Exam II - review

Question 1

Topic 6, slide 6

Why would a DNA virus and a Retrovirus be affected by Actinomycin D?

Answer 1

They use cellular RNA Pol II that is inhibited by Act. D

Question 2

Topic 6, slide 15

Which polynucleotide polymerases require divalent metal ions?

Bank: RdRp, DdRp, DdDp and RT

Answer 2

All of them

Question 3

Topic 6, slide 16

What attributes the NTP specificity over dNTPs in RNA polymerases?

Answer 3

The 2′hydroxyl of the ribose sugar

Question 4

Topic 6, slide 17

What domain of the hand ( fingers, thumb, palm ) is the RNA dependent RNA polymerase active site located in?

Answer 4

Palm

Question 5

Topic 6, slide 22

In dsRNA viruses ( Reovirus) , RNA dependent RNA polymerases are located in the viral core.
What special structure is here and what does it do?

Answer 5

Turrets ( 12 )

Each turret is associated with one of the RNA dependent RNA polymerases

Question 6

Topic 6, slide 24

In dsDNA viruses ( Reoviruses ), which of the following is correct?

A) The mRNAs are produced inside the viral core particle and never synthesized in the cytoplasm

B) The RNA dependent RNA polymerase is located inside the viral core below the turret proteins which synthesize the mRNAs

C) One of each of the 10 segments of double-stranded genomic RNA is associated with a viral RNA dependent RNA polymerase and is located under each “ turret proteins ” in each fivefold axis which synthesizes the mRNA

Answer 6

All of them

Question 7

Topic 6, slide 32

In which of the following ways are Poliovirus and Coronavirus replication strategy similar ( both + stranded RNA )?

A) Circularization of template for initiation of RNA synthesis

B) Extensive RNA secondary structures such as stem-loops

C) Long distance RNA -RNA interactions

Answer 7

All of them

Question 8

Topic 6, slide 38

What is the major difference between the Vesicular Stomatitis Virus (VSV) and Influenza Virus mRNA synthesis?

A) Genome is unimolecular (1 segment)

B) mRNAs and genomic RNAs are synthesized in the cytoplasm by viral RdRp

Answer 8

B; in the Flu, this occurs in the nucleus

Question 9

Topic 6, slide 41

In - strand RNA viruses ( VSV ), what causes polyadenylation of mRNA?

Answer 9

Slippage of the RNA polymerase and recopying over a seven-residue uridine (U7) at each intergenic region

Question 10

Topic 6, slide 42

In - strand RNA viruses ( VSV ), what causes genome RNA synthesis?

Answer 10

Encapsidation of the “leader RNA” by N protein acts as the “switch” from mRNA synthesis to genome RNA synthesis

RdRp reads through the intergenic region all the way to the end of template to synthesize the genome RNA

Question 11

Topic 6, slide 46

In - strand RNA viruses, ( Influenza virus ), what is the mRNA synthesis primer?

Answer 11

a snatched Portion of 5′ Capped of Host Nuclear Pre-mRNA

The 5’ cap is cleaved and snatched from host nuclear pre-mRNAs

Question 12

Topic 7, slide 56

Transcription of most but not all DNA viruses are carried out by RNA pol II – what is the exception?

Answer 12

Pox and giant viruses

Question 13

Topic 7, slide 58

What does TfIID bind to?

Answer 13

the TATA sequence

Question 14

Topic 7, slide 60

DNA binding protein can be enhancers or silencers. What are two examples of enhancer binding proteins?

Answer 14

Transcription factors in cis - within few 100 basepairs of the transcription initiation site

Transcription factors in trans - can be 1000s of base pair away from the transcription initiation site

Question 15

Topic 7, slide 62

Signature structure of a DNA binding domain of a transcriptional activator protein is ________

Answer 15

the Zinc Finger

Question 16

Topic 7, slide 66

When is the LT ( large T antigen ) created in SV40? What does it do?

Answer 16

the EARLY phase of transcription

Regulate DNA replication and expression of late genes

Question 17

Topic 7, slide 67

What binds to the initiator sequence in SV40 in order to repress regulation?

Answer 17

Ibp = initiator binding protein, a cellular protein

Question 18

Topic 7, slide 69

In Adenovirus transcription, what is produced…

• in the early phase and controls early gene expression?
• by the early phase that causes DNA replication and anti repression?
• in the late phase (2) and enhances the late phase gene expression?

Answer 18

• E1A
• E2
• IVa2 and L4
• Might be an exam question about which one is correct – all of them are correct

Question 19

Topic 7, slide 70

In Adenovirus transcription, E2F recruits the histone deacetylases ( Hdacs ). What is the result?

Answer 19

the DNA is wrapped more tightly and reduces transcription

Question 20

Topic 7, slide 72

The “ immediate early ” transcription factor ____ is packaged into the Herpesvirus virion because otherwise it cannot be recognized.

Answer 20

VP16

Question 21

Topic 7, slide 73

In Herpesvirus, transcription initiated by ____.
What is this the promoter of?

Answer 21

VP16

IE (immediate early ) transcription

Question 22

Topic 7, slide 75

In the modification of mRNA, in the 5’ cap structure, what is the first capping nucleotide? What is the second connected by? What do the second and third base have?

Answer 22

guanine ( at the seventh position )

a 5’ – 5’ triphosphate linkage

an O methylation ( can be viral or cellular )

Question 23

Topic 7, slide 77

In the modification of mRNA, where is Poly A added?

Answer 23

The cleaveage site of the pre mRNA

• No polyU tracts, no slippage

Question 24

Topic 7, slide 78

How is a poly A tail of mRNAs added to:

1) Adenovirus, HBV, HDV, Herpesvirus, Retrovirus

and

2) Influenza virus, VSV

and

3) Poliovirus, Coronavirus?

Answer 24

1) Cleavage of pre mRNA followed by polyadenylation
2) Copying at stretches of U in template RNA
3) Copying of long U stretch template RNA

Question 25

Topic 7, slide 80 How many trans-esterification reactions take place in the splicing of pre mRNA?

Answer 25

2

Question 26

Topic 7, slide 82 What does alternative splicing do?

Answer 26

creates different mRNAs and proteins so in a limited size genome, more proteins can be created

Question 27

Topic 7, slide 84 Why is splicing mRNAs necessary?

Answer 27

for the binding and activation of the nuclear export proteins for most viral mRNA export into the cytoplasm from the nucleus

Question 28

Topic 7, slide 85 To transport unspliced viral pre-mRNAs, Retroviral mRNAs must have a nuclear export signal known as _____. What is this is HIV?

Answer 28

CTEs ( Constitutive transport element ) RRE ( Rev responce element )

Question 29

Topic 7, slide 86 Why do mRNAs in HIV need RRE in order to be transported?

Answer 29

because it is unspliced ( not spliced)

Question 30

Topic 8, slide 92 Why do viruses need hosts for DNA replication (3)?

Answer 30

1) Viral DNA replication always requires synthesis of at least one viral protein, sometimes many (hence always delayed after infection) 2) Simple viruses require more host proteins - smaller genomes 3) Complex viruses encode many, but not all proteins required for replication

Question 31

Topic 8, slide 94 Which of the following proteins / enzymes is not involved in viral DNA replication? A) Helicases B) Topoisomerases C) Exonucleases D) None of the above

Answer 31

D

Question 32

Topic 8, slide 98 In the SV40 large T antigen, what does the host range have?

Answer 32

the ATPase function, helicase function, and the phosphorylation of the threonine ; needed for binding the Rb

Question 33

Topic 8, slide 100 What is Rb loss associated with? What binds to Rb and makes it lose its function?

Answer 33

Tumors; it is a tumor suppressor gene LT; makes tumors

Question 34

Topic 8, slide 101 ___, ____ or ___, ___ can all bind to Rb. Makes the Rb not able to bind ( causes tumors ).

Answer 34

SV40 HPV-16 or HPV-18 Ad5

Question 35

Topic 8, slide 106 In SV 40... LT is a ____ that binds on the opposite side of the origin ____ ( single strand binding protein ) binds LT LT shows helicase activity when bound to ___ LT has intrinsic ____ helicase activity

Answer 35

hexamer RpA RpA 3′→ 5′

Question 36

Topic 8, slide 107 In SV40 synthesis of leading and lagging strands, what is the clamp and what is the clamp promoter?

Answer 36

PCNA RFC

Question 37

Topic 8, slide 108 In SV40 synthesis of leading and lagging strands, what does gap repair?

Answer 37

DNA pol delta ( δ )

Question 38

Topic 8, slide 110 During DNA replication, _____ or ____ reduced the strain on the supercoiling ( relaxes ) At the end, the _______ does the resolution

Answer 38

topoisomerase I or II topoisomerase II

Question 39

Topic 8, slide 112 In Parvoviruses, DNA replication, what does Rep78/68 do?

Answer 39

required for initiation and resolution: endonuclease, helicase, binds 5′-terminus

Question 40

Topic 8, slide 117 In Herpesvirus ignition of DNA replication, what is responsible for circularization of the incoming viral DNA immediately after its delivery into the nucleus?

Answer 40

DNA ligase IV/XRCC4

Question 41

Topic 9, slide 129 ( +) strand RNA viruses usually have naked genomic RNA ( no nucleocapsid ), exceptions are what (2)?

Answer 41

Retroviruses and Coronaviruses

Question 42

Topic 9, slide 133 Every virus that codes  reverse transcriptase (does or does not) have integrase to integrate the converted DNA

Answer 42

does not

Question 43

Topic 9, slide 137 In HIV-1 reverse transcriptase, how many divalent metal ions are needed?

Answer 43

4

Question 44

Topic 9, slide 139 Why are retroviruses relatively resistant to UV and ionizing radiation?

Answer 44

Copy – choice rebuilds the genome ( two copies of all genes into one )

Question 45

Topic 9, slide 140 What is the signature structure of the tRNA used in the reverse transcription of the primer and the binding of the primer binding site in a retrovirus?

Answer 45

ΤψC ( T psi C ) loop and arm is the pbs ( primer binding site )

Question 46

Topic 9, slide 141 / 142 In Retroviral Reverse Transcription, first template exchange (of 2)... Priming of (‒) DNA strand synthesis is from ___ Priming of (+) DNA strand synthesis is from ___

Answer 46

tRNA PPT (polypurine tract; A and Gs)

Question 47

Topic 9, slide 143 In Retroviral Reverse Transcription, what happens (2)?

Answer 47

In two different template exchanges... 1) Degradation of the viral RNA by RNase H 2) Generation of two LTRs ( at each end of the DNA )

Question 48

Topic 9, slide 148 What is the BAF? What does it do?

Answer 48

BAF = barrier of autointegration factor = prevents autointegration of the retroviral DNA Tick question: Which interaction is incorrect? All interactions are correct

Question 49

Topic 9, slide 153 More than ___% of the human genome comprises mobile genetic elements, including endogenous proviruses and other retroelements

Answer 49

40

Question 50

Topic 9, slide 154 ________ and _______ both have LTRs ________ and ________ do not have LTRs

Answer 50

Endogenous retrovirus retrotransposons LINEs SINEs

Question 51

Topic 9, slide 156 ______ are produced during normal human embryogenesis

Answer 51

HERV-K mRNAs

Question 52

Topic 9, slide 158 How does a capsid allow entry into a cell?

Answer 52

Has a pore

Question 53

Topic 9, slide 159 _____ happens only in the core particle with partially assembled capsid

Answer 53

Reverse transcription

Question 54

Topic 9, slide 161 A Second template exchange is what kind of formation?

Answer 54

Hairpin

Question 55

Coronavirus RNA Synthesis, slide 165 What is the structure of the Coronavirus and what is it similar to?

Answer 55

Plus ( + ) strand RNA viruses with encapsidated genomic RNA in the form of the nucleocapsid also seen in retroviruses

Question 56

Coronavirus RNA Synthesis, slide 167 In the full length genome, what is manufactured first?

Answer 56

Two long polyproteins are translated by the ribosome by ribosomal frameshifting

Question 57

Coronavirus RNA Synthesis, slide 170 In differential synthesis, what would happen with... No slippery sequence & yes pseudoknot or No slippery sequence & no pseudoknot

Answer 57

No slippery sequence & yes pseudoknot – add viral genome and translation – small amount of transcription product No slippery sequence & no pseudoknot – add viral genome translation – virus dead

Question 58

Coronavirus RNA Synthesis, slide 173 What do NSP7 and NSP8 do? What is responsible for genome maintenance?

Answer 58

processivity factors and confer the stability of the RNA duplex Exonucleases and endonucleases

Question 59

Coronavirus RNA Synthesis, slide 178 Coronavirus produces two polyproteins – ______ Subgenomic mRNAs are of ____ lengths Only the _____ is translated

Answer 59

1a and 1ab variable first open reading frame

Question 60

Coronavirus RNA Synthesis, slide 180 _____ of template for initiation of RNA synthesis with the help of extensive RNA secondary structures such as stem-loops and long-distance RNA -RNA interactions

Answer 60

Circularization Like poliovirus!

Question 61

Coronavirus RNA Synthesis, slide 181 What does the cap do? What does it not do?

Answer 61

Cap confers stability to the genome/mRNA but NOT maintenance of large genomes