Chapter 7

Question 1

1. Where do most DNA, RNA retro and para-retro viruses replicate their genomes?

Answer 1

genomes of most DNA viruses are replicated in the nucleus

Question 2

Some viruses that replicate their genome in the cytoplasm, tend to synthesize the new genomes inside structures.

1. What kind of viruses are these?
2. Why is this?
3. What kind of structures do the genomes get replicated in?

Answer 2

1. Viruses aRE dsRNA viruses, the retroviruses and pararetroviruses
2. this is to protect them from defense mechanisms of the host cells
3. RT ase (structural)

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Question 3

1. What are the ways that virus genome replication can be initiated in respect to primers and genome sequences

Question 4

1. What part of the a protein primer serves as the treatment of the first nucleotide in nucleic acid? (chemical groups and types of residues)

Answer 4

1. Some DNA and RNA viruses use protein primer 3’ -OH of the Serine and Tyrosine residues

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Question 5

1. What is an inverted terminal repeat?
2. How does ITR relate to genome replication of adenovirus associated virus (parvoviridae)?
   
   1. has ssDNA genome
3. How is replication primed

Answer 5

1. a single stranded sequence of nucleotides followed downstream by its reverse compliment
   
   1. (where the sequence at one end is complementary to, and in the opposite orientation to, the sequence at the other end)
2. The ITRs work as primers when the repeat bends over itself and a nucleotide binds to the same nucleotide and from there acts as a primer
   
   1. hair pin formation

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Question 6

1. What is theta mode replication
2. what kind of genomes replicate this way
3. where does genome replication start
4. Draw a cartoon
   
   1. labels
   2. explain how this replication is carried out

Answer 6

1. theta mode replication is term that refers to the shapes of the replicating molecule. the theta structure forms due to the two replication forks as result of the bidirectional replication from ori
   
   1. there is both continuous and discontinuous replication
2. dsDNA and ssDNA , both of which replicate their genomes via dsDNA ???
3. Genome replications starts at the two origins of replication “ori”
4. Check this slide

Question 7

1. What is sigma mode replication
2. what kind of genomes replicate this way
3. where does genome replication start
4. Draw a cartoon
   
   1. labels
   2. explain how this replication is carried out

Answer 7

1. Sigma mode replication is circular dsDNA replication that occurs in a sigma shape formation . it is also called rolling circle replication. occurs later in infection
2. dsDNA genomes replicate this way
3. replication starts at the origin of replication
4. Picture
   
   1. one strand is nicked by endonuclease. this nicked strand is the primer for continuous replication
   2. The free 3’ end is extended by DNA poly merase while displacing the complementary template strand
   3. simultaneously the complementary template strand its coped in short fragments by DNA poly (Okazaki fragments)
   4. replication continuous until at least one new copy is made
5. multiple copies may result chained together = concatemer
   
   1. eventually they will be cut by endonuclease

Question 8

1. How does replication of virus dsDNA genomes compare to replication of cellular genomes?

Answer 8

1. They both use DNA polymerase
2. 5’ → 3’ leading strand and also lagging strand with Okazaki fragments
3. origin of replication helices unwinds the double helix at the sire of replication
4. ssDNA binding protein keeps the two DNA strands apart

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Question 9

1. concameter
2. how are they processed

Answer 9

1. Concameters are multiple copies of the virus genome
   
   1. they can be branched
2. when the DNA becomes packaged during the iron assembly an endonuclease will come in a cut the genome length from a concameter

Question 10

1. How does the replication of dsRNA genomes compare to dsDNA genomes

Answer 10

1. Compare
   
   1. dsRNA must be unwound with helicase
   2. some replicate via a semi-conservative mechanism like dsDNA (ds progeny molecules are made up of a parental strand and a daughter)
   3. some dsRNA viruses replicate by conservative mechanism , this because the double stranded molecule infecting the genome is conserved

Question 11

1. what is conservative and non-conservative replication

Answer 11

1. conservative= the two strands of the parent genome stay togethe
   
   1. double strnded molecule of the infecting genome is conserved
2. semi-conservative= each of the double stranded progeny molecule is made up of a parent strand and a daughter strand

Question 12

1. Does rotavirus replicate by conservative or semi conservative mode?
2. why does it never expose its dsRNA to the cellular environment
3. how does it avoid exposure to intracellular environment?

Answer 12

1. #
2. viroplasm, a viral enclosure made of proteins

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Question 13

1. How are ssRNA circular genomes replicated?
2. what is the significance of pseudoknots in this situation
3. another name for these pseudo knots

Answer 13

1. replicate by continuous rolling replication using RNA polymerase
   
   1. ssRNA genomes are replicated by synthesis of complementary strands of RNA that are then used as templates for synthesis of new copies of the genome
2. psuedoknotso/ribozymes are of tertiary structure
   
   1. they allow cleavage to occur at the end of each concatamere
   2. self cleavage
3. this results in antigenes
   
   1. antisense genomes that are recircualrized and then reentered into the same process to produces progeny genomes

Question 14

question 15