week 2 Flashcards
multiplicity of infection
the number of virus infecting a cell. calculated using poisson distribution bcviral infection is a random event
tropism
which cells a virus can infect. determined by cell surface receptors (if cell is susceptible), the cell also need to be permissive to allow virus replication
uptake of virus into the cell
virions enter the cell only by receptor mediated endocytosis or fusion. this happend by invaginatiom of a clathrin-coated pit forming an endosome. some viruses uncoat by fusing their envelope with the cell plasma membrane (uncoating by the membrane). other viruses uncoat after endocytosis, can be by lowering oh pH in endosome causing conformational changes in viral proteins exposing a fusion region
class 1 fusion proteins
found in the envelope of virus and assist in the fusing of viral envelope with target cell membrane/ endosomal membrane. they are composed of 3 identical subunits and their functional form is generated via cleavege. the n-terminal has a 20 aa stretch known as the fusion peptide that becomes exposed and inserted into the clel membrane
covid spike protein
S1 subunit mediates ACE2 attachment
S2 subunit contains the fusion peptide
to be activated for fusion, the spike protein must be cleaved at 2 sites firectly ay the cell membrane or through endosomes
class 2 fusion proteins
non-helical compared to class 1. beta sheet structure. not cleaved during biosynthesis. the portion that inserts into the target membrane is thought to be an internal hydrophobic fusion loop. pH plays a crucial role to expose their fusion loop.
entry of adenovirus
the penton fiber on adenovirus interacts with cell adenovirus receptor (CAR). these are integrins/ immunoglobin like molecules. endocytosis via endosomes (clathrin covered). uncoating perceeds in endosome and release of penton base breaks the endosome releasing a modified capsid. the capsid is then transported to the nuclear pore along microtubule
penetration of non-enveloped viruses: polio
binds a cellular receptor causing loss of VP4 capsidprotein. a hydrophopic internal VP1 sequence becomes exposed and then the RNA can enter cytopasm from endosome
HIV entry
HIV-1 encelope glycoproteins are highly variable but they all bind to the CD4 receptor on cells. a glycoprotein 160 envelope percursor is processed into a gp120 surface and a gp41 transmembrane protein. these bind to CD4 which induces a conformational change in gp120 exposing a binding site for the chemokine receptor CXCR4 or CCR5. binding of gp120 to CCR unduces a conformational change in gp41 that leads to insertion of fusion peptide into membrane.
how to determine it a virus enters cell by endocytosis or direct fusion
expose cells to a weak base during infection. this treatment will block infection via endocytosis by preventing the acidification of endosomes
general features of +RNA viruses
+RNA functions directly as mRNA and is used to make for example rdrp to produce -RNA as a template to create genome. most have a 5´ cap and poly A tail and the coding regions are flanked by UTRs
translation of poliovirus and flavivirus genome
they encode a large polyprotein which is cleaved into mature viral proteins by host or virus encoded proteases. poliovirus uses viral proteases 2A and 3C and flaviviruses uses host peptidase and viral protease NS3
poliovirus initiation of translation
using an “internal ribosome entry site” (IRES) which is an RNA structure that binds directly to translation factors and coordinates to start codon.
since it does not have a 5´cap to initiate translation
IRES formed by 5´ UTR
poliovirus control of translation
poliovirus 2A protease cleaves eIF4G TF which blocks the ability for cells to translate capped mRNAs -> stops cellular translation and virus completely takes over
other viruses phosphorylates eIF4G so it doesn’t work
hepacivirus (ex hepC) translation
IRES at 5´
uses host an viral proteases to produce mature proteins from polyprotein
does not destroy cellular protein translation and therefore does not directly kill hepatocytes
type of flavivirus
norovirus translation
viral protein VPg acts as a cap substitute and recruits factors for translation
replication of ssRNA
performed by rdrp that creates complementary strand of ssRNA. encoded in the genome of +rna viruses. the complex is partly double stranded and known as a replicative intermediate. transcriptio is 5´to 3´. initiation and termination occurs at specific sites on RNA, may require a primer.
poliovirus solution to clash problem
since translation and transcription moves in opposite direction on the +RNA, they will collide in the middle. the interaction of cellular an viral proteins with the 5´ UTR might determine if genome is translated or replicated. binding of poly rC -binding protein 2 initially stimulates translation. when the viral protease has been synthesized, it cleaves this protein which then binds to a different site and stimulates replication instead.
flavivirus solution to clash problem
?
togavirus repliaction
translation from genomic rna yields rna polymerase and accessory proteins. a subgenomic promoter within the -rna creates a smaller +rna that encodes the structural proteins. this is not initially translated by the host ribosome but is hidden within the genome. sub-genomic rnas are not packaged into virions but are only produced during active replication.
subgenomic mRNAs
produced by togavirus and norovirus. this overcomes problems with genome structure to ensure that structural proteins are only made once replication has been established.
coronavirius replication
produces subgenomic RNAs by skipping by rdrp. this is caused by several repeated transcription-regulating sequences (TRS) that interacts with the rdrp causing it to skip. the SARS-cov2 replicase complex is very big and contains many accessory proteins such as proofreading and unwinding proteins
different types of -RNA genomes
- unimolecular: one rna segment for genome. paramyxovirus, rhabdovirus, filovirus. genes far from the start of transcription may be copied less frequently because the ability to reinitiate lessens along the length of the rna. the genes are sepaated by start and stop signals
- segmented: serveral rna molecules. orthomyxovirus and bunyavirus
switch from mrna synthesis to genome replication in paramyxo and rhabdovirus
translation produces nucleoprotein N which is the most abundant viral protein in infected cells. it self assembles to form the nucleocapsid. N binds to intergenic regions and promote rna polymerase read-through and prodiction of full-lenght +RNA template
