Understand relative size ranges of molecules viruses bacteria and eukaryotic cells as measured by appropriate units o Micron o Nanometer 1 micron 1 micrometer Bacterial and eukaryotic cells are in this range 10 100 micrometers A filter with 0 2 micron sized pores will effectively remove bacterial contamination by trapping them in the filter nm Viruses are in this range 20 100 nm is typical range of diameters for viruses Same filter mentioned above will not remove most viruses angstrom A A Molecules are in this range A nanometer nm 10 o Angstrom Understand difference between light microscopes and electron microscopes o Sources of illumination are different photons light vs electrons o Level of resolution o Different types of EM techniques TEM SEM cryoEM EM tomography Know viral causes of some common diseases o Common cold rhinovirus flu influenza virus warts human papillomavirus 1 2 4 cold sores herpes virus diarrhea enterovirus AIDS HIV poliomyelitis Poliovirus hemorrhagic fever Ebola dengue SARS coronavirus Definitions o Virus obligatory intracellular parasite that carries nucleic acid viruses that have additional lipid membrane also called virus particles A virion refers to physical particle o Virions o Enveloped viruses genome enclosed by protein coat surrounding protein coat whereas a virus is a more general term solo entities o Resolution of a microscope o Bacteriophages viruses that infect bacterial cells ability to distinguish between 2 objects as Definitions o Viral receptor o Transmembrane protein bilayer at least once mediate its entry into host cells cell types but not others o Tropism a cell surface molecule that is bound by a virus to phenomenon that viruses are capable of infecting certain a protein that spans across membrane lipid o Endocytosis o Highly pathogenic avian influenza HPAI virus cellular uptakes of materials from extracellular space using membrane bound vesicles called endosomes Avian flu virus that has crossed over from waterfowl to domestic birds and causes high rate of death in latter population Understand general steps of virus life cycle o Entry which includes receptor binding all the way to membrane o Replication of viral genomes which requires expression of replication o Viral assembly and exit which requires the expression of structural penetration enzymes proteins Understand structure of biological membranes o Lipid bilayer with embedded transmembrane proteins o A barrier that viruses must cross to deliver its genome into cells Understand importance of studying viral receptors o Elucidation of viral tropism o Help predicting viral pathogenesis o Reveal drug targets for therapy Know 4 possible routes of viral entry following receptor binding o Pore formation at cell surface neutral pH o Membrane fusion at cell surface neutral pH o Pore formation in endosomes acidic pH o Membrane fusion in endosomes acidic pH Definitions o Nucleic acid o Reverse transcriptase o Semiconservative replication polymer made up of repeating units of nucleotides can either be DNA or RNA during DNA replication each daughter DNA contains one strand of parental DNA and one strand of new DNA enzyme that uses RNA as template to produce DNA By in large absent from host cells and has to be carried in by virions enzyme that uses RNA as template to produce RNA By in large absent from host cells it has to be either carried in by virions or encoded by viral genome o RNA dependent RNA polymerase Know 7 types of viral genes Notice the lack of X2 stranded genome type with one strand of DNA and one strand of RNA These molecules are physically unstable o dsDNA o ssDNA o dsRNA o ss RNA o ss RNA o ss RNA RT o dsDNA RT Understand why viruses are successful despite having limited coding capacity in their genomes o Host provides much of the service o Viral genomes are more efficient in carrying information i e overlapping reading frames Why do RNA viruses have a much higher mutation rate o The enzymes used to copy RNA genomes have low fidelity during replication make more mistakes These include reverse transcriptase and RNA dependent RNA polymerase The DNA polymerases which the host cell and DNA viruses use have much higher fidelity Understand general scientific principles of reconstructing extinct o Obtain viral genome sequence and use it to synthesize a man made Understand difference between positive sense and negative sense RNA o Positive sense RNA directly spells out code for protein translation o Negative sense RNA needs to be converted to positive sense RNA via the base pair rule to spell out code for protein translation As a result negative sense RNA viruses need to carry their own RNA dependent RNA polymerase in their viral particles Definitions o Icosahedron by having 20 faces and 3 types of symmetries 5 fold 3 fold 2 fold a common shape adopted by viruses It is characterized viruses genome genomes o Packaging signal o Metastable state a piece of viral DNA RNA sequence that is necessary a long lived stable state that is less stable than most and sufficient for incorporation into virions It is unique for each virus stable lowest energy state virus encoded proteins displayed on membrane surface of virion These proteins are typically glycoproteins having sugars added to them common motifs include stem loops hairpins and kissing loops partially double stranded structures o RNA secondary structure o Envelope proteins Understand general consideration of viral assembly and the 2 general shapes of viruses o Should be able to use very simple single repeating protein units o Structure needs to close o Virions should be mobile easy to roll helical and icosahedron o Should be amenable to scaling up Know basic traits of icosahedron o 20 faces and 3 types of symmetry o Sphere like properties readily scalable Understand 3 modes of virus assembly o Self assembly o Chaperones and scaffolds o Virion maturation Understand different ways that assembled virions exit from host cell o Cell lysis o Budding out at plasma membrane o Exocytosis endocytosis reversal Definitions o Cytoskeleton a network of interconnected filaments and tubules that extends t o cytosol from nucleus to inner surface of plasma membrane 3 major parts are MT MF and IF proteins to the outside of cell via membrane enclosed vesicles reverse of endocytosis The cellular pathway for secreting o Exocytosis Understand difference b w in vitro in vivo studies of viral infection o In vitro outside a body and in cultured cells o In vivo in
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