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BIO 315 > Module 10: Viral Rep. Strategies (Viral Replication) > Flashcards

Module 10: Viral Rep. Strategies (Viral Replication) Flashcards

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1
Q

What determines HOW viral genome replication and viral mRNA production occur?

A

The TYPE of genome of a given virus!

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2
Q

What are the seven classes of viruses?

A

I) dsDNA
II) ssDNA
III) dsRNA
IV) (+) ssRNA
V) (-) ssRNA
VI) ssRNA with RT
VII) dsDNA with RT

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3
Q

What determines which of the 7 viral classes a virus falls into?

A

Based on two factors:

1) The TYPE of viral genome

2) HOW viral mRNA is produced

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4
Q

Class I virus: Genome replication

A

dsDNA genome is replicated in the hosts’s NUCLEUS with host’s DNA polymerase

dsDNA –> dsDNA

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5
Q

Class I virus: Transcription

A

viral dsDNA genome acts as the direct template for mRNA production

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6
Q

Class II virus: Genome replication

A

–> Replication occurs through a dsDNA intermediate that serves as the template for new copies of ssDNA genome

1) ssDNA genome + HOST DNA polymerase = dsDNA intermediate!

2) dsDNA intermed. + HOST DNA polymerase = ssDNA product!

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7
Q

What enzymes do Class I and II viruses use for genome replication and mRNA production?

A

Genome rep. = Host DNA Polymerase!

mRNA prod. = Host RNA polymerase

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8
Q

Class II virus: Transcription

A

–> ssDNA is first converted to a dsDNA intermediate which serves as template for mRNA by RNA polymerase

1) ssDNA genome + HOST DNA polymerase = dsDNA intermediate!

2) dsDNA intermed + HOST RNA polymerase = mRNA

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9
Q

Class III Virus: Genome Replication

A

–>dsRNA genome is replicated in CYTOPLASM with viral Rd-RP!

1) Rd-RP uses (-) strand of dsRNA genome as template for a new (+) ssRNA strand

2) Rd-RP forms second strand of ssRNA strand == dsRNA genome copy made

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10
Q

Class III Virus: Transcription

A

–> dsRNA genome serves as template for mRNA produced by Rd-RP!

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11
Q

Class IV Virus: Genome Replication

A

–> (+)-ssRNA genome is replicated in the CYTOPLASM with viral Rd-RP!

1) Rd-RP makes new strand bound to (+)-ssRNA genome ==dsRNA

2) Produced dsRNA is then used to make new copies of (+)-ssRNA by Rd-RP

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12
Q

Class IV Virus: Transcription

A

NO TRANSCRIPTION OCCURS!

–> (+)-ssRNA genome is used directly in translation! (b/c (+)-ssRNA = mRNA!)

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13
Q

Class V Virus: Genome Replication

A

–> (-) ssRNA genome is replicated in the CYTOPLASM with viral Rd-RP

1) Rd-RP first makes a dsRNA molecule
2) New (-) ssRNA genome copy is made from (+) strand of the dsRNA

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14
Q

Class V Virus: Transcription

A

(-) ssRNA genome serves as template for mRNA synthesis by Rd-RP

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15
Q

Class VI: Genome Replication and Transcription

(Process)

A

(+) ssRNA genome goes through a DNA intermediate!

1) REV. T forms dsDNA intermediate from (+) ssRNA genome

2) dsDNA copy (proviral DNA) integrates into host cell genome

3) Host RNA polymerase used to produce mRNA and ssRNA genome copies from

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16
Q

Class VII: Genome Replication and Transcription

(process)

A

dsDNA genome goes through an ssRNA intermediate

1) Host RNA polymerase acts on dsDNA genome to produce an ssRNA intermediate

2A) ssRNA intermediate is used directly in translation (as mRNA)

2B) REV. T acts on ssRNA intermediate to produce dsDNA copies of the original genome

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17
Q

What are the enzymes used by each class of viruses

A

Class I and II (DNA viruses) == Use HOST RNA + DNA polymerase

Class III, IV, V (RNA viruses) == Uses VIRAL RNA Dependent-RNA polymerase (Rd-RP)

Class VI (Retrovirus) == Uses VIRAL reverse transcriptase + HOST RNA polymerase

Class VII (Reverse-transcribing) == Uses VIRAL reverse transcriptase + HOST RNA polymerase

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18
Q

TYPICAL DNA Virus Replication Process

A

1) Entry + uncoating (in the cytoplasm)

2) DNA entry into nucleus

3) Replication and transcription of viral DNA genome by HOST enzymes!

4) Any produced mRNA leaves the nucleus and gets translated to produce the viral proteins

5) Viral proteins RE-ENTER nucleus

6) Nucleocapsid is assembled IN THE NUCLEUS

7) Nucleocapsid leaves nucleus and exits cell! (acquiring envelope if applicable)

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19
Q

WHERE does genome replication AND transcription typically occur in DNA viruses (Classes I and II)?

A

Within the NUCLEUS (using host enzymes)

–> mRNA is then trafficked out into cytoplasm for protein synthesis

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20
Q

WHERE does viral assembly typically occur in DNA viruses? (Classes I and II)

(Based on logic, why?)

A

Viral assembly occurs in the NUCLEUS

(Viral proteins made in the cytoplasm are trafficked BACK into the nucleus for this assembly)

WHY = Because DNA CANNOT leave the nucleus!!! So assembly must happen where the DNA is == nucleus

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21
Q

What is special about poxvirus replication?

A

Have dsDNA genome BUT DO NOT REPLICATE IN NUCLEUS!!

–> All genome replication occurs within the CYTOPLASM!!

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22
Q

Due to location of poxvirus replication, what enzymes are used?

Why?

A

VIRAL RNA-polymerase and DNA-polymerase!

Host RNApol and DNApol are only found within the NUCLEUS == if the poxvirus does not enter the nucleus, these enzymes CANT be used

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23
Q

What viruses are the exception to typical DNA virus replication process?

A

Poxviruses

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24
Q

Poxvirus Replication Process

A

1) Entry + uncoating of viral dsDNA AND release of viral RNApol (into cytoplasm)

2) Viral RNApol transcribes “early genes” == mRNA for viral DNApol

3) Early genes mRNA is translated to produce viral DNApol

4) Viral DNApol uses viral dsDNA genome as template for genome replication

5) Viral RNApol transcribes “late genes” == mRNA for viral capsid proteins AND viral RNApol

6) “Late genes” mRNA is translated to produce viral capsid proteins + RNApol

7) Assembly occurs
= Capsid proteins, dsDNA genome copy, and RNApol!

8) Viral particle exits and acquires envelope as it leaves

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25
Poxviruses: What are "late" and "early" genes?
Early + Late refers to locations on the viral dsDNA genome (early being closer to where transcription begins and late being farther) **Early Genes** = Contain the sequences for Viral DNApol **Late Genes** = Contain the sequences for viral capsid proteins AND viral RNApol
26
What do poxvirus particles need to carry with them for genomic replication and transcription?
**VIRAL RNA POLYMERASE** and their own **Transcription Factors (TF)** (plus dsDNA genome)
27
Poxvirus "Early genes" encode for...
Viral DNApol and other proteins needed for DNA replication
28
Poxvirus "Late genes" encode for...
Structural proteins needed for capsid and envelope formation
29
What is the main challenge RNA viruses must face when replicating in host cell? What is the "solution"?
**Problem** Their genome (RNA) does NOT match that of their host genome (DNA) == **host lacks machinery to make RNA copies from an RNA template** **Solution:** As a result, RNA viruses employ a VIRAL RNA-dependent RNApol (Rd-RP)
30
RNA-Dependent RNA Polymerase
Rd-RP = a viral polymerase that produces RNA from and RNA template strand
31
Where does RNA viral replication usually occur?
In the cytoplasm (because no host proteins can be used, so why waste the time to enter the nucleus)
32
(+)ssRNA Virus Replication Process (Class IV virus)
1) Viral entry and uncoating 2) (+)ssRNA genome DIRECTLY enters into translation 3) Translation produces capsid proteins AND **Rd-RP** 4) Translated Rd-RP uses (+) ssRNA genome as template for genome replication = produces (+) ssRNA copies 5) Viral capsid proteins and the (+) ssRNA genome copies assemble into progeny
33
How do (+) ssRNA viruses "get" Rd-RP?
They DO NOT carry Rd-RP itself --> Instead, these viruses **have Rd-RP encoded in their genome** which gets immediately translated and produced upon entry into cell
34
Infectious RNA
Genome of a (+) ssRNA virus that can direct the production of new viral particles after being injected into host cell
35
What is the difference between products of: Cells infected with isolated (+) ssRNA genome vs Cells infected with full (+) ssRNA viral particle
Products are the SAME! Because (+) ssRNA viruses have their genomes directly translated, the complete virion is NOT needed for proper viral replication!
36
For (+) ssRNA viruses, what parts of the viral particle are needed for proper replication? (What is NOT needed?)
ONLY the genome is needed! --> The complete virion (with capsids and all) is NOT needed!
37
In (-) ssRNA viruses, the genome has what relationship to mRNA?
(-) ssRNA genome is COMPLEMENTARY to mRNA!
38
What is the difference between (-) ssRNA viruses and (+) ssRNA viruses in their genome relationship to mRNA?
(-) ssRNA = Complementary to mRNA sequence (+) ssRNA = Identical to mRNA sequence!
39
(-) ssRNA virus replication process (Class V)
1) Viral entry + uncoating = releases (-) ssRNA genome AND viral Rd-RP! 2) Rd-RP uses (-) ssRNA genome as template to produce a dsRNA intermediate 3) dsRNA is then used by Rd-RP to produce mRNA transcripts AND full (-) ssRNA copies 4) mRNA is translated to produce viral capsid proteins AND viral Rd-RP 5) Assembly occurs = (-) ssRNA copies, capsid proteins, Rd-RP all combine together!
40
How do (+) ssRNA and (-)ssRNA viruses differ in the contents of their particles?
(+) ssRNA = just has its genome (-) ssRNA = has BOTH its genome and functional Rd-RP
41
Why do (-) ssRNA viruses need to carry Rd-RP with them in their nucleocapsid?
Because their genomes are not able to be directly translated to produce the necessary Rd-RP --> SO in order to get replication and transcription going, they must bring it with them into the cell to allow for transcription to occur (then triggering the rest of replication)
42
How do (+) ssRNA and (-) ssRNA viruses differ in how they begin replication?
**(+) ssRNA** = begins replication by being directly translated to give Rd-RP and mRNA **(-) ssRNA** = begins replication by the carried Rd-RP to produce mRNA and ssRNA copies immediately upon entry
43
What was the first identified retrovirus?
RSV (Rous Sarcoma Virus)
44
What is one of the most major retroviruses?
HIV (Human Immunodeficiency Virus) (Causes AIDS)
45
What enzyme do retroviruses depend on for genome replication?
Multifunctional Viral Reverse Transcriptase (Rev. T)
46
What is meant by "multifunctional" reverse transcriptase?
Rev. T used by retroviruses has two main abilities: 1) Work as an RNA-dependent DNA polymerase 2) Work as an endonuclease (RNAse H)
47
What is reverse transcriptase? (Rev. T)
An RNA-dependent DNA polmerase! --> = enzyme that uses RNA strand as a template for DNA strand synthesis
48
Rev. T Process with ssRNA
1) Rev. T uses ssRNA as template to synthesize a complementary DNA strand == HETERODUPLEX forms (Molecule with RNA + DNA strand) 2) Rev. T uses its RNAse H activity to degrade the RNA strand in the heteroduplex == ssDNA strand! 3) Rev. T uses synthesizes a second DNA strand from the generated ssDNA template == **dsDNA molecule!**
49
DNA:RNA Heteroduplex
Double-stranded nucleic acid molecule with: 1 RNA strand + 1 DNA strand
50
What virus class do retroviruses belong to?
Class VI --> (+) ssRNA viruses with RT
51
Retrovirus replication process:
1) Viral entry and uncoating = Releases (+) ssRNA genome, Rev. T, integrase 2) Reverse Transcription: a) Rev. T forms heteroduplex from (+) ssRNA genomic template b) RNAse H activity of Rev. T degrades the RNA strand in the heteroduplex to form ssDNA c) Rev. T makes second strand on ssDNA template = dsDNA copy 5) Viral dsDNA and integrase are transported into the host nucleus 6) viral dsDNA is integrated into the host genome, becoming a provirus 7) Host RNApol transcribes proviral DNA, making viral mRNA and ssRNA full-length viral genome copies 8) Viral mRNA + ssRNA genome copies leave nucleus 9) viral mRNA is translated == capsid proteins, Rev. T, integrase are produced 10) Viral assembly occurs in cytoplasm (Capsid, Rev. T, ssRNA genome, and integrase form one particle)
52
What enzymes do retroviruses depend on that they CARRY with them?
Rev. T + INTEGRASE
53
Integrase
Enzyme that mediates integration of viral DNA into a host cell genome
54
What is the role of integrase in retrovirus replication?
Integrase helps to integrate proviral DNA (DNA made from Rev. T) into the host genome
55
Provirus
Viral DNA integrated into host genome
56
What are the contents of a retrovirus particle?
1) (+) ssRNA genome 2) Rev. T 3) Integrase 4) Capsid (+ possible envelope)
57
With retroviruses, where does genome replication occur?
Within the nucleus --> Integrated DNA is transcribed by host RNApol
58
What are ALL the enzymes used in the entire retrovirus pathway?
1) Rev. T 2) Integrase 3) Host RNApol
59
Most currently known bacteriophages have what kind of genome?
(+) ssRNA genome
60
Lytic Phages are AKA...
"Virulent Phages"
61
Lytic Phage
A phage whose ONLY mode of replication involves lysing (killing) the host cell upon exit
62
Temperate Phages
Phages that have the OPTION of existing in a quiescent/latent state within a host cell or entering the lytic pathway
63
Prophage
The quiescent phage genome (latent form of a temperate phage genome within a host cell)
64
Prophages can exist one of what 2 forms?
1) Plasmid 2) Integrated into host cell genome
65
What is an example of a plasmid prophage?
Phage P1 in E. coli
66
What is an example of an integrated prophage?
Lambda phage in E. coli
67
How do plasmid and integrated prophages differ in replication?
**Plasmid Prophage** = Separate from host genome so host cell can replicate it separately from the host genome **Integrated Prophage** = Replicated ALONG with the host genome whenever the host cell divides
68
Lysogen
A bacterial cell containing a prophage
69
INDUCTION of the lytic pathway is possible in what type of bacterial strains?
In LYSOGENIC bacterial strains (lysogens)
70
What happens when lambda phage genome is injected into host cell? (Explain Process)
1) Injected lambda phage genome immediately circularizes upon entry into host cell 2) Transcription of viral genome occurs (dsDNA) 3) mRNA is translated; one product is viral integrase 4) Viral integrase facilitates integration of phage DNA into the host genome via recombination == Prophage forms
71
For lambda phage, what determines whether the phage undergoes lytic or lysogenic phase?
The ratio of repressor proteins cI and cro
72
cI gene
Gene on lambda phage genome that encodes for the **cI repressor** protein
73
cro gene
Gene on lambda phage genome that encodes for the **cro repressor** protein
74
What does cI repressor do?
Binds to promoter of cro gene = blocks transcription of genes needed for LYTIC cycle
75
What does cro repressor do?
Binds to cI gene promoter = blocks transcription of genes needed for LYSOGENIC Phase
76
cI high : cro low =
Lysogenic phase! (cI high = more blocking of the cro promoter = less transcription of genes needed for lytic phase)
77
cI low : cro high =
LYTIC phase (cro high = more blocking of the cI promoter = less transcription of genes needed for lysogenic phase)
78
What is the default cI : cro ratio within temperate phages?
Default = **cI HIGH** (lysogenic/quiescent phase is the "default")
79
What causes the "default" latent phase of a temperate phage to switch to the lytic phase?
A drop in cI levels! == triggered by cellular damage
80
What triggers cI levels to drop?
**Cell damage** (Ex: by mutagens, UV light, etc.)
81
Temperate phages TOGGLE between lytic and lysogenic phases in response to what?
In response to overall cellular health! (cell damage)
82
For most icosahedral viruses, how does capsid assembly occur?
Occurs via automatic SELF-ASSEMBLY! --> Capsid proteins "self-assemble" to form the full capsid structure
83
Capsid Self-Assembly
Chemical interactions between capsid proteins cause them to bind to each other == formation of capsomeres --> Chemical interactions between proteins of the capsomeres then cause the capsid as a whole to be assembled
84
What is an example of a that virus does not self-assemble viral capsid?
HIV
85
What special requirement does HIV capsid assembly have?
HIV capsid assembly requires virally encoded proteins that DO NOT reside within the mature virion! --> These "extra" proteins help to FORM the capsid but do not end up as part of the capsid in the mature particle
86
HIV capsid assembly
1) Viral proteins come together to form a non-infectious precursor capsid particle == has both the permanent capsid proteins AND helper proteins 2) Precursor capsid undergoes proteolytic processing == helper proteins are cleaved/removed from the capsid structure 3) mature infectious particle is produced
87
What drugs target the proper formation of HIV capsid?
Antiretroviral Protease Inhibitors
88
Antiretroviral Protease Inhibitors
Drugs that block proteolytic processing enzyme in retroviruses (Like HIV) == preventing non-infectious precursor from converting to mature infectious particle
89
What is the "extra step" that HIV must undergo during capsid assembly?
Must undergo proteolytic processing of precursor particle!
90
What are the 2 main ways that viral genomes are packaged into their viral particles?
1) Assembly AROUND viral genome 2) Partial capsid assembly
91
For viral genome packaging AROUND the genome, what element must the genome contain?
A PACKAGING SEQUENCE
92
Packaging Sequence
A sequence-specific assembly motif; specific sequences of viral genome that direct the selective packaging of the genome into the viral particle
93
How does viral genome packaging AROUND the genome occur?
Viral capsid proteins interact with the packaging sequence of the viral genome == causes the capsid proteins to come together AROUND the genome containing the motif
94
Partial Capsid Assembly
“Empty” capsids are partially assembled first and then the viral genome is inserted into these capsids
95
What is an example of a virus that assembles via partial capsid assembly?
Poliovirus
96
Process of poliovirus assembly
1) Capsid proteins assemble into capsomeres 2) Capsomeres assemble into small units 3) Small capsomere units coalesce around the genome molecule == formation of nucleocapsid
97
What 2 factors determine the EXIT mechanism a virus uses?
1) The host cell type 2) The virus type
98
General Enveloped Virus Egress Process
1) Viral proteins destined for viral envelope are inserted into a region of the host cell PM 2) Specific AAs in the tails of the viral envelope proteins embedded in the PM interact with the viral nucleocapsid, brining it close to the PM 3) Nucleocapsid BUDS OUT of the cell == Mature virion is formed as envelope is acquired through this process
99
What is a challenge Influenza faces upon egress from host cell?
THe HA proteins on the newly released virion immediately bind to the terminal sialic acid residues of the glycoprotein receptors of the host cell it just left == virion gets stuck! Can't actually spread to anywhere new
100
During Influenza egress, what molecule helps to "unstick" newly formed influenza particle from the host cell it came from?
NA (neuraminidase) == one of the viral envelope proteins of influenza
101
What is NA's role in influenza egress?
Cleaves the terminal SA off of the glycoprotein receptor of the host cell that the newly exited influenza particle bound to == FREES the influenza particle, allowing it to float away and spread!
102
Tamiflu
A drug that helps with the flu **An NA inhibitor**
103
How does Tamiflu work>
The drug prevents NA from cleaving terminal SA, ultimately preventing the freeing of newly formed influenza viruses == decreased viral spread!
104
For non-enveloped viruses, egress almost ALWAYS involves...
LYSIS of the host cell!
105
How do phages exit host cell?
By producing enzymes that destroy the bacterial host cell PM + cell wall! == Induces cell lysis!
106
How do non-enveloped mammalian viruses exit host cell?
Host cell becomes progressively more unstable as viral reproduction increases == cell LYSIS due to instability!
107
How does egress of phages + non-enveloped mammalian viruses differ? (Logically, why do these differences exist?)
**Phages** = Uses viral proteins to induce lysis **Mammalian** = Does NOT use protiens but rather relies on the natural instability of the host cell due to viral reproduction Why? == most likely b/c phage host cells are bacteria which have a cell wall, making them less susceptible to instability, SO creating instability by degrading the cell wall allows for lysis to occur (mammalian cells do not have this cell wall and therefore are susceptible to instability)
108
How do plant viruses exit host cells?
By plasmodesmata (moves into adjacent cell of same plant) or by outside forces (moves virus to cells of new plant)

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