Viral Replication Part II Flashcards
1
Q
have distint lineages that predate the origin of LUCA
A
viruses
2
Q
mutation rate and genome size relationship
A
inversely related
3
Q
have lower mutation rates than its counterpart (ss)
A
ssDNA
4
Q
viral genomes consist of either
A
DNA or RNA
5
Q
viral genome shape
A
linear or circular
6
Q
single-stranded viral genomes may be of either the
A
plus sense
minsu sense
7
Q
have the exact same base sequence as that of the
viral mRNA
A
plus configuration
8
Q
are complementary in base sequence to viral
mRNA
A
minus configuration
9
Q
- typically smaller than those of cells - encoding about __ genes
viral genome
A
350
10
Q
tiny viruses contain fewer than __nucleotides and only two genes
A
2000
11
Q
writing across of genetic information from a sequence of nucleic acid to the complementary sequence in messenger RNA (mRNA)
A
transcription
12
Q
converts genetic information from the language of bases in nucleic acid to the language of amino acids in proteins
A
translation
13
Q
DNA viruses after transcription, does this process to translate its proteins
A
transport
14
Q
if the enzymes are not present in the location they prefer, then the virus should do what
A
bring it along its capsid
15
Q
typical mRNA in eukaryotes are ___
A
monocistronic
16
Q
cystron means
A
gene
17
Q
1 mRNA is equal to how many genes
A
3 genes
18
Q
where does DNA virus do transcription
A
nucleus
19
Q
where do RNA viruses do transcription
A
cytoplasm
20
Q
why do RT viruses need to convert +ssRNA to -ssDNA
A
to introduce their genome as DNA
21
Q
type of Retrovirus where they have an option to do RT since they have the necessary enzyme
A
dsDNA
22
Q
virus enzyme for dsDNA to be converted to mRNA
A
DdRp
23
Q
virus enzyme for dsRNA to be converted to mRNA
A
dsRdRp
24
Q
virus enzyme for +RNA to be converted to mRNA
A
ssRdRp
25
virus enzyme for -ssRNA to be converted to mRNA
ssRdRp
26
can dsDNA do transcription in cytoplasm?
yes
27
general term for an enzyme that carries out transcription
transcriptase
28
virus that replicate in the nucleus generally use a _ enzyme
cell
29
virus that replicate in the
___ enode their own
cytoplasm
30
class of viruses that encode their own enzyme
III
IV
V
31
perfrom reverse transcription using reverse transcriptase (RdDp) but also have DdDp activity
retroviruses
pararetroviruses
32
generally replicate as an independent episome
which have a DNA genome but also use reverse transcription during replication
pararetroviruses
33
are transported from the nucleus to the cytoplasm, and virus proteins may be transported to various locations, including the nucleus
virus mRNAs
34
mRNA have several __
open reading frames (ORF)
35
which are sequences within the RNA that can be translated into proteins.
open reading frames
36
re rarely present in bacteria and their viruses.
introns
37
Some ___use the host DNA-dependent RNA polymerase for their transcription, while
others encode their own.
phage
38
enzyme for genome replication of class I-II
DdDp
39
enzyme for genome replication of class III-V
RdRp
40
enzyme for genome replication of class VI
RNA > RdDp > DNA >
DdRp > RNA
41
enzyme for genome replication of class VII
DNA > DdRp > RNA > RdDp
42
viruses that copy genome directly to DNA
DNA viruses
43
some DNA viruses replicate their genomes with an ___ intermediate
RNA
44
enumerate virus enzymes for genome replication
DdDp
RdRp
RdDp (RT)
45
enumerate cell enzyme
DdDp
DdRp (RNA poly II)
46
DdDp is brought by the virus if ther replicate in the ___
cytoplasm
47
location of viral genome replication of
some dsDNA viruses
cytoplasm/nucleus
48
location of viral genome replication of
dsRNA viruses
cytoplasm
49
location of viral genome replication of
+RNA viruses
cytoplasm
50
location of viral genome replication of
-RNA viruses (non-segmented genomes)
cytoplasm
51
location of viral genome replication of
retroviruses and pararetroviruses
cytoplasm/nucleus
52
location of viral genome replication of
ssDNA viruses
nucleus
53
location of viral genome replication of
-RNA (segmented genomes)
nucleus
54
DNA viruses replication depends on what __ they carry
enzyme
55
locations of virus genome replication in eukaryotic cells
cytoplasm
nucleus
dsDNA
cytoplasm - some
nucleus - some
56
locations of virus genome replication in eukaryotic cells
cytoplasm
nucleus
ssDNA
cytoplasm - /
nucleus - all
57
locations of virus genome replication in eukaryotic cells
cytoplasm
nucleus
dsRNA
cytoplasm - all
58
locations of virus genome replication in eukaryotic cells
cytoplasm
nucleus
+RNA
cytoplasm - all
59
locations of virus genome replication in eukaryotic cells
cytoplasm
nucleus
-RNA (non segmented)
cytoplasm - all
60
locations of virus genome replication in eukaryotic cells
cytoplasm
nucleus
-RNA (segmented)
nucleus (all)
61
These viruses replicate entirely in the cytoplasm because they carry their own RNA-dependent RNA polymerase (RdRp)
non-segmented RNA viruses
62
example of non segmented RNA viruses
rhabdoviruses
paramyxoviruses
filoviruses
63
These viruses require the host’s nuclear machinery for efficient replication, particularly cap-snatching, where they steal host mRNA caps to initiate viral transcription.
segmented RNA viruses
64
following attachment, entry, and uncoating, viral DNA is released into the ___
nucleus
65
transcription of the portion of the viral DNA into ___
early genes
66
genes required for the multiplication of viral DNA
early genes
67
after transcription of early genes, these stages occur
transcription and translation of late viral genes
genome replication
capsid synthesis
capsid proteins migrate to nucleus (maturation) to assemble
release of virus from host cell
68
replicate their DNA in the nucleus of the host cell by using viral enzymes
DNA viruses
69
synthesize their capsid and otherp proteins in the cytoplasm by using host cell enzymes
DNA viruses
70
in DNA viruses, ___ proteins migrate into the nucleus, join newly synthesized DNA to form virions
capsid
71
Following attachment, entry and
uncoating, viral DNA released into the
___.
cytoplasm
72
can transcription happen after translation?
yes
73
RNA viruses multiply in the host cell's ___
cytoplasm
74
major differences among the multiplication processes in how mRNA and viral RNA are produced
RNA viruses
75
how does -ssRNA replicagte?
-ssRNA > +ssRNA > -ssRNA
76
how does dsDNA reproduce?
translation begins immediately since transcription happens in capsid
77
+ssRNA, how do they reproduce
-ssRNA thru rdrp
78
79
origin of transcriptional components of retroviruses with simple genomes, caulimoviruses
host only
80
origin of transcriptional components of bacteriophages T3 and T7
host plus one viral protein (viral protein transcribes late genes)
81
origin of transcriptional components of parvoviruses, papillomaviruses, polyomaviruses, retroviruses with complex genomes, geminiviruses
host plus viral protein regulating transcription
82
origin of transcriptional components of adenoviruses, bacteriophages T4, herpesviruses
host plus several viral proteins
83
origin of transcriptional components of poxviruses
viral
84
for early proteins through viral RNA
polymerase – for __for transcription of viral DNA templates
poxvirus
85
In general, enzymes and regulatory
proteins needed in smaller quantities
made during the initial period of infection termed
early proteins
86
early/late viral proteins - necessary for efficient
viral gene expression, viral DNA synthesis,
or other regulatory functions.
early
87
Replicate DNA in the nucleus of the host cell by using
viral enzymes – cause inhibition of cell DNA synthesis
DNA animal viruses
88
by replication of DNA in the nucleus of DNA containing Animal virus, it creates __ near nucleus
replication centers
89
Template-directed; semi-conservative; by DNAdependent DNA polymerases
DNA containing animal virus
90
Transcription of the ___genes, most of which encode
structural proteins, requires genome replication.
late
91
___proteins of virus particles are made only
after viral DNA synthesis – late proteins
structural
92
93
structural proteins of virions include
capsid and other proteins
94
__proteins migrate into the nucleus, join newly
synthesized DNA to form virions.
capsid
95
RNA viruses multiply in the host cell’s
__.
cytoplasm
96
genome consists of two identical single-stranded RNAs of the
plus sense (only 1 is processed to become dsDNA) – security
copy
retroviruses
97
retroviruses have their genome coated by
nucleocapsid
98
enzymes in retroviruses
RT (50 to 100 molecules)
integrase
retroviral-specific protease
99
prefix retro means “backward,” and the term ___
refers to the fact that these viruses transfer information
from RNA to DNA
retrovirus
100
first viruses shown to cause cancer, and the human
immunodeficiency virus (HIV) is a ___ that causes
acquired immunodeficiency syndrome (AIDS).
retrovirus
101
enzyme for synthesis
of DNA from an RNA template
reverse transcriptase
102
enzyme for synthesis of
DNA from a DNA template; and
DNA polymerase
103
enzyme for digestion of
the RNA strand from an RNA:DNA
hybrid to leave single
-stranded
DNA.
Rnase H activity
104
can be
initiated in virus particles as soon
as the viral envelope is made
permeable to dNTP substrates
reverse transcription
105
it has been established that DNA
synthesis takes place in the
cytoplasm shortly after entry,
within a subviral nucleoprotein
structure that retains a partially
dissociated capsid.
what kind of virus
retroviruses
106
reverse transcription
in fact starts near the 5’ end of
the viral genome; 5’ end of the
genome RNA is degraded by
the RNase H domain of RT,
after (or as) it is copied to form (-) strand DNA.
what type of initiation of DNA syntehsis
- strand DNA synthesis
107
. RNA fragment by
Rnase H serves as the primer
for (+) strand DNA synthesis,
which begins even before (
-)
strand DNA synthesis is
completed
what strand of initiation of DNA synthesis
+DNA synthesis
108
One genus of retrovirus, ___,
includes the subspecies HIV-1 and HIV-2,
which cause AIDS
lentivirus
109
genome is replicated inside the host cell via
a DNA intermediate
what kind of virus?
retroviridae
110
uses the viral RNA as a template to
produce complementary double-stranded
DNA, however, lacks proofreading
reverse transcriptase
111
occurs without full
uncoating of the genome – prevents
translation
reverse transcription
112
usesd to degrade the original viral RNA of retroviruses
enzyme
113
viral DNA integrated into a host cell chromosome as a ___, indefinitely
provirus
114
115
retroviruses are released by ___
budding
116
viral DNA integrated into a host cell chromosome as a
provirus, indefinitely by what enzyme
integrase
117
* The __ carries two identical copies of the RNA
genome (orange).
virion
118
Reverse transcriptase, carried in the virion, makes
single-stranded DNA from viral ___and then
double-stranded DNA that integrates into the host
genome as a provirus.
RNA
119
Reverse transcriptase, carried in the virion, makes
single-stranded DNA from viral RNA and then
double-stranded DNA that integrates into the host
genome as a __.
provirus
120
Infected cells contain __ copies of pro-viral DNA.
1-20 copies
121
Transcription and translation of proviral genes leads
to the production of new virions that are then
released by ___.
budding
122
* first step in viral maturation is the assembly of the
protein ___; this assembly is usually a spontaneous
process.
capsid
123
* first step in viral maturation is the assembly of the
protein capsid; this assembly is usually a ___
process.
spontaneous
124
capsids of many animal viruses are enclosed by an
envelope consisting of
protein
lipid
carbohydrate
125
is encoded by the viral genes and is
incorporated into the plasma membrane of the host
cell.
envelope protein
126
___protein is encoded by the viral genes and is
incorporated into the plasma membrane of the host
cell.
envelope protein
127
* envelope protein is encoded by the viral genes and is
incorporated into the ___ ___ of the host
cell.
plasma membrane
128
portion of the plasma membrane, now the __, adheres to the virus.
envelope
129
assembled capsid containing nucleic acid pushes through the __membrane
plasma membrane
130
This extrusion of a virus from a host cell is one method of release called
budding (may not kill cells)
131
Nonenveloped viruses are released through ___in the host cell plasma membrane –
ruptures
132
* Nonenveloped viruses are released through ruptures in the host cell plasma membrane –
do they kill cells
yes
133
___, in hepadnaviral RT, as an intermediate in the replication of a virus with
a DNA genome – came as another surprise after
discovery of reverse transcription.
RNA
134
* incoming hepadnaviral genome is seen as “___” by the
cell – hence the cell enzymes do routine repair works.
damaged
135
No integrase; the repaired DNA remains in nucleus as
minichromosome which is transcribed to mRNAs.
which virus
hepadnaviral
136
what is the RT in hepadnaviruses
p particle
137
The DNA in
extracellular ___particles is a
partially duplex molecule of 3 kb with
circularity that is maintained by overlapping 5’
ends.
hepadnavirus
138
In mammalian hepadnavirus genomes, the (+)
strand is ___than the (-) strand and has
heterogeneous ends.
shorter
139
uses the host cell’s nucleotides and several of its
enzymes to synthesize many copies of itsDNA
phage
140
___transcribed from phage DNA for the biosynthesis of
phage enzymes and capsid proteins.
mRNA
141
host cell’s ribosomes, enzymes, and amino acids are used
for translation for this virus
phage
142
early/late messages are translated into early phage proteins,
the enzymes used in the synthesis of phage DNA.
early
143
___ messages are translated into late phage proteins for
the synthesis of capsid proteins.
late
144
in more complex DNA viruses such as bacteriophage T4, the
virus encodes its own
DNA polymerase
145
primases and helicases that function in viral DNA replication
are also encoded by the __ genome.
what phage genome
T4
146
T4 genome encodes three major sets of proteins
early
middle
late
147
proteins include enzyme in replisome for phage-specific genome; and modification proteins to modify host RNA poly in T4
early
148
include other proteins, structural and release proteins in T4 phage
middle and late
149
____polymerase is modified to recognize only phage promoter regions.
host RNA
150
* precursors of the bacteriophage head called __are assembled.
proheads
151
* precursors of the bacteriophage head called proheads are assembled.
what stage
maturation
152
* a __ ___ded by viral gene) is assembled at the opening to the prohead –
viral motor
153
is forcibly pumped into the prohead using an energy-linked packaging motor (ATP from host)
DNA genome
154
* ___ __ itself is discarded and the capsid head is sealed in phage
packaging motor
155
* tail, tail fibers, and the other components of the virion are added, primarily by ___ in phages
self assembly
156
* final stage of viral multiplication
release
157
is generally used for this stage in the multiplication of T-even
phages.
lysis
158
release where plasma membrane breaks open
lysis
159
phage genome encodes a pair of very late enzymes that combine to
breach the two major barriers to virion release: the host ___ and ___ layer
cytoplasmic membrane
peptidoglycan layer
160
which is encoded by a phage gene, synthesized within the
cell.
lysozyme
161
enzyme causes the bacterial cell wall to break down, and the
newly produced bacteriophages are released from the host cell
lysozyme
162
double-stranded DNA bacterial viruses, although able to catalyze a
virulent cycle, can also infect their host and establish a long-term stable relationship -
state called lysogeny
temperate viruses
163
double-stranded DNA bacterial viruses, although able to catalyze a
virulent cycle, can also infect their host and establish a long-term stable relationship -
state called
lysogeny
164
most virus genes are not transcribed, instead, the virus genome is replicated in
synchrony with the host chromosome and passed to daughter cells at cell division
what kind of virus-host state
lysogeny
165
Maintenance of the lysogenic state is due to a phage-encoded __ ___
repressor protein
166
in lambda lysogenic cycle, the originally linear phage DNA forms a __
circle
167
3B. circle can recombine with and become part of the
circular bacterial DNA (___).
prophage
168
Replication of bacterial chromosome replicates
the prophage DNA - prophage remains __within
the progeny cells.
latent
169
spontaneous event, or the action of UV light or
certain chemicals, can lead to the __(poppingout) of the phage DNA, and to initiation of the lytic
cycle.
excision
170
* a. ___cells are immune to reinfection by the same phage
lysogenic
171
which causes diphtheria,
synthesis of a toxin when it carries a lysogenic phage.
corynebacterium diphtheriae
172
toxin produced by ___ __, which causes
botulism, is encoded by a prophage gene, just as
clostridium botulinum
173
produced by pathogenic strains of E. coli.
shiga toxin
174
genes from previous host are
transferred to new host
specialized transuction
175
___viruses can undergo processes very
similar to lysogeny.
animal
