General Biology 116 – Introductory Virology, Classification & Evolution

Course Information & Logistics

• Instructor: Dr. Daniel Stern Cardinale
  • Office: Room 108A, Douglass Bio Building
  • Contact: genbio@dls.rutgers.edu – WRITE THIS DOWN
• Synchronous support
  • Weekly review sessions (3 × week)
  • Tues & Fri 10{:}20{-}11{:}40\,\text{am} in Hickman 205
  • Thurs 12{:}10{-}1{:}30\,\text{pm} via ZOOM
• Course text: Same textbook as GB 115
• Workshops
  • Begin week of 1/22
  • Policy-Acknowledgment Form due by noon 1/26 (Friday) – must be complete or no credit for Workshop 2 →
  • Weighting: 10\% participation, 30\% graded assignments
  • Success tip: “Don’t go in cold” – do the worksheet before workshop; graded quiz each week covers current + prior material.

Memory & Learning Review (Why workshops matter)

• Long-term retention is based on USE (active practice).
• Model introduced (slide diagram):
  • Encoding → Sensory Store → Short-Term/Working Memory → Long-Term Memory (LTM) via Long-Term Potentiation (LTP).
  • Retrieval reinforces pathways; lack of retrieval leads to “Forgotten.”
• Workshops = scheduled retrieval & practice to drive info into LTM.

Scope of GB 116

• Major thematic buckets
  • Chemistry, Cellular Biology, Gene Expression, Energetics
  • Diversity, Systems, Ecology, Evolution (today’s focus)
• Today’s lecture subtitle: “Virology! (and a bit of review)”
  • Learning Outcomes flagged by verbs: SEQ (sequence), INTERPRET, CC (compare/contrast).

Slide-Reading & Lecture Etiquette

• Formatting conventions
  • Bold red text = instructor expects you to know the term.
  • True definitions follow a colon (:) not a dash.
  • Slides are arranged like outlines—follow indentation.
• Participation
  • Raise hand; if unseen, speak up.

Classification & Evolution

A. Classification (Systematics)

• Study of biological diversity & evolutionary relationships. Two intertwined parts:
  1. Taxonomy – naming, describing, classifying (binomial nomenclature).
  2. Phylogeny – evolutionary history of a species or group.

Linnaean Hierarchy refresher

• Hierarchical = each level more inclusive.
• Any level is a taxon. Example dog:
  • Domain: Eukarya
  • Kingdom: Animalia
  • Phylum: Chordata
  • Class: Mammalia
  • Order: Carnivora
  • Family: Canidae
  • Genus: Canis
  • Species: Canis lupus
  • Subspecies: Canis lupus familiaris (domestic dog)

B. Evolution (Definition level)

• Evolution = change in allele frequency from generation to generation.
  • NOT change within an individual’s lifetime.

Natural Selection recap

• Mechanism of evolution (one of many).
  • Requires heritable, phenotypic variation + differential success.
• Berkeley “beetle cartoon” example: predators prefer green beetles → over generations, brown allele frequency ↑.
  • Note connection to earlier GB 115 unit on Mendelian genetics & population genetics (Hardy–Weinberg).

C. Phylogeny Basics

• Phylogenetic tree = hypothesis of evolutionary relationships, not necessarily morphological similarity.
  • Branching order represents pattern of descent from common ancestors.
  • Terms: outgroup, node, branch, sister taxa.
• Example tree (lancelet, lamprey, fish, frog, turtle, leopard) with derived traits (vertebral column, jaws, amnion, hair) mapped onto branches.

Connecting Taxonomy & Phylogeny / Tree of Life

• Goal: modern taxa should reflect monophyletic clades.
• “3-Domain System” (Woese): Bacteria, Archaea, Eukarya emanate from a Universal Ancestor.
• Representative lineages shown (Proteobacteria, Euryarchaeotes, plants, animals, fungi, etc.)
• Key question raised: “Where are viruses on the tree?” → Answer: nowhere — they are non-living (by traditional criteria) & not cellular.

Virology

Are Viruses Alive? — Guided Socratic images

• Instructor displayed side-by-side photos (bacteria, bacteriophage, nanoarchaea, mini bacs, viroids, etc.) and asked repeatedly “Are these alive?”
  • Consensus: bacterial cells = yes; bacteriophages/viruses = generally considered non-living because they cannot self-sustain metabolism or reproduction.

General Characteristics

• Subcellular, intracellular parasites.
  • Basic parts: Capsid + Genome (some also an envelope).
  • Size: typically 20{-}300\,\text{nm} (exception: giant viruses up to >500\,\text{nm}).
  • Replication strictly inside host cells; usurp host resources.
• Rule-breakers: there are exceptions to nearly every generalization in virology.

What viruses do NOT do

• No metabolic processes (no ATP production, etc.)
• Cannot reproduce independently of host
• No nucleus/cytoplasm/organelles – they are not cells
• Caveat: complexity possible (e.g., Mimivirus micrographs, Amoeba-infecting giant viruses with numerous genes, membrane layers, fibrils).

Viral Structure

Genome Diversity

• Possible nucleic acid options:
  • DNA or RNA
  • Single-stranded (ss) or double-stranded (ds)
  • May switch forms during life cycle (“ambisense”, dsDNA→mRNA etc.).
  • Architecture: linear, circular, or segmented (Influenza = 8 RNA segments).
  • Gene count spans 2{-}1000+.

Capsid

• Protein coat comprised of repeating capsomeres.
• Determines morphology (helical, icosahedral, complex) & host-cell attachment.
  • Ex: Helical (TMV), Icosahedral (Human Rhinovirus 14).
• Image Fig 21.7 referenced.

Envelope (optional)

• Derived from host phospholipid bilayer during budding.
• Contains mixture of host lipids + viral glycoproteins (key to cell entry).
• Typical diameters 80{-}200\,\text{nm} (Influenza example).
  • Electron micrograph emphasises spikes = hemagglutinin (HA) & neuraminidase (NA).

Viral Replication Concepts

Host Range & Tissue Tropism

• Host range = species/tissues virus can infect. Often narrow (1 species or even single tissue).
  • West Nile Virus cycle: mosquitos ↔ birds (primary), incidental hosts = humans, horses.
  • Measles ≈ only human respiratory/epithelial.
  • Determinant = lock-and-key interaction between viral surface proteins & host receptors.

Generic Replication Cycle (Influenza example)

1. Attachment to host receptor.
2. Entry – membrane fusion or endocytosis; genome released.
3. Genome replication with viral or host polymerase; gene expression to make proteins.
4. Assembly of capsids + genomes.
5. Release/Exit – lysis (non-enveloped) or budding (enveloped). Often kills host cell.
   • Key note: for flu, viral RNA enters nucleus (unusual for RNA viruses) where viral RNA polymerase replicates genome.

Two Canonical Cycle Types (from bacteriophage model)

• Terminology lytic & lysogenic derived from phage but similar logic in eukaryotic viruses.

Lytic Cycle (Virulent phage)

• Steps: Attachment → Inject DNA → Circularization → Phage DNA replication + protein synthesis → Assembly → Lysis (host cell bursts) → release.
• Transmission = horizontal (host → host).
• Outcome: host death.

Lysogenic Cycle (Temperate phage)

• Integration: phage DNA inserts into host chromosome ⇒ prophage.
• Host replicates, thereby copying viral genome (vertical transmission, parent→offspring).
• Generally non-destructive; prophage may confer benefits (toxins, immunity to superinfection).
• Environmental stress (UV, nutrient shortage) can induce prophage excision → lytic switch.

Temperate Phage λ (lambda) as exemplar

• Demonstrates ability to toggle cycles; decision governed by regulatory proteins (cI repressor vs Cro).
• Diagram on slide 32 shows bifurcation.

Bacterial Defenses Against Phage

• Restriction enzymes cut foreign DNA at specific sites.
• Other systems (CRISPR not shown but implied).
• Citations: Labrie et al. 2010 Nature; He et al. 2015 Sci Rep.

Summary Slide Recap

• Viruses = subcellular, intracellular parasites with vast genomic & morphological diversity.
• Two major replication strategies: lytic (kills host) & lysogenic (integrates).
• Constant host–virus arms race (restriction enzymes, etc.).

Practice Question (Outcome: CC replication cycles)

Prompt recap: “Which statement is true of BOTH lytic and lysogenic cycles?”

• Options reviewed:
  a. Both involve horizontal transmission
  b. Only lysogenic involves vertical transmission
  c. Only lytic forms a prophage
  d. Both result in host cell death
• Evaluate:
  • Both cycles certainly involve horizontal transmission because infection must begin in a new host; lysogenic additionally involves vertical transmission once integrated.
  • So (a) is the only universally true statement for both.
• Teachable moment: vocabulary horizontal vs vertical.