size of a virus

• 5-10 nm

basic structure of a virus

• nucleic acid wound up inside a protein capsid
• ssDNA is used to make dsDNA intermediates, which get used to make more ssDNA
• dsDNA is used in DNA replication to make more dsDNA
• dsRNA is used to make more dsDNA 
• and ssRNA (both +/- strands) used to make complements and viral proteins

plus strand RNA

• used as mRNA in viruses
• is single stranded
• can bind to the ribosome
• can be used to make protein in translation 

minus strand RNA

• used as a template (along with RNA replicase) to make plus strand RNA 
• is single stranded
• eventually used to make viral proteins and more minus strand RNA

Baltimore scheme for virus classification

• uses the tpye of nucleic acid INSIDE the virus for classification
• also uses the type of nucleic acid metabolism during replication for classification

bacteriophage

• infect bacterial cells
• 1-10 mm 

steps of the reproductive cycle of a T4 lytic phage

• Attachment: virus finds host cell
• Penetration: the nucleic acid enters the cell
• Synthesis: viral nucleic acid is transcribed into RNA and translated into viral proteins
• Assembly: assembling protein capsids and packaging DNA/RNA inside them
• Release: lysis of the cell, excretion of the protein capsids

latent period of a phage lytic infection

• number of plaque forming units vs. time
• stays fairly constant for a while, viable phage count remains the same
• synthesis is occuring
• nucleic acid is being created

reproductive cycle of a Lambda lysogenic phage

• a silent, dormant state
• 1/1000 lambda cells will take a lysogenic pathway
• lambda DNA enters the host cell and circulates, but shuts off it's gene expression 
• no synthesis occurs 
• as the cell divides, the lambda DNA is passed on the chromosome
• one day (with stress) the prophage comes out of dormancy

prophage

• when the lambda injects its DNA into a host chromosome and lays dormant for a period of time

lysogen

• the cell that carries the prophage 

phage forming units 

• unlike bacteria, phages cannot form colonies
• thousands of cells are spread on a plate, which produce a lawn of growth

reproductive cycle of a retrovirus

• genome made up of ssRNA, which enters the host cell, as is used as a template to make dsDNA (with reverse transcriptase)
• genome gets inserted into the host chromosome
• genome gets transcribed in the host RNA polymerase to make new copies of the RNA genome
• these new copies of RNA get packaged into new virus particles

enveloped viruses

• envelope is made up of a lipid bilayer membrane that comes from the previous host cell
• when the virus gets excreted out of the host cell, the viral particles bud out, pinching off a part of the membrane -- becomes the envelope
• "spikes" or viral proteins stick out of the membrane
• only found in viruses that infect Eukaryotes

polyprotein

• found in viruses that infect Eukaryotic cells
• contains the sequences for RNA replicase, protease, spikes, and capsids
• protease can cut at each of the sequences to make smaller pieces of protein
• generally only for an RNA virus

reverse transcriptase

• takes the RNA template and makes dsDNA
• this dsDNA gets inserted into the host chromosome

RNA replicase

• takes ssRNA template and makes it into dsRNA
• the dsRNA ultimately ends up as ssRNA again

antigenic shift - influenza

• undergo dramatic genetic changes from one year to the next 
• genome is made up of 8 ssRNA molecules
• one cell can get infected by two different flu viruses, which can then alter themselves
• our immune system no longer recognizes the sequence of the virsues - new flu shot every year

viroid

• a naked, ssRNA molecule
• looks like a ssRNA virus, but without a capsid
• does not encode for eny proteins
• enters a cell, gets replicated, and passed on 
• only found in plants

prions

• an infectious protein
• does not carry any nucleic acid with it
• gets reproduced by bumping into normally folded prions, causing them to miss-fold