Virology Assignment 6a Quiz
Which of the following RNA viruses does NOT encode an RNA dependent RNA polymerase? a. flaviviruses b. picornaviruses c. alphaviruses d. retroviruses
Retroviruses
The RNA in RNA viruses can have looped portions due to intrastrand complementarity.
True
All RNA viruses encode their own replication system. True or False? Why? (Short answer)
"The genomes of all RNA viruses except retroviruses encode an RNA-dependent RNA polymerase to catalyze the synthesis of new genomes and mRNA.." "Retroviruses encode an RNA-dependent DNA polymerase, and therefore mRNA synthesis and genome replication are very different from those of other RNA virus."
Influenze viruses are unusual among RNA viruses in that all RNA synthesis occurs
In the nucleus
RNA-dependent RNA polymerases are targets for inhibition by antiviral compounds since they are not found in mammalian cells
True
Double stranded RNA genomes
Cannot be copied into mRNA by the cell so the virions must carry their own RNA polymerase.
RNA synthesis in (+) RNA viruses take place
In the cytoplasm
What is the function of reverse transcriptase in retroviruses?
It uses viral RNA as a template for DNA synthesis
The polio and corona viruses are not capped. They are translated immediately to make proteins but at some point you need to make more genomes. You do that by making a kinus strand. A full-length copy of the plus-stranded genome and then from that you make more plus strands to make new virus ______________. (Completion)
Particles
So this is just one of the many polymerase structures that have been solved. But those are some of the basic principles that emerge. That this area where the catalysis occurs is a protected area in the middle of the enzyme made by this hand folding around it. So that's the polio RNA dependent RNA __________________. (Completion)
Polymerase
In the middle is a structure called a pseudo-knot. Because as the name implies, it looks like a knot but it's not really a knot in the sense of a piece of string tied into a knot. A _____________ is a stem loop where the bases in a loop can base pair with sequences just downstream of the stem that is indicated on the top there by these dotted lines. (Completion)
Pseudo-knot
Now when we were able to sequence polymerase as we found some remarkable relationships. There are four different kinds of nucleic acid polymerase. No more no less. We have RNA dependent RNA polymerase which we are talking about today. We have RNA dependent DNA polymerase, __________________, which we'll talk about today. (Completion)
Reverse transcriptase
dsRNA genomes of viruses can be translated by ribosomes
False
Which is a universal rule about RNA directed RNA synthesis? a. RdRP may initiate de novo or require a primer b. RNA synthesis initiates randomly on the RNA template c. RNA is synthesized in a 3'-5' direction d. RNA synthesis is always template-directed
RdRp may initiate de novo or require a primer
Now you'll notice there is one other virus on the slide with an RNA genome that's (the group six) the plus RNA viruses that go through a DNA intermediate. They utilize, they employ a ________________ enzyme which is quite unique so that we'll talk about that in a lecture of its own. (Completion)
Reverse transcriptase
We'll see some of those today where bases are added to a product that are not in the original template. There area couple of interesting examples of that. That we will get into later on. So the initiation step shown here. Two modes of initiation of RNA synthesis- denovo or primer ____________ (Completion)
dependent
And in contrast, the negative strand RNA viruses those genomes have to be copied into mRNAs so they need to be coated with protein. Of course, there are exceptions for these plus-stranded genomes. I show 2 of them here. The third virus from the left is a ________ which we haven't mentioned yet, we will encounter just a bit in this course. But these are viruses with the longest RNA genomes that we know of. Up to 40,000 bases of RNA and these RNAs are coated with protein in the particle. (Completion)
Coronavirus
The influenza virus has eight nucleocapsids each attached to an RNA polymerase
True
So people would see a sequence genome and say ah this looks like a polymerase, then they would take the gene and put it in a plasmid, put it in a cell and show that you could make a protein that had polymerase activity. And then finally when we were able to make enough of these proteins, people started solving crystal structures of these polymerases typically by _____________ and now we have hundreds and hundreds of structures of viral RNA polymerases. (Completion)
X-ray crystallography
RNA viruses require their own supply of certain enzymes because
Host cells lack enzymes that can replicate the viral genome
And here is the addition of the third base in progress. This is a reaction catalyzed by the polymerase. It enables this to happen. You add a triphosphate, so the T that is being added here is coming in as TTP thymidine triphosphate for DNA or uridine triphosphate for RNA. This addition reaction is catalyzed in the active site of the polymerase. Te active site is characterized by having two amino acids, typically asp-asp as part of the GDD sequence that coordinate two ________________ metals. (Completion)
Magnesium
So this was one of the first demonstrations that there is an enzyme induced in infected cells that can copy the genome because you are measuring copying of the viral genome that you infected the cells with by incorporation of these triphosphates into cells into RNA product. Now this experiment was also done using inhibitors of cellular _____________. (Completion)
Polymerases
RNA synthesis begins and ends at very specific places on the template and here in the top is a generic example of a template being copied by an RNA polymerase. And there happens to be a ___________ there that is initiating synthesis (Completion)
Primer
Then finally, we have double stranded RNA genomes and as I told you a while ago, dsRNA cannot be translated by ribosomes because it's in a double strand the ribosomes cannot access the plus strand. So there has to be an _________ polymerase in these particles but the RNA is naked. It's not coated in protein. (Completion)
RNA
Tobacco mosaic virus was first crystallized in 1935. Remember, that was the first virus discovered at the end of the 1800s and so a lot of people began to work on it as a model system was easy to grow a lot of it. So, in 1935 crystals were grown by William Stanley and in 1930 at the time we couldn't solve structure by x-ray crystallography. They were too big, we didn't have the computational power. That came later. But in 1936 those crystals were found to contain about 5% _________ and no one at the time knew what that means (Completion)
RNA
Why do RNA viruses appear to have higher rates of mutation?
Replication of their genomes does not involve proofreading
Which viruses have single-stranded RNA that acts as a template for DNA synthesis? a. lytic phages b. proviruses c. viroids d. bacteriophages e. retroviruses
Retroviruses
The flu, the influenza RNP is colored so that this is a charged coloring of the protein and the blue is plus charged and that makes sense because the negatively charged RNA is binding to the blue regions and so these are nucleocapsids and each one is attached to an RNA polymerase which as you can see here we're going to talk about this in some detail. It's a ___________ subunit RNA polymerase. (Completion)
Three
Select all that are true regarding viruses with RNA genomes: (Multiple Response) a. (-) strand RNA genomes have RNA-dependent RNA polymerase in the particle b. The RNA is coated with the protein in (-) strand RNA genomes c. (+) strand RNA genomes have RNA-dependent RNA polymerase in the particle d. (-) strand RNA genomes have a nucleocapsid
a. (-) strand RNA genomes have RNA-dependent RNA polymerase in the particle b. The RNA is coated with the protein in (-) strand RNA genomes d. (-) strand RNA genomes have a nucleocapsid
Select all that are true regarding viruses with RNA genomes: (Multiple Response) a. dsRNA genomes have RNA-dependent RNA polymerase in the particle b. The RNA is coated with protein in all (+) strand RNA genomes c. (+) strand RNA genomes do not have RNA-dependent RNA polymerase in the particle d. (-) strand RNA genomes have a nucleocapsides e. Coronavirus and retrovirus have nucleocapsides
a. dsRNA genomes have RNA-dependent RNA polymerase in the particle d. (-) strand RNA genomes have a nucleocapsides e. Coronavirus and retrovirus have nucleocapsides
RNA synthesis requires the assistance of two Mg2+ that are co-ordinated by the amino acid
aspartate
Which of the following are "universal" rules for RNA-directed RNA synthesis of viral genomes? (Multiple response) a. Only cell proteins are required for RNA-directed RNA synthesis b. RNA is synthesized by template-directed stepwise incorproation of nucleotide triphosphate enlongated in a 5'-3' direction c. The RNA genome must be copied end to end with no loss of nucleotide sequence d. Synthesis always requires a template in RNA viruses e. RNA-dependent RNA polymerase may initiate synthesis de novo or it may require a primer.
b. RNA is synthesized by template-directed stepwise incorproation of nucleotide triphosphate enlongated in a 5'-3' direction c. The RNA genome must be copied end to end with no loss of nucleotide sequence e. RNA-dependent RNA polymerase may initiate synthesis de novo or it may require a primer
Which of the following are "universal" rules for RNA-directed RNA synthesis of viral genomes? (Multiple response) a. The genome and mRNA in RNA viruses is always the same thing b. Viral mRNAs must be produced that can be efficiently translated be cellular protein synthesis machinery c. The RNA genome must be copied end to end with no loss of nucleotide sequence d. Synthesis always requires a template in RNA viruses
b. Viral mRNAs must be produced that can be efficiently translated be cellular protein synthesis machinery c. The RNA genome must be copied end to end with no loss of nucleotide sequence
Which of the following are "universal" rules for RNA-directed RNA synthesis of viral genomes? (Multiple response) a. RNA synthesis initiates and terminates at random sites on the template b. Viral mRNAs must be produced that can be efficiently translated be cellular protein synthesis machinery c. The RNA genome must be copied end to end with no loss of nucleotide sequence d. Synthesis always requires a template in RNA viruses e. RNA-dependent RNA polymerase may initiate synthesis de novo or it may require a primer.
b. Viral mRNAs must be produced that can be efficiently translated be cellular protein synthesis machinery c. The RNA genome must be copied end to end with no loss of nucleotide sequence e. RNA-dependent RNA polymerase may initiate synthesis de novo or it may require a primer
