Viro 2

Front 1

1. What is the time after injection until new extracellular virions are detected?
2. What is the time after infection where little or no infectious virus can be detected?
3. What is the viral yield?

Back 1

1. Latent period = eclipsed period plus the time till virus is released
2. Eclipse period, during this period gene expression, genome replication, and assembly is occurring
3. Amount of virus produced after infection

Front 2

1. What proteins are expressed by early genes/
2. What proteins are expressed by late genes/
3. What are 2 ways that early and late genes are separated in DNA viruses?

Back 2

1. regulatory proteins and enzymes needed for viral transcription and DNA synthesis
2. Encode structural proteins and proteins that will be packaged into progeny virus
3. Temporally and spatial separation

Front 3

1. What is DDDP?
2. What direction is DNA always synthesized in?
3. What does any DNA polymerase require to initiate synthesis?
4. What are the 3 components for DNA virus replication?

Back 3

1. DNA dependent DNA polymerase
2. 5' to 3'
3. A template and a primer
4. DDDP, double stranded primer with free 3'OH end, single stranded template

Front 4

1. Do DNA or RNA viruses mutate more rapidly, and why?

Back 4

1. RNA, b/c DNA has polymerases that facilitate proof reading

Front 5

1. What is the shape of the Parvovirus DNA/
2. What does the Rep sequence do?
3. The Cap sequence?
4. Although this only has 2 genes how does it make more than 2 proteins?

Back 5

1. A hammer shaped ds unit on either end (inverse terminal repeat) with a ss, linear genome in the middle
2. Replication - occurs early
3. Cap- capsid occurs late
4. Alternative splicing to get more than 1 protein from a gene, and by having more than 1 promoter on a gene

Front 6

1. What is an acceptor site in terms of splicing?
2. How does parvovirus replicate its genome?

Back 6

1. site that accepts splicing
2. Host polymerase uses hammerhead end as a primer and single-stranded viral genome as a template. Rep 68/68 acts as a nickase and helicase to cleave ds viral DNA at specific site and promote separation of DNA strands, this reforms the hammer head

Front 7

1. What are the 2 subclasses of papovavirus?
2. Type of DNA?

Back 7

1. Polyomavirus (ka BKV in humans) and papillomavirus
2. circular ds DNA genome

Front 8

Notes about the papovaviruses:
1. nonenveloped virus with icosahedral capsids
2. ds, small, cc genomes
3. Have single origin of replication and physical separation of early and late genes
4. More proteins than ORFs (genes)

Back 8

5. T antigens (early gene products) involved in transcriptional regulation and genome replication
6. VP1-3 are late gene products and are capsid proteins

Front 9

1. How does theta (ring) replication work?

Back 9

1. Very early on have ds ring with a small ss bubble. Then a polymerase binds and creates a theta looking circle in a circle. The polymerase continues bidirectional replication until you have a circle in a circle. The entwined circles are resolved by a host topoisomerase

Front 10

1. What are the only viral proteins necessary to initiate DNA replication of polyomaviruses and papillomaviruses?
2. What is the fxn of 1?
3. What resolves the entwined circles?

Back 10

1. Poly- T antigen and the pap- E1 | All the rest are from the cell
2. Recognition proteins that act as a helicase to unwind the ds DNA at the origin producing a ss DNA
3. Host toposiomerase

Front 11

Features of adenovirus:
1. Noneneveloped, icosahedral capsid
2. Linear, ds, genome with covalently linked protein on 5' end of each strand

Back 11

3. No physical separation of early and late genes
4. Makes numerous proteins by a combination of multiple proteins and differential splicing

Front 12

1. What are the 2 classes of early genes in adenoviruses?
2. What virus was used to discover splicing?

Back 12

1. immediate early and early
2. adenovirus- splices more than any other virus

Front 13

1. How does an adenovirus replicate?
2. What does it mean that synthesis is continuous?
3. Synthesis is semiconservative, what does this mean?

Back 13

1. uses its own DNA polymerase and a unique terminal protein (TP) that provides a free OH group (from serine) for the addition of the first CTP (cystein)
2. Only occurs on the leading strand (from 5' to 3'), so there is no lagging strand or okazaki fragments
3. one new strand, and one from the parent

Front 14

In the herpesvirus virion
1. What is the region between the capsid and envelope, what does it contain?
2. What is the genome?
Herpes has an icosahedral capsid surrounded by host-cell derived lipid envelope with glycoprotein spikes

Back 14

1. Tegument- numerous viral proteins
2. Genome is linear, ds,

Front 15

Herpesvirus Genome
1. What are the box regions in the genome?
2. What are the areas between box regions ka?
3. Isomerization of the genome means what?

Back 15

1. Repeated sequences (some are inverted repeats IR)
2. Unique (can be unique long or unique short)
3. Recombination between adjacent IR sequences leads to inversion of the intervening genome region leading to different isomeric forms

Front 16

Realize that alpha equals early, beta is intermediate early, and gamma are late genes in the herpes virus
1. How is herpes trancription regulated?

Back 16

1. Alpha genes turn on beta and gamma, but turn off alpha. Gamma genes turn off alpha and beta and produce the virion. Beta does not turn anything off, it just is necessary to turn gamma on

So lot of autofeed back and regulation

Front 17

1. How does the herpes virus replicate itself?
2. Use host proteins?

Back 17

1. The genome circularizes, then replicates using the theta nick. Then it uses a rolling circle mechanism that generates long chains (concatemers). Concatemers are cleaved into genome length segments for packaging
2. No, it encodes all of its own replication proteins

Front 18

Hepatitis B virus- only human agent in this family
- enveloped virion (lipid membrane)
- Small, partially ds, genome with 4 overlapping ORFS
- only 1 s is transcribed
- generates more than 4 proteins with splicing and other mechs.

Back 18

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Front 19

How does the Hep B virus replicate?

Back 19

1. upon entry the partially ds genome is completed. the ds genome is transcribed by host RNAP
2. Viral transcripts are translated to make viral proteins, one of which is reverse transcriptase RT
3. The longer than genome lenght viral RNA is packaged into a virion with RT protein
4. RT converts the viral RNA into a ds DNA. The RT runs out of dNTPs so synthesis does not complete and you get a partial ds sequence

Front 20

1. How does Hep B genome appear in the host?
2. Outside?
3. cycle of it?

Back 20

1. Complete
2. Partial
3. Partial DNA -> DNA completed in cell -> RNA + RT (released) -> DNA partial

Front 21

Characteristics of Poxviruses
- linear, ds genome covalently closed at both ends
- enveloped
- extremely complex virion, over 100 proteins

Back 21

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Front 22

1. What is the only DNA virus that replicates in the cytoplasm (lacks a nuclear phase)?
2. In order to do 1, what does the virion carry?

Back 22

1. Poxvirus
2. RNA polymerase, Poly (A) polymerase and capping enzyme