Lecture 1- Phylogenetics Review & Virology

Question 1

What are the two types of phages discussed in lecture?

Answer 1

Virulent (T4) & Temperate (lamda)

Question 2

A(n) _______ is the protein shell of a virus, enclosing its genetic material

Answer 2

Capsid, they determine morphology and attachment to host cell

Question 3

True or False: The lytic cycle results in the death of the host

Answer 3

True

Question 4

What are capsids composed of?

Answer 4

Capsomeres (proteins)

Question 5

True or False: Temperate phages undergo only the lytic cycle

Answer 5

False; temperate phages can undergo lytic and lysogenic cycles

Question 6

Which viral replication cycle(s) do virulent phages undergo?

Answer 6

Lytic cycle ONLY

Question 7

A(n) ______ is the latent form of a bacteriophage genome inserted and integrated into the circular bacterial DNA chromosome

Answer 7

Prophage

Question 8

Taxon

Answer 8

Grouping of organisms at any level

Question 9

Evolution

Answer 9

Changes in allele frequency in a population over time

Question 10

Taxonomy

Answer 10

Naming, describing, classifying re binomial nomenclature

Question 11

Phylogeny

Answer 11

Evolutionary history of species or group

Question 12

Natural selection ensures that _________ traits increase in frequency over time

Answer 12

Beneficial

Question 13

Difference between taxonomy and phylogeny

Answer 13

Taxonomy groups organisms based on shared phenotypic traits, while phylogeny shows the descent from common ancestor (descendants do not always have the same traits)

Question 14

Big idea re taxonomy and phylogeny

Answer 14

Taxonomy should reflect phylogeny

Question 15

Envelope

Answer 15

Phospholipid bilayer surrounding capsid, only present in some viruses

Question 16

Host range

Answer 16

Species or tissue that a particular virus can infect, usually narrow- 1 or a few

Question 17

General Replication Cycle

Answer 17

Bind to host cell, genome enters cell, genome replication and gene expression, assembly, exit

Question 18

Lytic cycle

Answer 18

1. The phage infects a cell
2. The phage DNA circularizes, remaining separate from the host DNA
3. Phage DNA replicates and phage proteins are made. New phage particles are assembled.
4. The cell lyses, releasing phage

Question 19

Lysogenic cycle

Answer 19

Replication of viral genome without destroying host cell. Phage genome integrates into bacterial chromosome. When host replicates, phage genome replicates.

Question 20

What does capsid determine?

Answer 20

Morphology, involved in attachment to host cell

Question 21

What is vertical transmission?

Answer 21

Parent to offspring- Phage genome is integrated into bacterial chromosome and when the host replicates, the phage genome replicates

Question 22

What is horizontal transmission?

Answer 22

Host-to-host- Replication occurs (phage DNA replicates) and phage proteins are made. The cell lyses and releases phage

Question 23

Temperate phage- what is it capable of?

Answer 23

Both lytic and lysogenic replication

Question 24

Virulent phage- what is it capable of?

Answer 24

Only lytic replication (horizontal transmission)

Question 25

What are bacterial defenses?

Answer 25

Resistance to infection and restriction enzymes

Question 26

A prophage forms ONLY during the __________ cycle

Answer 26

Lysogenic

Question 27

Basal Taxon

Answer 27

Near common ancestor (First to branch from common ancestor)

Question 28

Extant species

Answer 28

Tips of branches/non-extinct

Question 29

Clades

Answer 29

Monophyletic (CA and all descendants)/ paraphyletic (CA and some descendants)/ polyphyletic (some descendants)

Question 30

Homologous traits

Answer 30

Similar because of shared CA

Question 31

Analogous traits

Answer 31

A result of convergent evolution (have similar structure or function but don't share a CA)

Question 32

Dichotomy

Answer 32

2 way branch points- where common ancestor diverged into two new species

Question 33

Rooted tree

Answer 33

Represents MRCA of all taxa on tree

Question 34

Branch point

Answer 34

Divergence of 2 species from a common ancestor

Question 35

Node

Answer 35

Branch point

Question 36

Branch

Answer 36

Each line

Question 37

Sister taxa

Answer 37

Groups or organisms that share and immediate CA

Question 38

Basal taxa

Answer 38

Lineage that diverged early in history of group

Question 39

Polytomy

Answer 39

More than 2 groups emerge from one branch (Uncertainty=polytomy)

Question 40

Derived trait

Answer 40

Separates you from common ancestor