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CMMB 421 > MT 1 > Flashcards

MT 1 Flashcards

1
Q

What is the size range of a virus?

A

Viruses can vary in size in which some are as small as ribosomes or bigger than the smallest bacterial forms.

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2
Q

What are viruses?

A

They are obligate intracellular parasites that can only replicate within a living cell. They lack basic functions such as synthesis of nucleic acids, protein synthesis (no ribosomes), and the generation of ATP.

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3
Q

What is uncoating?

A

The break down and release of the virus particle in which releases the genomes within the cell or injects it.

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4
Q

Genomes can be:

A

RNA or DNA (not both), circular or linear, and ss or ds.

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5
Q

The protein coat of a virus that contains capsomeres

A

Capsid

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6
Q

Nucleocapsid

A

The capsid with an enclosed genome

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7
Q

Virion

A

The complete, infectious virus particle that contains a capsid, genome, and maybe an envelope.

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8
Q

Proteins that cover and protect the genome of the virus that can also hold enzymes or proteins to be carried with the genome

A

Capsomeres

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9
Q

The phospholipid bilayer that contains virals proteins which a virus acquires when it buds out of the host cell

A

Envelope

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10
Q

What was the first genome to be sequenced?

A

Microviridae

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11
Q

What are the five morphological structures of a virus?

A
  1. Naked polyhedral
  2. Naked helical
  3. Enveloped polyhedral
  4. Enveloped helical
  5. Complex coated virus that can contain both or defy morphological classifications.
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12
Q

What was the first virus ever discovered?

A

Tobacco mosaic virus

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13
Q

What is enveloped complex?

A

When a virus has a capsid that is neither helical or icosahedral with an envelope.

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14
Q

T-even Bacteriophages contain what type of structure?

A

The capsid is icosahedral while the sheath is helical and has no envelope.

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15
Q

-virales is …
-viridae is …
-virinae is …
-virus is …
-viriodae is …
What system is this?

A
  1. Order
  2. Family
  3. subfamily
  4. genus
  5. sub-viral agents
    The international committee on taxonomy of viruses.
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16
Q

What classification system is based on genome and replication?

A

The Baltimore classification of viruses

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17
Q

What are the seven Baltimore groups?

A
  1. dsDNA - transcription of - strand to make mRNA. Normal transcription.
  2. ssDNA (+ sense) - synthesis of dsDNA intermediates and then transcribe it into mRNA from + strand. Uses host cell’s proteins.
  3. dsRNA - Transcribes the -strand into +strand mRNA using viral RNA pol.
  4. +ssRNA - used directly as mRNA.
  5. -ssRNA - Synthesizes +ssRNA by viral RNA pol then into mRNA.
  6. ssRNA (reverse) - The virus packages a reverse transcriptase that produces dsDNA copies from RNA. dsDNA is integrated into the genome and transcribed into mRNA by cellular RNA pol II.
  7. dsDNA - transcribed and then reverse transcribed by reverse transcriptase.
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18
Q

Protomer

A

one viral protein or complex of proteins in a capsomer.

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19
Q

hexamer

A

contains 6 protomers.

Can be calculated using 10(T-1)

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20
Q

pentamer

A

contains 5 protomers.

There are 12 in an icosahedral.

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21
Q

T/F - A capsid contributes most of the mass to a small virus

A

True

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22
Q

Assemble spontaneously

A

self-assembly

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23
Q

Genomic economy

A

composed of may copies of identical subunits

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24
Q

How to calculate protomers in an icosahedral?

A

60 * T

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25
Q

What is quasi-equivalent?

A

When complex capsids have repeating subunits that interact with one another that is similar to a smaller virus. So, 6 tails is similar to 5 tails.

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26
Q

What is triangulation number?

A

T = h^2 + hk + K^2

calculated from center of one penton to the next using the shortest path.

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27
Q

T/F - Envelopes are more common in plants than anima viruses?

A

False

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28
Q

What is chloroform sensitive or ether sensitive?

A

If a virus contains an envelope, the ether or chloroform destroys the envelope which is essentially killing the virus.

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29
Q

T/F - The complete virion of all viruses enters the host during infection?

A

False

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30
Q

T/F - Some viruses have an inner and outer capsid?

A

True

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31
Q

T/F - All virus genomes must code for one protein

A

True

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32
Q

Scaffolding proteins

A

Assist in the formation of the pro-capsid by coassembling with the capsid proteins.

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33
Q

Core proteins

A

Condense viral DNA by neutralizing the negative charges of the phosphate groups.

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34
Q

T/F - Envelopes that bud outward have the same levels of cholesterol and phospholipids of the membrane.

A

True

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35
Q

T/F - Capsids usually assemble around the genome

A

True

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36
Q

Which capsid needs ATP hydrolysis?

A

Scaffold icosahedral capsid

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37
Q

T/F - Every virion assembled is functional

A

False

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38
Q

T/F - Tobacco mosaic virus is icosahedral

A

False, helical

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39
Q

When is quantitative PCR used?

A

Want to measure the abundance of a virus when you know the genome of a virus but do not know what host it infects.

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40
Q

What size of pore in the filter is suitable for collecting and concentrating viruses on the surface of that filter?

A

0.02 um

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41
Q

What size of pore in the filter is suitable for removing large molecules and other contaminants (viruses, bacteria, etc) on the surface of that filter?

A

0.2 um

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42
Q

T/F - The first gene sequenced was the MS2 coat protein gene

A

True

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43
Q

T/F - A bacterium can be lysogenic for a phage that belongs to the family Inoviridae.

A

True

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44
Q

Which gene is never present in the genome of viruses from the leviviridae familiy

A

the scaffolding protein gene

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45
Q

The genome of which of these bacteriophages encodes the most proteins

A

M13 - 11 proteins

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46
Q

T/F - There is only one family of bacteriophages that have single stranded DNA genomes.

A

False

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47
Q

Tailed phages are best classified as a part of what group

A

claudovirales

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48
Q

T/F - There is only one family of bacteriophages with ssRNA genomes

A

True

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49
Q

A complete carpet growth of bacteria in an agar plate

A

Lawn

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50
Q

Plaques

A

Zones of clearing in the lawn when a phage will attach to one bacterium by infecting it and lysing it then spreading to adjacent cells.

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51
Q

How do you purify a phage?

A

Successive repetitions of plaque assay

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52
Q

What is confluent lysis?

A

When the lawn gets completely wiped out by the phage.

53
Q

Titre

A

the number of particles per unit volume of suspension. PFU - plaque forming units.

54
Q

Ratio of PFU in viral suspension to number of cells plated or infected in some other way.

A

Multiplicity of infection

55
Q

T/F - Direct counts with an electron microscope or with fluorescence microscopy after staining nucleic acid is used for viruses that have hosts.

A

False, no hosts

56
Q

What methods are used for a known virus?

A

ELISA or fluorescence with labelled antibodies.

57
Q

T/F - isopycnic centrifugation separates viruses based on their buoyant densities

A

true

58
Q

What type of growth do viruses go through in host cells?

A

Exponential

59
Q

what does P = P0 x B^2 calculate?

A

The growth of a virus. Where P = final, P0 = initial, B = burst size, and N = generation time.

60
Q

A virus that infects bacteria

A

bacteriophage

61
Q

Who discovered bacteriophages?

A

Twort and D’Herelle

62
Q

What is phage transduction?

A

Bacterial donor and a recipient which both are susceptible to infection by the phage of interest. The phage is propagated in the donor in which some of the phages retain the bacterial DNA of the donor. This mutant phage binds to the recipient cell in which it replace the target allele with the donor’s allele.

63
Q

What is phage therapy?

A

Use of a phage to kill specific bacteria.

64
Q

Phage whose infection always results in production of new phages and usually cell lysis/

A

Virulent phage, lytic cycle

65
Q

What is a temperant phage?

A

Phage that can either replicate to produce progeny virions and cell lysis or enter a repressed state that can be harbored in the cell for multiple generations. Lysogeny.

66
Q

Integrates into plasmid or chromosome

A

prophage

67
Q

What group has not been discovered for phages?

A

ssRNA minus sense

68
Q

How many families of phages are in dsRNA and ssDNA?

A

one and two, respectfully.

69
Q

Lysogenic bacteria

A

when it harbors a prophage.

70
Q

What are the receptors of phages?

A

pili, flagella, capsular polysaccharide, S-layers, lipopolysaccharide, and outer membrane proteins/porins.

71
Q

Leviviridae

A

+ssRNA and it is icosahedral

Need RDRP

72
Q

Levivirus

A

genera of leviviridae that includes MS2, f2, and R17.

Encodes protein A, CP, lysis, and RDRP.

73
Q

who isolated the first RNA phage and which one?

A

Loeb and Zinder which was f2

74
Q

Allolevivirus

A

phage Qbeta

No lysis protein and encodes the same as levivirus

75
Q

f1

A

DNA phage

76
Q

Phage MS2

A

first gene ever sequenced –> coat protein gene.

Complete genome sequenced

+ssRNA genome

icosahedral.

77
Q

Maturation protein

A

called protein A, involved in attachment, entry and lysis

78
Q

Receptors of leviviridae?

A

The F-pilus in E. coli in which protein A binds to.

79
Q

T/F - simultaneous translation and transcription of RNA occurs in RNA phages

A

False

80
Q

What controls translation of lysis and replicase genes in phage RNA

A

RNA secondary structure.

81
Q

T/F - Translation of mature protein occurs only in nascent mRNA

A

True

82
Q

T/F - phage polymerase is a complex of 3 viral proteins and one cellular protein

A

False, one viral protein and three cellular proteins

83
Q

T/F - translation and replication compete in RNA phages

A

True based on replicase and ribosome

84
Q

Microviridae

A

Icosahedral phages with circular ssDNA genomes includes phage PhiX174

85
Q

microvirinae

A

subfamily of microviridae t

86
Q

gokushovirinae

A

subfamily of microviridae that includes chlamydia.

87
Q

Structure of microviridae

A

no envelope with T =1 with twelve spikes on capsid (G proteins)

88
Q

1st DNA genome sequenced

A

PhiX174

89
Q

how many proteins does phiX174 have

A

11 proteins –> look at notes for types

90
Q

T/F - genome synthesis and packaging occurs simultaneously in microviridae

A

True, circular ssDNA

91
Q

What does protein E do

A

Inhibits PG formation causing cell lysis

92
Q

Inoviridae

A

filamentous ssDNA which do not lyse the cell, it is not lysogenic. Includes M13 and f1. Helical

93
Q

What phages are ssDNA

A

f1 and M13

94
Q

Persistent infection

A

phages that are virulent but do not lyse their hosts.

95
Q

T/F - Both ssDNA and ssRNA using rolling circle mechanism

A

True

96
Q

When a phage changes the host’s properties that make it more pathogenic

A

lysogenic conversion

e.g. cholera toxin genes

97
Q

what are morons

A

extra genes from phages in a bacteria

98
Q

protein 3

A

binds to the F-pilus on E. coli cells for M13 and f1 (inoviridae)

99
Q

what phages are used in phage display assays

A

filamentous phages (inoviridae)

100
Q

T/F - some phages of the inoviridae are temperant phages

A

True

101
Q

What phage can reverse amyloid plaques in Alzheimers and parkinson’s

A

M13

102
Q

Replicative form (RF)

A

dsDNA intermediates

103
Q

phagemid

A

plasmid that can also be replicated as a phage using a helper phage that coinfects the cell

104
Q

Smith and Winter did what

A

phage display assays

105
Q

Caudovirales

A

tailed phages with dsDNA genomes. Includes pdoviridae, myoviridae, and siphoviridae.

106
Q

short non-contractile tails that include T7

A

podoviridae

107
Q

myoviridae

A

long rigid contractile tails, T2

108
Q

long flexible non-contractile tails

A

siphoviridae, lambda

109
Q

phage revealed that genes can overlap one another

A

PhiX174

110
Q

T/F - Not all phages need to bind to a receptor to initiate infection

A

False, always

111
Q

what is the T for leviviridae

A

T =3

112
Q

T/F - PhiX174 belongs to leviviridae

A

false, microviridae

113
Q

what genome does PhiX174 have

A

ssDNA

114
Q

what structure is PhiX174

A

icosahedral

115
Q

what phage has a naked helical structure

A

f1 and M13

116
Q

What order has ssDNA?

A

microviridae

117
Q

what phages cause persistent infection?

A

M13 and f1 –> inoviridae

118
Q

what phage does not have a RNA genome

A

f1 and M13, PhiX174

119
Q

T/F - PhiX174 contains a linear genome

A

False, circular

120
Q

what phage is tail-less

A

phiX174

121
Q

T/F - RNA phages contain a maturation protein that binds to the receptor

A

true

122
Q

T/F - DNA phages have a maturation protein

A

False, only RNA phages

123
Q

How many different proteins are present in a virion of phage M13?

A

5

124
Q

Estimates of the abundance of phages in environmental samples have primarily been made using:

A

Fluorescence microscopy and nucleic acid binding dyes

125
Q

T/F - The genome of adenovirus is replicated in the nucleus

A

true

126
Q

Which of these genes of phage T7 is transcribed by the E. coli (host) RNA polymerase:

1) RNA polymerase
2) Spanin
3) Terminase
4) DNA polymerase

A

1

127
Q

T/F - The genome of phage MS2 is larger than that of PhiX174

A

true

128
Q

Which protein encoded by the phage PhiX174 genome is part of the virion, but present at a lower copy number than other capsid proteins.

A

H

129
Q

T/F - The Phage T7 genome encodes a single-gene lysis protein

A

False

CMMB 421 (2 decks)

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