Microbio 310 1st EditionExam # 2 Study Guide Lectures: 10 - 20Lecture 10 (February 20)9.1 General Properties of Viruses• Virus: genetic element that cannot replicate independently of a living (host) cell (metabolicallyinert)• Virus particle (virion): extracellular form of a virus; facilitate transmission– 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• Viruses can be classified on the basis of the hosts they infect:• Bacterial (bacteriophage), Archael, Animal, Plant viruses 9.2 Nature of the Virion • Viral Structure– Capsid: the protein shell that surrounds the genome of a virus particle– Capsomere: smallest subunit of the capsid– Nucleocapsid: complete complex of nucleic acid and protein packaged in the virion• Enveloped Viruses– Have membrane surrounding nucleocapsid • Complex Viruses: Virions composed of several parts, each with separate shapes and symmetries• Some virions 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 and allow viruses to leave 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; 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 cell metabolism 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 virus (ex: Maltose receptors used by lambda in E. coli)– 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• 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 effective against 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 DNA • Viral mechanisms to evade bacterial restriction systems– Chemical modification of viral DNA (glycosylation or methylation)– Production of proteins that inhibit host cell restriction system9.8 Overview of Bacterial Viruses • Viral Life Cycles– Virulent mode: viruses lyse host cells after infection– Temperate mode: viruses replicate their genomes in tandem with host genome and without killing host9.10 Temperate Bacteriophages, Lambda, and P1• Temperate viruses: can undergo a stable genetic relationship within the host– But can also kill cells through lytic cycle (end up exploding the host cell)• Lysogeny: state where most virus genes are not expressed and virus genome (prophage) is replicated in synchrony with host chromosome• Lysogen: a bacterium containing a prophage• Under certain conditions, such as environmental stress (UV radiation), lysogenic viruses may revert to the lytic pathway and begin to produce virions • Bacteriophage lambda– Linear, double-stranded DNA genome– Complementary, single-stranded regions at 5’ terminus of each strand– Upon penetration, DNA ends base-pair, forming the cos site, and the DNA ligates and forms a double-stranded circle– When lambda is lysogenic, its DNA integrates into E. coli chromosome at the lambda attachment site (attl• Regulation of lytic vs. lysogenic events in lambda is controlled by a complex genetic switch– Key elements are two repressor proteins: cl protein and Cro repressor9.11 Overview of Animal Viruses• Consequences of Virus Infection in Animal Cells– Persistent infections: slow release of virions from host cell does not result in cell lysiso Infected cell remains alive and continues to produce virus– Latent infections: delay between infection by the virus and lytic events; virus may be present but not replicating and then suddenly revert to lytic infection– Transformation: conversion of normal cell into tumor cell– Cell fusion: two or more cells become one cell with many nuclei9.12 Retroviruses• Retroviruses: RNA viruses that replicate through a DNA intermediate– Enveloped viruses that contain reverse transcriptase (copies information from its RNA genome into DNA), integrase, and protease enzymes– Virion contains specific tRNA molecules• Retroviruses have a unique genome– Two identical single-stranded RNA molecules of the plus (+) orientation• Process of Replication of a Retrovirus:– Entrance into the cell– Removal of virion envelope at the membrane– Reverse transcription of one of the two RNA genomes– Integration of retroviral DNA into host genome– Transcription of retroviral DNA– Assembly and packaging of genomic RNA– Budding of enveloped virions; release from cell9.13 Defective Viruses• Defective viruses: viruses that are parasitic on other viruses– Require other virus (helper virus) to provide some function• Some rely on intact virus of same type• Satellite viruses: defective viruses for which no intact version