2.6 Molecular (Chemo) Taxonomy

Question 1

Molecular Taxonomy

Answer 1

Molecular Chronometer: ribosomal RNA (rRNA)

DNA -> Replication / Gene expression + transcription -> RNA -> (Ribosomes) -> Translation -> Protein

Ribosomes play key role in protein synthesis.

Ribosomes are composed of (ribosomal) RNA and various proteins

Question 2

Different types of Ribosomes

Prokaryotes

Prokaryotic and Eukaryotic ribosomes are different

Answer 2

Nucleotides : 165 (~1500)

21 proteins
30 S subunits

~34 proteins

50 S subunits -> 5S (~120) / 23 S (~2900)

70 S ribosome

Question 3

Different types of Ribosomes

Eukaryotes

Prokaryotic and Eukaryotic ribosomes are different

Answer 3

185 small subunit rRNA

5.0 S / 5.8 S / 28 S
40 S / 60 S

80 S ribosome

Question 4

Molecular Taxonomy by
CARL WOESE

‘Molecular Tree of Life’

Answer 4

Cells -> isolate DNA -> DNA -> gene encoding, ribosomal RNA / PCR -> DNA sequencing

DNA sequencing -> sequence analysis -> Alligned rRNA gene sequences -> generate phylogenetic tree

Question 5

Molecular Tree of Life

simplified

Answer 5

Observation 1:
Three domains of life: (EU)bacteria, Archaea, and Eukarya
(previously five kingdoms: animals, plants, fungi, bacteria and protists)

Observation 2:
The three domains of life diverged from an universal ancestor

Observation 3:
Bacteria and Archaea share a prokaryotic cell structure, but differ dramatically in their evolutionary history - Archaea are closer related to Eukarya than to Bacteria.

Observation 4:
Microorganisms branching off close to root show ancient traits.

Observation 5:
Unicellular eukaryotic microorganisms (protists) were the ancestors of the multicellular crown group organisms.

Observation 6:
Mitochondria and chloroplasts are derived from ancestors of specific lineages of Bacteria that established stable residency in cells of the Eukarya.

Question 6

Endosymbiont Hypothesis

Answer 6

Mitochondria evolved after the symbiotic uptake of a respiring alpha-proteobacteria.

Chloroplasts evolved after the symbiotic uptake of phototrophic algae.

Universal ancestor -> Nuclear line -> increased cell size -> origin of nucleus -> primitive eukaryote -> modern eukaryotes lacking mitochondria -> modern eukaryote -> loss of organelles -> protozoa, animals / Algae, plants

Universal ancestor -> Archaea

Universal ancestor -> Bacteria -> symbiotic uptake of a respiring cell (primitive mitochondrian)

Universal ancestor -> Bacteria -> symbiotic uptake of a phototrophic cell (primitive chloroplast)

Question 7

The ‘Omics’ Era

Craig Venter

Answer 7

• Sequencing at an industrial scale
• First complete DNA sequence of a microorganism (Haemophillus influenza, 1995)
• Draft human genome (2001, with Francis Collins)
• Thousands of completed genomes
• Metagenomics: whole genome sequencing

1986 
Phylogenetic stains (Normal Pace)

1987
Community sampling of ribosomal RNA genes reveals enormous diversity of bacteria in nature (Normal Pace)

1992
Discovery of marine Archeae (Jed Fuhrmann + Ed Delong)

1995
First genome sequence (Craig Venter + Hamilton Smith)

2004 - 2010
First large scale metagenomics project (Craig Venter)

=> Genomics
=> Proteomics
=> Transcriptomics
=> Metabolomics