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.
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.
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.
4
Q
Genomes can be:
A
RNA or DNA (not both), circular or linear, and ss or ds.
5
Q
The protein coat of a virus that contains capsomeres
A
Capsid
6
Q
Nucleocapsid
A
The capsid with an enclosed genome
7
Q
Virion
A
The complete, infectious virus particle that contains a capsid, genome, and maybe an envelope.
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
9
Q
The phospholipid bilayer that contains virals proteins which a virus acquires when it buds out of the host cell
A
Envelope
10
Q
What was the first genome to be sequenced?
A
Microviridae
11
Q
What are the five morphological structures of a virus?
A
- Naked polyhedral
- Naked helical
- Enveloped polyhedral
- Enveloped helical
- Complex coated virus that can contain both or defy morphological classifications.
12
Q
What was the first virus ever discovered?
A
Tobacco mosaic virus
13
Q
What is enveloped complex?
A
When a virus has a capsid that is neither helical or icosahedral with an envelope.
14
Q
T-even Bacteriophages contain what type of structure?
A
The capsid is icosahedral while the sheath is helical and has no envelope.
15
Q
-virales is …
-viridae is …
-virinae is …
-virus is …
-viriodae is …
What system is this?
A
- Order
- Family
- subfamily
- genus
- sub-viral agents
The international committee on taxonomy of viruses.
16
Q
What classification system is based on genome and replication?
A
The Baltimore classification of viruses
17
Q
What are the seven Baltimore groups?
A
- dsDNA - transcription of - strand to make mRNA. Normal transcription.
- ssDNA (+ sense) - synthesis of dsDNA intermediates and then transcribe it into mRNA from + strand. Uses host cell’s proteins.
- dsRNA - Transcribes the -strand into +strand mRNA using viral RNA pol.
- +ssRNA - used directly as mRNA.
- -ssRNA - Synthesizes +ssRNA by viral RNA pol then into mRNA.
- 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.
- dsDNA - transcribed and then reverse transcribed by reverse transcriptase.
18
Q
Protomer
A
one viral protein or complex of proteins in a capsomer.
19
Q
hexamer
A
contains 6 protomers.
Can be calculated using 10(T-1)
20
Q
pentamer
A
contains 5 protomers.
There are 12 in an icosahedral.
21
Q
T/F - A capsid contributes most of the mass to a small virus
A
True
22
Q
Assemble spontaneously
A
self-assembly
23
Q
Genomic economy
A
composed of may copies of identical subunits
24
Q
How to calculate protomers in an icosahedral?
A
60 * T
25
What is quasi-equivalent?
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.
26
What is triangulation number?
T = h^2 + hk + K^2
calculated from center of one penton to the next using the shortest path.
27
T/F - Envelopes are more common in plants than anima viruses?
False
28
What is chloroform sensitive or ether sensitive?
If a virus contains an envelope, the ether or chloroform destroys the envelope which is essentially killing the virus.
29
T/F - The complete virion of all viruses enters the host during infection?
False
30
T/F - Some viruses have an inner and outer capsid?
True
31
T/F - All virus genomes must code for one protein
True
32
Scaffolding proteins
Assist in the formation of the pro-capsid by coassembling with the capsid proteins.
33
Core proteins
Condense viral DNA by neutralizing the negative charges of the phosphate groups.
34
T/F - Envelopes that bud outward have the same levels of cholesterol and phospholipids of the membrane.
True
35
T/F - Capsids usually assemble around the genome
True
36
Which capsid needs ATP hydrolysis?
Scaffold icosahedral capsid
37
T/F - Every virion assembled is functional
False
38
T/F - Tobacco mosaic virus is icosahedral
False, helical
39
When is quantitative PCR used?
Want to measure the abundance of a virus when you know the genome of a virus but do not know what host it infects.
40
What size of pore in the filter is suitable for collecting and concentrating viruses on the surface of that filter?
0.02 um
41
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?
0.2 um
42
T/F - The first gene sequenced was the MS2 coat protein gene
True
43
T/F - A bacterium can be lysogenic for a phage that belongs to the family Inoviridae.
True
44
Which gene is never present in the genome of viruses from the leviviridae familiy
the scaffolding protein gene
45
The genome of which of these bacteriophages encodes the most proteins
M13 - 11 proteins
46
T/F - There is only one family of bacteriophages that have single stranded DNA genomes.
False
47
Tailed phages are best classified as a part of what group
claudovirales
48
T/F - There is only one family of bacteriophages with ssRNA genomes
True
49
A complete carpet growth of bacteria in an agar plate
Lawn
50
Plaques
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.
51
How do you purify a phage?
Successive repetitions of plaque assay
52
What is confluent lysis?
When the lawn gets completely wiped out by the phage.
53
Titre
the number of particles per unit volume of suspension. PFU - plaque forming units.
54
Ratio of PFU in viral suspension to number of cells plated or infected in some other way.
Multiplicity of infection
55
T/F - Direct counts with an electron microscope or with fluorescence microscopy after staining nucleic acid is used for viruses that have hosts.
False, no hosts
56
What methods are used for a known virus?
ELISA or fluorescence with labelled antibodies.
57
T/F - isopycnic centrifugation separates viruses based on their buoyant densities
true
58
What type of growth do viruses go through in host cells?
Exponential
59
what does P = P0 x B^2 calculate?
The growth of a virus. Where P = final, P0 = initial, B = burst size, and N = generation time.
60
A virus that infects bacteria
bacteriophage
61
Who discovered bacteriophages?
Twort and D'Herelle
62
What is phage transduction?
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
What is phage therapy?
Use of a phage to kill specific bacteria.
64
Phage whose infection always results in production of new phages and usually cell lysis/
Virulent phage, lytic cycle
65
What is a temperant phage?
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
Integrates into plasmid or chromosome
prophage
67
What group has not been discovered for phages?
ssRNA minus sense
68
How many families of phages are in dsRNA and ssDNA?
one and two, respectfully.
69
Lysogenic bacteria
when it harbors a prophage.
70
What are the receptors of phages?
pili, flagella, capsular polysaccharide, S-layers, lipopolysaccharide, and outer membrane proteins/porins.
71
Leviviridae
+ssRNA and it is icosahedral
Need RDRP
72
Levivirus
genera of leviviridae that includes MS2, f2, and R17.
Encodes protein A, CP, lysis, and RDRP.
73
who isolated the first RNA phage and which one?
Loeb and Zinder which was f2
74
Allolevivirus
phage Qbeta
No lysis protein and encodes the same as levivirus
75
f1
DNA phage
76
Phage MS2
first gene ever sequenced --> coat protein gene.
Complete genome sequenced
+ssRNA genome
icosahedral.
77
Maturation protein
called protein A, involved in attachment, entry and lysis
78
Receptors of leviviridae?
The F-pilus in E. coli in which protein A binds to.
79
T/F - simultaneous translation and transcription of RNA occurs in RNA phages
False
80
What controls translation of lysis and replicase genes in phage RNA
RNA secondary structure.
81
T/F - Translation of mature protein occurs only in nascent mRNA
True
82
T/F - phage polymerase is a complex of 3 viral proteins and one cellular protein
False, one viral protein and three cellular proteins
83
T/F - translation and replication compete in RNA phages
True based on replicase and ribosome
84
Microviridae
Icosahedral phages with circular ssDNA genomes includes phage PhiX174
85
microvirinae
subfamily of microviridae t
86
gokushovirinae
subfamily of microviridae that includes chlamydia.
87
Structure of microviridae
no envelope with T =1 with twelve spikes on capsid (G proteins)
88
1st DNA genome sequenced
PhiX174
89
how many proteins does phiX174 have
11 proteins --> look at notes for types
90
T/F - genome synthesis and packaging occurs simultaneously in microviridae
True, circular ssDNA
91
What does protein E do
Inhibits PG formation causing cell lysis
92
Inoviridae
filamentous ssDNA which do not lyse the cell, it is not lysogenic. Includes M13 and f1. Helical
93
What phages are ssDNA
f1 and M13
94
Persistent infection
phages that are virulent but do not lyse their hosts.
95
T/F - Both ssDNA and ssRNA using rolling circle mechanism
True
96
When a phage changes the host's properties that make it more pathogenic
lysogenic conversion
e.g. cholera toxin genes
97
what are morons
extra genes from phages in a bacteria
98
protein 3
binds to the F-pilus on E. coli cells for M13 and f1 (inoviridae)
99
what phages are used in phage display assays
filamentous phages (inoviridae)
100
T/F - some phages of the inoviridae are temperant phages
True
101
What phage can reverse amyloid plaques in Alzheimers and parkinson's
M13
102
Replicative form (RF)
dsDNA intermediates
103
phagemid
plasmid that can also be replicated as a phage using a helper phage that coinfects the cell
104
Smith and Winter did what
phage display assays
105
Caudovirales
tailed phages with dsDNA genomes. Includes pdoviridae, myoviridae, and siphoviridae.
106
short non-contractile tails that include T7
podoviridae
107
myoviridae
long rigid contractile tails, T2
108
long flexible non-contractile tails
siphoviridae, lambda
109
phage revealed that genes can overlap one another
PhiX174
110
T/F - Not all phages need to bind to a receptor to initiate infection
False, always
111
what is the T for leviviridae
T =3
112
T/F - PhiX174 belongs to leviviridae
false, microviridae
113
what genome does PhiX174 have
ssDNA
114
what structure is PhiX174
icosahedral
115
what phage has a naked helical structure
f1 and M13
116
What order has ssDNA?
microviridae
117
what phages cause persistent infection?
M13 and f1 --> inoviridae
118
what phage does not have a RNA genome
f1 and M13, PhiX174
119
T/F - PhiX174 contains a linear genome
False, circular
120
what phage is tail-less
phiX174
121
T/F - RNA phages contain a maturation protein that binds to the receptor
true
122
T/F - DNA phages have a maturation protein
False, only RNA phages
123
How many different proteins are present in a virion of phage M13?
5
124
Estimates of the abundance of phages in environmental samples have primarily been made using:
Fluorescence microscopy and nucleic acid binding dyes
125
T/F - The genome of adenovirus is replicated in the nucleus
true
126
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
1
127
T/F - The genome of phage MS2 is larger than that of PhiX174
true
128
Which protein encoded by the phage PhiX174 genome is part of the virion, but present at a lower copy number than other capsid proteins.
H
129
T/F - The Phage T7 genome encodes a single-gene lysis protein
False
