Unit 2 Viral Replication Strategies Flashcards
Viruses are very ______ to a host cell/organism
What is an exception?
Specific
Influenza, it can target bird or swine in some strands
The possible range of interactions a virus can have with different host cells is dictated by the interaction between _______ and host cell receptor molecules
Viral Attachment Proteins
It is not wise to block receptors on cells that are used in viral infection because they have important cellular _____
Therefore, we try to block the______
functions
attachment
E. coli has many strains belonging to the same species, and these have antigenic variation for different surface proteins. Phage T2 and phage PP01 can infect different strains (K12 and O157), but what happens when you switch the surface proteins of the phages?
They infect the other strain that they couldn’t originally infect but that the other could.
Thus, host range is determined by phage attachment proteins (in this case, tail fibers)
Bacteriophages typically have what type of attachment proteins?
Enveloped viruses, like influenza, typically have what type of attachment proteins?
Non-enveloped (naked) viruses can have what two types of attachment proteins?
Tail fibers
Spike Proteins
Spike extending from viral capsid and attachment proteins that are a part of the viral capsid (capsomere proteins)
Can strain specificity exist within a single species?
What example of disease was used in class?
Explain what scientists observed
What human disease is a good example of this?
Yes
Mouse Hepatitis Virus
Mice with the Bgp1a receptor on host cells got infected with MHV while those without Bgp1b did not get infected. The small change in shape did not allow the attachment fibers to bind
HIV
Influenza is what type of virus?
What type of attachment protein does it have? What’s its name?
What type of capsid structure is it?
Enveloped
Spike protein, hemaglutinin(HA)
Helical
By what process does influenza enter the host cell?
What structure forms around the virus?
Endocytosis
Endosome
What structure helps beind the viral envelope and the plasma membrane of the host cell during entry of enveloped viruses?
Fusion peptide
What causes the endosome to break down and expose the viral membrane fusion peptide in the entry of enveloped viruses into host cells. It causes a change in shape of the protein (hemaglutinin in the influenza example)
What occurs after?
Then….
How?
Low pH (acidification)
Membrane fusion
Release of viral nucleocapsid
Enzymes
In the case of HIV, an enveloped virus, what is the surface protein it binds to on the host cell?
What are the spike proteins on the surface of HIV called?
CD4
gp120 and gp41
Which HIV spike protein binds to CD4?
What occurs next?
This triggeres a conformation change, what becomes exposed? It helps facilitate membrane fusion
After binding, this spike protein becomes exposed and interacts with the host membrane
What occurs next
gp120
It bonds to the co-receptor
Fusion peptide
gp41
gp41 folds and brings the viral envelope and PM together
What does Fuzeon do to block HIV?
It blocks gp41 folding in order to inhibit fusion
How is fuzeon imperfect?
It only lowers the amount of HIV, it is not perfect
It has to be in the right place at the right time
Viruses that enter bacteriophages are typically what kind of structure?
What cuts the peptidoglycan wall of the bacteriophage?
The virus can be ___ or _____
Does the capsid enter the bacteriophage?
Complex
Lysozyme
Lytic or Lysogenic
No, the genome is injected into the bacteriophage and the capsid remains outside of it
Plant viruses often require damage induced by insects to infect the plants cells because or tough.
what can cause this damage?
cell walls
Weather, insects, humans
Each virus may use a different method for viral uncoating, but the viral genome must be inserted into the host cell.
This exception we went over in class injects its genome into the host cell with the capsid staying on the outside of the host cell, pretty unusual.
Poliovirus
When poliovirus infects human cells, the poliovirus receptor on the host cell attaches to the caspid, and a conformational change causes it to be lost and replaced by a receptor from the virus that forms a pore in the host cell. What are the names of these proteins?
After the aforementioned process, the genome is inserted into the host cell
VP4 and VP1
What classes can DNA viruses be?
What classes can RNA viruses be?
What are these classes based upon?
What do those depend upon?
Class 1, 2, and 7
Class 3,4,5,6
Replication strategies
Replication strategies depend upon genome type
In class 1, what is the genome?
What is used to replicate this?
What occurs next?
which strand is read to make the mRNA?
Double stranded DNA
DNA polymerase
transcription
the negative strand is read to make +mRNA
In class 2, what is the genome?
For replication, what must be formed first?
For transcription, what must be formed first?
What type of mRNA is formed from transcription?
What strand is read, then?
Single stranded DNA (+ or -)
Temporary double stranded DNA intermediate
Temporary double stranded DNA intermediate
Always +mRNA for mRNA in all classes
(-) DNA strand
In class 7, what is the genome?
For replication, what is formed first?
What occurs next for replication? What carries this process out?
For mRNA formation, what occurs next?
Which strand is read to make the RNA?
Double stranded DNA
Single stranded RNA (+)
Reverse transcription. Reverse transciptase (a viral enzyme)
Transcription
the negative strand is read to make +mRNA
In class 3, what is the genome?
For transcription, which strand is used to make the
mRNA?
For genome replication, what is made first?
Double stranded mRNA
The minus strand is used to make +mRNA
+mRNA intermediate
In class 4, what is the genome?
For mRNA formation, what occurs?
For genome replication, what is made first?
Single stranded mRNA (+)
the +mRNA genome is used directly to make proteins
Double stranded RNA intermediate
In class 5, what is the genome?
For mRNA formation, what occurs?
For genome replication, what is made first?
Single stranded mRNA (-)
transcription to +mRNA
double stranded mRNA
For class 6, what is the genome?
For mRNA formation, what occurs first?
For genome replication, what occurs first
Single stranded mRNA (+)
Reverse transcription to double stranded DNA. Transcription to +mRNA follows from the negative DNA strand
Reverse transcription to double stranded DNA. the replicated genome is formed from the negative strand
During the replication of typical eukaryal DNA viruses, the DNa goes to the nucleus after the enzymes in the cytoplasm release them from the capsid. What do they do there?
Where do they go after and for what purpose?
Where do the resulting structures go?
Transcription
The transcribed viral DNA goes back to the cytoplasm for translation of proteins
The proteins go back into the nucleus
During the replication of typical eukaryal DNA viruses, once the proteins have been formed from the viral genome and returned to the nucleus, what happens?
What other structures are on the virion?
Assembly of the capsid with the replicated genome and exit
Spike proteins
What was the example of atypical replication of eukaryal DNA viruses?
What is unique about it?
Poxvirus
transcription takes place in the cytoplasm, so it brings its own viral RNA polymerase
In the replication of the poxvirus, there are two types of genes. What are they?
Early and Late genes
This poxvirus gene leads to DNA polymerase after translation
Early Genes
This poxvirus gene leads to proteins for capsid contstruction
Late Genes
In the replication of positive sense RNA viruses, what is created initially by translation (this occurs sometimes, can also come packaged)
What does it make?
RNA dependent RNA polymerase
The complimentary -RNA strand
In replication of positive sense RNA viruses, if there is no envelope, what might occur?
Lysing by weakening of the cell membrane
In the replication of negative sense RNA, what must always occur?
Once the above occurs, protein translation or genomic replication can occur
Production of +RNA
In the replication of retroviruses, what is the first thing that occurs to the genome once inside the nucleus?
Note that spike proteins are eventually made too
Reverse transcription
In the replication of retroviruses, once the double stranded DNA has been made by reverse transcription, the DNA and viral protein integrase go into the nucleus and insert the DNA into the chromosome at a random positive. What is the viral DNA that has been inserted called? It doesn’t have to cut itself out.
Provirus
Where do spike proteins made coded for by the viral genome but made by the host cell go?
The host cells plasma membrane
What breaks down the packaging of enveloped viruses liked HIV?
Enzymes in the cytoplasm. There is polymerase in the cytoplasm which allows the DNA to be coded for
What two things occur for both lytic and lysogenic bacteriophages?
Assembly and penetration
A virulent bacteriophage is…
A temperate bacteriophage is…
Lytic
Lysogenic
What does the lytic virus code for that the host cell produces that eventually causes the cell to break and release mature phages?
Lysozyme
The lysogenic bacteria joins the host cell DNA to make a
How does it replicate
What might cause the prophage to become permanently integrated?
prophage
It replicates when the host cell divides
Mutation
With a bacterial provirus, what causes excision and return to the lytic cycle?
The environment (UV light, slowing of replication)
AKA bad environments
What two things are largely influential in determining whether a bacteriophage enters the lytic or lysogenic phase?
C1 and Cro
When there is a high amount of Cr1 promoter being expressed by RNA polymerase, creating the Cro repressor protein, which cycle occurs?
Lysogenic
When there is a high amount of Cro promoter being expressed by RNA polymerase, creating the C1 repressor protein, which cycle occurs?
Lytic Phase
The most common type of viral assembly is fast and cheap from an energetic perspective
Self-Assembly
These structures of viruses may interact with packaging sequences on the viral genome to coalesce around the nucleic acid (ex, tobacco mosaic virus)
Additionally, like the poliovirus, empty ____ may partially form then have the viral genomes inserted into them
Capsid proteins
Capsids
This means viral exit from the cell
Is the mechanism universal to all viruses?
Egress
No.
This type of viruses put viral proteins (spikes) in the host membrane, dock to them, and bud out of the cell, taking a portion of the plasma membrane with them
Enveloped Viruses
This virus types almost always exit the cell by lysis
This virus type may move from cell to cell by specific cytoplasmic interactions.
What are the cytoplasmic connections called?
Naked Viruses
Plant viruses (they move within one plant)
Plasmodesmata
How do plant viruses move from one plant to another?
Disruption of the cell wall structures, often by insects
This antiviral drug is a nucleoSIDE analog used for HIV
AZT
What is different about AZT that allows it to work?
What does it inhibit?
Why doesn’t inhibit DNA polymerase?
It has an N2 group attached to the 3’ carbon instead of OH
Reverse Transcriptase
Reverse Transcriptase has a higher affinity for it.
Another good antiviral that works by p[reventing the activity of the enzyme that helps a new virus detach from the infected cell
Tamiflu
Which protein helps the flu virus get into the host cell and eventually gets stuck to the receptor requiring cleaving
This surface protein cleaves the aforementioned protein from the cell receptor
Which does tamiflu act on?
Hemaglutinin
Neuraminidase
Neuraminidase
