Taxonomy

Question 1

Nomenclature

Answer 1

• Binomial system used to name all cellular organisms
• Names are descriptive and derived from Latin and Greek

Question 2

What are stromatolites

Answer 2

Microbial mats consisting of layers of filamentous prokaryotes, sediments and extracellular matrix

Question 3

Origin or cellular life: Theories

Answer 3

• Surface origin hypothesis
• Subsurface origin hypothesis

Question 4

Surface origin hypothesis

Answer 4

• The first membrane-enclosed, self-replicating cells arose out of primordial soup rich in organic and inorganic compounds in ponds on Earth’s surface
• Dramatic temperature fluctuations (day/night) and mixing from meteor impacts, dust clouds, and storms argue against this hypothesis

Question 5

Subsurface origin hypothesis

Answer 5

• Life originated in hydrothermal springs on the ocean floor
• Conditions would have been more stable
• Steady and abundant supply of energy (e.g., H 2 and H 2 S) was likely available at these sites

Question 6

Origin of cellular life: Emergence steps

Answer 6

1. Prebiotic chemsitry:
   * Biological building blocks
2. Precellular life:
   * RNA world
   * Protein synthesis
   * DNA
3. Early cellular life:
   * Lipid bilayers
4. LUCA
5. Diversification of Bacteria & Archaea

Question 7

RNA world theory

Answer 7

First self-replicating system may have been RNA
* RNA can bind small molecules
* RNA has catalytic activity
* RNA can be copied like DNA

Question 8

LUCA

Answer 8

Population of early cells from which
cellular life may have diverged into ancestors of modern-day Bacteria and Archaea

Question 9

Origin of Life: Conditions

Answer 9

Early Earth was anoxic and much hotter than present day

Question 10

2 methods of classification

Answer 10

• Phenetics: Overall similarity
• Phylogenetics: Evolutionary relationships

Question 11

Phenetics: Rules

Answer 11

• All characteristics should be considered of equal importance
• Classification should be base on as many features as possible.
• Organisms should be grouped based on overall similarity

Question 12

Similarity/Jaccard coefficient

Answer 12

S = # shared/total
Sj = # shared/(total - negative shared)

• 0.85 = species similarity
• 0.65 = genus similarity

Question 13

Phenon

Answer 13

Group of organisms that have characters in common

Question 14

Phylogenetics

Answer 14

• Fossil record
• Ribosomal RNA sequencing
• Multi-locus sequence typing
• Whole genome sequencing

Question 15

Ribosomal RNA sequencing: Steps

Answer 15

• Amplification of the gene encoding SSU rRNA
• Sequencing of the amplified gene
• Analysis of sequence in reference to other sequences

Question 16

SSU rRNA

Answer 16

• Contains conserved & variable region
• Evolutionary relationship
  between 2 organisms = # of mutations in each region.
• Few differences: closely related
• Many differences: loosely related

Question 17

Multi-locus sequence typing (MLST)

Answer 17

• Method in which several different “housekeeping genes” from a species are sequenced and aligned to the respective sequences of other individuals of the same species
• Can distinguish between very closely related strains

Question 18

Phylogenetic tree

Answer 18

Graphic illustration of the relationships among sequences
* Branch length = the number of changes that have occurred along that branch
* Branches = the order of descent & ancestry of the nodes
* Nodes: putative common ancestor

Question 19

Polyphasic approach to taxonomy

Answer 19

1. Phylogenetic analysis (SSU rRNA)
2. Phentypic analysis (motility, capsule, virulence…)
3. Genotypic analysis (presence/absence of specific genes)

Question 20

Identification

Answer 20

• Comparison of its properties with those of organisms that have already been classified and named
• Dichotomous key
• Serotyping

Question 21

Serotyping

Answer 21

Based on the binding of specific antibody to surface structure:
* LPS: O serotypes
* Capsule: K serotypes
* Flagella: H serotypes
* H1N1, Hemagglutinin 1, Neuraminidase 1

Positive reaction: agglutination

Question 22

Ancient Vs Modern stromatolites

Answer 22

• Ancient stromatolites: Anoxygenic phototrophic filamentous bacteria
• Modern stromatolites: Oxygenic phototrophic cyanobacteri