Deck 10: Viral Genomics, Diversity, and Ecology

Question 1

In T7, the proteins that inhibit the host restriction system are synthesized

A) before the entire T7 genome enters the cell.
B) while the T7 genome is entering the cell but before it enters the nucleus.
C) after the T7 genome is completely within the host cytoplasm.
D) in response to the T7 genome binding to the host chromosome.

Answer 1

A

Question 2

Which type of viruses can be directly used for translation?

A) dsRNA
B) negative ssRNA
C) positive ssRNA
D) retroviruses

Answer 2

C

Question 3

A concatemer is a

A) combination of two or more repeated nucleotide sequences covalently linked together.
B) complex of RNA-specific polymerases found only in bacteriophages.
C) linker molecule that allows several phages to infect one host.
D) polymeric protein.

Answer 3

A

Question 4

Mu is a ________ virus with a ________ tail.

A) ssRNA / filamentous
B) dsRNA / helical
C) ssDNA / filamentous
D) dsDNA / helical

Question 5

Reoviruses contain ________ genomes, and their replication occurs within the hostʹs ________.

A) ssDNA / nucleus
B) dsDNA / nucleus
C) ssRNA / cytoplasm
D) dsRNA / cytoplasm

Question 6

If the hypothesis stating viruses evolved prior to living organisms on Earth is TRUE, the first type of viruses in the world were likely

A) bacteriophages.
B) DNA viruses.
C) retroviruses.
D) RNA viruses.

Question 7

Which feature, if changed, would NOT abolish M13ʹs utility as a cloning vector?

A) ssDNA genome becoming a dsDNA genome
B) loss of genes that make coat proteins
C) replacing the segment of non-coding DNA in its genome with an indispensible gene
D) switch from lysogenic to lytic lifestyle

Question 8

How could overlapping genes in a positive ssDNA virus genome be predicted?

A) Convert the positive ssDNA into its complementary ssDNA and search for genes in the negative ssDNA strand for sequences used in more than one predicted gene.
B) Directly search the three frames of the positive ssDNA for genes that have sequences where more than one gene is predicted.
C) Convert the positive ssDNA into negative ssDNA and search all six possible frames for genes that use part of the same sequence.
D) Convert the positive ssDNA into its complementary ssDNA and search for genes in the negative ssDNA strand that also share a complementary gene in the positive strand.

Question 9

What will happen if the Mu repressor is NOT synthesized?

A) Genome replication will not be able to occur.
B) It will lyse its host.
C) Mu will improperly synthesize its capsid.
D) Transposition will not be possible.

Question 10

Spindle-shaped viruses have been shown to infect only

A) Eukarya.
B) Bacteria.
C) Archaea.
D) plants.

Question 11

Integration of Mu DNA into the host genome is essential for

A) lytic growth.
B) lysogenic growth.
C) both lytic and lysogenic growth.
D) neither lytic nor lysogenic growth.

Question 12

Of the phages listed below, which creates mutations in its host genome via transposition?

A) lambda
B) M13
C) Mu
D) T7

Question 13

The filamentous DNA phages are unusual, because they

A) are released from the host without the host being lysed.
B) have linear genomes.
C) replicate without a host.
D) are released from the host without being lysed and have linear genomes.

Question 14

The phage Mu

A) has a circular genome.
B) repairs mutations in the host genome.
C) replicates by transposition.
D) has a circular genome, repairs host genome mutations, and can replicate by transposition.

Question 15

Early and late viral proteins are classified according to their relative

A) evolutionary appearance in virus genomes.
B) stability during infection.
C) time of synthesis following host infection.
D) transmission into virions.

Question 16

The Baltimore Scheme to classify viruses contains a total of ________ groups based on ________.

A) four / genome composition
B) four / genome composition and transcription mechanism
C) seven / genome composition
D) seven / genome composition and transcription mechanism

Question 17

How are T7 genes transcribed?

A) Host RNA polymerase is modified to recognize the T7 promoter.
B) Host RNA polymerase directly translates the T7 genes.
C) T7 has its own RNA polymerase, which is packaged in its capsid and injected into the host during infection to transcribe T7 genes.
D) T7 has its own RNA polymerase, which must first be synthesized by the host.

Question 18

Which type of viruses generally has the smallest genome?

A) bacteriophages
B) DNA viruses
C) RNA viruses
D) viroids

Question 19

Viruses that infect the hyperthermophilic Archaea tend to contain genomes that are composed of

A) ssDNA.
B) dsDNA.
C) ssRNA.
D) dsRNA.

Question 20

Unusually shaped viruses, such as lemon-shaped and spindle-shaped, have recently been discovered in

A) Archaea.
B) Bacteria.
C) Archaea and Bacteria.
D) Eukarya.

Question 21

What is the purpose of synthesizing a negative strand RNA in positive stranded ssRNA viruses?

A) enable rolling circle amplification of the genome, which requires both strands of RNA
B) enable transcription of genes occurring on both the negative and positive strands of the genome, such as overlapping genes
C) proofreading of the genome to minimize mutations generated by the polymerase being passed onto virion progeny
D) to serve as the complementary template sequence in genome amplification of the positive strand

Question 22

Proteins made by a ribosome reading through the stop codon of a transcript without their own discrete ribosome binding sites

A) are thought to be a primitive mechanism to avoid host defenses.
B) appear most abundant in archaeal viruses and relatively uncommon in bacteriophages.
C) suggest a relatively low level of protein product is essential for the virus due to the rare frequency of these events.
D) create opportunities for viruses to make different capsid proteins.

Question 23

Among the largest RNA genome viruses are ________ which contain a ________ genome.

A) coronaviruses / dsRNA
B) coronaviruses / positive ssRNA
C) polioviruses / dsRNA
D) polioviruses / positive ssRNA

Question 24

As a consequence of the immune system in humans recognizing dsRNA as foreign

A) dsRNA viruses rarely infect humans.
B) dsRNA viruses quickly transcribe their genes into mRNA which is insensitive to immune responses.
C) genomes of RNA viruses are often chemically modified to avoid recognition by human immune cells.
D) the genomes of dsRNA viruses must avoid human immune cells during infection, including replicating their genomes within their own nucleocapsids.

Question 25

Blocking polyomavirus SV40ʹs ability to integrate its genome into host cells would

A) avoid cancer development caused by the virus.
B) increase the rate of transformation.
C) increase the latent period of SV40.
D) switch SV40 into a lytic lifecycle which would be especially harmful to the host cells.

Question 26

In contrast to positive ssRNA viruses such as coronaviruses and polioviruses, the genome of retroviruses

A) lacks genes encoding for tRNA primers.
B) must first integrate into the hostʹs genome before transcription.
C) is negative ssRNA.
D) lacks ribonuclease activity.

Question 27

The unconventional dsDNA genome replication mechanism where no lagging strand exists is a hallmark of which group of viruses?

A) adenoviruses
B) coronaviruses
C) herpes viruses
D) pox viruses

Question 28

A drug designed to inhibit reverse transcriptase activity would target

A) coronaviruses and rhabdoviruses.
B) retroviruses.
C) hepadnaviruses and retroviruses.
D) viruses with RNA genomes.

Question 29

The family of reoviruses contain dsRNA genomes use a ________ replication process.

A) conservative
B) semiconservative
C) retroviral
D) rolling circle

Question 30

Which of the following conditions favors a lysogenic life cycle in bacteriophages?

A) Having ssDNA.
B) Having ssRNA.
C) A lack of host bacteria.
D) The presence of abundant hosts.

Question 31

The ________ has been especially useful for genetic engineering because it is capable of triggering a substantial immune response without causing major adverse health effects.

A) adenovirus
B) polymyxavirus
C) vaccina virus
D) herpesvirus

Question 32

Based on its function, which type(s) of viruses likely contain(s) a gene encoding for RNA replicase?

A) dsDNA and ssDNA viruses
B) positive ssRNA viruses
C) positive and negative ssRNA viruses
D) ssRNA and ssDNA viruses

Question 33

Herpes viruses can cause all of the following diseases in humans EXCEPT

A) cancer.
B) chicken pox.
C) cold sores.
D) spongiform encephalopathy.

Question 34

Identifying proteases being essential for the replication of a virus would suggest the virus

A) lyses its host following genome replication.
B) contains at least one polyprotein.
C) has a single-stranded RNA genome.
D) uses at least one set of overlapping genes.

Question 35

Polyproteins made from human viruses such as poliovirus must be ________ in order to yield the required functional units of the virus.

A) able to interact with VPg proteins
B) chemically modified with either glycolation or methylation
C) post-translationally cleaved
D) properly folded into secondary and tertiary structures

Question 36

What is unusual about phage MS2 infection of Escherichia coli?

A) All proteins are synthesized simultaneously during infection so there are no early and late proteins.
B) It attaches to the hostʹs pilus rather than the cellʹs surface.
C) It enters through a host cell porin.
D) More than one MS2 phage can be present in an individual E. coli cell.

Question 37

The hepadnavirus DNA polymerase acts as which of the following?

A) DNA polymerase
B) reverse transcriptase
C) protein primer for synthesis of a strand of DNA
D) DNA polymerase, reverse transcriptase, and protein primer for DNA synthesis

Question 38

When two different influenza viruses infect the same cell, their segmented genomes can undergo reassortment which will result in

A) antigenic drift.
B) antigenic shift.
C) loss of neuramidase.
D) loss of hemagglutinin.

Question 39

In designing a drug to inhibit poxvirus, the compound should localize in the hostʹs ________ to be most effective.

A) nucleus
B) endoplasmic reticulum
C) cytoplasm
D) Golgi complex

Question 40

How do reoviruses increase the translational activity of human ribosomes so that they can rapidly produce viral proteins during infection?

A) They chemically modify the RNA transcripts with methyl caps in a similar manner to normal eukaryotic RNA processing.
B) They keep a ribosome binding site specific to human ribosomes on their genome.
C) They have introns and sometimes extons in their genomes to make their RNA resemble eukaryotic mRNA.
D) They only adhere to and infect metabolically active host cells where protein synthesis is high.

Question 41

Despite viruses require a living hostʹs metabolism to replicate, it remains unclear whether viruses existed before living cells.

Question 42

By nature of its infectivity, M13 phages can be used in the laboratory to continually propagate a particular DNA sequence inside of Escherichia coli by simply culturing infected E. coli in LB.

Question 43

To date, there is no evidence that RNA viruses infect Archaea.

Question 44

Genomics analysis of recently isolated viruses indicate that some viruses contain larger genomes than some bacterial genomes.

Question 45

Varied transcription mechanisms distinguish the different DNA virus Baltimore classes, whereas varied translational mechanisms distinguish the RNA virus Baltimore classes.

Question 46

Some virus shapes that infect members of Archaea are unique from other viruses that infect eukaryotes and bacteria.

Question 47

Most archaeal viruses identified appear to have DNA genomes.

Question 48

Bacteriophages that have single-stranded genomes are specialized to minimize energy requirements because just one strand is necessary for replication.

Question 49

A bacteriophage that lacks its proteinaceous capsid structure is also called a viroid.

Question 50

Due to their indispensible role for copying its genome, an intracellular host protease that attacks the adenoviral protein ends would likely result in halting its replication.

Question 51

The Baltimore classification scheme is a useful way to categorize viruses based on their host infectivity.

Question 52

Nonfilamentous bacteriophages often can escape its host without lysing, whereas filamentous phages normally induce cell lysis once replicated inside their host.

Question 53

Viroids infect only fungi.

Question 54

Due to the genetic diversity of viruses and their lack of ribosomal RNA, nucleotide-based phylogeny studies are not applicable to virology.

Question 55

Viruses that contain positive-strand genomes do not share genetic elements with other positive-strand genomes.

Question 56

One hypothesis on the origin of DNA points to RNA viruses evolving a modified nucleotide that is insensitive to ribonucleases.

Question 57

In order to replicate its genome, a positive-strand RNA virus must produce a complete negative-strand RNA molecule that serves as the template for protein synthesis.

Question 58

Many viruses that infect humans may illicit a strong immune response causing additional harmful effects, so the discovery of a virus that can induce an immune response without causing harm made it attractive for vaccine development.

Question 59

Viruses are known to infect Bacteria, but no virus has yet been found that infects Archaea.

Question 60

Knowing the genome of Mu bacteriophages now enables researchers to locate where it incorporates into bacterial genomes.

Question 61

Why is so much emphasis placed on the genomic composition (e.g., ssRNA, dsDNA) of individual viruses? Provide examples to support your explanation.

Question 62

Is there a certain type of virus morphology that is especially known to cause disease in humans? Explain your reasoning.

Question 63

Describe one use of bacteriophage Mu for a bacterial geneticist, and explain why it is useful.

Question 64

Defend why the discovery of prions and viroids changes our view on what it takes to be an infectious particle. Be sure to explain the feature of each that distinguishes them from traditional viruses.

Question 65

Why are phylogenetic studies of viruses more challenging than Bacteria? Explain how genes are selected in viruses for phylogeny and the constraints those create.

Question 66

Describe how bacteriophages influence the oceans' bacterial populations and nutrient cycling.

Question 67

Explain why the viral genome of the MS2 phages can be immediately translated. What type of genome must it have for this to be the case?

Question 68

Describe the hypothesis of viruses occurring before living cells and how DNA might have evolved. What is the current hypothesis about the evolutionary relationships between RNA, DNA, viruses, and cellular life?