Viral Genomes (Lecture 6)

Question 1

3 basic principles behind the viral genome

Answer 1

genomes need to be copied to make mRNA; unity in viral diversity; genome is used as a template for new genomes for new progeny

Question 2

How is there unity in the 7 different types of viral genomes?

Answer 2

they all want to accomplish the same goal –> make mRNA

Question 3

Why are not all (+)ssRNA are mRNA?

Answer 3

they may not be ribosomal ready, they can be preliminary mRNA

Question 4

What are the 5 genes viruses need to have or already have with them?

Answer 4

genes that will help replicate viral genome | assembly/packaging genes | regulation and time of replication cycle | modulation of host defenses | genes that will allow it to spread and infect other cells

Question 5

What are 4 genes that viruses DON’T have encoded in their genome but may need?

Answer 5

protein synthesis machinery | synthesis of biomembranes | synthesis of energy | centromeres/telomeres

Question 6

Why would viruses need telomeres?

Answer 6

to maintain genome so as it replicates, it won’t get totally wiped out

Question 7

What are the 3 viral genes needed for infection?

Answer 7

capsid proteins | viral receptor-binding protein | polymerase (either to have it with them or something to induce activation host-cell polymerase)

Question 8

What are the 4 types of polymerases?

Answer 8

DdDp, DdRp, RdDp, RdRp

Question 9

What is DNA-dependent DNA polymerase?

Answer 9

replicates DNA

Question 10

What is DNA-dependent RNA polymerase?

Answer 10

makes mRNA and other RNA transcripts (such as RNA primers)

Question 11

What is RNA-dependent DNA polymerase?

Answer 11

reverse transcriptase; uses RNA as a template to make DNA

Question 12

What is RNA-dependent RNA polymerase?

Answer 12

copies viral RNA genome

Question 13

Which polymerases do eukaryotic cells NOT have? What does this mean for the virus?

Answer 13

ANY RNA-dependent polymerases (RdRp and RdDp) which means the virus needs to have genes to make RNA-dependent polymerases

Question 14

Which polymerases do DNA viruses use?

Answer 14

host-cell DNA-dependent polymerases

Question 15

Which polymerases do RNA viruses use?

Answer 15

need to have genes to make their RNA-dependent polymerases (can come with them)

Question 16

What are segmented genomes?

Answer 16

genome is cut into 8 different pieces (segments)

Question 17

What are gapped genomes?

Answer 17

part of the genome is single-stranded while rest of genome is double stranded

Question 18

What are ambisense genomes?

Answer 18

has both a (+) strand and a (-) strand

Question 19

What are genomes with cross-linked ends of dsDNA?

Answer 19

ends are cross-linked to each other = difficult to replicate/transcribe genome

Question 20

What are 3 basic strategies that viruses use to replicate their genome and synthesize mRNA?

Answer 20

based on host DNA (will use same strategies host already uses to replicate DNA) | emulate host (need DNA polymerase = only present during cell division = virus need to jump start cell cycle) | viral genomes are not chromosomes so don’t have telomerase = need to fix that issue

Question 21

Which type of viruses are more likely to cause cancer and why?

Answer 21

DNA virus, they need to jump-start and push cell cycle forward = causes cells to begin replicating (and may not stop)

Question 22

What are 2 common types of dsDNA viruses?

Answer 22

Herpes and HPV

Question 23

What is the first biosynthetic event dsDNA viruses undertake? The second?

Answer 23

1) make mRNA –> protein | 2) replicate genome (can be used to make more mRNA)

Question 24

What are the polymerases that dsDNA viruses use?

Answer 24

DdDp and DdRp

Question 25

Which type of virus has gapped dsDNA?

Answer 25

Hepadena virus

Question 26

What polymerases does this gapped-dsDNA virus use?

Answer 26

RdDp (RT), DdRp, DdDp

Question 27

What is the first biosynthetic event that gapped dsDNA viruses undertake?

Answer 27

repair and fill in the broken gaps of its genome --> mRNA --> protein

Question 28

What are common example(s) of gapped dsDNA viruses?

Answer 28

hepatitis viruses

Question 29

How do gapped dsDNA viruses replicate their genome?

Answer 29

dsDNA >>> (+)ssRNA via DdRp >>> (-)ssDNA via RT (RdDp) >>> enzymes make it gapped dsDNA

Question 30

What are the 3 benefits to having a gapped DNA genome?

Answer 30

more resistant against host cell defenses, mutations = evolutionary advantage, may assist with assembly of virus

Question 31

What is the first biosynthetic even ssDNA viruses need to undertake?

Answer 31

need to become dsDNA first

Question 32

Why can't you make mRNA with a ssDNA molecule?

Answer 32

DNA-dependent RNA polymerase ONLY recognize double-stranded molecules

Question 33

What are the polymerases that ssDNA viruses use?

Answer 33

DdDp and DdRp

Question 34

What are the 3 strategies that RNA viruses use to replicate their genome and make mRNA?

Answer 34

encode for RdRp (host cells don't have this), use RdRp, RdRp is used to replicate genome and make mRNA

Question 35

Which type of virus is the most abundant and why? (RNA or DNA viruses?

Answer 35

RNA viruses because they are always changing as RNA is less stable than DNA

Question 36

What is a key enzyme that scientists use to target RNA viruses and why?

Answer 36

RdRp or RdDp because host cells don't have this

Question 37

What is a common type of dsRNA virus?

Answer 37

rotavirus

Question 38

What is the first biosynthetic event dsRNA viruses undertake?

Answer 38

use RdRp to synthesize (-)ssRNA strand which will be then transcribed to mRNA by RdRp

Question 39

What polymerases do dsDNA viruses use?

Answer 39

RdRp

Question 40

How do dsRNA viruses replicate their genome?

Answer 40

encapsidate some newly synthesized mRNA in a vesicle and use RdRp to copy the second strand

Question 41

Why do dsRNA viruses need to encapsidate their mRNA in a vesicle to replicate their genome?

Answer 41

they are hiding from host-cell defenses since our cells have never seen dsRNA = once cell detects dsRNA it will destroy it asap

Question 42

Which type of virus can potentially be used to cure cancer?

Answer 42

dsRNA viruses

Question 43

Which type of RNA virus is the most abundant?

Answer 43

(+)ssRNA viruses

Question 44

What are common types of (+)ssRNA viruses?

Answer 44

Togavirus and Flavivirus

Question 45

What is the first biosynthetic event (+)ssRNA viruses undertake?

Answer 45

make protein IF genome/mRNA is ribosome ready

Question 46

What polymerases do (+)ssRNA viruses use?

Answer 46

RdRp

Question 47

How do (+)ssRNA viruses replicate their genome?

Answer 47

RdRp makes (-)ssRNA that serves as a template to make (+)ssRNA

Question 48

What is the first protein that (+)ssRNA will make?

Answer 48

RdRp

Question 49

What is a common type of (+)ssRNA w/DNA intermediate virus?

Answer 49

retroviruses = HIV

Question 50

What is the first biosynthetic event (+)ssRNA w/DNA intermediate viruses undertake?

Answer 50

reverse transcribe their (+)ssRNA to (-)ssDNA

Question 51

What enzyme copies the complementary strand of (-)ssDNA?

Answer 51

reverse transcriptase (RdDp)

Question 52

What enzyme(s) do (+)ssRNA w/DNA intermediate viruses use?

Answer 52

RdDp and DdRp

Question 53

How do (+)ssRNA w/DNA intermediate viruses replicate their genome?

Answer 53

uses newly synthesized mRNA as genome since they are (+)ssRNA (essentially)

Question 54

Do (+)ssRNA w/DNA intermediate viruses have to encode for the RdDp once they get into the cell or do they carry it with them?

Answer 54

carry it with them

Question 55

What is unique about (+)ssRNA w/DNA intermediate viruses and how do they do this?

Answer 55

insert their genome into our genome via integrase

Question 56

What are common types of (-)ssRNA viruses?

Answer 56

rhaboviruses = rabies

Question 57

What is the first biosynthetic pathway (-)ssRNA viruses undertake?

Answer 57

RdRp copies (-)ssRNA into (+)ssRNA

Question 58

What polymerases do (-)ssRNA viruses use?

Answer 58

RdRp

Question 59

Do (-)ssRNA viruses have to encode for the RdRp once they get into the cell or do they carry it with them? And why?

Answer 59

carry it with them since they are (-)ssRNA and it needs to be copied into (+)ssRNA; no way of making RdRp from (-)ssRNA

Question 60

How do (-)ssRNA viruses replicate their genome?

Answer 60

use RdRp to re-transcribe their newly synthesized mRNA to (-)ssRNA