Reading...
Play button
Play button
Use LEFT and RIGHT arrow keys to navigate between flashcards;
Use UP and DOWN arrow keys to flip the card;
H to show hint;
A reads text to speech;
136 Cards in this Set
- Front
- Back
|
What is the genome like of Picorna viruses?
|
linear, single stranded, ( + ) RNA, 7-8.5 kb
|
|
|
In what form are proteins translated for Picornaviruses?
|
One mRNA encodes for a single polyprotein that is cleaved by viral proteases to yield smaller functional proteins
|
|
|
What types of proteins does Picornavirus have?
|
4 capsid
1-3 proteases 6-8 replication proteins |
|
|
Where are the replication proteins often found?
|
Tethered to membranes in the cytoplasm (ie. ER membrane)
|
|
|
What type of capsid does the virus have?
|
Icosahedral
|
|
|
Do Picorna viruses have an envelope?
|
NO. The virus is naked
|
|
|
What is a protein that is unique to Picornaviruses?
|
VPg
|
|
|
What is VPg?
|
A small virus-coded protein that is covalently attached to the 5' end of the RNA genome
|
|
|
What is the function of VPg?
|
-Serves as a PRIMER for the viral polymerase to start replication
-Protects RNA from degradation by acting as a cap |
|
|
When does protease cleavage of the precursor polyprotein occur?
|
Immediately after translation
|
|
|
Why is the process of RNA replication so difficult to study?
|
Because RNA replication is associated with membranous vesicles in the cytoplasm, like the ER. Membrane proteins are hydrophobic and are difficult to study in vitro.
|
|
|
What are some members of the Picornavirus family?
|
Enteroviruses, Rhinoviruses, Cardioviruses, Foot and Moth Disease Virus
|
|
|
Where does poliovirus belong?
|
With the Enteroviruses
|
|
|
What do Rhinoviruses cause?
|
The common cold
|
|
|
What do Cardioviruses infect?
|
Mice, other animals
|
|
|
What does the Foot-and-Mouth Disease virus infect?
|
Cattle
|
|
|
How does death occur in viral infection?
|
Viruses do not directly kill the cells but rather take over the cellular machinery to multiply their virions
|
|
|
What are the triangles in the capsid of Picornaviruses formed by?
|
VP1/VP2/VP3
|
|
|
Which protein is cleaved to form VP1/VP2/VP3/Vp4?
|
P1
|
|
|
What is a protomer?
|
Size 5S
-Formed by VP1/VP2/VP3 |
|
|
What is a pentamer?
|
Size 14 S
-Formed by protomers |
|
|
What does the pentamer assemble to form?
|
The empty capsid, size 80S
|
|
|
How is the provirion formed from the empty capsid?
|
The genome is inserted into the empty capsid, leading to the provirion of size 150S
|
|
|
How does the provirion turn into an infectious virion?
|
VP0 is cleaved to VP2 + VP4
|
|
|
What are the two ways that RNA can be injected into the cytoplasm?
|
1) Endocytosis
2) Direct injection of RNA |
|
|
How is endocytosis of the Picornavirus particle achieved?
|
Binding of the picornavirus to its receptor, causing a conformational change of the receptor as well as endocytosis.
Once in the endocytotic vesicle, changes in pH allow the RNA to get into the cytoplasm through a hole made by VPg |
|
|
How is the direct injection of RNA into the cytoplasm achieved?
|
The virus can bind to the receptor, which will result in VP4 falling off. VP1 changes its conformation upon binding and forms a hole in the PM, allowing RNA to enter the cell.
|
|
|
What are three key components of the Picornavirus genome?
|
VPg protein at the 5' end
Poly (A) tail at the 3' end 5' non coding region has IRES (Internal Ribosome Entry Site) |
|
|
What is the difference between the picorna virus poly (A) tail and that of humans?
|
The virus codes for the poly (A) stretch in its genome, while in humans this tail is post-transcriptionally added by poly(A) polymerase.
|
|
|
What is the viral poly(A) tail used for?
|
It is used in replication, because the VPg primer has two U's, which will bind to A's after folding of the genome.
|
|
|
What are IRES? (Internal Ribosome Entry Site)
|
Long non-coding regions (500-600nt), forming a structure for non-conventional ribosomal attachment
|
|
|
Which protease is responsible for the first cleavage of the polyprotein into proteins P1, P2 and P3?
|
The protease encoded by the leader peptide
|
|
|
What are the P2 proteins and what are they used for?
|
2A, B, C
Needed to enable replication |
|
|
What are some key proteins that result from cleavage of P3?
|
3B= VPg
3C= main protease, conserved in all viruses 3D=RNA dep RNA polymerase |
|
|
What did Western-blots/x-ray analysis show about viral translation?
|
That while viral translation is on, cellular translation is shut off.
|
|
|
What does the IRES structure allow?
|
The ribosome to bind internally of the mRNA, while it normally binds to the 5' end
|
|
|
What are the two types of IRES structures?
|
Type 1: 6 stem looped
Type 2: 12 stem looped |
|
|
How does the Type1 IRES work?
|
A poly C binding protein binds to a stetch of C, either to loop 1 or 4
|
|
|
What happens when the polyC binding protein binds to loop 4?
|
This allows for ribosome binding and translation initiation
|
|
|
What happens when the poly C binding protein binds to loop 1?
|
It inhibits translation and activates replication
|
|
|
What is a key difference between Type 1 and Type 2 IRES?
|
In type 1, the AUG is NOT the initator sequence
In type 2, the AUG is the initiator sequence |
|
|
If you circularized ssRNA, what would be the only way you could get translation?
|
If the circularized ssRNA had IRES. (As there is no possibility for a cap its circularized!!!!!)
|
|
|
How is host translation shut off by the virus?
|
Proteases 2A or L cleaves off eIF-4G, which holds together the other proteins of the eIF-4F complex
|
|
|
What key protein falls off that prevents cellular translation?
|
eIF-4e (cap binding protein)!
|
|
|
Which components of the initiation complex are sufficient to drive viral translation?
|
Since the Picorna virus has an IRES, if it just has eIF4G with eIF4a it is sufficient for translation
|
|
|
While Picornaviruses use a protease to get rid of eIF4e, how do EMCV or Polioviruses do this?
|
Using 45-BP1. It will be activated by dephosphorylation and bind to eIF-4E and sequester it from the complex, preventing translation
|
|
|
Which viruses only have the 3C protease?
|
Hepatitis A, Parechovirus
|
|
|
What are some key features of the 3C protease?
|
It can cleave itself
Performs first three cleavages to get P1/P2/P3 Leads to chronic infections at low levels |
|
|
Which viruses also have 2A protease in addition to the 3C protease?
|
Rhinoviruses
|
|
|
What are some key features of the 2A protease?
|
-Can cleave itself
-Does not cleave other viral proteins -Can cleave host proteins |
|
|
What are some viruses that have the L protease in addition to 3C and 2A?
|
Cardioviruses, apthoviruses
|
|
|
Which virus has an exception relating to 3C?
|
Foot and mouth virus
-It has an 18 aa peptide inside the polyprotein instead of 3C which is a self-cleaving peptide. It is NOT a protease |
|
|
What is a final step to make the virus infectious?
|
Cellular protease Furin cleaves 1A to 1B
|
|
|
What is the difference between the replicative intermediate form of the Picornavirus RNA and the replicative form?
|
Replicative intermediate is (-) synthesized from (+) strands
Replicative form is the generation of (+) strands from these minus strands |
|
|
What is 3A?
|
Spans the ER, attatches to 3B
|
|
|
What are the three genera of the Flaviviridae family?
|
Flaviviruses
Pestiviruses Hepaciviruses |
|
|
What is an example of a Flavivirus?
|
Yellow Fever Virus that causes jauncdice
|
|
|
What are Pestiviruses?
|
Causes diarrhea in cows
|
|
|
What is an example of a hepacivirus?
|
Hepatitis C
|
|
|
How is Hepatitis C transmitted?
|
Through the blood (Percutaneous)
|
|
|
What does chronic hepatitis C infection lead to?
|
Progressively evolves to end-stage liver disease as cirrhosis and hepatocellular carcinoma
|
|
|
What is a therapy used to treat HCV patients?
|
Interferon-containing therapies
-they are cytokine homologs that induce an immune response |
|
|
What are some other treatments of chronic HCV?
|
Rebetron (Intron A + ribavirin)
Viraferon Peg Viraferon Peg+ ribavirin |
|
|
What is ribavirin?
|
A broad spectrum antibiotic
|
|
|
Which is the new "standard" therapy used to treat HCV?
|
Viraferonpeg + ribavirin
|
|
|
What are some limitations of these treatments for chronic HCV?
|
-Relatively limited efficacy (20-40%)
-Significant side effects leading to high discontinuation rates -High costs |
|
|
Does HCV have an envelope?
|
Yes! It takes the lipid bilayer from the cell
|
|
|
What are the structural proteins encoded by HCV?
|
E1/E2 and core proteins
|
|
|
What is the function of the E1/E2 proteins?
|
E1/E2 are glycoproteins inserted into the lipid bilayer. They bind receptors in the LIVER
|
|
|
What is the function of the core proteins?
|
They make the viral shell
|
|
|
What are the non-structural proteins?
|
NS3
NS5B P7 NS2 |
|
|
What is the purpose of NS3?
|
Acts as a protease at the N-terminus
Acts as an RNA helicase at the C-terminus |
|
|
What is NS5B?
|
RNA dependent RNA polymerase
|
|
|
What is P7?
|
An ion channel
|
|
|
What is NS2?
|
Cysteine protease, performs a single cleavage
After performing this single cleavage, functions in viral particle assembly |
|
|
What did treating the viral particle with detergents reveal?
|
In the presence of the detergents, the lipid bilayer fell apart. This suggests that the proteins cannot bind to each other and thus require a lipid bilayer to tether the proteins together in a complex
|
|
|
What are key enzymatic functions of HCV that are targeted by drugs?
|
Protease, helicase, polymerase activity
|
|
|
Where does the RNA replication complex form?
|
At the ER membrane
|
|
|
Where does maturation of the virus occur?
|
At the ER membrane
|
|
|
What does inhibition of NS3 result in?
|
Loss of production of 3A, NS4B, NS5A, NS5B
|
|
|
What type of protease is NS3?
|
Trypsin-like serine protease
Has a zinc-binding site |
|
|
What does Ns5A do?
|
It is a 6 amino acid cleavage product of NS3 which acts as a natural inhibitor of NS3 activity
|
|
|
How have scientists taken advantage of this natural inhibition of NS3 by NS5A?
|
They have used the hexapeptide NS5A as a template for drug production
|
|
|
What are two compounds that have been developed using NS5A as a template?
|
Compound A (hexapeptide)
BILN 2061 (tripeptide) |
|
|
Is there a primer for HCV replication?
|
NO! The NS5B initiates replication by associating with the IRES
|
|
|
Is there a poly A tail in the HCV genome?
|
NO! There is a 3' highly conserved, highly folded structure
|
|
|
Among HCV isolates, which components of the genome are variable and which are highly conserved?
|
The NS and S proteins can be different
The IRES and 3'UTR are highly conserved |
|
|
What is the HCV protein NS4A?
|
It is a small protein which is necessary for the NS3 protease to be functional
|
|
|
How does NS4 interact with NS3?
|
NS4 is released and beings to the NS3. Without NS4A, NS3 is not an efficient protease and it is also not attached to the membrane
|
|
|
What does HCV interact with at the cell surface?
|
CD81 and the LDL receptor
|
|
|
What are the three genera in the Flaviridae family?
|
Flavirus
Pestivirus Hepacivirus |
|
|
What are some examples of Flaviviruses?
|
West nile, Yellow fever, Dengue
|
|
|
Which of these viruses have a vaccine?
|
Yellow fever
|
|
|
What type of envelope do flaviruses have?
|
Spherical, with no projections
|
|
|
What is the diameter of the flavirus virion?
|
50 nm
|
|
|
What type of symmetry does the nucleocapsid have?
|
Icosahedral
|
|
|
What is the difference between flaviviruses, and polio/picornaviruses?
|
Polioviruses and Picornaviruses do not have an envelope, and flaviviruses do
|
|
|
What type of genome do flaviruses have?
|
linear, ssRNA, (+) sense, and has a size of 10-12.3 kB
|
|
|
What is a key difference between pestiviruses + HCV with flaviruses?
|
Flaviruses have a cap at the 5' end while pesitviruses and HCV have an IRES sequence!
|
|
|
Where do the capping enzymes of flaviruses reside?
|
Within the NS5 protein (RNA pol), ther is a methyl transferase that adds the cap
|
|
|
How are flavivirus virions assembled and released?
|
They are assembled by budding at the ER and are released by exocytosis
|
|
|
What are some diseases caused by flaviruses?
|
Yellow fever, Dengue fever, Japanese encephalitis, West Nile, TIck-borne encephalitis
|
|
|
What are the structural proteins of flaviruses?
|
Capsid protein C
Two envelope glycoproteins: M and E |
|
|
What is the function of capsid protein C?
|
Forms the shell that contains the RNA (Basic residues inside, bind RNA, hydrophobi residues outside and bind to envelope)
|
|
|
How are many flaviruses transmitted?
|
From host to host by mosquitoes or ticks
|
|
|
Which non-structural protein is a cofactor for the NS3 protease in flaviviruses? How does this differ from HCV?
|
The non-structural protein that is a co-factor for NS3 in flaviruses is NS2B. In HCV, it uses NS4A!
|
|
|
How are the envelope proteins arranged in the IMMATURE virion of flaviviruses?
|
M is in a preM form
E is in a monomer form and perpendicular to the plasma membrane. |
|
|
What happens to the envelope proteins when the viral particle gets close to the plasma membrane?
|
The host protease furin cleaves the prM to M
|
|
|
What does the cleavage of prM to M allow for the E envelope protein?
|
THe E protein is rearranged so it is now PARALLEL to the plasma membrane, and two E proteins bind together.
|
|
|
What does the rearrangement of E allow?
|
The exposure of the fusion peptide on E, resulting in fusion to the PM and release of the infectious viral particle!
|
|
|
What type of envelope do Coronaviruses have?
|
Spherical enveloped with clubbed spikes
|
|
|
How big is the Coronavirus virion?
|
120-160nm
|
|
|
What shape is the Coronavirus nucleocapsid?
|
Coiled helical
|
|
|
What type of genome do Coronaviruses have?
|
Linear ssRNA, (+) (27-32kB)
5' cap and poly A tail |
|
|
What forms do the (+) mRNA come in?
|
1 mRNA and many subgenomic mRNA
|
|
|
Which genes are translated first and from which type of mRNA?
|
The replicase genes are translated first, from the genomic mRNA that has two large ORFS joined by a frameshift. A polyprotein is synthesized which is cleaved to many functional proteins
|
|
|
What do the subgenomic mRNAs of Coronaviruses largely encode for?
|
The structural proteins: envelope, nucleocapsidm etc
|
|
|
What is the most common disease caused by coronaviruses?
|
Coronaviruses are responsbile for up to 30% of common colds
|
|
|
How are coronaviruses transmitted?
|
Many different routes of infection: Direct contact, aerosol, fecal-oral, contact w/ contaminated surfaces
|
|
|
What does gene 1 encode for?
|
It contains the two ORFS, ORF1a and 1b that encode many non-structural proteins
|
|
|
What are some proteins that ORF1b encodes for?
|
Pol, Hel, ExoN, EndoN, OMT
|
|
|
What are some proteins that ORF1A encodes for?
|
PLP1, PLP2, MP1, MP2
|
|
|
How is species specificity obtained with coronaviruses?
|
Through variations in the spike protein on the envelope
|
|
|
What is a key region at the 5' end of the Coronavirus mRNA?
|
There is a conserved leader region, 70bp long
|
|
|
How are subgenomic mRNAs generated?
|
The polymerase reads the leader region, and then jumps to other regions within the genome to yield different subgenomic mRNAs (-) strand templates
|
|
|
What happens when a cell is infected with two related coronaviruses?
|
High frequency recombination can occur by a copy-choice mechanism (not done by flavi or pesti)
|
|
|
Where does replication of coronaviruses occur?
|
In double membrane vesicles
|
|
|
Which receptor does HTLV use to interact with target cells?
|
Glucose-transporter type receptor
|
|
|
What are the two subunits of RT?
|
P66 and P51
|
|
|
What is P66?
|
The catalytic subunit: has the polymerase and RNaseH activity
|
|
|
What is p51?
|
It does not have an enzymatic acitvity. It is more for stability/structural function
|
|
|
Why do we get high levels of mutations in retroviruses?
|
Because the RTases lack proof-reading activity, there is no exonuclease acitivty
|
|
|
What is a quasi sopecies?
|
Variations of a virus due to the high level of mutation by RT
|
|
|
What do simple viruses like Murine Leukemia Virus require to enter the nuceus?
|
THey can only enter during mitosis/cell division, so they can only infect rapidly dividing cells
|
|
|
When can complex retroviruses like HIV/HTLV enter the nucleus?
|
They have enzymatic activities to get the pre-integration complex into the nucleus, therefore they can infect terminally differentiated cells such as macrophages because it doesnt require cell division to get into the nucleus as it has the enzymatic acitvity that allows it to do so
|
|
|
Which interactions allow trafficing of proviral DNA into the nucleus?
|
Nuclear pore complex protein interaction with viral proteins
|
