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Virology > Exam II - quizzes > Flashcards

Exam II - quizzes Flashcards

1
Q

Quiz 6

Which of the following group of viruses ALWAYS contain an encapsidated RNA in the form of nucleocapsid?

A) All of the RNA viruses have encapsidated RNA in the form of nucleocapsid

B) Double-stranded RNA viruses

C) Plus strand RNA viruses

D) Minus strand RNA viruses

A

D) Minus strand RNA viruses

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2
Q

Quiz 6

Which is a part of the Poliovirus replication strategy?

A) Circularization of template for initiation of RNA synthesis

B) De novo (without primer) initiation of RNA synthesis

C) The production of subgenomic mRNAs

D) All of the above

A

A) Circularization of template for initiation of RNA synthesis

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3
Q

Quiz 6

The mRNAs are synthesized by the Reovirus in which of the following structural state of the virus?

A) At the infectious sub viral particle (IVSP) stage after acid-dependent proteolytic cleavage

B) Double capsid virion stage of the virus after in the acidic endosome

C) When the core particle is released into the cytoplasm

D) After the genomic RNAs are released into the cytoplasm from the core

A

C) When the core particle is released into the cytoplasm

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4
Q

Quiz 6

Which of the following group of viruses pack RNA dependent RNA polymerase in the virus particle?

A) (C) minus strand RNA viruses

B) (B) plus strand RNA viruses

C) (A) double stranded RNA viruses

D) Both A and B are correct

E) Both A and C are correct

A

E) Both A and C are correct

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5
Q

Quiz 6

The catalytic site of the RNA dependent RNA polymerase is present in which of the domain?

A) The Knuckle

B) The Thumb

C) The Palm

D) The Finger

A

C) The Palm

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6
Q

Quiz 6

What strategy is used by the poliovirus to make many proteins from a single mRNA?

A) Alternative splicing

B) Proteolytic cleavage of a protein

C) Alternative translation stop

D) Alternative translation start

A

B) Proteolytic cleavage of a protein

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7
Q

Quiz 6

Which of the following group of viruses usually do NOT pack RNA dependent RNA polymerase in the virus particle?

A) Plus strand RNA virus

B) All of the above pack RNA dependent RNA polymerase in the virus

C) Double stranded RNA virus

D) Minus stranded RNA virus

A

A) Plus strand RNA virus

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8
Q

Quiz 6

Which of the following process acts as the primary “switch” from Vesicular Stomatitis Virus (VSV) mRNA synthesis to genome RNA synthesis?

A) Slippage of the RNA polymerase at the 5`end of the genome RNA

B) Encapsidation of the “leader RNA” by N protein and association of N protein with RNA polymerase which reads through the intergenic region

C) Production of a large amount of viral structural proteins in the cell helps the RNA dependent RNA polymerase to read through the intergenic region

D) Slippage of the RNA polymerase at the 3` end of the genome RNA

A

B) Encapsidation of the “leader RNA” by N protein and association of N protein with RNA polymerase which reads through the intergenic region

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9
Q

Quiz 6

How are the Influenza virus and VSV RNA synthesis similar?

A) Viral mRNAs are shorter than (-) genome RNA

B) The switch from mRNA to genome RNA synthesis is controlled by an RNA-binding protein

C) All of the above

D) Polyadenylation occurs at the short stretch of U residues

A

C) All of the above

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10
Q

Quiz 6

Which of the following type of metal ion coordinate the incoming nucleotide in a polymerization reaction catalyzed by polynucleotide polymerase class of enzymes like RNA or DNA polymerases?

A) Tetra-valent metal ion

B) Mono-valent metal ion

C) Di-valent metal ion

D) Tri-valent metal ion

A

C) Di-valent metal ion

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11
Q

Quiz 6

Which RNA polymerase mode of action “model” explains the VSV mRNA synthesis and attenuation at intergenic regions?

A) Moving template model

B) Stop-start model

C) Protein dependent priming model

D) Cap snatching model

A

B) Stop-start model

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12
Q

Quiz 6

Which of the following process form the 5` mRNA cap structure in the Influenza Virus?

A) The 5`cap is cleaved and snatched by the virus from host small nuclear (sn) RNAs

B) The RNA polymerase snatches a 5` binding protein cap to cap the mRNA and attach two uridine residues

C) The RNA polymerase catalyzes a 7-methyl guanosine formation followed by 5−5 triphosphate bridge formation to the second adenine base

D) The 5` cap is cleaved and snatched by the virus from host nuclear pre-mRNAs

A

D) The 5` cap is cleaved and snatched by the virus from host nuclear pre-mRNAs

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13
Q

Quiz 6

Which of the following method is used by the Influenza virus to synthesize its mRNAs?

A) Stop-start model

B) Moving template model

C) 3′co-priming and nested mRNA synthesis model

D) In-particle mRNA synthesis model

A

B) Moving template model

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14
Q

Quiz 6

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

A) VSV mRNA synthesis is carried out by viral RNA dependent RNA polymerase; in contrast, the Influenza virus steals/snatches the DNA dependent RNA polymerase from the nucleus of the host cell

B) VSV mRNAs are synthesized in the cytoplasm whereas the Influenza virus mRNAs are synthesized in the nucleus.

C) All of the other are major differences between Vesicular Stomatitis Virus (VSV) and Influenza Virus mRNA synthesis

D) VSV produce one genome length mRNA whereas Influenza Virus always subgenomic mRNAs from all of its individual segments

A

B) VSV mRNAs are synthesized in the cytoplasm whereas the Influenza virus mRNAs are synthesized in the nucleus.

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15
Q

Quiz 6

Actinomycin D was utilized in the experiments that lead to the discovery of the viral RNA polymerase. What was the principle of the experiment?

A) In the presence of dNTP and Actinomycin D; which inhibited cellular DNA dependent RNA polymerase; RNA synthesis occurred in the virally infected cell extract.

B) In the presence of dNTP and Actinomycin D; which inhibited cellular DNA dependent RNA polymerase; RNA synthesis occurred in the virally infected cell extract.

C) In the presence of NTP and Actinomycin D; which inhibited cellular RNA dependent RNA polymerase; RNA synthesis occurred in the virally infected cell extract.

D) In the presence of NTP and Actinomycin D; which inhibited cellular DNA dependent RNA polymerase; RNA synthesis occurred in the virally infected cell extract.

A

D) In the presence of NTP and Actinomycin D; which inhibited cellular DNA dependent RNA polymerase; RNA synthesis occurred in the virally infected cell extract.

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16
Q

Quiz 6

Which of the following enzyme/s has/have conserved GDD (or significantly close) amino acid motifs at their catalytic site?

A) RNA dependent RNA polymerase

B) All of the above enzymes have conserved GDD (or significantly close) amino acid motifs

C) DNA dependent DNA polymerase

D) DNA dependent RNA polymerase

E) RNA dependent DNA polymerase

A

B) All of the above enzymes have conserved GDD (or significantly close) amino acid motifs

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17
Q

Quiz 6

Which of the following acts as a primer for the initiation of poliovirus mRNA synthesis?

A) The 3` pseudoknot

B) The VPG protein and covalently bonded two uridine residues

C) The CRE element and covalently bonded two uridine residues

D) The VPG protein

A

B) The VPg protein and covalently bonded two uridine residues

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18
Q

Quiz 6

Coronavirus and Retrovirus are two unique viruses among the plus-strand RNA viruses. Which of the following feature make them unique?

A) They are the only enveloped viruses among plus-strand RNA viruses

B) Both of them carry reverse transcriptase

C) Both A and B are correct

D) They are the only plus-strand RNA viruses with encapsidated genomic RNA in the form of the nucleocapsid

A

D) They are the only plus-strand RNA viruses with encapsidated genomic RNA in the form of the nucleocapsid

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19
Q

Quiz 6

Which of the following strategy is observed in the Coronavirus reproductive events?

A) mRNAs are synthesized on (−) sense templates that use a 3′co-priming followed by a variable-length nested RNA synthesis and addition of the 5′leader sequence

B) All of the other events are observed in the Coronavirus reproductive cycle

C) Two long polyproteins are translated by the ribosome by ribosomal frame shifting

D) The genomic RNA is synthesized on a (−) sense template where the viral RdRp do not jump from any of the translational regulatory sequences (TRS) making the long (+) sense genomic RNA without any loss of nucleotides

E) Only the first open reading frame (ORF) is translated into the corresponding proteins in all subgenomic mRNAs of the Coronavirus

A

B) All of the other events are observed in the Coronavirus reproductive cycle

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20
Q

Quiz 6

Which of the following process describes the polyadenylation of mRNAs in Vesicular Stomatitis Virus (VSV)?

A) Snatching of poly(A) tails from cellular mRNAs

B) All of the above processes can polyadenylate VSV mRNAs

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

D) Addition of poly(A) with the help of Poly(A) binding protein, PABP

A

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

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21
Q

Quiz 6

Which of the following is NOT true about viral mRNAs?

A) All of the above are true about the viral mRNAs

B) Viral mRNAs could be genome length or shorter sub-genomic length

C) Viral mRNAs may be attached with a protein at its 5` end; instead of a cap

D) Uncapped viral mRNAs can’t be translated into protein by the ribosomes

A

D) Uncapped viral mRNAs can’t be translated into protein by the ribosomes

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22
Q

Quiz 6

Which of the following attributes to the specificity of RNA polymerases towards NTPs over dNTPs?

A) The 2` hydrogen of the ribose sugar

B) The 2` hydroxyl of the ribose sugar

C) The 2` hydroxyl of the deoxy-ribose sugar

D) The UTP

A

B) The 2` hydroxyl of the ribose sugar

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23
Q

Quiz 6

Which is a universal rule about RNA directed RNA synthesis?

A) RNA is synthesized in a 3’-5’ direction

B) RdRp may initiate de novo or require a primer

C) RNA synthesis is always template-directed

D) RNA synthesis initiates randomly on the RNA template

A

B) RdRp may initiate de novo or require a primer

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24
Q

Quiz 6

Which of the following is unique in Reovirus RNA dependent RNA synthesis?

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

D) All of the above are unique in Reovirus RNA dependent RNA synthesis

A

D) All of the above are unique in Reovirus RNA dependent RNA synthesis

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25
Q

Quiz 6

Which of the following group of viruses usually pack RNA dependent RNA polymerase in the virus particle?

A) Both A and B are correct

B) Both A and C are correct

C) (B) Plus strand RNA viruses

D) (C) Minus strand RNA viruses

E) (A) Double stranded RNA viruses

A

B) Both A and C are correct

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26
Q

Quiz 6

Which of the following group of viruses usually pack RNA dependent RNA polymerase in the virus particle?

A) Both A and B are correct

B) Both A and C are correct

C) (B) Plus strand RNA viruses

D) (C) Minus strand RNA viruses

E) (A) Double stranded RNA viruses

A

B) Both A and C are correct

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27
Q

Quiz 7

How many mRNA start sites may be present in an “initiator sequence” among DNA viruses?

A) 1 or multiple
B) Always one
C) 1 or 3
D) Always 3

A

A) 1 or multiple

“ In cells infected with DNA viruses, at least one protein, often many, are needed for DNA replication “

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28
Q

Quiz 7

Adenovirus E1A protein stimulating the expression of adenovirus E2 protein which then stimulates the expression of adenovirus IVa2 & L4 protein is an example of:

A) Dimerization
B) Cascade regulation
C) A negative auto regulatory loop
D) Repression of gene expression

A

B) Cascade regulation

Definition: “ Ensures that different classes of viral proteins are made during different periods of the infectious cycle “

Think of a cascading waterfall

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29
Q

Quiz 7

Which of the following reactions take place at the splicing site of a pre-mRNA?

A) Methylation
B) Cis-esterification
C) Trans-esterification
D) Acetylation

A

C) Trans-esterification

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30
Q

Quiz 7

Which statement about polyadenylation of DNA virus mRNAs is correct?

A) It is specified by a stretch of U residues in the template

B) It always occurs in the cytoplasm

C) It occurs after the cleavage of pre-mRNA

D) Poly(A) is added at the 5’ end of pre-mRNA

A

C) It occurs after the cleavage of pre-mRNA

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31
Q

Quiz 7

How is the “immediate early” transcriptional regulation of Herpesvirus is different from the Adenovirus?

A) Herpesvirus uses a cascade regulation unlike Adenoviral autoregulation

B) Herpesvirus packs its RNA polymerase but Adenovirus do not

C) The Herpesvirus “immediate early” transcription factor VP16 have cellular origin whereas adenovirus packs the “immediate early” E1A transcription factor in the virion

D) The “immediate early” transcription factor VP16 is packaged into the Herpesvirus virion but Adenovirus use cellular transcription factors for its “immediate early” transcription

A

D) The “immediate early” transcription factor VP16 is packaged into the Herpesvirus virion but Adenovirus use cellular transcription factors for its “immediate early” transcription

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32
Q

Quiz 7

DNA viruses require DNA binding proteins for transcriptional control. Which of the following may be the source of these DNA binding proteins?

A) Both virus and/or the host cell

B) Only the host cell

C) Only the virus

D) None of the choices are correct

A

A) Both virus and/or the host cell

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33
Q

Quiz 7

Which of the following is the signature structure of a DNA binding domain of a transcriptional activator protein?

A) Cloverleaf structure

B) Zinc finger

C) Dimerization domain

D) Leucine zipper

A

B) Zinc finger

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34
Q

Quiz 7

Which of the following proteins binds to the TATA sequence and regulate transcription?

A) TFIID

B) TFIIA

C) TFIIC

D) TFIIB

A

A) TFIID

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35
Q

Quiz 7

What is the first biosynthetic event that occurs in cells infected with dsDNA Viruses?

A) Membrane fusion

B) Transcription

B) Protein synthesis

D) DNA replication

A

B) Transcription

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36
Q

Quiz 7

The transcription of MOST but not all DNA viruses are carried out by which enzyme?

A) DNA pol III

B) DNA pol I

C) RNA pol II

D) RNA pol III

A

C) RNA pol II

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37
Q

Quiz 7

Which of the following process occurs, immediately after the release of a viral gapped DNA or viral plus-strand DNA?

A) Replication into double stranded RNA template for transcription

B) Replication into double stranded genomic DNA

C) Repairment of double stranded DNA template for transcription

D) Transcription into mRNA

A

C) Repairment of double stranded DNA template for transcription

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38
Q

Quiz 7

Spliceosomes - which of the following is found in a spliceosome?

A) Micro RNAs ( mi-RNA )

B) Silencing RNAs (siRNA)

C) Small nuclear RNAs (snRNA)

D) Ribosomal RNAs

A

C) Small nuclear RNAs (snRNA)

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39
Q

Quiz 7

Which of the following statement is true about Adenoviral transcriptional regulation?

A) E2 produced in early phase enhance DNA replication

B) E1A produced in the immediate-early phase enhance early phase gene transcription

C) All of the other choices are true

D) DNA replication exhibit anti-repression by relief of promoter occlusion

A

C) All of the other choices are true

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40
Q

Quiz 7

Which of the following phases of transcriptional regulation is observed in Adenovirus?

A) Early and Late

B) Immediate Early, Early, and Late

C) Early, Late and Very late

D) Early, Middle and Late

A

B) Immediate Early, Early, and Late

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41
Q

Quiz 7

Which of the following region is the actual start site for mRNA transcription?

A) Repressor sequence

B) Enhancer sequence

C) Initiator sequence

D) TATA sequence

A

C) Initiator sequence

42
Q

Quiz 7

Which of the following mode of repression is seen in the late phase genes of Simian Virus 40 (SV40)?

A) Initiation complex binding to an initiator sequence

B) RNA pol II binding to an initiator sequence

C) TFIID binding to TATA sequence

D) Initiator Binding Protein (IBP) binding to an initiator sequence

A

D) Initiator Binding Protein (IBP) binding to an initiator sequence

43
Q

Quiz 7

Which of the following is true about the splicing of viral Pre-mRNAs?

A) Splicing is necessary for the binding and activation of the nuclear export proteins for most viral mRNA export into the cytoplasm from the nucleus

B) Some retroviral RNA is exported “unspliced” out of the nucleus facilitated by special nuclear export binding proteins

C) All of the above are true about viral mRNA splicing

D) Alternative splicing can produce multiple proteins from the same Pre-mRNA

A

C) All of the above are true about viral mRNA splicing

44
Q

Quiz 7

Which of the following protein is produced in Simian Virus 40 (SV40) in the early phase of transcription and regulate DNA replication and expression of late genes?

A) E1A

B) E2

C) Large T antigen (LT)

D) Small T antigen (ST)

A

C) Large T antigen (LT)

45
Q

Quiz 7

Which of the following sequences is the part of the “core promoter” sequence for RNA polymerase II?

A) Trans-acting local regulatory sequences

B) Cis-acting local regulatory sequences

C) All of the choices constitute the “core promoter”

D) TATA sequence

A

D) TATA sequence

46
Q

Quiz 7

Which of the following process explains Adenoviral anti-repression of transcription by abrogation of Rb (Retinoblastoma protein)?

A) E1A binds to Rb and prevents Rb (Retinoblastoma protein) to be associated with E2F and Dp-1. In absence of Rb, no Hdacs (histone deacetylases) are recruited making the DNA loose and accessible around the nucleosome, and transcription complex can be formed and proceed.

B) E2f binds to Rb and prevents Rb Retinoblastoma protein) to be associated with E1A and Dp-1. In absence of Rb, no Hdacs (histone deacetylases) are recruited making the DNA loose and accessible around the nucleosome, and transcription complex can be formed and proceed.

C) E2f binds to Rb and prevents Rb (Retinoblastoma protein) to be associated with E2F and Dp-1. In absence of Rb, no Hdacs (histone deacetylases) are recruited making the DNA loose and accessible around the nucleosome, and transcription complex can be formed and proceed.

D) E1A binds to Rb and prevents Rb Retinoblastoma protein) to be associated with E2F and Dp-1. In absence of Rb, no Hdacs (histone deacetylases) are recruited making the DNA tightly wrapped around the nucleosome, and transcription complex can be formed and proceed.

A

A) E1A binds to Rb and prevents Rb Retinoblastoma protein) to be associated with E2F and Dp-1. In absence of Rb, no Hdacs (histone deacetylases) are recruited making the DNA loose and accessible around the nucleosome, and transcription complex can be formed and proceed.

47
Q

Quiz 7

Poxviruses and giant viruses never have to deliver their DNA into the nucleus. Which of the following would justify such a phenomenon?

A) Pox and giant viruses have all the transcription machinery packaged within the virion

B) Pox and giant viruses have all the mRNAs packaged within the virion

C) Pox and giant viruses have all the translational machinery packaged within the virion

D) Pox and giant viruses have all the DNA replication machinery packaged within the virion

A

A) Pox and giant viruses have all the transcription machinery packaged within the virion

48
Q

Quiz 7

Which of the following process may be responsible for the regulation of viral transcription through nucleosomal templates?

A) Histone de-acetylation

B) Histone methylation

C) Histone acetylation

D) All of the choices are correct

A

D) All of the choices are correct

49
Q

Quiz 7

Which of the following is unique of a 5′ cap structure of an mRNA?

A) Usually, the first capping base is adenine

B) None of the choices is correct

C) The 2nd base of cap 2 is always guanine, and the base is methylated at the 7th carbon (m7)

D) The first base adenine of cap 1 is bonded to the first base of cap 2 guanine by a 5’-5’ phosphate linkage

A

B) None of the choices is correct
__________________________
A) Usually, the first capping base is adenine
It is U ( uridine )

B) None of the choices are correct

C) The 2nd base of cap 2 is always guanine, and the base is methylated at the 7th carbon (m7)
This is true for cap 1

D) The first base adenine of cap 1 is bonded to the first base of cap 2 guanine by a 5’-5’ phosphate linkage
Triphosphate linkage

50
Q

Quiz 7

Which of the following is NOT true about mRNA polyadenylation of DNA viruses?

A) PolyA polymerase slips on a few U residues to incorporate about 200 A residues at the 3’ end of the RNA

B) The pre-mRNAs are cleaved at the prospective polyadenylation site for polyadenylation

C) The polyadenylation occurs in the nucleus before export into the cytoplasm

D) PolyA polymerase is the enzyme responsible for the polyadenylation of the mRNAs

A

A) PolyA polymerase slips on a few U residues to incorporate about 200 A residues at the 3’ end of the RNA

51
Q

Quiz 7

Which mode of transcriptional regulation is displayed; when transcription and translation of gene X results in the formation of protein X and protein X turn on the transcription of gene Y.

A) Cascade regulation

B) Positive feedback

C) Positive regulatory loops

D) Negative regulatory loop

A

A) Cascade regulation

52
Q

Quiz 8

Which of the following protein is NOT involved in viral DNA replication?

A) Exonucleases

B) Topoisomerases

C) All of the mentioned proteins are involved in viral DNA replication

D) DNA dependent DNA polymerases

E) Helicases

A

C) All of the mentioned proteins are involved in viral DNA replication

53
Q

Quiz 8

What makes poxvirus DNA replication different from all of the other viruses?

A) DNA synthesis occurs in the nucleus

B) DNA synthesis occurs by strand displacement

C) The complete replication machinery is encoded by the viral genome

D) None of the above

A

D) None of the above

__________________
Answer: Poxviruses replicate in the cytoplasm, all other viruses replicate in the nucleus

54
Q

Quiz 8

Which of the following features is NOT observed in DNA dependent DNA polymerases?

A) Have conserved GDD or close amino acid motifs at the catalytic site

B) Di-valent metal ions coordinate the incoming nucleotide to catalyze the reaction

C) The thumb domain acts as the catalytic site

D) They contain the thumb, palm and the finger domain

A

C) The thumb domain acts as the catalytic site

55
Q

Quiz 8

Which of the following is incorrect about the poxvirus DNA genome and its replication?

A) The ends of the poxvirus DNA contain inverted terminal repeats (ITRs)

B) Poxvirus DNA is a double stranded DNA with covalently joined ends

C) All the viral replication proteins are synthesized by the virus

D) Viral replication occurs in the cytoplasm of the cell

A

C) All the viral replication proteins are synthesized by the virus

56
Q

Quiz 8

Which of the following is NOT a viral origin binding protein?

A) Herpesvirus proliferative cell nuclear antigen (Pcna) protein

B) Parvovirus Rep 78/68 protein

C) Polyomavirus (SV40) Large T (LT) antigen protein

D) Adenovirus pre-terminal protein (pTP)

A

A) Herpesvirus proliferative cell nuclear antigen (Pcna) protein

57
Q

Quiz 8

Which of the following protein/protein-complex is NOT associated with priming of DNA synthesis?

A) Parvovirus: Rep78/68 protein

B) SV40: DNA pol α - primase complex

C) Herpesvirus: UL5, 8 and 53-primase

D) Adenovirus: pre-terminal protein (pTP)

A

A) Parvovirus: Rep78/68 protein

Is a recognition protein that binds at ends and unwinds DNA, also involved in terminal resolution

58
Q

Quiz 8

Which of the following is incorrect about Parvovirus DNA synthesis?

A) DNA replication requires DNA pol δ, Rf-C and PCNA

B) Replication is continuous

C) DNA synthesis is by strand displacement

D) Rep78/68 proteins are required for RNA primer synthesis, initiation, and resolution

A

D) Rep78/68 proteins are required for RNA primer synthesis, initiation, and resolution

59
Q

Quiz 8

Which of the following is NOT a mechanism of viral DNA synthesis?

A) All the mentioned processes are mechanisms of viral DNA synthesis

B) Rolling circle DNA synthesis

C) Replication fork formation at the origin of replication for DNA synthesis

D) Strand displacement DNA synthesis

A

A) All the mentioned processes are mechanisms of viral DNA synthesis

60
Q

Quiz 8

Which statement about viral DNA synthesis is NOT correct?

A) Small DNA viruses encode at least one protein involved in DNA synthesis

B) Large DNA viruses encode many proteins involved in DNA synthesis

C) Some viruses encode all proteins needed for DNA replication

D) Viral DNA replication is always delayed after infection because it requires the synthesis of at least one viral protein

A

C) Some viruses encode all proteins needed for DNA replication

61
Q

Quiz 8

Which statement about viral DNA synthesis is correct?

A) Viral DNA replication begins as soon as the genomic DNA is delivered into the nucleus

B) Some viruses encode all proteins needed for DNA replication

C) Small DNA viruses do not encode any protein involved in DNA synthesis

D) Large DNA viruses encode many proteins involved in DNA synthesis

A

D) Large DNA viruses encode many proteins involved in DNA synthesis

62
Q

Quiz 8

The SV40 genome is a circular dsDNA. Which statement about its replication is correct?

A) Has leading and lagging strand synthesis

B) Replication is bidirectional from a single ori

C) Viral Large T (LT) antigen protein binds and unwinds the ori

D) All of the above

A

D) All of the above

63
Q

Quiz 8

How is DNA replication of Parvovirus and Adenovirus similar?

A) None of the above

B) They both require protein-linked primers

C) Replication occurs by strand displacement

D) A replication fork forms at the origin of replication

A

C) Replication occurs by strand displacement

64
Q

Quiz 8

Which of the following protein complex is required for the synthesis of RNA primer during SV40 DNA replication?

A) DNA polymerase α and the primase complex

B) DNA polymerase δ and the primase complex

C) DNA pol I and the primase complex

D) DNA polymerase ε and the primase complex

A

A) DNA polymerase α and the primase complex

65
Q

Quiz 8

During SV40 DNA replication, the supercoiling of the dsDNA is inevitable. Which of the following statement correctly illustrates the different mechanisms of supercoiling removal during replication and after replication (terminal resolution)?

A) During replication single strand nicks are responsible for supercoil relaxation whereas double strand nicks are responsible for supercoil relaxation (terminal resolution) at the end of DNA replication

B) During replication both single and double strand nicks are responsible for supercoil relaxation whereas only double strand nicks are responsible for supercoil relaxation (terminal resolution) at the end of DNA replication

C) During replication Topoisomerase II and after replication Topoisomerase I and II both carry out relaxation of the supercoils

D) During replication Topoisomerase I and after replication Topoisomerase II carry out relaxation of the supercoils

A

A) During replication single strand nicks are responsible for supercoil relaxation whereas double strand nicks are responsible for supercoil relaxation (terminal resolution) at the end of DNA replication

66
Q

Quiz 8

Which of the following is incorrect regarding Adenovirus DNA replication?

A) The DNA is replicated by strand displacement

B) A pre-terminal protein (pTP) binds to DNA pol and the α phosphoryl group of a dGMP is bonded with a serine residue of the pTP; which acts as the primer for the DNA synthesis by bonding with the first dCMP on the template strand

C) The displaced strand during DNA synthesis is coated with a DNA binding protein and circularized where the inverted terminal repeats (ITRs) base pair and a new strand synthesis can initiate with the help of pre-terminal protein (pTP) using the 3` end as the template

D) DNA synthesis by strand displacement and DNA binding protein (DBP) coated displaced strand DNA synthesis both simultaneously participate in Adenovirus DNA replication

A

B) A pre-terminal protein (pTP) binds to DNA pol and the α phosphoryl group of a dGMP is bonded with a serine residue of the pTP; which acts as the primer for the DNA synthesis by bonding with the first dCMP on the template strand

Correction: Adenovirus DNA pol links α-phosphoryl of dCMP to OH of Ser residue only when pTP is assembled with DNA pol into preinitiation complex at Ori

67
Q

Quiz 8

Which of the following feature is NOT observed in SV40 Large T (LT) antigen protein?

A) Contain an ATPase domain

B) Contains DNA Pol α-Primase domain which synthesizes RNA primers

C) Contain replication origin binding domain

D) Contain a helicase domain which unwinds DNA in association with other proteins

A

B) Contains DNA Pol α-Primase domain which synthesizes RNA primers

68
Q

Quiz 8

Which of the following protein is involved in viral DNA replication?

A) Ribonucleotide reductase

B) Thymidine kinase

C) dUTPase

D) All of the above are involved in viral DNA replication

A

D) All of the above are involved in viral DNA replication

69
Q

Quiz 8

Which of the following is NOT a universal rule of viral DNA replication?

A) DNA synthesis may be primer dependent or independent

B) The DNA synthesis is always template directed

C) The dNTPs are incorporated at the 3′-OH of the DNA chain

D) Replication can initiate at random sites on templates called origin of replication

A

D) Replication can initiate at random sites on templates called origin of replication

70
Q

Quiz 8

Which of the following is NOT a characteristic associated with cellular retinoblastoma (Rb) protein?

A) Rb protein prevents the cells to enter into the S phase of the cell cycle

B) Loss of Rb protein is associated with childhood ocular malignant tumors

C) Rb protein is an oncogene

D) Rb protein is a tumor suppressor gene

A

C) Rb protein is an oncogene

71
Q

Quiz 8

Which of the following non-retro-viral DNA replication does not require an RNA primer?

A) Strand displacement DNA synthesis

B) Replication fork based DNA synthesis from a single origin

C) Replication fork based DNA synthesis from a multiple origins

D) Rolling circle DNA synthesis

A

A) Strand displacement DNA synthesis

72
Q

Quiz 8

Which of the following process is involved in the regulation of viral DNA synthesis?

A) Viruses must recruit host replication proteins to preferentially synthesize viral DNA

B) Host replication proteins are induced by early viral gene products

C) All of the mentioned processes are involved in the regulation of viral DNA synthesis

D) Virally encoded early gene products often induce quiescent cells to enter the cell cycle again into the synthesis (S) phase

A

C) All of the mentioned processes are involved in the regulation of viral DNA synthesis

73
Q

Quiz 8

What is the function of the cellular DNA ligase IV/XRCC4 in Herpesvirus DNA replication?

A) DNA ligase IV/XRCC4 is responsible sealing the gaps of the replicated DNA

B) DNA ligase IV/XRCC4 is responsible for end to end DNA ligation to form concatemers during rolling circle DNA synthesis

C) DNA ligase IV/XRCC4 is responsible for circularization of the viral DNA

D) DNA ligase IV/XRCC4 is responsible for the terminal resolution ligation of the separated DNA strands

A

C) DNA ligase IV/XRCC4 is responsible for circularization of the viral DNA

74
Q

Quiz 8

Which of the following is the correct function of the replication factor protein Rf-C?

A) All of the mentioned functions of Rf-C are correct

B) Rf-C release DNA pol α-primase complex

C) Rf-C acts as a clamp loading protein to allow clamping of Pcna onto the DNA

D) Rf-C binds to 3’-OH of the DNA, Pcna and DNA pol δ

A

A) All of the mentioned functions of Rf-C are correct

75
Q

Quiz 8

Which of the following mechanism explains the abrogation of cellular Rb protein by viral proteins?

A) Viral protein like E1A competitively binds to Rb protein which removes Rb protein bound to transcription factor E2f and Dp and Rb protein-free E2f and Dp induce transcription

B) Viral proteins like E1A competitively binds to Rb protein; which in turn binds to transcription factor E2F and Dp to form E1A, Rb, E2F, Dp complex which induces transcription

C) Viral protein like E1A binds to Rb and recruit histone deacetylases which lead to transcriptional activation

D) Viral protein like E1A binds to Rb protein and induce phosphorylation which dissociates Rb from E2f and Dp protein leading to transcriptional activation

A

A) Viral protein like E1A competitively binds to Rb protein which removes Rb protein bound to transcription factor E2f and Dp and Rb protein-free E2f and Dp induce transcription

76
Q

Quiz 8

Which of the following is NOT a function of the Large T (LT) antigen protein in SV40 DNA replication?

A) LT protein shows intrinsic 3’ to 5′ helicase activity and unwinds the SV40 DNA in an ATP dependent manner and Rp-A binds onto the separated single strands and Topoisomerases keep the unwound DNA relaxed

B) Two LT protein hexamers bind on the opposite end of the SV40 origin of replication

C) In presence of ATP, LT forms hexamer and binds to the SV40 origin of replication, and undergo conformational changes to denature the DNA strands

D) LT protein in association with DNA Pol𝛼 unwinds SV40 DNA in a 5′ to 3′ direction in an ATP dependent manner and Rp-A binds onto the separated single strands and Topoisomerases keep the unwound DNA relaxed

A

D) LT protein in association with DNA Pol𝛼 unwinds SV40 DNA in a 5′ to 3′ direction in an ATP dependent manner and Rp-A binds onto the separated single strands and Topoisomerases keep the unwound DNA relaxed

77
Q

Quiz 9

Which of the following steps occur during reverse transcription of retroviral genomic RNA?

A) Priming of (−) DNA synthesis by tRNA

B) All of the mentioned events occur during reverse transcription

C) Two template exchanges

D) Degradation of the viral RNA by RNase H

E) Generation of two LTRs

A

B) All of the mentioned events occur during reverse transcription

78
Q

Quiz 9

The HIV-1 reverse transcriptase contains p66 protein and p51 proteins and each contain the thumb, palm and finger domain. Which is the most logical way to describe the enzyme?

A) It is homodimeric protein

B) It is heterotrimeric protein

C) It is homotrimeric protein

D) It is heterodimeric protein

A

D) It is heterodimeric protein

79
Q

Quiz 9

Which of the following is NOT correct about the first strand DNA synthesis (the minus strand) in a typical retroviral (e.g. Avian Leukosis Virus: ALV) during reverse transcription?

A) RNaseH degrades the RNA template from the RNA-DNA duplex concurrently with the DNA synthesis

B) The initiation site is close but not exactly at the 3` end of the retroviral genome

C) The initial segment of the DNA is synthesized as “strong stop” DNA

D) All of the above/other are correct about the first strand DNA synthesis during reverse transcription

E) tRNA bound to pbs acts as the primer for DNA synthesis

A

B) The initiation site is close but not exactly at the 3` end of the retroviral genome

80
Q

Quiz 9

Which signature structure of the tRNA is used as a reverse transcription primer, binding to pbs (primer binding site) in a typical (e.g. Avian Leukosis Virus: ALV) retroviral genome?

A) The D loop and arm

B) The acceptor arm

C) The ΤψC loop and arm

D) The anticodon loop and arm

A

C) The ΤψC loop and arm

81
Q

Quiz 9

Which of the following statement is NOT correct about reverse transcriptase (RT)?

A) Every virus that codes reverse transcriptase must have integrase to integrate the reverse transcribed DNA into host DNA

B) RT was present in our common ancestor before the evolution and separation of the of Prokaryotes, Archaea and Eukaryotes

C) RT might be the bridge between the RNA and the DNA world

D) Prokaryotes, Archaea and Eukaryotes all have RT

A

A) Every virus that codes reverse transcriptase must have integrase to integrate the reverse transcribed DNA into host DNA

82
Q

Quiz 9

“Endogenization” is a term used to define which of the following statement?

A) Excision of the proviral DNA from the host germ cell DNA and passage onto the autosomes

B) Integration of the proviral DNA into the host chromosomes

C) Movement and reintegration of proviral and retrotransposons in host by reverse transcriptase

D) Integration of the proviral DNA in host germline and passage onto the next progeny

A

D) Integration of the proviral DNA in host germline and passage onto the next progeny

83
Q

Quiz 9

How many di-valent metal ion binding sites are present in reverse transcriptase holoenzyme?

A) 4

B) 2

C) 1

D) 3

A

A) 4

84
Q

Quiz 9

Reverse transcriptase is an enzyme with low fidelity and low processivity. Which of the following statement best suites the above definition?

A) The enzyme often incorporates wrong nucleotides as its synthesis rate is very fast

B) The enzyme is always capable of incorporating correct nucleotides at a very high rate of synthesis for a productive viral infection

C) The enzyme often incorporates wrong nucleotides and its synthesis rate is slow as well

D) The enzyme incorporates always correct nucleotides but in doing so the synthesis rate is also slow

A

C) The enzyme often incorporates wrong nucleotides and its synthesis rate is slow as well

85
Q

Quiz 9

Which of the following is NOT true about the second strand (+) strand DNA synthesis of a typical retroviral (e.g. Avian Leukosis Virus: ALV) reverse transcription?

A) The first template exchange synthesize the second DNA strand

B) A polypurine tract (ppp) from RNaseH terminal digestion product serves as the primer for the second strand synthesis

C) All of the other statements are true about the second strand (+ strand) DNA synthesis of a typical retroviral (e.g. Avian Leukosis Virus: ALV) reverse transcription

D) The second strand synthesis stops temporarily at the modified base of the tRNA attached to the first strand before template exchange

A

A) The first template exchange synthesize the second DNA strand

86
Q

Quiz 9

Which of the following might be the most probable cause of resistance of retroviruses against UV and ionizing radiation?

A) In between two RNA copies of the diploid genome is likely to build an error free functional genome; even if one of the gene is mutated due to UV and ionizing radiation

B) Reverse transcription is error prone and likely repair the mutation caused by UV and ionizing radiation; a mechanism not seen in any other viruses

C) Retroviruses use cellular RNA pol II to make mRNAs and proteins from the integrated provirus; which is resistant to UV and ionizing radiation

D) As the provirus is integrated in the host genome UV and ionizing radiation does not have any effect on the retroviruses

A

A) In between two RNA copies of the diploid genome is likely to build an error free functional genome; even if one of the gene is mutated due to UV and ionizing radiation

87
Q

Quiz 9

Which of the following is NOT true about the Long Terminal Repeat (LTR) in a retrovirus; such as HIV-1?

A) The LTRs have signature U3, R and U5 regions flanked by pbs (primer binding site) and ppt (poly purine tract)

B) The LTRs are found on both the 5’ and 3’ end of the diploid retroviral genome (+) RNA genome

C) The LTRs are essential for integration into the host genome

D) The LTRs have strong promoters

A

B) The LTRs are found on both the 5 and 3 end of the diploid retroviral genome (+) RNA genome

88
Q

Quiz 9

Which of the following statement about reverse transcriptase (RT) is NOT correct?

A) RT is unique to retroviruses

B) Might have bridged the ancient RNA world and the DNA world

C) The reverse transcriptase holoenzyme also has RNase H activity

D) The name of the enzyme comes from its ability to reverse the flow of genetic information

E) RT is packaged in the retrovirus particle

A

A) RT is unique to retroviruses

89
Q

Quiz 9

Which of the following statement is true about retroviral transformation?

A) All of the other statements are true about retroviral transformation.

B) The retroviruses cause permanent changes in cells

C) Retroviral DNA is integrated into host genome

D) The integrated retoviral genome is called a “provirus”

E) Become permanent part of the host DNA

A

A) All of the other statements are true about retroviral transformation.

90
Q

Quiz 9

Which of the following is NOT true about retroviral DNA integration into the host genome?

A) Integrase removes two nucleotides from the 5` ends of each retroviral DNA strands

B) All of the above/other are true about the retroviral DNA integration

C) Integrase makes a staggered nick (a single strand break slightly apart) on each strand of the host DNA

D) Integrase is a tetramer

E) It is catalyzed by enzyme integrase

A

A) Integrase removes two nucleotides from the 5` ends of each retroviral DNA strands

91
Q

Quiz 9

The reverse transcriptase enzyme is coded by which region of a typical (e.g. Avian Leukosis Virus; ALV) retroviral genome?

A) LTR

B) env

C) pol

D) gag

A

C) pol

92
Q

Quiz 9

Which of the following statements about retroelements is NOT correct?

A) None of the above/other

B) Retroelements in the human genome sometimes may be fully transcribed to produce infectious viruses

C) They can be beneficial

D) There are many retroelement copies in eukaryotic genomes

E) They are currently entering the Koala germline in south-eastern Australia

A

B) Retroelements in the human genome sometimes may be fully transcribed to produce infectious viruses

93
Q

Quiz 9

Which of the following is true about Hepadnavirus?

A) The viral reverse transcriptase is attached to the 5′ end of the (+) strand and immediately reverse transcribe the genome upon entry into the cytoplasm

B) The 5` end of the (-) strand DNA is attached to an RNA primer for reverse transcription

C) All of the other statements are true about Hepadnavirus

D) Reverse transcription happens only in the core particle with partially assembled capsid

E) They contain circular DNA as their genome where one strand is complete, circular and covalently closed and the other strand is only about 2/3 complete

A

D) Reverse transcription happens only in the core particle with partially assembled capsid

94
Q

Quiz 9

Which of the following is NOT true about retrotransposons with the fully functional native RT coded by the pol open reading frame?

A) They contain retroviral gag pol sequences and code reverse transcriptase

B) They can be present as LINEs (Long Interspersed Nuclear Elements) or SINEs (Short Interspersed Nuclear Elements)

C) They are likely progenitor of retroviruses

D) They can be mobile elements of the genome

E) All of the other statements are true about retrotransposons

A

B) They can be present as LINEs (Long Interspersed Nuclear Elements) or SINEs (Short Interspersed Nuclear Elements)

95
Q

Quiz 9

Which of the following is the most logical explanation behind the naming “reverse transcriptase”

A) All of the other statements are correct logics behind the naming

B) Because of the enzyme’s ability to reverse the flow of the genetic information

C) Because of the enzyme’s ability to reverse the process of translation followed by transcription

D) Because of the enzyme’s ability to synthesize the RNA from the DNA in a reverse order using 5′ end of the RNA as the initiation site

A

B) Because of the enzyme’s ability to reverse the flow of the genetic information

96
Q

Quiz 9

Which of the following define the most logical function of reverse transcriptase in most cases (ignoring the few exceptions)?

A) It is an RNA dependent DNA polymerase

B) It is an RNA dependent RNA polymerase

C) It is a DNA dependent DNA polymerase

D) It is a DNA dependent RNA polymerase

A

A) It is an RNA dependent DNA polymerase

97
Q

Quiz 9

Which of the following statement is NOT correct about a typical (e.g. Avian Leukosis Virus: ALV) retrovirus?

A) All of the other statements are correct about the typical (e.g. Avian Leukosis Virus: ALV) retrovirus

B) Protease processing/cleaving of the Gag precursor protein forms several viral proteins

C) The unspliced env pre-mRNA codes SU (surface) and TM (transmembrane) proteins

D) The pol region of the retroviral genome code for reverse transcriptase and integrase

E) The one strand of genomic RNA, Gag-pol-env mRNA and the unspliced pre-mRNA are all the same

A

C) The unspliced env pre-mRNA codes SU (surface) and TM (transmembrane) proteins

98
Q

Quiz 9

The SU (surface protein) and TM (transmembrane protein) are coded by which region of a typical (ex. Avian Leukosis Virus: ALV) retroviral genome?

A) Gag

B) Env

C) Pol

D) LTR

A

B) Env

99
Q

Quiz 9

Which of the following statement is NOT true about the regulation of retroviral DNA integration?

A) Preferential integration towards DNA sequences that are wrapped around nucleosomes

B) Integrase function is regulated by host as well as the viral Capsid (CA) protein

C) All of the above/other are true about retroviral DNA integration

D) The BAF protein prevents auto-integration of the retroviral DNA

E) Integrase bound to chromatinized retroviral RNA interacts with Capsid (CA) and LEDGF protein along with associated CPSF6 and RNA pol II and integrates in a region close to a transcriptionally active region

A

C) All of the above/other are true about retroviral DNA integration

100
Q

Quiz 9

Which of the following process facilitates the second template exchange of hepadnavirus reverse transcription?

A) Conformational change of TP (terminal protein) and reverse transcriptase exchange the template from 5′ end to 3′end of the pre-genomic RNA

B) RNase H digestion of the 3′ dr1 sequence and downstream secondary structure facilitates template switching in the pre-genomic RNA

C) A hairpin formation near the 3′ end of the DR1 sequence on the (−) strand DNA switches the RNA primer to the DR2 sequence near the 5′ end of the (−) strand DNA

D) Template switching is initiated by the 5′ end limit product of the RNaseH digestion of the pre-genomic RNA

A

C) A hairpin formation near the 3′ end of the DR1 sequence on the (−) strand DNA switches the RNA primer to the DR2 sequence near the 5′ end of the (−) strand DNA

101
Q

Quiz 9

Which of the following is NOT true about a typical (e.g. Avian Leukosis Virus: ALV) retrovirus genome and its function)?

A) The retroviral genome is (+) strand RNA with two identical copies in each virion

B) Host tRNAs are packaged in the virion bound to the pbs (primer binding site) of the genome

C) The (+) strand genome RNA is 5′ capped and 3′ polyadenylated and immediately translated into Gag and Gag-Pol polyprotein precursor immediately upon viral entry into the host cell

D) The viral genome is coated with nucleocapsid protein

A

C) The (+) strand genome RNA is 5′ capped and 3′ polyadenylated and immediately translated into Gag and Gag-Pol polyprotein precursor immediately upon viral entry into the host cell

102
Q

Quiz 9

The reverse transcriptase enzyme is coded by which region of a typical (e.g. Avian Leukosis Virus; ALV) retroviral genome?

A) Env

B) Gag

C) LTR

D) Pol

A

D) Pol

Virology (3 decks)

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