week 2

Question 1

multiplicity of infection

Answer 1

the number of virus infecting a cell. calculated using poisson distribution bcviral infection is a random event

Question 2

tropism

Answer 2

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

Question 3

uptake of virus into the cell

Answer 3

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

Question 4

class 1 fusion proteins

Answer 4

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

Question 5

covid spike protein

Answer 5

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

Question 6

class 2 fusion proteins

Answer 6

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.

Question 7

entry of adenovirus

Answer 7

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

Question 8

penetration of non-enveloped viruses: polio

Answer 8

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

Question 9

HIV entry

Answer 9

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.

Question 10

how to determine it a virus enters cell by endocytosis or direct fusion

Answer 10

expose cells to a weak base during infection. this treatment will block infection via endocytosis by preventing the acidification of endosomes

Question 11

general features of +RNA viruses

Answer 11

+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

Question 12

translation of poliovirus and flavivirus genome

Answer 12

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

Question 13

poliovirus initiation of translation

Answer 13

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

Question 14

poliovirus control of translation

Answer 14

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

Question 15

hepacivirus (ex hepC) translation

Answer 15

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

Question 16

norovirus translation

Answer 16

viral protein VPg acts as a cap substitute and recruits factors for translation

Question 17

replication of ssRNA

Answer 17

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.

Question 18

poliovirus solution to clash problem

Answer 18

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.

Question 19

flavivirus solution to clash problem

Answer 19

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Question 20

togavirus repliaction

Answer 20

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.

Question 21

subgenomic mRNAs

Answer 21

produced by togavirus and norovirus. this overcomes problems with genome structure to ensure that structural proteins are only made once replication has been established.

Question 22

coronavirius replication

Answer 22

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

Question 23

different types of -RNA genomes

Answer 23

• 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

Question 24

switch from mrna synthesis to genome replication in paramyxo and rhabdovirus

Answer 24

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

Question 25

influenzavirus structure

Answer 25

influenza virus is pleiomorphic in shape and has eight (-)RNA segments in its genome. Each genome segment is bound
to a virion RNA polymerase made up of three protein units PB1, PB2, and PA. The segments are each coated in nucleocapsid protein (NP). Viral membrane proteins include the HA - hemagglutinin, the NA - neuraminidase, and M2 -
an ion channel protein. The NEP protein, also called NS2, is in the capsid.

Question 26

influenza replication

Answer 26

influenza is unique among rna viruses because part of their replication cycle involves the nucleus. it also cleaves off the cap of host mRNAs and puts it on its own mRNA

Question 27

reovirus

Answer 27

reoviruses such as rotavirus have a segmented dsRNA genome which can easily be detected by host cell as forgein. therefore the transcription and replication is concealed inside the inner core of the virus. +RNA is transported through the cytoplasm and then the complementary strand is synthesized in the new virion.