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Chapter 28 Flashcards

Retroviruses

1
Q

Rous showed

A

Rous Sarcoma virus inducing tumor formation in chickens

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2
Q

Retroviridae has 7 genera, grouped based on

A

differences in morphology, genome organization

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3
Q

there is Lentivirus of

A

HIV type 1 with humans as host

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4
Q

general virion structure

A

enveloped, icosahedral or conical capsids with 3 different enzymes contained

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5
Q

the three different enzymes are

A

reverse transcriptase, integrase, protease; encoded by viral genome

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6
Q

the virion contains inside

A

tRNA, 2 copies of RNA genome (diploid and dimerized)

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7
Q

on the surface it has

A

transmembrane protein, surface protein (bound to TM), matrix protein

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8
Q

on the capsid it has

A

capsid protein (icosahedral) and nucleocapsid protein (coating genome)

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9
Q

inside the lipid bilayer, there is

A

matrix protein and capsid protein, cpsid protein and nucleocapsid proatein coating the genome

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10
Q

general genome structure

A

(+)-sensed ssRNA, 5’-capped and 3’-poly(A)
repeated sequence of R at 5’ and 3’ ends
unique regions of U5 and U3
primer binding sequence and polypurine tract
splice sites 5’SS and 3’SS
[psi] is at downstream of 5’SS

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11
Q

U5 contains

A

RNA dimerization hairpin that allows RNA to interact, where both RNAs interact with each other through U5 sequence

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12
Q

PBS binds to

A

tRNA in the virion. the type of tRNA packaged into genome is dependent on the virus.

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13
Q

SS is used to

A

splice out that part of genome and generate spliced mRNA.

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14
Q

[psi] is a packaging signal that

A

used to create an assembly of progeny virus

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15
Q

polypurine tract is important for

A

transcription reaction

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16
Q

there are three main polyproteins genes

A

group-specific antigen
polymerase (readthrough/framshift)
envelope (spliced mRNA)

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17
Q

surface protein (SU) recognizes

A

specific cell receptors, which indicates what type of cells the virus infect

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18
Q

after binding, the virus either

A

fuses with plasma membrane (endocytosis)

or pH-dependent fusion mediated by TM

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19
Q

once the penetration happens, capsid (CORE) is inside the cell, and

A

reverse transcriptase will start to copy RNA and synthesize dsDNA

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20
Q

after reverse transcription, dsDNA and proteins can be either

A

directly transported into nucleus as Lentiviruses and HIV, or must wait until nuclear envelope to desintegrate during the cell cycle

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21
Q

integration occurs to

A

the host’s genome

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22
Q

for synthesizing complementary DNA, both

A

RNA and DNA can be used as a template

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23
Q

RT starts as

A

tRNA inside the virion binds to PBS in the viral genome

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24
Q

RT needs

A

vRdDP and rDdDp

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25
once tRNA bound, enzyme uses this as
a primer to initiate synthesis of (-)-sensed DNA (Strong-stop DNA)
26
When the synthesis reaches the end of the genome,
it ends abruptly.
27
after the stop of synthesis,
RNAse H (Ribonuclease H) digestion occurs to get a complement of U5' and R5' regions of newly synthesized DNA to be exposed.
28
R is also present at 3' end, and the newly synthesized DNA is transferred to
R at the 3' end, to continue with the synthesis
29
after the continuation of DNA synthesis from the 3' end to PBS,
another RNAase H digestion occurs, with ppt remaining intact to the DNA
30
another synthesis occurs on ppt with
(+)-strand strong-stop DNA
31
once (+)-strand strong-stop DNA is made,
RNAse H digestion occurs with second strand of U3-R-U5-PBS to PBS' of the first synthesized genome
32
when two DNA genomes are hybridized,
extension of both DNA strands occur with forming LTR.
33
LTR is
a long terminal repeats on proviral DNA genome with U3, R, U5 sequences
34
RT is
RdDp and DdDp that is primer dependent for synthesis initiation
35
the order of RT is
(+)-stranded ssRNA -> (-)-stranded DNA -> dsDNA in CORE
36
RT has no
3'-to-5' exonuclease, consequently no proofreading
37
due to 1-10 substitutions per genome, the virus is considered
quasipecies that has variants in a single infeciton that differ by a small number of mutations
38
quasispecies are allowed for
rapid adapation, facilitating drug resistance
39
proviral integration happens at
random sites within the cellular genome
40
integration is catalyzed by
the viral integrase (IN)
41
to initiate, integrase binds to
both ends of dS DNA and brings them close to cDNA
42
near the cDNA, integrase
removes 2 nucleotids from each 3' end of the dsDNA, makes 4-6 nucleotides cut in cDNA, and ligate 3' ends of vDNA to cDNA
43
the ligation results mismatches of gaps that allow
host's enzymes to repair two unpaired viral nucleotides that stick out
44
provirus becomes part of host cell chromosome is replicated
along with host genome
45
proviral integration makes spread of infection by
infection of new cells with progeny virus, | multiplication of cells with integrated proviral DNA
46
integrated proviral DNA in egg or sperm can
transmit virus to offspring
47
integration makes the virus difficult to
be cured, because it is latent and does not express
48
after the RT and integration,
expression of viral RNA, viral protein synthesis, virion assembly are followed
49
in the genome replication, there are enhancer sequences and TATA in U3 sequence that recruit
TFs to U3 regiong, bringing cellular polymerase
50
when Pol II is brought to the LTR [L], it will begin
transcription initiation, with Pol III transcribing R sequence through U5 and to LTR [R]
51
in LTR [R], AAUAAA signal is for
cleavage and polyadenylation, with CF coming to cleave RNA after R sequence
52
transcribed RNA has
5'cap and poly[A] tails
53
full-length RNA transcribed can be for
mRNA or genome
54
translation of the RNA can be made for
Gag or Gag/Pol
55
transcribed RNA can be spliced to
remove Gag/Pol sites with 5'ss and 3'ss
56
the spliced mRNA can be used for
translating the Env gene
57
[psi] is the packaging signal only present in
full RNA, not present in spliced RNA
58
the LTR [L] is used for intiation, because
complex binding to it will dislodge the LTR
59
during transcription of proviral DNA, Promoter Occlusion TFs and RNA Pol complex that bind to the LTR [L] would
remove any complex bound to the LTR [R]. defining directionality
60
Only LTR [R] that gets transcribed is
U3, because it has signal function of directing poly[A] and cleavage with AAUAAA signal
61
U3 on LTR [L] is not
transcribed
62
the AAUAAA located in U3 allows the CF to find
cleavage signal in the R region, in which one from LTR [R] will enhance R to be recognized
63
however, AAUAAA is actually located in R, but it is U3 that contains
enhancer of AAUAAA that functions in RNA only
64
simple retroviruses make
full lengthed and spliced mRNAs
65
full length mRNA is used for
expression of Gag polyproteins that process into MA, NC, CA
66
ribosomes can also make
Gag/Pol to make PR, RT and INT as well, made in smaller amounts
67
synthesis of Pol is regulated to be less than
synthesis of Gag
68
for gamma, Gag/Pol is made by
readthrough at stop codon after Gag reading frame UAG->CAG (glu)
69
for HIV, Gag/Pol is done by
frameshift, moving one nucleotide backward to resume in translation
70
after spliced, mRNA with Env gene can generate
SU and TM proteins
71
normally, the ribosome in retrovirus stops translating Gag gene at
AAA/AAC, upstream of a hairpin
72
when stopped at the AAA/AAC, the ribosome occassionally moves one nucleotide backward to be in a frame of
AAA/AAA, not recognizing the stop codon
73
AAA/AAC and AAA/AAA can be possible, because both interact with
RNA codon and tRNA codons (Phe and Leu) are very similar
74
NC binds to
[Psi] which will nucleate assembly
75
SU and TM process from Env are translated in
ER and go through the Golgi and transported to PM
76
after nucleate assembly,
CA is added next to form a core
77
newly formed core buds from cytosol into
plasma membrane, along with SU and TM
78
PR mediates
maturation
79
two classes of oncogenic retrovirsues are
acute transforming and nontransforming
80
acute transforming is when
rapidly transformed cultured cells and induce cancer quickly
81
nontransforming is when
inducing cancer after a long latency period
82
acute transforming retroviruses encode
extra protein not required for virus replication
83
Rous contains
src, sarcoma
84
src is almost identical to a cellular gene of
c-src (tyrosine kinase) that regulates cell cycle
85
nontransforming retrovirus does not encode
an oncogen
86
nontransforming retrovirus results
loss of regulation from integration in or near cellular genes that alter normal expression fo cellular gene
87
when a promoter insertion happens with exon 1 in upstream of the viral genome,
the transcription from LTR [R] occurs without a proper amount or timing
88
a potential of gene-therapy can be found from
the retrovirus ability to integrate into host genome to "replace defective genes"
89
retroviral vectors often made with
Gag, Pol and Env deleted to prevent virus replication, and desired genes to take the place of viral genes
90
the limitation of the retrovirus-based gene-therapy is
size limit on RNA that can be packaged, and insertion of gene near oncogene can cause cancer
91
retroviral gene therapy has been used for treatment of
SCID, from a mutation in a cellular receptor required for differentiation of T-lymphocytes
92
SCID is treated with
removing hematopoietic stem cells, infect cells with retroviral vector containing normal gene, reintroduce cells into body to differentiate and proliferate

BIOL 3155 (16 decks)

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