CH. 6 RNA from RNA templates

Question 1

RNA Virus Genome Configurations:

Answer 1

Unimolecular, segmented, single stranded (+) or (-), double stranded, and circular

Question 2

For viral propagation, the genome must be _____ and ______

Answer 2

copied; transcribed into mRNA for protein synthesis

Question 3

Genomes of all RNA virus encode:

Answer 3

RNA dependent RNA polymerase; exception: Retroviruses

Question 4

RNA virus with (-) strand genomes must contain ____ within the _____

Answer 4

RNA dep. RNA Pol.; capsid

Question 5

Can RNA virus with (+) strand genomes still be infectious after protein denaturization?

Answer 5

Yes

Question 6

Make sure to study:

Answer 6

Flash cards 3,4

Question 7

How were RNA synthesis mechanisms researched?

Answer 7

Poliovirus and Mengovirus infected cell lysates were incubated with ATP, UTP, CTP, and GTP where one was radiolabeled. Treated with actinomycin D, (blocks DNA directed RNA synthesis)

Question 8

In RNA-dep. RNA pol. how many motifs were identified as being possible active sites? Which is most likely the active site?

Answer 8

4 (a-d); C. When C was altered, it rendered poliovirus inactive

Question 9

What does RNA-dep. RNA Pol. resemble?

Answer 9

A right hand

Question 10

What does a De Novo initiation require?

Answer 10

RNA-dep. RNA pol., an RNA template, initiating NTP and a second NTP

Question 11

What are the three types of RNA replication initiation strategies?

Answer 11

De Novo initiation, Prime and realign(- sense, internal initiation), primer dependent initiation (5’ Cap or primer protein)

Question 12

How does a dsRNA access its genome? How is this being researched?

Answer 12

Virus encoded helicases generate ssRNA from dsRNA, as well as preventing extensive base pairing between template and nascent complementary strands. RNA helicases for hepatitis and dengue are extensively studied in order to find ways of disrupting them

Question 13

Would Ribosomes and RNA Pol collide?

Answer 13

If there weren’t mechanisms in place to prevent this, yes they would. Ribosomes translate from 5’ to 3’, and RNA Pol replicates moving along from the 3’ end of the template strand to the 5’ end.

Question 14

Are there different RNA Pol for replication and mRNA synthesis?

Answer 14

Yes.Ex: for influenza, the presence of Nucleocapsid proteins inhibits mRNA synthesis.

Question 15

What are the two methods of replication used by dsRNA virus?

Answer 15

Semi-conservative (birnaviruses) and conservative (Reoviruses)

Question 16

Where does most RNA replication and mRNA synthesis occur?

Answer 16

In the cytoplasm, in specific structures.

Question 17

Where is Polioviral RNA Pol located?

Answer 17

On the surface of small membranous vesicles of ER and autophagosomes

Question 18

Why is membrane association useful to the virus?

Answer 18

It ensures a high local concentration of replication components (increases replication rate)

Question 19

Why are RNA viruses generally so diverse?

Answer 19

All polymerases insert the incorrect nucleotides on occasion. DNA Pol have proof-reading due to exonuclease activity. RNA dep. RNA Pol does not.

Question 20

What is a quasispecies? What does this influence

Answer 20

A population resulting from nonlethal mutations that have many different genome sequences. Evolution and pathogenesis.

Question 21

What is reassortment???

Answer 21

The exchange of entire RNA molecules between genetically related virus( ex. influenza)

Question 22

What is recombination?

Answer 22

The exchange of nucleotide sequences between different genomic RNA molecules. Important for the generation of a new genome with selective advantages. First discovered in Poliovirus. 10-20% of polioviral genomic RNA molecules recombinant. Can lead to production of pathogenic virus.

Question 23

What are the methods of RNA recombination?

Answer 23

It can occur by “copy switch” where an RNA dep. RNA pol. switches from one template strand to another.
Class 1: base pairing dependent ( strands are same length)
Class 2: Base pairing independent (strands switch without regard to alignment
Class 3: Base pairing assisted (strands switch with assistance from base pairing, but strands end up being different length anyways due to hairpins further down.