Viruses Individual Viruses = Virion Not cells – nonliving Size 0.02 -0.3 μm Bacterial Viruses = Bacteriophage T 4

Viral Genome Double Strand or Single Strand DNA or RNA Most Genomes Linear Overlapping genes Human Papillomavirus

Protein Coat Capsid, Coat, Shell Capsomer - Individual Proteins Self Assembly Nucleocapsid

Viral Symmetry Helical Icosahedral 20 faces, 12 vertices

Icosahedral Subunits

Tobacco Mosaic Virus Herpes Simplex Virus

Enveloped Virus

Complex Virus T 4 Bacteriophage

Enzymes in Viruses Reverse Transcriptase Lysozyme RNA Polymerase Neuraminidase

Viral Host Living Cells Animal Host Cell Culture Tissue Culture Monolayer

Cell Line Primary Culture Line Transformation Permanent Cell line Viruses Mutagen Permanent Cell line HELA –Henrietta Lacks

Quantification of Viruses Plaque Assay – Bacteria Efficiency of Plating Animal Infectivity Methods End Point Dilution

Bacteriophage Plaques

Plaques in Tissue Culture Monolayer

Viral Replication Attachment Penetration

1. Production of Early Proteins Replication of Nucleic Acids Synthesis 1. Production of Early Proteins Replication of Nucleic Acids 2. Production of Late Proteins Viral Coat

Assembly Release

One-step Growth Curve Latent Period

Some Host Cells Use Restriction Enzymes to Destroy DNA Viruses Some Viruses Can Modify Their Genome’s Restriction Sites for Protection

Baltimore Classification Scheme David Baltimore, Howard Temin, Renato Dulbecco 1975 Reverse transciptase Retro virus 6 Classes based on DNA→RNA→Protein 7th Class Hepadnaviruses added

6 Classes of Viruses Class I DS DNA Herpes virus Class II SS DNA ØX 174 Class III DS RNA Reovirus –rotavirus Class IV +SS RNA Polio Class V -SS RNA Influenza Class VI SS RNA Retrovirus Others?

HEPADNAVIRUS Class VII DS DNA virus Reverse transcriptase Use RNA intermediate Smallest genome 3-4 kb Hepatitis B

+/- SS RNA Viruses SS DNA Viruses DS Intermediates Reverse Transcriptase

Virulent Bacteriophage Lytic T Phages T4, T7 DS DNA Head, Tail, Spikes Base Plate, Tail Fibers, Contractile Sheath Hydroxymethyl-cytosine

Lambda Best Known Virus? Can be Virulent or Temperate Lysis or Lysogeny Becomes Prophage (Provirus) Gives Immunity to Host Specific Insertion Site

Maintenance of Lysogeny Lambda Repressor -Lysogeny CRO Protein - Lysis Induction

Animal Viruses DNA Viruses RNA Viruses

Eukaryotic Host Types of Infections: Lytic Persistent Latent Hepatitis A Herpes

Cancer Viruses Transformation Neoplasm Benign Malignant Metastasis Oncogene

Retrovirus RNA Genome Reverse Transcriptase DNA Copy Insert into Host Genome AIDS Acquired Immunodeficiency Syndrome HIV – Human Immunodeficiency Virus HIV

Subviral Entities Defective Viruses Parasitic? Helper Viruses Satellite Viruses AAV – Adenovirus Associated Virus Specific Insertion Sites

Viroids Naked Circles SS RNA 246-375 Nucleotides Plant Diseases Regulatory RNA -sRNA

Prions Infectious Proteins? Chaperone Protein Kuru Mad Cow Disease Scrapies Creutzfeldt- Jakob Disease 11/21/2018

Prion Infectious Cycle PrPc → PrPsc Infectious, Sporadic, or Inherited Prion Disease Mice with no PrPc are Normal?

Viruses Word List Virion Bacteriophage 28 –200 nm (0.2 μm) Genome SS/DS RNA/DNA Capsid, Coat, Shell Capsomer Self-Assembly Nucleocapsid Viral Symmetry Helical Icosahedral Enveloped Viruses Complex Viruses Enzymes in Virion Reverse Transcriptase Lysozyme Viral Host Living Organisms Cell (Tissue) Culture Monolayer Primary Culture Line

Viruses 2 Transformation Permanent Cell Line Quantification of Viruses Plaque Assay Efficiency of Plating Animal Infectivity Methods End Point Dilution Viral Reproduction Attachment Penetration Early Steps (Early Proteins) Replication of Nucleic Acids Synthesis of Proteins (Late) Assembly Release

Viruses 3 One-step Growth Curve Latent Period Restriction/ Modification Restriction Enzymes Modification +/- SS RNA Viruses SS DNA Viruses DS Intermediates Reverse Transcriptase   BACTERIAL VIRUSES Model Viruses Genetic Engineering RNA Bacteriophage +SS RNA Viruses MS2 “Male” Specific Phage

Viruses 4 4 Proteins4 Proteins Maturation, Coat, Lysis & RNA Replicase Overlapping Genes SS DNA Icosahedral Phage ФX 174 DS DNA Phage – Lytic T7, T4 Head, Tail, Base Plate, Spikes, Tail Fibers, Contractile Sheath Hydoxymethylcytosine Temperate Bacteriophage Lambda

Viruses 5 Virulent – Temperate Lysogeny Prophage – Provirus Immunity Lambda Repressor Cro protein Transposable Phage Insertion Elements Transposon Mu Phage – Mutator Animal Viruses Eukaryotic Hosts Lytic Infections Persistent Infections Latent Infections

Viruses 6 Cancer Transformation Neoplasm Benign Malignant Metastasis Oncogene +SS RNA Viruses Rhinovirus Foot-and-Mouth Virus Poliovirus Polyprotein Viral Protease -SS RNA Virus Rhabdovirus RNA Dep. RNA Polymerase Influenza Segmented Genome DS RNA Virus Reovirus Rotavirus

Viruses 7 DNA Virus Papovavirus SV 40 Herpesviruses Herpes simplex, Chickenpox, Shingles, Epstein-Barr, Burkitt’s Lymphoma Pox Virus Smallpox Adenovirus Retrovirus Reverse Transcriptase Acquired Immuno deficiency Syndrome – AIDS   Viroids SS RNA Circles

Viruses 8 Prions “Mad Cow Disease” Kuru Scrapies Creutzfeldt-Jakob Disease