Lecture 2

Question 1

What information is encoded in a viral genome?

Answer 1

Replication of viral genome
Assembly and packaging of the genome
Regulation and timing of the replication cycle
Modulation of host défenses
Spread to other cells

Question 2

All viral genomes must make ____ that can be read by host ribosomes.

Answer 2

mRNA

Question 3

Is mRNA + or - polarity

Answer 3

+

Question 4

What is the + strand?

Answer 4

DNA or RNA that is the coding strand (starts with AUG)

Question 5

What is the - strand?

Answer 5

DNA or RNA that is the template strand. Does not contain open reading frame

Question 6

True or false: All +RNAs are mRNAs

Answer 6

False. Ex: Genomic RNA vs sub-genomic mRNAs

Question 7

What are the seven Baltimore classes?

Answer 7

1. ds DNA
2. • ssDNA
3. ds RNA
4. • ssRNA
5. • ssRNA
6. • ss RNA reverse transcriptase
7. ds DNA reverse transcriptase

Question 8

Describe Baltimore Class I viruses

Answer 8

Transcribe dsDNA to +mRNA

Question 9

What are two Baltimore class I viruses whose genomes are copied by host DNA polymerases?

Answer 9

Polyomaviridae, Papillomaviridae

Question 10

What are two Baltimore Class I viruses that encode their own DNA polymerase?

Answer 10

Adenoviridae
Poxviridae (replicates in cytoplasm, therefore needs to create its own DNA pol)

Question 11

Describe Baltimore Class II viruses

Answer 11

Convert - or + ssDNA to dsDNA and then transcribes to mRNA

Question 12

True or false: Baltimore class II viruses can be circular or linear

Answer 12

True

Question 13

Which Baltimore class viruses use an RdRp?

Answer 13

dsRNA, + RNA and - RNA

Question 14

What is RdRp?

Answer 14

RNA-dependent RNA polymerase
To make mRNAs and RNA genomes from RNA templates

Question 15

Which Baltimore class viruses use reverse transcriptase

Answer 15

ssRNA-RT and dsDNA-RT

Question 16

Describe Baltimore Class III viruses

Answer 16

dsRNA converted to mRNA by RdRp

Question 17

Describe Baltimore Class IV viruses

Answer 17

mRNA can be directly translated

Question 18

Describe Baltimore Class V viruses

Answer 18

-RNA gets converted to +RNA through RdRP
Can be segmented or non-segmented

Question 19

Describe Baltimore Class VI viruses

Answer 19

+RNA gets converted - ssDNA by reverse transcriptase and then to dsDNA

Question 20

Describe Baltimore Class VII viruses

Answer 20

Gapped dsDNA converted to full dsDNA and then transcribed to mRNA

Uses reverse transcriptase when turning +RNA to dsDNA (replicating genome)

Question 21

What is reassortment?

Answer 21

Multiple viruses co-infect the same cell
Leads to rapid evolution

Question 22

How were viral stocks maintained in the 1900s?

Answer 22

Continual passage from animal to animal

Question 23

Before cell culture, how were viruses propagated?

Answer 23

In embryonated chicken eggs
5-14 days after fertilization, hole drilled in shell, the location of viral injection depends on site appropriate for its replication

Question 24

What are the two types of cell cultures?

Answer 24

Primary cell cultures
- prepared from animal tissues
- limited life span

Continuous cell lines
- single cell type that can be propagated indefinitely in culture
- HeLa cells: cancer cells
- Tumor tissue or immortalized primary cells
- May not resemble the cell of origin

Question 25

What is evidence of viral growth in culture cells?

Answer 25

Rounding up of cells, detachment, cell lysis, syncytial formation (cell fusion), nuclear shrinking/swelling, accumulation of virions/viral proteins, membrane alteration

Question 26

What is the virus titer?

Answer 26

Concentration of a virus in a sample

Question 27

What is the plaque assay?

Answer 27

Quantitative measure of infectious virus Count # of infectious viral particles in a suspension

Question 28

How do you calculate the titer in a plaque assay?

Answer 28

#PFU/volume plated x dilution factor

Question 29

What is a focus-forming unit assay?

Answer 29

Modification of the plaque assay for viruses that do not lyse cells After viral infection, cells are permeabilized and stained with an antibody against a viral protein

Question 30

What is the particle-to-PFU ratio?

Answer 30

# of physical particles divided by the # of infectious particles

Question 31

Why are viral particles not always successful at infection?

Answer 31

Damaged particles, mutations, empty particles, complexity of viral life cycles, antiviral defenses

Question 32

What is MOI

Answer 32

Multiplicity of infection Average number of cells added per cell (not the same as the # of infectious particles each cell receives) Depends on random collision of virions and cells

Question 33

How do you calculate the fraction of cells infected by one or more viral particles?

Answer 33

P(k) = (e^-m) (m^k)/k! P(k) = fraction of cells infected by k virus particles m=MOI e = Euler’s number (approx 2.72) k! = factorial of k Fraction of uninflected cells = P(0) = e^-m Fraction of cells infected with one particle = P(1) = (e^-m)m Fraction of cells multiply infected = P(>1) = 1-(e^-m)(1+m)

Question 34

How is MOI used in research?

Answer 34

Low MOI: experiment requires multiple cycles of infection High MIO: when every cell in culture needs to be infected Optimal MOI: optimize number of cells that will be infected with a single viral particle