Virology – Exam 1 – Flashcards
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| Terminal Direct Repeats |
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| In Herpes, circularize when the ends are chewed back. |
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| Terminal Inverted Repeats |
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| In Adenovirus, cause it to form a loop when single stranded. |
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| dsDNA that forms a circle |
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| Polyoma, Papilloma |
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| Multipartite viruses |
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| Genome separated into segments that are in separate capsids. Brome Mosaic Virus has three. |
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| Viruses with a primer protein attached on the 5' end. |
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| Adenovirus, Picornavirus |
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| Overlapping ORFs |
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| In viruses, can have up to three reading frames. |
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| Which is larger: amino acids or nucleotides? |
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| Nucleotides. |
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| How does capsid volume relate to genome size? |
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| To fit the genome, a capsid must be made up of subunits, or else it could not be packaged inside. |
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| Explain how to calculate the triangulation of an icosahedron. |
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| Using an image of the virus, count how many steps (h) and turn-steps(k) it takes to get from one vertex to another while only stepping on hexamer points. T = h^2 + hk + k^2 |
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| What is the number of subunits in a capsid? |
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| T(60) |
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| As T value increases, capsid volume generally... |
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| increases |
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| Where is the beta-sheet jelly roll seen? |
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| In subunits of the icosahedral capsid proteins. |
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| What type of hosts are non-enveloped icosahedral viruses common in? |
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| Plants and animals. |
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| What type of hosts are non-enveloped helical viruses common in? |
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| Plants |
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| How were the attachment factors of LPS determined? |
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| Randomly mutated viruses, and looked for those that were newly susceptible or newly resistant to a virus. Then looked at the structure of LPS to determine what changed. |
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| Describe the Head and Tail method of penetration. |
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| The tail fibers connect, then pull the baseplate to connect to the host. Once that connects, the tail contracts and pushes the nucleic acid into the host. |
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| How are ICAM-1 and PVR related? |
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| Both are Ig-like domains on the host cell that a virus (i.e. picorna) can bind to. |
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| Which virus uses a host carbohydrate group to attach? |
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| Influenza (orthomyxo) -- to sialic acid |
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| What virus fuses at the plasma membrane? |
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| HIV |
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| What virus fuses at endosomal membrane and requires low pH? |
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| Influenza (orthomyxo) |
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| What virus uncoats (no fusion) at the endosomal membrane? |
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| Polio (picorna) -- capsid remains outside. |
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| Which virus lyses the endosome to uncoat in the cytoplasm? |
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| Adenovirus, which uses its spike proteins to lyse the endosome. |
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| Which virus uses histones to uncoat at the nuclear pore? |
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| Adenovirus |
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| Which 2 viruses change conformation of receptor/fusion peptides when they bind? |
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| HIV (retro) and Paramyxo |
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| Which virus uses ribosomes to uncoat? |
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| Togavirus (IV), after fusion in the endosome. |
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| Which virus depends on lysosomal enzymes to uncoat? |
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| Reovirus (rota)-- after uncoating the ISVP (intermediate subviral particle) is left. |
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| What is the role of the canyon cleft and VP1 in picornavirus? |
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| Canyon is where the PVR binds, and is hidden from immune system. The VP1 changes conformation to slide into host membrane and make a pore for the viral genome to enter. |
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| What characterizes a Nuclear Localization Signal? |
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| Stretch or patch of basic amino acids. |
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| What is a positive autoregulatory loop? |
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| When an expressed protein further activates its own expression. |
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| What is a transcriptional cascade? |
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| When one protein activates the expression of another, etc. |
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| What are the main steps of prokaryotic transcription? |
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| Sigma factor binds to RNA polymerase, which finds a promoter and initiates transcription. |
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| What are the main steps of eukaryotic transcription? |
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| A closed initiation complex must for and be phosphorylated, then binds to the promoter and initiates transcription. |
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| What strategy does T4 use for transcription? |
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| Sequential modification of RNA polymerase/sigma factor so that the promoters for the late genes are nothing like the host promoters. |
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| What strategy does bacteriophage lambda use for transcription? |
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| Antitermination and repression of promoters. |
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| What is a cellular transcription factor that viruses use? |
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| NFkB |
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| How does Tat relate to NFkB? |
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| Once NFkB initiates transcription, short abortive transcripts are made, but eventually Tat is made. Tat binds to the Tar region of the RNA made and stabilizes the polymerase. |
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| What do VP16, Oct1, and Hcf have to do with each other? |
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| VP16 is from Herpes (HSV) and Oct1 and Hcf are from the host. All three must bind for transcription to occur. |
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| What does E1A do in a virus? |
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| E1A binds to Rb and releases it from E2F. E2F then can activate E2 genes. E1A comes from Adenovirus. |
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| What is Ibp? |
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| Initiator binding protein, a host protein. Virus uses it to bind to late gene promoters so they won't be expressed until the end. |
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| Which viruses use a replication fork? |
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| Papilloma, polyoma, herpes, retro. |
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| Which viruses use strand displacement? |
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| Adeno, parvo, pox. |
