Lecture 1- Phylogenetics Review & Virology Flashcards
What are the two types of phages discussed in lecture?
Virulent (T4) & Temperate (lamda)
A(n) _______ is the protein shell of a virus, enclosing its genetic material
Capsid, they determine morphology and attachment to host cell
True or False: The lytic cycle results in the death of the host
True
What are capsids composed of?
Capsomeres (proteins)
True or False: Temperate phages undergo only the lytic cycle
False; temperate phages can undergo lytic and lysogenic cycles
Which viral replication cycle(s) do virulent phages undergo?
Lytic cycle ONLY
A(n) ______ is the latent form of a bacteriophage genome inserted and integrated into the circular bacterial DNA chromosome
Prophage
Taxon
Grouping of organisms at any level
Evolution
Changes in allele frequency in a population over time
Taxonomy
Naming, describing, classifying re binomial nomenclature
Phylogeny
Evolutionary history of species or group
Natural selection ensures that _________ traits increase in frequency over time
Beneficial
Difference between taxonomy and phylogeny
Taxonomy groups organisms based on shared phenotypic traits, while phylogeny shows the descent from common ancestor (descendants do not always have the same traits)
Big idea re taxonomy and phylogeny
Taxonomy should reflect phylogeny
Envelope
Phospholipid bilayer surrounding capsid, only present in some viruses
Host range
Species or tissue that a particular virus can infect, usually narrow- 1 or a few
General Replication Cycle
Bind to host cell, genome enters cell, genome replication and gene expression, assembly, exit
Lytic cycle
- The phage infects a cell
- The phage DNA circularizes, remaining separate from the host DNA
- Phage DNA replicates and phage proteins are made. New phage particles are assembled.
- The cell lyses, releasing phage
Lysogenic cycle
Replication of viral genome without destroying host cell. Phage genome integrates into bacterial chromosome. When host replicates, phage genome replicates.
What does capsid determine?
Morphology, involved in attachment to host cell
What is vertical transmission?
Parent to offspring- Phage genome is integrated into bacterial chromosome and when the host replicates, the phage genome replicates
What is horizontal transmission?
Host-to-host- Replication occurs (phage DNA replicates) and phage proteins are made. The cell lyses and releases phage
Temperate phage- what is it capable of?
Both lytic and lysogenic replication
Virulent phage- what is it capable of?
Only lytic replication (horizontal transmission)
What are bacterial defenses?
Resistance to infection and restriction enzymes
A prophage forms ONLY during the __________ cycle
Lysogenic
Basal Taxon
Near common ancestor (First to branch from common ancestor)
Extant species
Tips of branches/non-extinct
Clades
Monophyletic (CA and all descendants)/ paraphyletic (CA and some descendants)/ polyphyletic (some descendants)
Homologous traits
Similar because of shared CA
Analogous traits
A result of convergent evolution (have similar structure or function but don’t share a CA)
Dichotomy
2 way branch points- where common ancestor diverged into two new species
Rooted tree
Represents MRCA of all taxa on tree
Branch point
Divergence of 2 species from a common ancestor
Node
Branch point
Branch
Each line
Sister taxa
Groups or organisms that share and immediate CA
Basal taxa
Lineage that diverged early in history of group
Polytomy
More than 2 groups emerge from one branch (Uncertainty=polytomy)
Derived trait
Separates you from common ancestor
