Unit 4/5

Question 1

Negative sense genomes are of the same polarity as mRNA.

Answer

true

Question 2

No dsDNA [blank_start]plant[blank_end] viruses are known

Accepted Answer

plant

Question 3

RNA genomes need to be smaller

Answer

true

Question 4

RdRp has high fidelity and a low error rate.

Answer

true

Question 5

RNA breaks less often than DNA.

Answer

true

Question 6

Host cells have defenses against [blank_start]dsRNA[blank_end].

Accepted Answer

dsRNA

Question 7

ssRNA(+) viruses drastically limit the amount of ssRNA([blank_start]-[blank_end]) used for replication.

Accepted Answer

-

Question 8

ssRNA(-) viruses keep the genome covered in viral proteins to avoid [blank_start]complementary[blank_end] RNA binding.

Accepted Answer

complementary

Question 9

Viruses (and all genomes) have what is called “the [blank_start]end[blank_end] problem”. This problem involves the loss of genetic information through copying the genome.
DNA viruses are often [blank_start]circular[blank_end]
ssRNA(-) viruses often have special [blank_start]secondary[blank_end] structure such as cloverleaves. 
ssRNA(+) viruses often have  5’ [blank_start]caps[blank_end] and [blank_start]polyA[blank_end] tails.

Accepted Answer

end

Accepted Answer

circular

Accepted Answer

secondary

Accepted Answer

caps

Accepted Answer

polyA

Question 10

Segmented genomes have the problem that each segment must be [blank_start]recognized[blank_end] for inclusion into the virion, however, they have the benefit of allowing faster genetic [blank_start]shift[blank_end].

Accepted Answer

shift

Accepted Answer

recognized

Question 11

RNA viruses that are nonsegmented cannot be made segmented while still retaining their functionality.

Answer

true

Question 12

Satellite, dependent and defective genomes
Some viruses require a [blank_start]coinfection[blank_end] with a completely separate virus to allow  the expression of their own genetic material and formation of their own virions.

Accepted Answer

coinfection

Question 13

All virus genomes experience pressure to minimize their [blank_start]size[blank_end].
Prokaryotic viruses require a small genome to be able to keep up with bacterial [blank_start]growth[blank_end].
Eukaryotic viruses require a small genome usually for [blank_start]packaging[blank_end] reasons.

Accepted Answer

size

Accepted Answer

growth

Accepted Answer

packaging

Question 14

Things that researchers will look for when examining a virus:
[blank_start]Composition[blank_end] – DNA or RNA, single-stranded or double-stranded, linear, or circular, complete or segmented/multipartite
If segmented or multipartite, size and number of segments
[blank_start]Terminal[blank_end] structures
Nucleotide sequence
[blank_start]Coding capacity[blank_end] – open reading frames
[blank_start]Regulatory signals[blank_end] – transcription enhancers, promoters and terminators

Accepted Answer

Composition

Accepted Answer

Terminal

Accepted Answer

Coding capacity

Accepted Answer

Regulatory signals

Question 15

DNA virus genomes can be analysed directly by restriction endonuclease digestion without resorting to molecular cloning

Answer

true

Question 16

Direct analysis of RNA sequences is usually fairly easy.

Answer

true

Question 17

RNA sequence analysis did not begin to advance rapidly until the widespread use of [blank_start]reverse transcriptase[blank_end] (isolated from avian myeloblastosis virus) to convert RNA into [blank_start]cDNA[blank_end] in the 1970s

Accepted Answer

reverse transcriptase

Accepted Answer

cDNA

Question 18

(+)sense RNA virus genomes are often infectious when the purified RNA (vRNA) is applied to cells in the absence of any virus proteins.

Answer

true

Question 19

Virus genomes which are composed of double-stranded DNA are also usually infectious.

Answer

true

Question 20

Cloned cDNA genomes of ([blank_start]+[blank_end])sense RNA viruses are infectious, although less efficient at infecting cells than vRNA.

Accepted Answer

+

Question 21

All (–) sense viruses all require Reverse Transcriptase. Without it they cannot replicate.

Answer

true

Question 22

In [blank_start]vitro[blank_end] complex formation – genome is mixed with the appropriate enzymes prior to introduction into the test system: paramyxoviruses, rhabdoviruses and bunyaviruses.

Accepted Answer

vitro

Question 23

In [blank_start]vivo[blank_end] complex formation – helper viral strains co-transfect/infect and provide the needed enzymes: influenza virus, bunyaviruses and double-stranded RNA viruses such as reoviruses and birnaviruses.

Accepted Answer

vivo

Question 24

More recently, [blank_start]plasmids[blank_end] bearing the anti-genome (cDNA) can be introduced along will the genes for the required proteins for viral replication (such as RdRp and NC).

Accepted Answer

plasmids

Question 25

Reverse transcriptase has a lower error rate than DNA polymerase.

Answer

true

Question 26

Chemically induced mutations are not used much any more since PCR is so much safer and much more precise.

Answer

true

Question 27

Often to knock out a gene in a virus, a [blank_start]frameshift[blank_end] is added so that the genome size doesn’t actually change and thus affect [blank_start]packaging[blank_end]. This is a common way of studying the importance and role of viral genes.

Accepted Answer

frameshift

Accepted Answer

packaging

Question 28

Due to genomic space issues, any ncRNAs have a specific role. They aren’t frivolous.

Answer

true

Question 29

ncRNAs may function like a [blank_start]protein[blank_end] since they are less [blank_start]immunogenic[blank_end] and cheaper to produce.
They associate with proteins that are vital to the viral replication cycle.
They are often expressed at [blank_start]high[blank_end] levels during an infection.

Accepted Answer

protein

Accepted Answer

immunogenic

Accepted Answer

high

Question 30

Many viruses have [blank_start]auxilary metabolic genes[blank_end] (AMGs) which is a non-random event where a virus steals a host gene that helps the virus compete. Some AMGs have been shown to be involved with photosynthesis, nutrient stress, motility, chemotaxis, showing that the viruses can manipulate the host in a variety of ways.

Accepted Answer

auxilary metabolic genes

Question 31

While [blank_start]dsDNA[blank_end] viruses are the easiest to discover and expand our knowledge of, techniques have been developed to accurately find RNA viruses. Currently, it appears that [blank_start]ssRNA[blank_end]([blank_start]+[blank_end]) viruses dominate the RNA virus world.

Accepted Answer

ssRNA

Accepted Answer

+

Accepted Answer

dsDNA

Question 32

Label Picture.

Accepted Answer

phenotyp

Accepted Answer

genome

Question 33

In regards to Class I: dsDNA viruses:
Can be divided into two groups:
replication is exclusively [blank_start]nuclear[blank_end] (e.g. Adenoviridae, Polyomaviridae, Herpesviridae) 
replication occurs in the [blank_start]cytoplasm[blank_end] (Poxviridae)

Accepted Answer

nuclear

Accepted Answer

cytoplasm

Question 34

dsDNA viruses:

Since their genomes all resemble double-stranded cellular DNA, they are essentially transcribed by the same mechanisms as cellular genes
However, there are profound differences between them relating to the degree to which each family is reliant on the host cell [blank_start]machinery[blank_end].

Accepted Answer

machinery

Question 35

RNA is fragile and long strands break easily

Answer

true

Question 36

RNA genomes tend to have lower mutation rates than those composed of DNA.

Answer

true

Question 37

RNA is fragile and long strands break easily.
RNA genomes tend to have higher mutation rates than those composed of DNA.
This drives RNA viruses to [blank_start]smaller[blank_end] genomes.

Accepted Answer

smaller

Answer

bigger

Question 38

Nested Genomic Sets Label Picture

Accepted Answer

internal initiation

Accepted Answer

premature termination

Accepted Answer

discontinuous transcription sgRNA synth.

Question 39

Picornavirus  genomes consists of a single-stranded, (+)sense RNA molecule of between 7.2 kb to 8.5 kb, containing features conserved in all picornaviruses:
The 5' UTR contains a '[blank_start]clover[blank_end]-[blank_start]leaf[blank_end]' secondary structure known as the IRES ([blank_start]Internal Ribosome Entry Site[blank_end]).
The rest of the genome encodes a single polyprotein of between 2100 and 2400 amino acids
Both ends of the genome are modified, the 5' end by a [blank_start]covalently[blank_end] attached protein (VPg), the 3' end by [blank_start]polyadenylation[blank_end].

Accepted Answer

clover

Accepted Answer

leaf

Accepted Answer

Internal Ribosome Entry Site

Accepted Answer

covalently

Accepted Answer

polyadenylation

Question 40

Togavirus genomes comprise single-stranded, (+)sense, non-segmented RNA of approximately 11.7 kb with the following features:
They resemble cellular mRNAs in that they have a 5' [blank_start]methylated[blank_end] cap and 3' [blank_start]poly[blank_end]([blank_start]A[blank_end]) sequences.
Expression is achieved by two rounds of translation, producing first non-[blank_start]structural[blank_end] proteins encoded in the 5' part of the genome and later structural proteins from the 3' part.
Use both subgenomic RNA as well as polyproteins.

Accepted Answer

methylated

Accepted Answer

poly

Accepted Answer

A

Accepted Answer

structural

Question 41

[blank_start]Subgenomic[blank_end] RNAs of positive-strand viruses have the same 3' ends as genomic RNA, but have deletions at the 5' ends to bring the 5' end of the RNA in proximity with the [blank_start]start[blank_end] codon of downstream (on genomic RNA) ORFs . Because replication is required for sgRNA synthesis, the RNA-dependent RNA polymerase (RdRp) is always translated first, directly from genomic RNA of positive-strand RNA viruses. sgRNAs express products needed during intermediate and late stages of infection, such as structural or movement proteins.
These sgRNA are not part of the genome because they don’t comprise encapsidation signals and therefore are not carried out by virions to new infected cells.

Accepted Answer

Subgenomic

Accepted Answer

start

Question 42

Flavivirus genomes are comprised of one single-stranded, (+)sense RNA molecule of about 10.5 kb with the following features:
A 5' methylated cap, but not [blank_start]polyadenyl[blank_end]ated at the 3' end.
Genetic organization differs from that of the togaviruses - structural proteins are encoded in the 5' part of the genome and non-structural proteins in the 3' part.
Expression is similar to that of the picornaviruses, involving the production of a polyprotein.

Accepted Answer

polyadenyl

Question 43

Viruses with negative-sense RNA genomes are less diverse than positive-stranded viruses.

Answer

true

Question 44

Class V: ssRNA(-) virus replication:
Possibly because of the difficulties of expression, they tend to have [blank_start]larger[blank_end] genomes.
Because of this, [blank_start]segment[blank_end]ation is a common, although not universal feature.
Some of these virus genomes are [blank_start]ambisense[blank_end] - part (–) sense and part (+) sense.

Accepted Answer

larger

Accepted Answer

segment

Accepted Answer

ambisense

Question 45

Class VI RNA viruses have a [blank_start]DNA[blank_end] intermediate in regards to replication.

Accepted Answer

DNA

Question 46

Class VI: ssRNA with DNA intermediate virus replication:
After entry, the ssRNA genome goes through [blank_start]reverse transcription[blank_end] via the viral enzyme [blank_start]reverse transcriptase[blank_end] (RT).
The [blank_start]cDNA[blank_end] genome is taken into the [blank_start]nucleus[blank_end] and integrates.
vRNA is made, which is used both as a template for proteins as well as new genomic ssRNA(+).
The genomic ssRNA(+) strands (2 of them) get incorportated into [blank_start]capsid[blank_end]s and bud from the host cell.

Accepted Answer

reverse transcription

Accepted Answer

reverse transcriptase

Accepted Answer

cDNA

Accepted Answer

nucleus

Accepted Answer

capsid

Question 47

Retrovirus genomes have four unique features:
They are the only viruses which are [blank_start]diploid[blank_end]
They are the only RNA viruses whose genome is produced by [blank_start]cellular[blank_end] transcriptional machinery
They are the only viruses whose genome requires a specific cellular RNA ([blank_start]tRNA[blank_end]) for replication
They are the only (+) sense RNA viruses whose genome does not serve directly as [blank_start]mRNA[blank_end] immediately after infection

Accepted Answer

diploid

Accepted Answer

cellular

Accepted Answer

tRNA

Accepted Answer

mRNA

Question 48

Class VII dsDNA use an [blank_start]RNA[blank_end] intermediate during replication.

Accepted Answer

RNA

Question 49

Class [blank_start]VII[blank_end]: dsDNA with an RNA intermediate virus replication:

After entry, the genome, which is an open loop (relaxed circular DNA), gets taken into the [blank_start]nucleus[blank_end] to be completed and [blank_start]ligated[blank_end] (covalently closed circular DNA).
Transcription and translation occur as normal.
Pre-genomic RNA is made and  in the [blank_start]cytoplasm[blank_end] is encapsidated.
The RT makes [blank_start]ssDNA[blank_end](-), from which [blank_start]dsDNA[blank_end] is made.
The capsid buds out of the cell.

Accepted Answer

nucleus

Accepted Answer

ligated

Accepted Answer

cytoplasm

Accepted Answer

VII

Accepted Answer

ssDNA

Accepted Answer

dsDNA

Question 50

Class VII: dsDNA with an RNA intermediate virus replication:
Virions contain a partially [blank_start]double[blank_end]-stranded ('gapped') DNA genome, plus an [blank_start]RNA[blank_end]-dependent DNA polymerase ([blank_start]reverse transcriptase[blank_end]).

Accepted Answer

RNA

Accepted Answer

reverse transcriptase

Accepted Answer

double

Question 51

Although multipartite genomes are also segmented, each genome segment is packaged into a separate virus particle.

Answer

true

Question 52

Segmentation of the virus genome has the advantage of counteracting strand [blank_start]breakage[blank_end] of [blank_start]long[blank_end] RNA molecules, as well as more rapid [blank_start]recombination[blank_end] of genetic material.

Accepted Answer

breakage

Accepted Answer

long

Accepted Answer

recombination

Question 53

The disadvantage of segmentation is that all the individual genome segments must be [blank_start]packaged[blank_end] into each virus particle.

Accepted Answer

packaged

Question 54

Shut off of host [blank_start]mRNA[blank_end] expression is important for efficient viral gene expression.

Accepted Answer

mRNA

Question 55

The figure shown depicts [blank_start]suppression of termination[blank_end].

Accepted Answer

suppression of termination

Question 56

In suppression of termination the [blank_start]pseudoknot[blank_end] blocks the eRF release factor from recognizing the amber (UAG) or opal (UGA) stop codon, allowing translation to sometimes continue.

Accepted Answer

pseudoknot

Question 57

The figure depicts [blank_start]ribosomal frameshifting[blank_end].

Accepted Answer

ribosomal frameshifting

Question 58

The figure depicts [blank_start]ribosome skipping[blank_end].

Accepted Answer

ribosome skipping

Question 59

Ribosome skipping allows for the production of separate proteins without the need for [blank_start]peptidases[blank_end].

Accepted Answer

peptidases

Question 60

The figure depicts [blank_start]termination and reinitiation[blank_end].

Accepted Answer

termination and reinitiation

Question 61

In [blank_start]termination and reinitiation[blank_end] The [blank_start]pseudoknot[blank_end] allows for the machinery to get stuck long enough after termination to reinitiate on the new codon without the typical effort involved.