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Viruses - Lecture 1

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MICB 202
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Viruses Lecture 1 • Viruses=obligate intracellular parasites o Extracellular: inert virion o Intracellular: nucleic acid replication (gene expression, viral protein synthesis) • Viruses vs Organisms o No plasma membrane o Require ATP, nucleotides from host o No independent translation o No metabolism • Origin of viruses?—uncertain o Were cells that became parasitic and lost lots of cellular components o Mobile genetic agents that could enter cells o Were self replicating units then evolved to live in other cells o Don’t really know for sure since rapid mutation/evolution and no fossils  Rapid evolution due to: short generation time, lots of progeny, high mutation rate • Mutation rate: 10^-6 to 10^-7 for viral DNA POL, vs 10^-4,-5 for RNA POL • Compare to humans of 10^-11 • New viruses from mutations of pre-existing strains o Eg. Smallpox from camelpox o Eg. HIV from SIV o H1N1 from recombination(combine with host genome) and rearrangement of segmented genome of bird swine flu located in 1 host cell • Viruses diverse: o Replication strategy, genetics, structure, type of host • Viral Structure o Naked: genome surrounded by protein coat=capsid  Capsid made of repeating capsomers  If more than 1 capside, inner capsid=nucleocapsid o Enveloped: has a phospholipid bilayer covering capsid, thru budding  Can have GPs embedded to attach to host  Some have matrix proteins to link capsid with envelope  Some enveloped have CORE instead of capsid. Is capsid that doesn’t immediately break apart upon entering host cytoplasm. Instead, docks to nucleus before releasing genetics into nucleus o Genome: linear, circular, segmented o Some viruses contain own enzymes necessary for replication  If they replicate in cytoplasm can’t use DNA pol from host’s nucleus or host pol not appropriate eg. retrovirus • 5 structural forms of viruses o Naked, icosahedral: eg. Polio o Naked, helical o Enveloped icosahedral: eg. HIV o Enveloped, helical. Eg flu o Complex eg. Pox • Enveloped vs naked viruses o Enveloped viruses use budding for prolonged viral synthesis in cell “(doesn’t kill host right away)  But envelope sensitive, and dies quickly in outside environment thru dessication or harsh chemicals o Naked viruses=hardier • Viral Replication Cycle: o Adsorption, attach to host  By chance. Host has receptors that virus takes advantage of. Virus has anti-receptors. If fit, enter. o Genome (and enzymes) go into cell  Dif for dif types of viruses • A: only genome enters • B: enter via endosome, then genome released • C: envelope fuse, capsid moves to nucleus eg. HIV o Synthesis of viral genome, synthesis of viral proteins, synthesis of viral mRNA  Doesn’t always occur in this order. Depends on the virus o Assembly  Viral components have affinity for each other  Can be spontaneous or require host mechanism for assembly o Release: thru budding or lysis =egress o Viruses must infect a cell that is: permissive, susceptible  Susceptible=has virus receptor and virus has antireceptor=ability for virus to infect cell • Note: receptor is for normal host function but exploited by virus  Permissible=ability for virus to replicate inside cell LECTURE 2 • Central dogma=DNARNAproteins o Only applies to cells, not to viruses • DNA viruses=use central dogma • RNA viruses=RNAproteins aka bypass DNA part • Retrovirus=RNADNARNAproteinsgenome replication • Eukaryotics : o DNA Pol III recgonize dsDNA, synthesize 5’ to 3’  Requires primer o RNA Pol recognize dsDNA, synthesize 5’ to 3’  No primer o Ribosomes read mRNA from 5’ to 3’  polyA tail, 5’ cap  translates 1 gene at a time  mRNA=+ sense like template strand aka the strand NOT replicated • VIRAL genome replication o dsDNA viruses  use host DNA pol and RNA Pol if in nucleus  if in cytoplasm, must encode own DNA Pol + package it with virus • DNA dependent DNA polymerase • Encode own RNA pol and packaged with capsid o ssDNA viruses  DNA can be + or – sense  Convert ssDNA to dsDNA with host enzyme + viral primer • Viral ssDNA folds over to form self-template for replication o Also used for translation o RNA viruses ( nucleus or cytoplasm, ss, or ds)  Gene that codes for enzyme (RNA dependent RNA pol) • (+) sense RNA viruses synthesize it after infecting cell • (-) sense RNA virus brings it in capsid  Encode own RNA Pol to produce genome and mRNA (RNA dependent RNA pol) • Packaged with capsid if – sense • Make upon entry if + sense o Retrovirus  Must convert ssRNA to dsDNA • Then dsDNA transcribed to make more ssRNA genome • Requires enzyme REVERSE TRANSCRIPTASE • Since viral mRNA is made by viral RNA pol, maybe no 5’cap which is needed to bind ribosome o Incorporates special sequence that can bind ribosome (OR) o Steals 5’ cap from cell mRNA • Some viral genes contain more than 1 gene when translated. One of the genes codes for a protease which is activated when protein folds to cause sself-proteolytic cleavage • Baltimore Classification System of Viruses: based on how mRNA is made o Some similarities:  All viruses make mRNA and use host ribosome  All viruses make protein  All viruses must replicate genome  **see graph • 4 possible outcomes for infected Cells o LYTIC:  Naked virus: DNA or RNA  If cell routinely replaced, no permanent damage  If cell not routinely replaced, permanent damage  Eg. Cold, polio o Persistent Infections  Enveloped: DNA, RNA  Budding. Prolonged cell death. Evades immunity but stimulates itchronic inflammation, long-term damage  Eg. Measles, rubella o Latent Infections  DNA or retrovirus  Viral genome persists in cell but NOT REPLICATED  Viral production may resume after period of latency  Eg. Herpes, HIV o Oncogenic infection  DNA or retrovirus  Integrated into host cell genome and replicated with host genome  Some viral genes expressedloss of growth control of cellcancer  Eg. Hepatitis B, HPV • Cellular responses to infection o No change o Cytopathic effect (cell injury, fusion, death) o Loss of growth control (neoplasmic transformation) o Form inclusion bodies (aggregates of viral protein in cytoplasm or nucleus of cell) o Formation of multi-nucleate giant cells=syntcytium • Growing Viruses o Primary cell culture (initial isolation) o Continuous cell culture (good for vaccines)—immortalized cell lines o Embryo egg (good for vaccine) 
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