
    - - RNA viruses often need viral RNA polymerases (cells usually don’t copy RNA from RNA).
      - Retroviruses (e.g., HIV) use reverse transcriptase:
        
        Converts RNA → DNA → integrates into host genome as a provirus.
        
        Provirus never leaves the host genome.
- - - - Plasmids: Small DNA molecules that move between cells.
      - Transposons: DNA segments that jump within genomes.