Infectious agents Eukaryotic- parasites, protists, fungi Prokaryotes Nonliving- viruses, viroids, prions Viruses apparen

1. Infectious agents Eukaryotic- parasites, protists, fungi Prokaryotes Nonliving- viruses, viroids, prions Viruses apparently infect every living thing (bacterio)phages- bacteria plant and animal viruses

2. All viruses have a protein capsid Capsid shape is characteristic of the virus Viruses are naked Or enveloped Much smaller than cells

4. General features of viruses, continued All have nucleic acid (DNA or RNA, but not both) genome is very small gene sequences sometimes overlap Must have genes to: make the capsid replicate itself (special polymerases) get into and out of the cell Viruses use the host replication processes

5. What do viruses do to cells? Some viruses kill the host cell (lytic; virulent) Some viruses are released from living cells (not lytic, but still productive) Some viruses become integrated into the DNA of the host (temperate: latent infection. Infection is lysogenic)

7. Viral “life cycles” especially well-studied in bacteriophages, esp. T4

8. Bacteriophage are classified according to host range attachment site genome (DNA or RNA) shape effect on host cell

9. Temperate phages can either lyse their host or replicate with it Bacteriophage lambda () is especially well analyzed Why lytic? Why lysogenic? Lytic if bacteria are actively dividing; otherwise lysogenic How are viruses maintained this way?

10. Virus becomes prophage (integrated into host genome)  has gene sequences homologous to sequences in E. coli, and integrates at that site Is excised in a reverse process In lysogen, some viral genes are repressed (prevented from being expressed)

11. How does phage become lytic again? loss or inactivation of repressor damage to bacterium Bacteria that already are lysogenic are immune to infection by the same type of phage

12. Lysogenic conversion

13. Transduction- phage-mediated genetic transfer Generalized- any bacterial gene can be transferred Specialized- virus inserted in a specific site so only genes adjacent to it are transferred (i.e., temperate phages)

14. Why can phages infect some bacterial strains but not others? Phage must attach to specific receptors on host cell Restriction-modification- prevents the “right” phage DNA from being degraded

15. Infectious agents of animals and plants Analogous biologically to bacteriophages Taxonomic grouping according to: mode of replication (genome structure) shape of capsid presence of envelope Both RNA and DNA genomes; wide variety of arrangement of nucleic acid

16. RNA viruses even more diverse (p. 343)

17. Some other grouping may be more useful, e.g., mode of transmission

18. Growing and studying viruses Tissue culture propagation cytopathic effect Quantitation plaque assay titration hemagglutination antibody titer

19. adenovirus Herpes simplex

20. Viruses may be pathogenic or have no apparent effect May cause acute or persistent infections

21. Entry of enveloped viruses into animal cells

22. Many viruses have genomes that cannot be transcribed by host enzymes They must encode their own How are viruses released? from dead cells (not actually lysed by virus) budding shed from host In persistent infections, viruses are continuously produced by budding Infected person is a carrier

24. Retroviruses are analogous to bacteriophage such as  Can be integrated (randomly) into host genome Reverse transcriptase Retroviruses (and other, DNA viruses) can cause tumors in susceptible animals

25. Viruses and tumors When viral genome gets inserted into a host genome, it can cause changes Activation of host genes Mutation of host genes If these genes regulate the cell cycle, this can lead to tumors (e.g., proto-oncogenes) Papilloma, herpes, Epstein-Barr

26. Retroviruses and cell transformation Viruses are integrated into host DNA and later excised May incorporate regulatory gene Virus polymerase is error-prone; may mutate gene This gene may then be transferred to a new host

27. Host range: the type of organism (or tissue) that a virus can infect Some can infect many species (zoonoses) Some can acquire that wide range through modifications Phenotypic mixing Mutation

29. Probably how influenza virus changes so rapidly

30. Viruses infect plants, too Wounds Contaminated soil Vectors Spread through plasmodesmata in cell walls Viruses can cause a variety of pathologies in plants

32. Other, novel infectious agents Prions- infectious proteins Viroids- naked, small RNA molecule replicate autonomously single viroid can infect cell resistant to proteases and nucleases only infect plants (as fas as we know)

33. Replication of prions?

34. Prions are species-specific Some apparently can cross species, e.g., mad cow disease