Micro Exam Chapter 9

17) 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.

A) Archaea.

23) 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

A) adenoviruses

25) Gene therapy viruses are usually constructed from which type of virus? A) adenoviruses B) cytomegaloviruses C) polyomaviruses D) poxviruses

A) adenoviruses

6) 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.

A) are released from the host without the host being lysed

26) Blocking polyomavirus SV40's ability to integrate its genome into host cells would A) avoid cancer development from 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.

A) avoid cancer development from the virus.

9) 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.

A) before the entire T7 genome enters the cell.

13) 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.

C) both lytic and lysogenic growth

22) In designing a drug to inhibit pox viruses, the compound should localize in the host's ________ to be MOST effective. A) nucleus B) endoplasmic reticulum C) cytoplasm D) Golgi complex

C) cytoplasm

29) 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

C) positive and negative ssRNA viruses

4) Which type of viruses can be directly used for translation? A) dsRNA B) negative ssRNA C) positive ssRNA D) retroviruses

C) positive ssRNA

30) 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

C) post-translationally cleaved

11) 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

C) replicates by transposition.

39) Proteins made by a ribosome reading through a transcript's stop codon 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 bacteriophage. C) suggest a relatively low level of protein product is essential for the virus due to its rare frequency. D) create opportunities for viruses to make different capsid proteins.

C) suggest a relatively low level of protein product is essential for the virus due to its rare frequency.

3) 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.

C) time of synthesis following host infection

24) 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

D) DNA polymerase, reverse transcriptase, and protein primer for DNA synthesis

5) 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) bacteriophage. B) DNA viruses. C) retroviruses. D) RNA viruses

D) RNA viruses

34) To promote the translational activity of ribosomes in human cells for synthesizing viral proteins during viral infection, viruses A) chemically modify (e.g., cap and methylate) the transcripts. B) keep a ribosome binding site specific to human ribosomes on their genome. C) maintain introns and sometimes extrons in their genomes to appear as eukaryotic mRNA. D) only adhere to and infect metabolically active host cells where protein synthesis is high

A) chemically modify (e.g., cap and methylate) the transcripts.

10) 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.

A) combination of two or more repeated nucleotide sequences covalently linked together.

35) The family of reoviruses contain dsRNA genomes that replicate from the template of ________ which makes it a ________ replication process. A) only the positive ssRNA strand / conservative B) only the positive ssRNA strand / semiconservative C) both RNA strands /conservative D) both RNA strands / semiconservative

A) only the positive ssRNA strand / conservative

15) Which feature, if changed, would NOT abolish M13's 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

A) ssDNA genome becoming a dsDNA genome

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

Answers will vary but should highlight the difference of viral genome diversity in composition compared to the three domains of life which are dominated by dsDNA genomes. Because different viruses genomes composition is so diverse, where some are positive ssRNA, negative ssRNA, dsRNA, positive ssDNA, and dsDNA, fundamental molecular mechanisms are also diverse. The genome composition often dictates which proteins must be carried and not made by the host, the type of genome replication mechanism, and the way transcripts are synthesized.

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

Answers will vary, but bacteriophage Mu integrates into its host's genome and when doing so induces mutations. Bacterial geneticists can use Mu to create a library of mutations, which is an especially useful technique in reverse genetics approaches.

7) 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.

B) Directly search the three frames of the positive ssDNA for genes that have sequences where more than one gene is predicted.

28) 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 host's pilus rather than the cell's surface. C) It enters through a host cell porin. D) More than one MS2 phage can be present in an individual E. coli cell.

B) It attaches to the host's pilus rather than the cell's surface.

19) 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.

B) It will lyse its host.

36) Identifying proteases being essential for 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.

B) contains at least one polyprotein.

32) 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

B) coronaviruses / positive ssRNA

20) Viruses that infect the hyperthermophilic Archaea tend to contain genomes that are composed of A) ssDNA. B) dsDNA. C) ssRNA. D) dsRNA.

B) dsDNA.

37) A drug designed to inhibit reverse transcriptase activity would target A) coronaviruses and rhabdoviruses. B) hepadnaviruses and retroviruses. C) retroviruses. D) viruses with RNA genomes

B) hepadnaviruses and retroviruses.

38) 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 host's genome before transcription. C) is negative ssRNA. D) lacks ribonuclease activity

B) must first integrate into the host's genome before transcription.

14) Most known plant viruses have ________-strand RNA genomes, because small genomes ________. A) negative / facilitate cell-to-cell transfer B) positive / facilitate cell-to-cell transfer C) negative / interact more readily with host DNA D) positive / interact more readily with host DNA

B) positive / facilitate cell-to-cell transfer

21) Spindle-shaped viruses have been shown to infect only A) Eukarya. B) Bacteria. C) Archaea. D) plants.

C) Archaea.

16) Of the phage listed below, which creates mutations in its host genome via transposition? A) lambda B) M13 C) Mu D) T7

C) Mu

1) Which type of viruses generally has the smallest genome? A) bacteriophage B) DNA viruses C) RNA viruses D) viroids

C) RNA viruses

8) 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.

D) T7 has its own RNA polymerase, which must first be synthesized by the host.

12) Mu is a ________ virus with a ________ tail. A) ssRNA / filamentous B) dsRNA / helical C) ssDNA / filamentous D) dsDNA / helical

D) dsDNA / helical

18) Reoviruses contain ________ genomes, and their replication occurs within the host's ________. A) ssDNA / nucleus B) dsDNA / nucleus C) ssRNA / cytoplasm D) dsRNA / cytoplasm

D) dsRNA / cytoplasm

2) 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

D) seven / genome composition and transcription mechanism

27) Herpesviruses can cause all of the following diseases in humans EXCEPT A) cancer. B) chicken pox. C) cold sores. D) spongiform encephalopathy.

D) spongiform encephalopathy.

33) 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.

D) the genomes of dsRNA viruses must avoid human immune cells during infection, including replicating their genomes within their own nucleocapsids.

31) 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

D) to serve as the complementary template sequence in genome amplification of the positive strand

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

False

True or False. A negative-stranded RNA virus produces a complete positive-stranded RNA virus that serves as template DNA for other proteins in order to replicate the complete negative-stranded RNA genome.

False

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

False

True or False. Nonfilamentous bacteriophage often can escape its host without lysing, whereas filamentous phage normally induce cell lysis once replicated inside their host.

False

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

False

True or False. To date, no virus that infects Archaea is known to have an RNA genome.

False

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

False

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

False

True or False. Viruses that contain positive-strand genomes are incompatible to share genetic elements other positive-strand genomes.

False

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

Fasle

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

No, there is not a particular morphology of viruses that is known to cause diseases in humans. Viral proteins often cause sicknesses, and certain viral morphologies are not strongly correlated with particular proteins. Only one viral morphology has not been described in animal (human) viruses, which is the head and tail morphology typical of bacteriophages.

2) 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?

One hypothesis on the origin of viruses states they developed prior to the living cells they infect. RNA viruses likely were the first to come about, and when host cells evolved ribonucleases to combat infection by RNA viruses, DNA might have evolved in viruses and a way to circumvent this defense. Because DNA is more stable than RNA, its evolution would also be advantageous and maintained in the cellular hosts.

1) Describe how bacteriophages influence the ocean's bacterial populations and nutrient cycling.

Phages are responsible for killing up to 50% of the marine bacterial population each day. They also play a major role in horizontal gene transfer due to their ability to package DNA from one host and integrate the DNA it carries into other host bacterial cells. With cellular constituents released that would otherwise not be available for other organisms, cycling of these nutrients might be expected to occur at a quicker rate. Another potential hypothesis could be that nutrients are consumed during phage replication that other bacteria might use and are no longer available to the bacteria by instead being incorporated into phage particles.

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

The MS2 phage has a positive ssRNA genome. Once the genome enters into the host cell, the host's RNA polymerase can directly bind to the mRNA transcript-like genome to translate the genome into proteins.

8) 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.

Traditionally viruses are thought of as protein-encapsulated genetic elements that exclusively replicate inside a living cell yet prions and viroids each lack one of these characteristics. While neither is a true virus, both are infectious particles, so it is clear a diversity of infectious particles exist. Prions lack nucleotide sequences altogether but one could also argue the protein conformation PrPSC itself serves as the blueprint to make available other PrPSC misfolded proteins. The gene for the prion, present in host cells, encodes for PrPC which is functionally different than its propagative and infectious form. Viroids on the other hand lack protein in their structure and their RNA genomes also do not encode for proteins. Viroids being infectious exclusively as RNA, and prions being infectious exclusively as protein expands our knowledge on the minimal requirements to be infectious.

True or False. By nature of its infectivity, M13 phage 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.

True

True or False. Despite viruses require a living host's metabolism to replicate, it remains unclear whether viruses existed before living cells.

True

True or False. 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.

True

True or False. Genomics analysis of recently isolated viruses indicate some viruses contain larger genomes than the some bacterial genomes.

True

True or False. Knowing the genome of Mu bacteriophage now enables researchers to locate where it incorporates into bacterial genomes.

True

True or False. Many human-infecting viruses that illicit a strong immune response cause additional harmful effects on humans, so the discovery of a virus that can induce an immune response but not cause harm made it attractive for vaccine development.

True

True or False. Most archaeal viruses identified appear to have DNA genomes.

True

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

True

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

True

True or False. The diversity of genome type and the overall number of bacteriophage that infect Escherichia coli is numerous, but many other bacterial taxa that thrive in the environment are likely infected by a variety of phage as well.

True

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

Viruses lack ribosomal RNA gene sequences present in Bacteria that are commonly used for phylogenetic studies. A universal gene in all viruses is absent, which means only subgroups are used for phylogenetic studies where the gene(s) is/are present. In a similar way as rRNA genes, phylogenetic genes selected in viruses often target essential functions for a particular group of viruses such as capsid proteins. Because no single gene is essential in viruses, whichever gene or genes selected constrains the phylogenetic study to only a subset of viruses.