RNA Synthesis (Lecture 11)

Question 1

What direction does RdRp read in and synthesize in?

Answer 1

reads 3’-5’ and synthesizes 5’-3’

Question 2

Why is it important for viral RNA to be different from eukaryotic RNA?

Answer 2

capsid proteins and RdRP needs to recognize viral RNA ONLY

Question 3

Which viruses encode for RdRp?

Answer 3

ALL RNA viruses EXCEPT Retroviruses

Question 4

What are the 5 rules for RNA-dependent RNA synthesis?

Answer 4

1) RNA synthesis starts and stops at specific sites on template || 2) RdRp can initiate via de novo or primer-dependent || 3) usually requires a template || 4) RdRp never copies cellular mRNA || 5) other viral or cellular proteins may be required to help with RNA synthesis

Question 5

What is the benefit of starting and stopping RNA synthesis at specific sites on the template?

Answer 5

more genes for the same protein on viral genomes

Question 6

What are the 2 ways to start RNA synthesis?

Answer 6

de novo or primer-dependent

Question 7

What is the de novo way of initiating RNA synthesis?

Answer 7

virus will bring together 2 rNTPs to form a phosphodiester bond taking place at the 3’ end of template

Question 8

What is the primer-dependent way of initiating RNA synthesis?

Answer 8

can use either a terminal protein that provides a free OH group (ie: tyrosine or serine) or snatch a 5’ cap fragment from host transcript and begin RNA synthesis on 3’ end

Question 9

What is a special feature of RdRp?

Answer 9

has endonuclease activity

Question 10

What are 2 ways do viruses obtain the 5’ cap?

Answer 10

recognizes capping sequence on ribosomal ready host mRNA and cleaves it OR steals cap during capping step of host mRNA synthesis

Question 11

Why is RdRp very efficient?

Answer 11

its very processive = does not easily fall off its template

Question 12

What are 4 ways that RdRp determines which are viral templates from host-RNA?

Answer 12

1) RdRp does not recognize adenosine (polyA tail on mRNA) || 2) secondary RNA structures (not very common in cell mRNA) || 3) internal RNA sequences that RdRp recognizes and loads onto || 4) membrane-bound replication complexes where reaction components and viral RNAs are centralized

Question 13

What helps load RdRp onto internal sequences in RNA templates?

Answer 13

secondary RNA structures

Question 14

What are the 2 roles of RdRp?

Answer 14

synthesize mRNA molecules and replicate genome; switches off between these roles?

Question 15

What regulates the initiation and termination of RNA synthesis?

Answer 15

RdRp switching roles

Question 16

What is one of the first proteins made from (+)ssRNA viruses?

Answer 16

RdRp

Question 17

What is the first thing that happens when (+)ssRNA viruses deliver its genome in the cytoplasm?

Answer 17

RdRp attaches 5’ cap &raquo_space;> host ribosomes recognize it and begin translation

Question 18

How does Polio replicate its genome?

Answer 18

uses a terminal protein as a primer and forms membrane-bound vesicles at the site of replication

Question 19

What is the method of translation that Polio takes?

Answer 19

full genomic translation, no sub-genomic particles; protein will be cleaved off into multiple different proteins

Question 20

In what structure do (+)ssRNA viruses replicate their genomes?

Answer 20

in membrane-bound structures

Question 21

What is the difference in genome replication between Polio and Togaviruses?

Answer 21

Togavirus uses a 5’cap primer to initiate RNA synthesis

Question 22

What is the method of transcription that Togaviruses take?

Answer 22

transcription can begin at internal sequences = subgenomic mRNAs = helps form capsid proteins

Question 23

How will (-)ssRNA viruses make RdRp if it isn’t (+)sense?

Answer 23

it can’t so it brings RdRp with them

Question 24

What is the method of transcription that (-)ssRNA viruses take?

Answer 24

mRNAs are made through a series of start/stop sequences (sub-genomic sequences)

Question 25

What dictates that the full genome will be replicated?

Answer 25

a viral protein (such as L protein) that will silence the start/stop sequences

Question 26

What is the strategy that Rabies viruses use?

Answer 26

can make a bunch of mRNA transcripts due to the start/stop sequences in the genome

Question 27

How does dsRNA viruses accomplish hiding of genome differently than (-)ssRNA viruses?

Answer 27

has 2 distinct viral particles one containing newly synthesized genome and one transcribing mRNA

Question 28

What is the first biosynthetic event that dsRNA viruses must undertake?

Answer 28

transcribe mRNA via RdRp

Question 29

In order to replicate the genome, what happens to mRNA once it leaves its viral particle?

Answer 29

gets encapsidated which then RdRp synthesizes second strand

Question 30

What are the 3 distinguishable characteristics/features of dsRNA viruses?

Answer 30

dsRNA is always found in a coat, 2 processes occurs in 2 separate respective virion particles, viral genome itself never leaves the particle as a double strand

Question 31

What are the 3 cellular sites of viral RNA synthesis?

Answer 31

nucleocapsids (in –ssRNA viruses); subviral particles of dsRNA viruses; membrane bound replication complexes

Question 32

Why would a virus want to make replication complexes? What is the benefit?

Answer 32

protection against host cell defenses, increases replication efficiency, protect from nucleases

Question 33

What are 3 reasons why RNA viruses are more diverse than DNA viruses?

Answer 33

RNA polymerase lacks proofreading = more mutations, reassort genomes, recombination during RNA synthesis when RNA polymerase copies one strand and then jumps on the other strand and continues synthesis, RNA editing when there’s no template