Microbio 310 1st Edition Lecture 10Outline of Last Lecture I. 6.15 The Unit of TranscriptionII. 6.16 Polypeptides, Amino Acids, and the Peptide BondIII. 6.17 Translation and the Genetic CodeIV. 7.2 Transcription and RNA Processing in ArchaeaV. 7.4 Shared Features of Bacteria and ArchaeaVI. 7.5 Genes and Chromosomes in EukaryaVII. 7.8 RNA ProcessingVIII. 7.9 Transcription and Translation in EukaryaIX. 7.10 RNA Interference (RNAi)X. 7.11 Regulation by MicroRNAXI. 8.3 Negative Control of Transcription: Repression and InductionXII. 8.4 Positive Control of TranscriptionXIII. 8.5 Global Control and the lac OperonXIV. 8.7 Two-Component Regulatory SystemsXV. 8.8 Regulation of ChemotaxisXVI. 8.9 Quorum SensingXVII. 8.14 RNA Regulation and Antisense RNAXVIII. 8.15 RiboswitchesXIX. 8.16 AttenuationThese notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.Outline of Current Lecture I. 9.1 General Properties of VirusesII. 9.2 Nature of the VirionIII. 9.3 The Virus HostIV. 9.4 Quantification of VirusesV. 9.5 General Features of Virus ReplicationVI. 9.6 Viral Attachment and PenetrationVII. 9.7 Production of Viral Nucleic Acid and ProteinVIII. 9.8 Overview of Bacterial VirusesIX. 9.9 Virulent Bacteriophages and T4X. 9.10 Temperate Bacteriophages, Lambda, and P1XI. 9.11 Overview of Animal VirusesXII. 9.12 RetrovirusesXIII. 9.13 Defective VirusesXIV. 9.14 ViroidsCurrent Lecture9.1 General Properties of Viruses• Virus: genetic element that cannot replicate independently of a living (host) cell• Virology: the study of viruses• Virus particle (virion): extracellular form of a virus– Exists outside host and facilitates transmission from one host cell to another– Contains nucleic acid genome surrounded by a protein coat and, in some cases, other layers of material• Viral Genomes– Either DNA or RNA genomes – Can be single or double stranded– Some circular, but most linear• Viral Hosts and Taxonomy– Viruses can be classified on the basis of the hosts they infect:• Bacterial viruses (bacteriophages) • Archaeal viruses• Animal viruses• Plant viruses• Other viruses9.2 Nature of the Virion• Viral Structure– Capsid: the protein shell that surrounds the genome of a virus particle• Composed of a number of protein molecules arranged in a precise and highly repetitive pattern around the nucleic acid– Capsomere: subunit of the capsid• Smallest morphological unit visible with an electron microscope– Nucleocapsid: complete complex of nucleic acid and protein packaged in the viriono Constructed in highly symmetrical wayso Enveloped virus: virus that contains additional layers around the nucleocapsid (steals some of the cell membrane of the host it infects)• Enveloped Viruses– Have membrane surrounding nucleocapsido Lipid bilayer with embedded proteins– Envelope makes initial contact with host cell• Complex Viruses– Virions composed of several parts, each with separate shapes and symmetries– Bacterial viruses contain complicated structures o Icosahedral heads and helical tails• Somevirions contain enzymes critical to infection (bring their own proteins)– Lysozyme• Makes hole in cell wall • Lyses bacterial cell– Nucleic acid polymerases- HIV brings its own polymerase– Neuraminidases• Enzymes that cleave glycosidic bonds • Allows viruses to leave the cell9.4 Quantification of Viruses• Titer: number of infectious units per volume of fluid; calculate by counting number of plaque-forming units• Plaque assay: analogous to the bacterial colony; one way to measure virus infectivity– Plaques are clear zones that develop on lawns of host cells- Plaque is where bacteria were killed/lysed by a virus• Lawn can be bacterial or tissue culture• Each plaque results from infection by a single virus particle9.5 General Features of Virus Replication • Phases of Viral Replication:– Attachment (adsorption) of the virus to a susceptible host cell– Entry (penetration/injection) of the virion or its nucleic acid– Synthesis of virus nucleic acid and protein by cellmetabolism as redirected by virus– Assembly of capsids and packaging of viral genomes into new virions (maturation)– Release of mature virions from host cell by exploding the cell9.6 Viral Attachment and Penetration• Attachment of virion to host cell is highly specific– Requires complementary receptors on the surface of a susceptible host and its infecting viruso Ex: Maltose receptors used by lambda in E.coli– Receptors on host cell carry out normal functions for cell (e.g., uptake proteins, cell to cell interaction)– Receptors include proteins, carbohydrates, glycoproteins, lipids, lipoproteins, or complexes• The attachment of a virus to its host cell results in changes to both virus and cell surface that facilitate penetration• Permissive cell: host cell that allows the complete replication cycle of a virus to occur• Bacteriophage T4: virus of E. coli; one of the most complex penetration mechanisms– Virions attach to cells via tail fibers that interact with polysaccharides on E. coli cell envelope– Tail fibers retract and tail core makes contact with E. coli cell wall– Lysozyme-like enzyme forms small pore in peptidoglycan– Tail sheath contracts and viral DNA passes into cytoplasm• Many eukaryotes possess mechanisms to diminish viral infections–Ex: immune defense mechanisms, RNA interference• Prokaryotes also possess mechanisms– CRISPR• Similar to RNA interference– Restriction modification system– DNA destruction system; only effectiveagainst double-stranded DNA viruses– Restriction enzymes (restriction endonucleases) cleave DNA at specific sequences (in sequence specific manner)o Restriction enzymes can also be used to make recombinant DNA– Modification of host’s own DNA at restriction enzyme recognition sites prevents cleavage of own DNAo This ensures the enzymes only work on invading viral DNA• Viral mechanisms to evade bacterial restriction systems– Chemical modification of viral DNA (glycosylation or methylation)– Production of proteins that inhibit host cell restriction system9.7 Production of Viral Nucleic Acid and Protein • Viral Proteins– Production follows synthesis of viral mRNA – Early proteinso Synthesized soon after infection o Necessary for replication of virus nucleic acid o Typically act catalyticallyo