Paige Lake
General Biology II
Dr. Stern Cardinale
General Biology II
Lecture Notes
. ݁₊ ⊹ . ݁˖ . ݁EXAM 1 . ݁₊ ⊹ . ݁˖ . ݁
☆ Lecture 1/21/25 (Virology)
☆ I. Classification & Evolution
- SEQ natural selection
- Interpret phylogeny
A. Classification (& Systematics)
- Study of diversity & evolutionary relationships.
- Taxonomy: naming, describing, classifying (binomial
nomenclature).
- Phylogeny: Evolutionary history of species or group.
Linnaean Classification
- Domain, kingdom, phylum, class, order, family,
genus, species
- Hierarchical: each level = more inclusive than the one
below
- All species at a level share characteristics of that group
- Taxon: grouping at any level.
,B. Evolution
- Changes in allele frequency from generation to generation;
no changes in allele frequency = no evolution.
- Natural selection: mechanism of evolution (1 of
many), beneficial traits ↑ in frequency over
generations; requires heritable phenotypic variation.
C. Basics of Phylogeny
- Evolutionary history of a species / group of species.
- Phylogenetic tree: representation of evolutionary
relationships – not phenotypic similarity.
- Pattern of descent from common ancestors.
- Trees = hypotheses!
- Every time more data = collected, hypothesis = tested.
- PSC (Phylogenetic species concept): The
smallest group of organisms that share an
evolutionary history.
- Dichotomies: Two-way branch points in a
phylogenetic tree.
- Branch points: Represent divergence from a
common ancestor.
- Sister taxa: Two taxa sharing an immediate
common ancestor.
- Basal taxon: Diverges early in evolutionary
history.
- Polytomy: Branch where more than
two groups emerge, indicating
uncertainty.
- Monophyletic: common
ancestor + all descendants.
, - Paraphyletic: common ancestor
+ some (not all) descendants.
- Polyphyletic: no common
ancestor.
- Connecting Classification & Phylogeny
- Main idea: Taxonomy should reflect phylogeny →
classification of organisms should be based on their
evolutionary history & relationships (phylogeny).
- Tree of Life
- 3 Domains: Archaea, Eukarya, Bacteria
☆ II. Virology
- SEQ viral replication cycle
- CC types of replication cycles
A. General Characteristics
- Subcellular, intracellular, parasites.
- Capsid (protein shell that protects & contains a virus’s
genetic material) + genome
- Smaller than cells (usually), “less than” cells.
- Replicate within cells (CANNOT replicate independent of
their host).
- Use the cell's resources to complete its own life cycle.
- Note: Viruses = weird, break all the rules, ALWAYS
exceptions
- Viruses DO NOT or CANNOT
- Carry out metabolic processes.
, - Reproduce independently of host cells.
- Contain nucleus, cytoplasm, organelles (they
are NOT cells).
- But they can still be complex!!!!
B. Viral Structure
- Often very small — 20-300 nm (smaller than average
eukaryotic cell).
- Rod-shaped, irregularly shaped, etc.
- Genetic material
- Can pretty much be anything.
- RNA and/or DNA
- Single stranded (SS) or double stranded (DS) or
BOTH.
- Linear, circular, or segmented.
- 2-1,000+ genes (need gene to make coat + gene
that directs replication once it has infected the
host cell).
- Capsid: protein coat, made of
capsomeres: capsid proteins.
- Determines morphology,
involved in the virus’s attachment
to the host cell.
- Envelopes
- Phospholipid bilayer surrounding
capsid.
- Only present in some viruses.
- Acquired from the host.
- Contains host + virus proteins.
General Biology II
Dr. Stern Cardinale
General Biology II
Lecture Notes
. ݁₊ ⊹ . ݁˖ . ݁EXAM 1 . ݁₊ ⊹ . ݁˖ . ݁
☆ Lecture 1/21/25 (Virology)
☆ I. Classification & Evolution
- SEQ natural selection
- Interpret phylogeny
A. Classification (& Systematics)
- Study of diversity & evolutionary relationships.
- Taxonomy: naming, describing, classifying (binomial
nomenclature).
- Phylogeny: Evolutionary history of species or group.
Linnaean Classification
- Domain, kingdom, phylum, class, order, family,
genus, species
- Hierarchical: each level = more inclusive than the one
below
- All species at a level share characteristics of that group
- Taxon: grouping at any level.
,B. Evolution
- Changes in allele frequency from generation to generation;
no changes in allele frequency = no evolution.
- Natural selection: mechanism of evolution (1 of
many), beneficial traits ↑ in frequency over
generations; requires heritable phenotypic variation.
C. Basics of Phylogeny
- Evolutionary history of a species / group of species.
- Phylogenetic tree: representation of evolutionary
relationships – not phenotypic similarity.
- Pattern of descent from common ancestors.
- Trees = hypotheses!
- Every time more data = collected, hypothesis = tested.
- PSC (Phylogenetic species concept): The
smallest group of organisms that share an
evolutionary history.
- Dichotomies: Two-way branch points in a
phylogenetic tree.
- Branch points: Represent divergence from a
common ancestor.
- Sister taxa: Two taxa sharing an immediate
common ancestor.
- Basal taxon: Diverges early in evolutionary
history.
- Polytomy: Branch where more than
two groups emerge, indicating
uncertainty.
- Monophyletic: common
ancestor + all descendants.
, - Paraphyletic: common ancestor
+ some (not all) descendants.
- Polyphyletic: no common
ancestor.
- Connecting Classification & Phylogeny
- Main idea: Taxonomy should reflect phylogeny →
classification of organisms should be based on their
evolutionary history & relationships (phylogeny).
- Tree of Life
- 3 Domains: Archaea, Eukarya, Bacteria
☆ II. Virology
- SEQ viral replication cycle
- CC types of replication cycles
A. General Characteristics
- Subcellular, intracellular, parasites.
- Capsid (protein shell that protects & contains a virus’s
genetic material) + genome
- Smaller than cells (usually), “less than” cells.
- Replicate within cells (CANNOT replicate independent of
their host).
- Use the cell's resources to complete its own life cycle.
- Note: Viruses = weird, break all the rules, ALWAYS
exceptions
- Viruses DO NOT or CANNOT
- Carry out metabolic processes.
, - Reproduce independently of host cells.
- Contain nucleus, cytoplasm, organelles (they
are NOT cells).
- But they can still be complex!!!!
B. Viral Structure
- Often very small — 20-300 nm (smaller than average
eukaryotic cell).
- Rod-shaped, irregularly shaped, etc.
- Genetic material
- Can pretty much be anything.
- RNA and/or DNA
- Single stranded (SS) or double stranded (DS) or
BOTH.
- Linear, circular, or segmented.
- 2-1,000+ genes (need gene to make coat + gene
that directs replication once it has infected the
host cell).
- Capsid: protein coat, made of
capsomeres: capsid proteins.
- Determines morphology,
involved in the virus’s attachment
to the host cell.
- Envelopes
- Phospholipid bilayer surrounding
capsid.
- Only present in some viruses.
- Acquired from the host.
- Contains host + virus proteins.
