EXAM 2: Taxonomy

Question 1

Taxonomy

Answer 1

the science of biological classification

Question 2

Nomenclature

Answer 2

the choosing of names for things

Question 3

Phylogeny

Answer 3

the evolutionary development/history of a taxonomic grouping of organisms

Question 4

Oligonucleotide

Answer 4

short single-stranded DNA or RNA molecules

Question 5

Species

Answer 5

collection of organisms that share the same sequences in their core housekeeping genes

Question 6

Strain

Answer 6

a genetic variant descended from a single, pure, microbial culture

Question 7

Biovars

Answer 7

a genetic variant that differs biochemically and physiologically

Question 8

Core housekeeping genes

Answer 8

genes that are essential for life (organism can’t survive without it)

Question 9

Taxon

Answer 9

is a unit of any rank (i.e. kingdom, phylum, class, order, family, genus, species) designating an organism or a group of organisms

Question 10

Morphovars

Answer 10

a genetic variant that differs morphologically

Question 11

Serovars

Answer 11

a genetic variant that differs in antigenic properties

Question 12

Clade

Answer 12

a group consisting of an organism and its descendants

Question 13

Parsimony

Answer 13

adoption of the simplest assumption in the formulation of a theory or in the interpretation of data

Question 14

Explain the binomial nomenclature and how to properly identify organisms in this format

Answer 14

• Developed by Carolus Linnaeus
• Can be abbreviated after 1st use (H. sapiens)
• Each organism has 2 names
  Genus name
• Italicized and capitalized (Homo)
  Species epithet/name
• Italicized, not capitalized (sapiens)

Question 15

List taxon categories used in the classification of organisms. What is a strain?

Answer 15

Life, Domain, KPCOFGS
- Species are collections of strains that share stable properties and differs significantly from other strains

Question 16

Describe the 3 domains and the 6 kingdoms of organisms. Explain the key differences between organisms in each group.

Answer 16

3 Domains:
- bacteria, eukarya, archaea
6 Kingdoms:
- Eubacteria, Archaeabacteria, Protist, Fungi, Plantae, Animalia

Main differences:
- Bacteria have peptidoglycan in cell wall
- Archaea have NO peptidoglycan in cell wall
- Eukarya are multicellular

Question 17

Describe traditional and modern methods used to classify microorganisms

Answer 17

Taxonomy consists of three separate by interrelated principles:
1. Classification → arrangement of organisms into groups (taxa/taxon)
2. Nomenclature → assignment of names to taxa
3. Identification → determination of taxon to which an organism belongs

Older method (Phenetic Classification)
Newer method (Phylogenetic Classification)
- uses SSU rRNAs

Question 18

Phylogenetic trees

Answer 18

• Show inferred evolutionary relationships in the form of multiple branching lineages connected by nodes
• Nodes represent divergence event
• Length of branch represents the number of molecular changes between two nodes

Question 19

SSU rRNA?

Answer 19

• Small subunit rRNAs (16S for prokaryotes)
• Highly conserved (least changes) so it is good for determining ancestors → genes encoding SSU rRNAs are the most frequently used sequence in phylogenetics
• 70% cutoff value for species definition (sequence homology)