Chapter 2 - V Flashcards
Key steps in virus replication
- Virus adsorption and attachment to susceptible host, occurs by chance
- Adsorption: 2 solid things bind tgt - Inject genomes into cell - genome enters cell and any other needed proteins
- This step varies
- stnthesis of viral mRNA
- Synthesis of viral proteins
- Synthesis of viral genome (for next generation?) - Assembly of virus particle from parts
- release from host
Virus structure
All virus genomes are surrounded by proteins
the virus particle is a gene delivery system - it moves the virus’ genome from one host cell to another host cell
The genome is packaged in a protein known as capsid
Some viruses, the virion consist of only genome and the capsid (nucleocapsid, capsid with enclosed genome)
others may have an additional layer
- lipid bilayer envelope
- layer of protein between capsid and envelope (matrix)
- internal lipid laters
- protein occlusion bodies
Capsid protein
Capsid proteins are structural proteins
the function of the proteins that make up the capsid include:
- protection of chemically labile virus genome
- from nucleases in the environment
- from agents that might damage the base of nucleotide
- shearing of viral genome from mechanical forces - Delivery of the virus’ genome to the location within the cel where the genome can be replicated and expressed
if virus is naked particle, the capsid has the structure to bind to host cell
If enveloped, the envelope has the structure to bind to host cell.- capsid does not have the correct structure (aka if envelope gone, no invasion)
Step 1: Virus - host cell Invasion
Adsorption and attachment to susceptible host:
Virus and host cell must have complementary structures to be able to interact - chance event (recognition specificity)
Host cell has a virus receptor - a normal cell structure that virus exploits as a binding site
the cell structure can be - protein or carbohydrate attached to a protein
Virus has an anti-receptor -
- structure that bind to host cell
A host is susceptible if it has the proper virus receptor
Step 1: Virus entry
The virus’ genome and replicative enzyme needs to enter the cell
Different strategies for different viruses,
but a given species of virus always use the same method
After binding to cell’s virus receptor, for some viruses
- only genome enters
- the whole virus enters the cell in an endosome
- the virus envelope fuses to the cell membrane releasing the genome into cytoplasm
Virus entry is necessary cuz
Viral genome needs to gain access to hosts translation machinery for replication
Some genomes have their own transcription machinery but no virus has translation machinery
Virus entry
Virus particle itself is inert with respect to its metabolism
The virus particle is designed to interact with host cell receptor to initiate the process of infection
for virus particles, the capsid is stable enough to persist in the environment but unstable enough to allow the release of the genome into cells cytoplasm
What type of interactions exist between the protein subunits in the capsid
interactions with other proteins
changes in pH
cleavage of proteins
Unfolding proteins
Susceptibility and permissiveness
For viruses to become successful in nature, it must encounter host cell that is both susceptible to viral infection and permissive to viral replication
Susceptibility
- host cells structure - viral receptor that specific virus can attach to for delivering the virus and its genome into the host ell
- virus has an anti-receptor structure that recognizes the virus receptor on the cell
Susceptibility and permissiveness - polio eg
poliovirus in human cells and mouse
- polio virus known to only infect human cells
- certain human cells express protein CD155 (aka poliovirus receptor) also act as virus receptor for polio
Polio binds to CD155 infecting them and kills them - increase in virus particle (spreads)
While in mouse, they have their own version of CD155, but slightly different than humans
- polio still cannot bind to mice CD155, so it cannot infect mouse cells
- mouse cell survives and three is no increase in number of virus particles
Susceptibility and permissiveness: Are mice really resistant to polio or not permissive to its replication
Determining if mouse cells are permissive:
isolate the mRNA from poliovirus and then find a way to introduce them into mouse cell
results: poliovirus are produced in both human and mouse cells
- mouse are permissive to polio replication even though they are not susceptible
Permissive
Ability to replicate the viral genome in the cell and
produce more viral particles
Susceptible
Ability of a given virus to infect
- virus receptor fits with anti receptor
Determining if mouse cells are permissive:
-II
Another experiment that we can do to confirm mouse cells permissiveness to polio
- transfect the mouse cells with the gene for the human version of CD155
- Transfecting means that we introduce a gene so that it can be expressed by the new cell - they have a transgene
- allow mouse cells to have human CD155 as well
result: transfected mice are susceptible to polio - we see an increase in the number of the virus particle
Susceptibility and permissiveness
For viruses to be successful, they need to:
- infect susceptible and permissive host
- package functional enzymes involved in the replication of its genome
- be able to remain intact and capable of infecting a new host when it is in the environment ( exposure to the environment should not damage the virus in such a way that it can no longer infect new host)
- virus must have multiple structures to interact with the surface of the host cell - ensures that in the event that some are damaged (by oxidation/enzymes) the virus can stull infect a new cell
Susceptibility and permissiveness
Susceptibility and permissiveness can be demonstrated experimentally
The virus that persist in natures have been successful at encountering host cells that are both susceptible and permissive
Baltimore classification of viruses
based on how viral mRNA is made
- group by starting material dna or RNA ds or ss
Key concepts - review
Polymerases work the same way in all cells - applies to both DNA and RNA pol
- All read a template in the 3-5’ direction
- all synthesize a complementary strand in the 5’-3’ direction
Differences between viruses and cells
Cell template is always DNA, virus can be DNA or RNA
Cells does transcription in nucleus,
Key concepts - review
All ribosomes work the same way
- read mRNA template 5-3’ direction
- Synthesize the polypeptide from N to C direction
with viruses they differ in how they start process of translation:
can be cap-dependent or cap independent
Viral Replication Enzymes
Some viruses package their own replicative enzymes in their capsids for 2 main reasons
- some species of viruses replicate their genomes in the cytoplasm of the cell
- can’t use cell’s DNA or RNA polymerases that are located inside the nucleus
- these viruses also must encode the genes for the polymerase - For RNA viruses, the Cell’s RNA polymerase cannot read RNA template (only DNA)
All RNA viruses must have in their genome a gene that encodes a polymerase that can read RNA as a template and synthesize RNA or DNA - some even have a functional enzyme copy readily inside the capsid
(RDRP)
Viral Genomes
RNA viruses need an enzyme that can read RNA as a template and make RNA for both their genomes and mRNA - excluding RT
The cell do not have a polymerase that can read RNA as a template
The virus must have a gene that encomds such an enzyme:
+ sense RNA can synthesize it right after infecting the cell- sense RNA viruses must have some packaged within their capsid
RNA dependent RNA polymerase
+ and - Sense
normal mRNA is defined as being + sense (same as host cell mRNA
+ sense is like normal mRNA can be translated right away and the RDRP produced and cango back to transcribe the - sense mRNA from the + sense and then more + again
While - sense needs to have RDRP packaged with it so it can use to make the + sense
Retroviruses
RT use an alternative approach –> transcribe the ssRNA to dsRNA first
dsDNA is transcribed to makes more of the ssRNA viral genome
need enzyme that reads RNA and synthesizes DNA = RT
RT
RT has 3 distinct enzyme activities
- RNA dependent DNA polymerase
- result in DNA-RNA hybrid molecule - RNaseH
- an enzyme that removes RNA in the DNA-RNA hybrid molecules - DNA dependent DNA polymerase
- makes the complementary DNA strand so that the ssDNA becomes ds DNA
mRNA synthesis
DNA viruses that replicate their genomes in cells nucleus can use the cells DNA polymerase
- DNA viruses can then use the cells RNA polymerase to transcribe their DNA
Retroviruses that have copied their genome to DNA can use the cell’s RNA pol to transcribe their DNA
- so now they can make multiple copies of that RNA
All DNA viruses that replicate in the cytoplasm and are all RNA viruses must encode their own RNA polymerase (except Retroviruses cuz they make DNA then use RNA pol in nucleus)
- they must package itw tih genome
Translation of viral m RNA
All viruses translate their mRNA (+sense RNA) on the cell’s ribosome
Eukaryotic ribosomes like:
- mRNA with 5’ cap, start codon, single ORF, stop codon, poly A tail
- cellular mRNA has these more favorable
Sometimes assembly of the mRNA on the ribosome is a big challenge, eukaryotic ribosomes are designed to translate eukaryotic mRNA not viral mRNA
some types of viruses have mRNA without the 5’cap - they use secondary structure instead
- not as efficient as 5’ cap but adequate
although some viruses do have 5’cap and poly-A tail
Translation of viral m RNA
monocistronic mRNA - one gene
Polycistronic mRNA multiple genes, multiple reading frames (multiple start stop codon)
- common in bacteria/viruses
Translation of viral m RNA
Eukaryotic ribosomes are not good at translating polycistronic mRNA
Only 1 gene would be translated. the ribosome would dissociate at the first stop codon and would not reassemble on the downstream start codon
- not good for viruses that need to make several proteins
Prokaryotic ribosomes might be able to reassemble on such mRNA but eukaryotic ribosomes cannot
- the cap is essential in ribosome assembly on mRNA
In cap-independent translation, a secondary mRNA structure takes place of the 5’ cap
Translation of viral m RNA
Viruses have evolved a simple strategy to overcome the problem of translating multiple proteins in a eukaryotic cell
- entire mRNA is translated into a polyprotein, which gets cleaved up into several individual proteins
- one ORF (like operons
SARS - CoV -2
Coronaviruses have one ss + sense RNA as their genome
they replicate and express their genomes in the cytoplasm of the infected cell
- they cannot use host cells RNA pol to replicate/transcribe their genomes
We would not find RDRP packaged in capsids cus plus sense
