L21 RNA replication

Question 1

Possible RNA genome configurations

Answer 1

linear: whole or fragmented
ss: +ve or -ve
ds (rare)
circular ss/ds (extremely rare)

Question 2

most common configuration

Answer 2

ssRNA

Question 3

label +ve and -ve strands as coding or non-coding

Answer 3

+ve: coding

-ve: non-coding

Question 4

what does having a +ve strand mean

Answer 4

proteins can be directly synthesised once in the cell using host ribosome machinery

Question 5

what must -ve strand do before synthesising proteins

Answer 5

use rdrp to make a +ve strand

Question 6

where does the rdpd come from

Answer 6

virus

Question 7

what happens in the first cycle of +ve sense RNA replication

Answer 7

proteins will be directly synthesised from the +ve strand

-one of which is rdrp

Question 8

what happens in the second cycle of +ve sense RNA replication

Answer 8

the rdrp produced in the first cycle is then used to transcribe genomic RNA or mRNA

Question 9

why dont -ve strand viruses have to make rdrp

Answer 9

it is already in the capsid

Question 10

what happens during -ve sense RNA replication

Answer 10

the rdrp from the capsid transcribes the strand into mRNA

the mRNA is translated into proteins

Question 11

during gene expression what does the genome code for (+ve RNA)

Answer 11

one or two polyproteins

Question 12

what is a polyprotein

Answer 12

covalently joined smaller proteins

Question 13

what can a -ve RNA gene encode for

Answer 13

one protein or

two or more proteins

Question 14

why is the ability to produce multiple proteins from one gene advantages

Answer 14

they have a very small genome so they can make more proteins with less genome

Question 15

how are polyproteins cleaved

Answer 15

initially by self or host protease

subsequently by viral

Question 16

example of viruses that form one or two polyproteins from +ve RNA

Answer 16

polio
hep C
SARS-CoV-2

Question 17

three ways one gene encodes for many proteins

Answer 17

alternative initation
alternative splicing
ribosomal frameshifting (slippage)

Question 18

what is alternative intiation

Answer 18

using the different methionine start codon down the gene

Question 19

example of virus that uses gene expression with a segmented genome

Answer 19

influenza

Question 20

what is alternative splicing

Answer 20

different splice sites are chosen

Question 21

what is ribosomal frameshifting

Answer 21

the skipping of nucleotides

Question 22

what is the intermediate of +ve strand RNA replication

Answer 22

-ve strand

Question 23

what is the intermediate of +ve strand RNA replication

Answer 23

-ve strand

Question 24

what is the intermediate of -ve strand RNA replication

Answer 24

+ve strand

Question 25

characteristic of ssRNA replication

Answer 25

5’-3’, like DNA
RNA primer independentant
mostly uses viral components

Question 26

what happens during dsRNA replication

Answer 26

after entry the rdrp present in the capsid trancirbes the negative strand into multiple +ve strands while still in the capsid
-the +ve strands are then released into the cell to translate viral proteins (rdrp incl.)

Question 27

example of virus that undergoes dsRNA replication

Answer 27

Rotavirus

Question 28

what kind of genome does rotavirus have

Answer 28

ds segemented

Question 29

how retrovirus replicate +ve strand RNA

Answer 29

reverse transcribe to dsDNA in the cytoplasm

dsDNA is transported into the nuclear and integrated into host DNA

Question 30

example of retrovirus

Answer 30

HIV

Question 31

what enzyme reverse transcribed the +ve RNA to dsDNA

Answer 31

reverse transcriptdase

Question 32

what enzyme integrates the double-stranded DNA into the host DNA

Answer 32

integrase

Question 33

where are integrase and reverse transcriptase packed

Answer 33

viral capsid

Question 34

what makes reverse transcriptase multifuctional

Answer 34

cna act as
rdrp
dpdp (no proofreading)
ribonuclese H

Question 35

what does ribonuclease H do

Answer 35

degrade DNA

Question 36

is reverse transcriptase RNA primer dependant or independent

Answer 36

dependant

Question 37

how many copies do retroviruses have of the genome in the capsid

Answer 37

two

Question 38

what do the genomes have on the end

Answer 38

direct repeats

Question 39

what is the first thing that reverse transcriptdase does

Answer 39

pick up host tRNA that has a similar sequence to the end of the RNA and uses it as a primer to synthesis a DNA version of the end of the DNA
-the DNA then moves on the other end of the second strand and uses it as a template, creating a DNA/ RNA hybrid