MST 1 (1-10) Flashcards
1
Q
what family is Influenza? and what genome is it?
A
Orthomyxoviridae
-ssRNA
2
Q
does influenza use splicing
A
-6 of its proteins code for 1 protein only
however 2 of them can use splicing to make non-structural proteins like NS1 (for immune evasion)
3
Q
are Paramyxoviridae enveloped?
A
Yes
4
Q
Does polio produce a long poly-protein? or individual proteins? How?
A
-polio will produce a large poly-protein
-this will then be cleaved by the viral protease
proteins are in Equimolar amounts
5
Q
what capsid does influenza have?
A
Helical
6
Q
What genome does Coronaviridae have?
A
+ssRNA
7
Q
where does reovirus replicate?
A
in its capsid - in the cytoplasm
as dsRNA is highly immunogenic
8
Q
How does Togaviridae regulate translation of its proteins?
A
- by using a sub genomic promoter
- structural proteins are made from the sub-genomic promoter which is not transcribed straight away
9
Q
What capsid does Poliovirus have
A
Icosahedral
10
Q
What capsid does Paramyxoviridae have?
A
helical
11
Q
is reovirus enveloped?
A
no
12
Q
How does Polio control transcription?
A
- it has a 5’ cloverleaf and a 3’ Pseudoknot that cell proteins bind to - they bring the ends together to form a loop
- this activates the RdRp, which will use the 5’ Vpg to start transcription
13
Q
What virus is in Caliciviridae?
A
Norovirus
14
Q
How does polio control translation?
A
- it has an IRES on the 5’ end
- ribosome and other translation factors will bind to IRES
- translation will occur CAP independent
15
Q
where does Paramyxoviridae replicate?
A
cytosol
16
Q
what capsid does Parvoviridae have?
A
icosahedral
17
Q
is influenza enveloped
A
yes
18
Q
where does Parvoviridae repliciate?
A
nucleus
19
Q
How does Coronaviridae control transcription?
A
- the common leader sequence is joined to one of several IG sequences
- it causes the RdRp to skip/frameshift
- this produces a nested set of discontinuous sub-genomic mRNA
- similar to splicing
20
Q
How does adenovirus enter the cell?
A
- penton spike binds to CAR receptor on host cell
- enters via endocytosis
- penton base’s release in the endosome which cause the endosome to lyse
21
Q
What viruses are in the Flaviviridae family?
A
Flavivirus and Hep. C
22
Q
Are Flaviviridae enveloped?
A
Yes
23
Q
What is the capsid structure for Flaviviridae?
A
Icosahedral
24
Q
Does influenza carry a RdRp in its capsid?
A
Yes
25
how does influenza enter the cell?
- HA attaches to sialic acid
- enters via endocytosis
- the acidification of the endosome causes a change in the HA which exposes a fusion domain that embeds into the target membrane and causes fusion
26
what capsid does reovirus have
icosahedral
27
what genome does Rhabdoviridae have?
-ssRNA
28
does paramyxoviridae have a segmented genome?
no - it is unimolecular
29
What capsid does Coronaviridae have?
Helical
30
How does LT protein drive DNA replication for SV40?
- in late gene transcription LT will form a hexamer around the Ori
- the hexamer will unwind the dsDNA and promote full dsDNA replication
- the transcription complex will bind and make lots of copies of circular dsDNA
31
what is the transcription process for SV40?
-early mRNAs are transcribed using the cells RNA pol. counter clockwise
-early proteins produced include Large T protein (LT) and short t protein (sT)
-LT will bind to the early gene promoter and make transcription fore efficient
-so many mRNAs will be made that it dilutes the inhibatory binding proteins present on the late gene promoters
-LT will then bind to the late gene promoters to drive late gene transcription - they will transcribe late mRNA as they are not repressed anymore
(LT dilutes the inhibatory proteins of the late genes)
-full DNA replication will also then occur - it occurs via fork replication from the Ori with a hexamer of LT
32
is herpes linear or circular
linear - but becomes circular in replication
33
how does influenza control transcription?
- the PB2 protein of the viral polymerase will bind to the 5' cap on cellular mRNA, and the PA protein will cleave it off and add it to the viral mRNA to use as a primer
- the RdRp will now use the viral -ssRNA to make + and - mRNA strands
34
Is Coronaviridae enveloped?
No
35
is adenovirus linear or circular
linear
36
what is significant about pox virus?
-it is the largest dsDNA virus, with a complex capsid
| IT IS THE ONLY DNA virus to replicate in the cytoplasm
37
What virus is in the Togaviridae family
Ross river
38
how does transcription occur for reovirus?
- it occurs in the capsid as the dsRNA genome is highly immunogenic
- the rdrp will transcribe mRNA
- the mRNA will be pushed out of the capsid into the cytosol for translation
39
is SV40 linear or circular
circular
40
how many segments does influenza have?
8
41
how does SV40 get over the end replication problem?
anti-repression
42
what genome does norovirus have?
+ssRNA
43
does reovirus have a rdrp?
yes
44
what dsDNA viruses use antirepression
adenovirus, herpes virus, SV40
45
How does Flaviviridae transcribe?
- it has complimentary sequences on its 5' and 5' end which come together to form a circle via complementarity
- the RdRp (NS5) recognises this and transcribes
- the NS5 is also a methyltransferase which adds a 5' CAP onto the new mRNA
46
What genome does poliovirus have
ss+RNA
47
where does influenza replicate?
nucleus! (rare for RNA virus)
48
what genome is SV40?
dsDNA circular
49
What virus is in the Picornaviridae Family
Poliovirus
50
what genome does Parvovirus have
ssDNA! (only ssDNA virus)
51
What genome does Togaviridae have?
+ssRNA
52
what virus out of all the dsDNA viruses is ss?
Parvovirus
53
what capsid does Togaviridae have
Icosahedral
54
what genome does reovirus have?
dsRNA! (the only dsRNA virus)
55
What genome does Flaviviridae have?
+ssRNA
56
what virus is in the Rhabdoviridae family?
Rabies
57
how does measles/mumps enter the cell?
it uses a fusion glycoprotein to enter via fusion at the plasma membrane!
58
how can polio dominate host translation?
- viral protein 2A will cleave cellular protein ELF4G which stops the cells ability to translate capped mRNA
- virus dominates the cell and cell will die after 4 hours
59
How does reovirus enter the cell
- virus enters via receptor mediated endocytosis
- the particle undergoes proteolysis by the cell proteosome and creates the ISVP
- the ISVP penetrates the membrane
60
how does poliovirus enter the cell
- binds to CD155 on host cell
- enters via receptor mediated endocytosis
- receptor binding causes a loss of VP4
- VP1 will now insert into the endosome membrane form a pore
61
How does norovirus control transcription?
-uses a sub genomic promoter to encode its structural proteins
62
What virus is in Paramyxoviridae family?
-measles and mumps
63
how does transcription occur for Parvoviridae
-as Parvoviridae is ssDNA it uses the cell transcription machinary to produce a dsDNA copy
-it has complementary sequences (inverted terminal repeat sequences) on its ends that fold back on each other to form pan handle structures
the ITR's act as a primer for transcription of a dsDNA strand
64
how does nucleoprotein assist Paramyxoviridae
-nucleoprotein is the first gene on the genome
-it is produced first, lots of it is made in early gene transcription (most abundant protein in the infected cell)
nucleoprotein can form the RNP complex which binds to the ig regions on the RNA to stabilise them - this allows for full sequence readthrough of the genome
-the nucleoprotein also self assembles to become the nucleocapsid
65
Does Flavivirus produce singular proteins, or a large polyprotein that is cleaved?
- it produces a large poly-protein that is cleaved by the viral protease enzyme
- all proteins are produced in equimolar amounts
66
How does Hep. C control translation
- it has IRES on the 5' end
- the host cell translation proteins will bind to this and start translation CAP independent
- Hep. C has a IRES but DOES NOT destroy the host cell machinary as polio does
67
how does norovirus control translation?
- translation is mediated by the VpG on the 5' end of the mRNA (called NS5 for norovirus)
- the translation machinery recognises the VpG and translates
68
how does HIV enter the cell
- gp160 is cleaved into gp120 and gp41
- gp120 and gp41 bind to CD4 which reveals a binding region on gp120 for CCR co-receptor
- when CCR is bound gp140 will bind to PM and cause fusion at the PM
69
how does Paramyxoviridae control transcription?
- in early transcription lots of early mRNA will be produced first (structural genes)
- the RdRp falls off at the ig regions on the genome hence lots of early genes made
- when nucleoprotein is produced it will form the RNP complex and bind to the Ig regions to stablise them
- full genome copies will then be produced
70
where does SV40 replicate?
nucleus
71
what family is Rotavirus in?
Reoviridae
72
Is Poliovirus enveloped
No
73
does Paramyxoviridae have a Rdrp in its capsid?
yes
74
Norovirus, is it enveloped?
No
75
How does Togaviridae control transcription?
- the Togaviridae has a sub-genomic promoter
- the subgenomic promoter can only be produced from the - strand of mRNA hence will not be produced straight away
- the sub genomic promoter encodes for the structural proteins
76
name the 6 DNA viruses
```
Pox
Herpes
Hepadna
Parvo
Papovavirus - SV40
Adenovirus
```
77
what is the only ssDNA virus
Parvovirus
78
what DNA virus replicates in the cytoplasm
Poxvirus
79
what type of genome does Herpes virus have
dsDNA linear but it can become circular during replication
80
what are the 3 structural proteins for SV40
VP1, VP2 and VP3
81
is SV40 circular or linear?
circular
82
how does SV40 replicate?
| early and late phase
- in the nucleus
- host cell polymerase will bind to the Ori and transcribe the early proteins first, including the transcription of LT protein (made by splicing)
- LT protein will bind to the early promoter and increase efficiency of early gene transcription
- when there is lots of protein produced - the inhibitory protein on the late promoter will be diluted. (anti-repression)
- LT will now bind to the late gene promoter and drive transcription of late genes
- LT will then form a hexamer around Ori, and unwind the dsDNA which will drive dsDNA replication. lots of dsDNA copies will be made
83
where does herpes virus replicate
nucleus
84
how does herpes virus replicate?
- it has terminal repeat sequences on its genome that ligate together to form a circle during replication
- it introduces a nick in one of the strands
- leading and lagging strand synthesis will begin, using the viruses own polymerase
- genome length copies of dsDNA will be made (concatemers) that are cleaved and encapsidated
- this is called 'rolling circle' and is a solution to the end replication problem
85
is adenovirus circular or linear
linear
86
what is adenovirus's solution to the end replication problem
- it uses its own protein primer - terminal protein
- which binds to the 5' end of the DNA strand to attract its own viral polymerase
- (DNA synthesis will occur in a 5' to 3' direction)
87
How does adenovirus regulate replication?
- early proteins will be transcribed first, and alternatively spliced
- early protein EIA will be translated, this will go back into the nucleus and increase transcription of early proteins
- EIA will also bind to the promoter of early protein E2 which will make lots of viral mRNA
- this will dilute the inhibitory proteins on the late gene promoter (anti-repression)
- E2 will now bind to the late gene promoter and drive transcription of late genes (structural genes)
88
what type of genome does parvovirus have?
| how does it replicate
- parvo has a ssDNA genome (rare)
- it replicates in the nucleus
- it has inverted terminal repeats that fold back on each other to form pan handles via complementarity
- the ITR sequence is used as a primer to synthesise DNA on one strand, then a dsDNA strand is formed
89
what type of genome does Hep. B have
| is it linear, or circular
dsDNA
| incomplete circular 'relaxed circle'
90
where does Hep. B replicate
in the nucleus
91
what type of capsid does hep b have
icosahedral
92
does hep b have a polymerase
-yes it is included in the capsid, bound to the genome
93
how does Hep. B produce 4 different mRNAs from its genome?
| what is the most important mRNA
- it has 4 different promoters that encode for 4 different mRNAs
- the most important mRNA is the pregenome mRNA which is more than one lap of the circle
- the pre-genome is important for producing infectious particles
94
what does the pre-genome mRNA of Hep. B make?
- the pre-genome makes the capsid and polymerase proteins
| - itself is also packaged into the capsid to make infectious particles
95
explain the replication process for hep. b
- enters hepatocyte cell
- the incomplete circular dsDNA enters the nucleus where the cellular machinary repairs it - to make a full covalently closed loop of dsDNA (the episome)
- the episome makes mRNA with the cell transcription machinery, and capsid and polymerase proteins are made
- a copy of the pregenomic mRNA will now be encapsidated by a capsid with a polymerase
- in the capsid (in the cytoplasm) reverse transcription of pregenome mRNA to dsDNA will occur
- the virus particle will then be released
96
explain the reverse transcription process for hep. b
| where does it occur
- it occurs in the capsid in the cytoplasm
- cis-acting signals will allow pregenome to be packaged into the capsid with a polymerase
- the Direct repeats on the mRNA are at the 5' and the 3' end
- the polymerase will bind to the 5' end and synthesise
- it will then template switch to the 3' end and finish the strand
- the RNA is degraded by RNAseH
- the dsDNA will then be made
97
where does retrovirus replicate?
nucleus
98
what is a simple retrovirus, what is a complex retrovirus
koala retrovirus
| HIV and HTLV
99
what genome does HIV have?
+ssRNA diploid
100
does HIV have an envelope?
| what is its capsid
yes
| icosahedral
101
what genes does the pro-viral HIV genome encode?
Gag Env and Pol proteins
gag - matrix, capsid and nucleocapsid
pol - reverse transcriptase
env - TM and SU glycoproteins
102
what genes have high sequence variability in retroviruses?
| why
gag and env genes
| the RT is highly error prone
103
retrovirus is diploid, how is it joined?
-joined loosely on the 5' end
-cellular tRNA binds to the primer binding site on each strand
the TRNA acts as a primer!
104
in koala retrovirus the gag-pol proteins are produced via frameshifting - how does this work
- -the provirus can express gag and pol via frame-shifting
- gag will be translated, the polymerase will hit a stem loop structure called a slippery sequence this will cause the polymerase to skip - the gag-pol polyprotein is produced this way
- gag-pol encodes a bunch of viral proteins
105
explain simple retrovirus replication process (koala retrovirus)
- the genome will not translate upon entry into the cytoplasm - first the pro-virus is made
- the virus enters via binding to CCR and CD4
- the capsid is released and will let DNTPs in (in cytoplasm)
- it will now make a dsDNA strand using its reverse transcriptase (dsDNA=provirus)
- the intergrase will bind to the dsDNA will translocate it to the nucleus -it becomes randomly integrated into the host DNA
- mRNA will be produced from the pro-virus to make proteins, others will become packaged into new virus particles
106
can simple retroviruses incorporate their DNA into terminally differentiated cells?
no (koala retrovirus)
| however complex retroviruses can - HIV
107
the intergrated provirus of retrovirus has a structure that is on either side of it - what is this called?
-the LTR sequences are on either side of the integrated viral DNA
-they are formed via the integration process
it will look like U3-R-U5-(viral DNA)-U3-R-U5
108
what are the differences between HTLV and HIV?
| what are the similarities
Differences:
HIV- spread by infectious particles, kills cells, makes more pro-virus to spread
HTLV - spread by infected cells, drives cell poliferation, uses cell mitosis to spread
both infect CD4 cells and have lifelong infection
109
where does HIV assemble?
at the PM in the cytosol
110
why is HIV a complex retrovirus?
it is complex because it can produce additional proteins via splicing
111
name the genes encoded on the provirus of HIV
Env- GP160 which is cleaved into gp120 SU and gp41 TM
Gag- matrix, capsid, nucleocapsid
pol - reverse transcriptase, integrase, protease
112
what genes encode for the structural genes of HIV?
gag and gag-pol
113
explain the replication cycle of HIV
- enters the cell via CD4 and CCR
- genome is released into cytoplasm
- here it will use its RT to make a dsDNA strand
- the integrase will recognise the LTR's on the ends of the dsDNA strand and translocate it to the nucleus where it will randomly integrate it into the host DNA
- the incorporated provirus can now produce mRNAs
- splicing of the mRNA can occur to produce around 40 different proteins - most of these will assemble on the PM
- after virus exit the gag-pol proteins will cleave all the proteins into their active form
114
when is HIV most suceptible to host recognition
when its assembling on the PM
115
what are the resevoirs for HIV infection?
resting memory t-cells
116
how do LTR sequences form on the HIV dsDNA
-it occurs when the RT duplicates the sequences at the ends of the viral RNA - this forms the LTRs on the DNA copies
117
what does the LTR sequence in the integrated HIV pro-virus do?
it acts as a promoter
the LTR has a binding site for TAT protein which increases transcription. it also has binding sites for cellular factor NFkB which increases transcription also
118
what are the two HIV regulatory proteins?
when are they made?
what do they do?
-Tat and Rev - they are produced via splicing
-TAT is made during early transcription
-initially lots of tat will be made which binds to TAR protein. it will bind to the start of the genome, make the RNA polymerase more effective and drive the transcription of lots of viral mRNA, including spliced mRNA
-Rev is produced a bit after, it will bind to the unspliced RNAs and stabilise them - to stop them being spliced. these mRNs will become structural proteins
(this is a timing mechanism - early lots of mRNAs, late - structural proteins produced)
119
what are the accessory proteins produced from HIV provirus? what do they do?
- Vif - blocks cell defence against ssRNA
- Vpr - allows the virus to infect a resting t-cell
- Nef -downregulates MHC
- Vpu - downregulates MHC
120
what gene has the most variability in HIV? why
the envelope gene
the RT is highly error prone
this allows the virus to escape immunity
121
how do viruses distinguish themselves from cellular rna?
packaging signals
| they are called psi sequences in the genome
122
how does the packaging signal for HIV work?
- the packaging signal is only retained in the RNAs that are not spliced
- there is a sequence loop (kissing loop) in the packaging signal that will hybridise to another kissing loop. this will form a dimer of -ssRNA
- the binding of the loops reveals a packaging signal that allows them to become encapsidated
123
what viruses form their virion structural units from individual proteins that come together during assembly?
- SV40 Vp1, Vp2 and Vp3 are formed seperately and come together during assembly
- so do adenovirus hexamers and penton spikes
124
what 2 viruses form large polyprotein units that are cleaved during assembly?
poliovirus - uses its own ribonuclease
| retrovirus
125
what is a virus that uses a viral chaperone to assemble? what is the chaperone called
Adenovirus uses L4 chaperone to assemble monomers into hexon trimers
126
what is a DNA virus that assembles in the cytoplasm?
Hep. B - it is a DNA virus, but it has a RNA pre-genome hence it assembles in the cytoplasm?
127
what are the two RNA viruses that replicate in the nucleus?
Retrovirus and influenza virus
128
SV40 is a dsDNA virus that assembles in the nucleus. How does its structural proteins enter the nucleus?
-Vp1 Vp2 and Vp3 have nuclear localisation signals that cell proteins bind to and take them into the nucleus
129
what is a NLS?
nuclear localisation signal
they are a string of basic amino acids flanked by hydrophobic amino acids
cell transport proteins bind to them to transport them into nucleus
130
How does herpes virus encapsidate its concatemers?
- viral DNA replication occurs in a rolling circle motion in the nucleus
- the capsid will form in the nucleus
- a bunch of proteins will bind to the 'portal' on the capsid
- the portal proteins will recognise the packaging signal on the concatemer (in the 'a' sequence at the start and end of the concatemer, has a PAC1 and PAC2 sequence)
- the proteins will begin stuffing the concatemer into the capsid and will cleave it off at the end
- now the viral genome is fully encapsidated
131
how does herpes exit the cell? what path does it take
it leaves the cell via the exocytosis route
it collects envelope and viral proteins along the way
exits via an exosome
132
how are mRNAs directed to the ER to be translated?
- these mRNAs have a string of 20 hydrophobic amino acids at their beginning that direct them to the ER
- the proteins will be translated into the RER
- they can undergo a range of modifications there
133
how to MOST enveloped viruses leave the cell?
| what are the exceptions?
- enveloped viruses leave via the golgi network
| - influenza and HIV are an exception. they assemble at the PM
134
what is the process of influenza assembly and exit
- influenza assembles in the nucleus
- the viral proteins that are expressed in the cytoplasm (M1, nucleoprotein and NEP) will translocate to the nucleus and attach to the influenza RNA
- they will transport influenza to the PM where it will assemble with the glycoproteins and bud off
135
how does Flavivirus exit the cell?
-it will assemble in the RER and use the golgi network to leave the cell via exocytosis
-in the process the cell enzyme furin will cleave the viral PrM to M
-this allows E to fuse with the plasma membrane and leave the cell
the pH also helps the virus to mature
136
how do the proteins for HIV assemble on the plasma membrane?
-they all have a code at their N terminus that sends them to the PM
137
what does host enzyme furin cleave on HIV?
it cleaves the Env. protein to produce active subunits on virus exit
138
how will non-enveloped viruses exit the cell?
most will lyse the cell upon exit!
139
how could a non-enveloped virus leave the cell without lysing it?
- enrobe themselves in lipid bilayer that is not an envelope
- this protects them from detection from Ab's and the in the blood stream
