Chapter 17 Notes PDF

virus/virion (infectious virus) ○ Shape evolution ○ Present in large numbers ○ Not organisms (dont have metabolism) ○ Nucleic acid (DNA or RNA) + protein shell called capsid Some surrounded by envelope aka membrane called envelope virus ○...

virus/virion (infectious virus) ○ Shape evolution ○ Present in large numbers ○ Not organisms (dont have metabolism) ○ Nucleic acid (DNA or RNA) + protein shell called capsid Some surrounded by envelope aka membrane called envelope virus ○ Common shapes Icosahedron (20 sided triangles) Helical filament ○ Classification Host Size and shape Genome (DNA or RNA and single or double stranded) Enveloped or not Mode of replication Viral replication: attachment then penetration then uncoating then replication then assembly then release ○ Requires host and is fast ○ 1) attachment of virus to host cell: ligands (capsid proteins or envelope proteins) bind to host receptors ○ 2) penetration: virus’s nucleic acids enters cell, virus can be intact or disassemble on entry but always ends up disassembled Membrane fusion: Enveloped viruses can fuse with host membrane Endocytosis Injection (done by bacteriophage) ○ 3) make mRNA and complying genome for viral proteins DNA viruses gDNA –(host) → mRNA using RNA polymerase gDNA –(host) → gDNA using DNA polymerase, can proofread gssDNA –(host) → complementary/template cDNA using DNA polymerase –(host) → gssDNA using DNA polymerase RNA viruses (generally single stranded) Positive polarity: gRNA=mRNA (used to make proteins)  Negative polarity: gRNA= complement of mRNA ○ First make mRNA then proteins ○ RNA –(viral RNA replicase which cant proofread) → mRNA, genome ○ gRNA(-) –(viral RNA replicase) → mRNA (+), template –(viral RNA replicase) → gRNA (-) Retroviruses: RNA based genome but not RNA virus gRNA –(viral reverse transcriptase) → ssDNA –(host DNA polymerase) → dsDNA –(viral integrase) → host genome becoming provirus –(host RNA polymerase) →mRNA, gRNA ○ 4) viral protein synthesis mRNA –(host ribosome) → protein Subvert host metabolism so only viral proteins made Ex sigma factor to control mRNA produced Host genome broken down so no host proteins made Viral translational regulators made which stops host translation so only viral proteins made ○ 5) virus assembly Self assembled Capsids filled with nucleic acids ○ 6) virus release Budding for enveloped viruses Cell lysis Ex how does an RNA virus with positive polarity like hepatitis A replicate its genome and make viral proteins? What host and viral proteins are involved? ○ Quiz ○ Sec transport system has covalent modification, ATP hydrolysis, and chaperones  ○ Trigger factors rotates proline bonds ○ Main carrier of nitrogen assimilation when ammonia is high is glutamate ○ RNA polymerase catatlyzes transcription ○ Gyrate fixes bacterial supercoiling ○ Phosphatase which removes phosphate from organic P is not ABC transporters and not redox reaction ○ Aerobic marin organism uses sulfate for s assimilation Quantifying viruses ○ 1) plaque count ○ 2) # of lesions ○ 3) electron microscopy ○ 4)fluorescence microscopy ○ 5) qPCR= quantitative PCR for DNA viruses qRT-PCR for RNA viruses because you have to do reverse transcriptase Types of viral lifestyles ○ Virulent: actively replicating, kill host by inducing lysis ○ temperate/latent: can live in harmony with host Reversibly integrates into host DNA and is replicated with the host chromosome Becomes episome (plasmid like virus) (bacteriophage is temperate) Temperate phage lifecycle ○ Lysogeny → lysis Process of induction: when conditions threaten host life ex DNA damage Lambda phage ○ Infects E.coli ○ Ds linear DNA ○ Becomes circularized when injected into E. coli using complementary ends ○ Integrates at specific site using viral integrase ○ Lambda repressor keeps phage genes from being expressed ○ Induction when things go poorly for E.coli (SOS response) ○ SOS response → cleavage of lambda repressor → expression of lambda genes including excisionase → removal of prophage  ○ Lysis or lysogeny? (depends on lambda repressor) ○ Environment ex lysis in rich media with fast growing cells (diluting repressor) ○ # of infecting particles/cell More phage/cell→ more repressor → lysogeny ○ Physiological state of cell Ex stationary phase is lysogeny since repressor builds up Viroids ○ Circular RNA particles, no coat proteins ○ Infects plants only because they use plant RNA dependent RNA polymerase (specific RNA replicase) ○ Do not encode protein ○ Enter through wound Prions: protein molecules that are misfolded and can catalyze misfolding of other proteins with same sequence ○ Can cause degeneration of central nervous system ex mad cow, scrapie, Kuru, cancer, alzherimers, Parkinsons ○ PrP^c → PrP^sc (irreversible, happens spontaneously) Normal (high in alpha helices) → diseased prion (high in B sheets) → amyloid fibers Resistant to heat and harsh chemicals  ○ Influenza ○ Negative polarity RNA virus ○ Enveloped ○ RNA has 8 segments ○ Influenza strains very specific for host but occasionally strains infect multiple species ○ Enters human epithelial cells in nasal passages ○ Evolution of influenza No proofreading Rarely see same strain twice Influenza types ○ Type A: birds and mammals (pandemic causing) Types based on HA and NA antigens which can bind different types of sugar residues on cell surfaces Characterized by 2 surface proteins (uses RNA replicase) Hemagluttin: 6 variances Nuramidase: 9 variances ○ Type B,C: predominantly found in humans ○ Type D: found in cattle Antigenic drift: gradual changes in proteins so our immune systems no longer recognize them ○ Caused by high error in replication and always happening Antigenic shift: genome shuffling with 2 strains that infect same host ○ If viruses encode different types of HA or NA antigens sometimes replicated genome pieces get mixed up and create new virus Flu vaccine: Protects you and vulnerable people (50% effective) ○ Public monitoring of patients with flu like symptoms ○ Worldwide public health officials meet and discuss data ○ Shot is inactivated influenza (cant replicate) or weakened virus called live attenuated vaccine