1. Viruses I. What are they (and what aren’t they)? II. Virus structure and classification III. Viral infection Herpesvirus Foot and Mouth Disease virus Ebola virus

2. Characteristics of Viruses Somewhere between life and non-life  Can’t reproduce or __________________ independently  But can direct living cells to do so for them  “___________________ intracellular parasites” “Infectious particles” rather than “organisms”, “active” or “inactive” rather than “alive” or “dead”. Bacteriophage Phi X 174

3. General Structure Small -- _______________ nm in diameter Small -- _______________ nm in diameter All have nucleocapsid composed of ______________ and nucleic acid All have nucleocapsid composed of ______________ and nucleic acid Some have a phospholipid bilayer membrane (envelope) Some have a phospholipid bilayer membrane (envelope)Nucleocapsid DNA or RNA Capsid Enveloped virus Spike Envelope

4. Viral envelope Common in animal and plant viruses Common in animal and plant viruses Membrane is required for ______________ Membrane is required for ______________ Viral envelopes are actually portions of the infected host cell _____________________ (viruses do not form their own) Viral envelopes are actually portions of the infected host cell _____________________ (viruses do not form their own) Often replace ______________ proteins with viral glycoproteins Often replace ______________ proteins with viral glycoproteins

6. Nucleocapsid architecture Two most common shapes: helical & icosahedral. Both are regular, geometric shapes determined by the structure and orientation of proteins in the ________________________

7. Helical structure Capsomeres (___________ building blocks) Virus _________

8. Helical structure: Tobacco Mosaic Virus TMV is composed of only_________ types of molecules: a single ________ molecule and one type of protein

9. Icosahedral structure Note that in both of these architectures, only one or two types of proteins used. Means that the virus needs only one or two protein-coding ________________. Composed of only one or two different proteins + nucleic acid

10. Adenoviruses -- non-enveloped icosahedral viruses which are generally mild pathogens in humans, birds, etc. causing ___________________ (‘pink eye’) and _________________ illnesses.

11. Complex viruses A number of types with somewhat more ___________ structures One is typical bacteriophage, with icosahedral head, helical tail, fibers for attachment Bacteriophage lambda

12. Nucleic acid content Viral genomes are very small  ___________ base pairs (enough to encode 3 or 4 proteins) to 200,000 bp  Small compared to bacteria (~10 6 bp) and human (~2 X 10 9 bp). Characterized by __________________ genes Viral genomic DNA mRNA transcripts (overlapping)

13. Viral genomes. The genomes of viruses can be either _________ or ________ (or some use both at different stages in their life cycle)

15. E. coli bacteriophages

16. Viral classification

17. Viral classification (cont.)

18. Viral Infection -- Overview 1) Adsorption 2) ____________ (either of nucleocapsid or of nucleic acid only) 3a) Viral _______________ (lytic phase) or 3b) Integration of viral genome into host cell genome (lysogenic phase) 4) Exit from cell

19. Adsorption Specific interaction of viral surface with cell surface. This is the reason viruses only infect certain cell types, for example: HIV only infects cells (such as T cells) with the CD4 glycoprotein on their surface. HIV only infects cells (such as T cells) with the CD4 glycoprotein on their surface. Influenza virus (an orthomyxovirus) only infects mucosal cells of upper ____________________ tract. Influenza virus (an orthomyxovirus) only infects mucosal cells of upper ____________________ tract. Bacteriophages are highly ___________________ for certain hosts (e.g. coliphages only infect E. coli) Bacteriophages are highly ___________________ for certain hosts (e.g. coliphages only infect E. coli)

20. Entry 1) ______________ of nucleic acid (e.g. T4 phage)

21. 2) Entry of ___________ nucleocapsid (most common in animal and plant viruses) Endocytosis: Virus in vescicle Vesicle and capsid break down, releasing nucleic acid Cell membrane

22. Membrane ____________ (only in enveloped viruses) Out In Out In Out In In Out Cell membrane

23. Viral replication Once inside, one of several things occurs, depending on the virus.Once inside, one of several things occurs, depending on the virus. However, the end result is always ________ ________________However, the end result is always ________ ________________ Involves:Involves: 1) Replication of the nucleic acid 2) Synthesis of capsid proteins 3) ________________ of nucleocapsids

24. General stages of (lytic) virus replication

26. One-step growth curve of virus replication

27. Lysogeny or ‘integration’ vs. lytic pathways

28. Exit Cell lysis or Cell lysis or Budding Budding

29. HIV movie