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Viruses, Bacteria and Archaea - Coggle Diagram

- - - - shorter duration, results in death of host cell
      - virulent phage
        
        virus that reproduces only by the lytic cycle
        
        ex. flu, COVID
      - shows symptoms within hours to days
      - produces new phages and lyses the host cell wall, releasing the viruses
    - - allows replication of the phage genome without destroying the host
      - temperate phage
        
        phages that use both the lytic and lysogenic cycles
        
        ex. lambda
      - viral DNA is incorporated into the host cell's chromosome
      - prophage
        
        integrated viral DNA; temporary
      - every time the host divides, it replicates the phage DNA and passes it down to daughter cells
    - - natural selection favors bacterial mutants w/ surface proteins that can't be recognized as receptors by a certain type of phage
      - phage DNA is often identified as foreign and cut up by restriction enzymes, which restrict the phage's ability to replicate
      - bacterial DNA is methylated and therefore protected from the restriction enzymes
      - bacteria and archaea also use the CRISPR-Cas system (CRISPR = clustered regularly interspaced palindromic repeats)
      - Cas proteins can identify and cut phage DNA, defending against infection
  - - - animal viruses with envelopes use them to enter the host cell
      - glycoproteins on the envelope's outer surface bind to receptor molecules on the surface of the host cell
      - the viral envelope is usually derived from the host cell's plasma membrane as the viral capsids exit
      - other viral membranes form from the host's nuclear envelope and are then replaced by an envelope made from golgi apparatus membrane
    - - all viruses that use an RNA genome as a template for the synthesis for mRNA transcription require RNA → DNA synthesis
      - retrovirus
        
        viruses that initially have RNA in their genome
        
        use reverse transcriptase to copy their RNA genome into DNA
      - the broadest variety of RNA genomes are found in animal viruses
      - HIV (human immunodeficiency virus) is the retrovirus that causes AIDS (acquired immunodeficiency syndrome)
        
        HIV's reverse transcriptase molecules catalyze synthesis of viral DNA in the cytoplasm of the host cell after entering
        
        the integrated viral DNA is called a provirus, and it remains in the host's genome permanently
- - - - can be double-stranded DNA or RNA; can be single-stranded DNA or RNA
      - genome is organized as a single linear or circular molecule of nucleic acid (although some have multiple molecules)
    - - capsid
        
        the protein shell enclosing the viral genome
        
        made of protein subunits called capsomeres
        
        capsids can be rod-shaped, polyhedral, or more complex depending on the virus
      - viral envelopes
        
        derived from membranes of host cells and contain host cell phospholipids and membrane proteins
        
        surround the capsids of influenza viruses and many other viruses found in animals
    - - viruses that infect bacteria by attaching to a host via protein tails and injecting their DNA inside
- - - - harmless component of a pathogen that stimulates the immune system to mount defenses against the harmful pathogen
      - can prevent certain viral infections, but do not cure them once they occur
  - - - widespread outbreak
      - occur when genetic changes allow a new viral strain to be easily transmitted between humans
    - - global epidemic
    - - type A: infects wide range of animals; type B/C: only infect humans
      - have high rates of mutation b/c they have 8 segments of RNA in their genome
  - - - horizontal transmission
        
        external source infects the plant by entering through damaged cell walls
      - vertical transmission
        
        virus is inherited from parent
  - - - infectious proteins that appear to cause degenerative brain diseases in animals (ex. mad cow disease, FFI)
      - incorrectly folded proteins that act very slowly, can be transmitted in food, and are virtually indestructible
- - - - technique to classify bacteria by cell wall composition
      - gram-positive
        
        simple walls w/ a thick layer of peptidoglycan
        
        shows up purple on gram stain
      - gram-negative
        
        less peptidoglycan and more complex with an outer membrane containing lipopolysaccharides
        
        shows up pink on gram stain
        
        more resistant to antibiotics
    - - if the layer is dense and well-refined, it is called a capsule
      - if it is not well organized, it is called a slime layer
      - both types enable prokaryotes to adhere to their substrate or other individuals in a colony
    - - resistant cells that bacteria develop when they lack water or essential nutrients
      - the original cell copies its own chromosome and surrounds it with a multilayered structure
  - - - directed movement towards or away from a stimulus