2.  Viruses are not alive  A virus in an obligate intracellular parasite  Requires host cell to reproduce  Can be seen at magnifications provided by the electron microscope (they are microscopic)

3.  1.) Contains a single type of nucleic acid: either DNA or RNA but not both  2.) Has a protein coat (capsid) surrounding the nucleic acid, some also have a lipid envelope around the capsid  3.) multiply inside living cells by using the synthesizing machinery of the host cell  4.) Cause the synthesis of specialized viral structures that can transfer the viral nucleic acid to other cells  5.) Have a specific host range

4.  Usually much smaller than bacteria  must be smaller than the cells they infect:  20-14,000nm in length

6.  Virion = infectious viral particle: completely assembled with a protein coat surrounding the nucleic acid  All viruses are made of at least 2 parts  Inner core of nucleic acid  Enclosed in protein capsid  * Some also contain lipoprotein envelope

7.  1.) Nucleic Acids:  Either DNA or RNA, but not both  Single or Double Stranded (SS or DS)  if RNA, it can be plus sense strand (has codons) or minus/antisense (need to make complement sense strand for translation)  If DNA- usually double stranded  Linear or circular  Genome is SMALL  Only a few genes (most have 6-10 genes)

8.  2. Capsid – protein coat (protein shell)  Surrounds the nucleic acid  protects the virion in the external environment  Aids in transfer between host cells  Composed of subunits called capsomeres  some capsids have protein-carbohydrate pointed projections called pentons  if pentons are present they are used for attachment to the host cell

9.  *3. Envelope (not all viruses)  Function is to protect the virion  some viruses have an envelope around the capsid consisting of lipids, proteins and carbohydrates (cell membrane like)  with envelope = enveloped virus  the envelope may be coded for by the virus or taken from the host cell plasma membrane  some envelopes have carbohydrate-protein complexes called spikes which are used for attachment to the host cell  if a virus does not have an envelope it is called a non-enveloped virus, “naked”

11. Capsomere protein

12.  The capsid can be distinct and sometimes identifies a particular virus. It is constructed in a highly symmetrical manner  Helical  Cylindrical capsid, hollow  Can be rigid or flexible  Made up of a helical structure of capsomeres with the nucleic acid wound up inside  Examples: Rabies virus, Ebola virus, tobacco mosaic virus (TMV) Rabies Virus

13.  Polyhedral  Most are icosahedrons (icosohedral)  20 equilateral triangle faces and made from capsomeres  12 corners made form capsomeres called pentons which contain 5 protomers each  Appear spherical  Examples: Adenovirus, Polio virus Polio virus

14.  Complex  Several types of symmetry in one virus  Unique shape  Examples:  Bacteriophage: capsid and accessory structure  Pox virus: no clear capsid, just several protein layers around the nucleic acid Glass sculpture of pox virus

15.  Replication must occur in a host cell (multiply only when inside a living cell)  The viral genome codes for viral structural components and a few viral enzymes needed for processing the viral enzymes  Everything else is supplied by the host:  Ribosomes, tRNA, nucleotides, amino acids, energy etc.  The DNA or RNA of the virus takes control of the host cell' metabolic machinery and new viral particles are produced utilizing the raw materials from the host cell.

16.  Replication of viruses is studied in great detail in bacteriophages  Bacteriophages are viruses that infect a specific bacteria  Two possible types of infection cycles:  1.) Lytic cycle (virulent)  Ends with the lysis and death of the host bacterial wall  2.) Lysogenic cycle  Host cell remains alive, but carries the virus in its genome

17.  1.) Attachment- phage contacts a bacterium (attachment to host) and uses the tail fibers to attach to proteins on the bacterial cell wall http://sites.fas.harvard.edu/~biotext/animations/lyticcycle.html

18.  2.) Penetration/Entry- the phage injects its DNA into the bacterium  The phage tail releases lysozyme to break down the bacterial cell wall  The sheath contracts to drive the tail core through the weakened cell wall and plasma membrane  The DNA is injected into the bacterium through the tail core  Uncoating- During or before penetration  3.) Synthesis of new virus particles (Multiplication)  Once inside, host protein synthesis is stopped  Virus has host make proteins and nucleic acid  Virus directs viral nucleic acid replication and transcriptions and translation of viral genes (host’s cell transcription stops)  This results in a pool of viral genomes and capsid parts

19.  4.) Assembly  “eclipse period” – the time of viral entry  The bacteriophage DNA and capsid spontaneously assemble into complete virons  5-10 hrs DNA viruses  2-10 hrs RNA viruses

20.  5.) Lysis- release of virus and death of host cell  A single virus can give rise to up to 1000 new virus particles from on host cell  Virions will leave bacteria (host)  Lysozyme encoded by viral genes causes the cell wall to break down  The bacteria lyses releasing the virions  Cycle will then repeat with new phages

21.  The lysogenic phage infects the cell, but remains inactive in a stage called lysogeny  1.) the phage attaches to the host cell and injects DNA  2.) the phage genome circularizes  At this point, the phage could begin a normal lytic cycle or it can begin the lysogenic cycle/lysogeny http://sites.fas.harvard.edu/~biotext/animations/lysogeny.html

22.  Latency- “dormant” state- unpredictability  Viral DNA/RNA  integrated into DNA of host = hidden DNA=provirus  Can be reactivated in the future  Factors that influence: stress, other viral infections, UV light  Example: fever blisters, chicken pox, HIV 2+ years

23.  Embryonated eggs  Refer to handout given in class