Exam 1 Notes: Chapters 1-3

Chapter 1: Introduction to Virology and Viruses

Learning Objectives

1. Advances in Techniques and Technology for Studying Viruses:
   • Chamberland porcelain ultrafilters to separate viruses from bacteria.
   • Dmitri Ivanovski's work with tobacco mosaic virus.
   • Martinus Beijerinck's concept of "contagium vivum fluidum."
   • Bacteriophage plaque assays for quantifying bacteriophages.
   • Transmission electron microscope to visualize viruses.
   • Hershey-Chase Blender Experiment established DNA as genetic material.
   • Single-virus tracking and bioinformatics tools for evolutionary studies.

Key Terms

• Bacteriophages: Viruses that infect bacteria, isolated from natural sources.
• Plaques: Clearings in bacterial lawns indicating lysed cells.
• Lysogenic vs. Lytic Infection: Lysogenic preserves host cells, lytic causes cell lysis.
• Virophages, ORFans, Homologs, and Retroid Viruses: Definitions and roles.

2. Definition of a Virus:

   • Submicroscopic agents replicating within living cells, not cells themselves, with both beneficial and harmful impacts.

3. Origin Theories of Viruses:

   • Panspermia hypothesis: extraterrestrial origins.
   • Precursors to cells or degeneration from cells.
   • LUCA and diversity of viral genomes.
   • Hydrothermal origin hypothesis: formation at oceanic vents.

4. Virus Transmission and Disease Causation:

   • Direct vs. Indirect transmission; role of reservoirs and portals of entry.
   • Pathogenesis and diseases like HPV, chickenpox, and shingles.

5. Beneficial Viral Infections:

   • Parasitoid wasps and polydnaviruses as mutualistic.
   • Role of cryptic viruses and bacteriophage "BAM Velcro" in defense.
   • Herpesvirus in immune protection.

6. Applications of Viruses in Health Treatments:

   • Bacteriophage therapy against antibiotic-resistant bacteria.
   • Gene therapy using viral vectors.
   • Vaccine development.

7. Historical and Contemporary Viral Epidemics:

   • Influenza pandemics, AIDS, SARS, and other notable outbreaks.

Chapter 2: Virus Definition and Classification

Learning Objectives

• Defining a Virus: Challenges due to size and genome diversity.

  • Giant viruses (gyruses) and virophages.

• Baltimore Classification System: Seven classes based on genome and replication:

  1. dsDNA
  2. ssDNA
  3. dsRNA
  4. +ssRNA
  5. -ssRNA
  6. DNA reverse transcription
  7. RNA reverse transcription

• Discovery of Giant Viruses: Mimivirus, Mamavirus, Megavirus, and others.

• Virology Taxonomy: Role of ICTV in virus naming and classification.

Chapter 3: Virus Structure and Replication

1. Basic Virus Structure:

   • Naked vs. Enveloped viruses.
   • Capsid shapes: icosahedral and helical.
   • Components: Capsomers, protomers, nucleocapsid, glycoprotein spikes.

2. Molecular Challenges and Overcoming Them:

   • Overcoming the lack of host polymerases, receptor binding, and mRNA translation issues.

3. Host Protein Synthesis Machinery:

   • Viruses rely on host machinery due to their limited genome size and lack of organelles.

4. One-Step Growth Curve Procedure:

   • Understanding viral replication kinetics.

5. Viral Replication Cycle Steps:

   • Attachment, penetration, uncoating, replication, assembly, maturation, release.

6. RNA Virus Mutation Rates:

   • Higher due to lack of proofreading in RNA polymerases.

7. Challenges in Antiviral Development:

   • Avoiding toxicity to host cells while targeting viral replication.

8. Viruses as "Eyes" into Cells:

   • Educational role in understanding cellular processes like protein synthesis.

Study Tips

• Focus on historical figures and transcription/translation processes.
• Use Quizlet for key terms.
• Review lecture slides for any missing information.