A3.2.9 Classification of all organisms using evidence from rRNA base sequences (HL) Notes

rRNA Analysis Revealed Three Evolutionary Domains

1. Early classification used five kingdoms: Monera, Protista, Fungi, Plantae, and Animalia.
2. However, this system ignored key molecular differences between organisms.
3. rRNA analysis later revealed these groups didn't reflect true evolutionary relationships.

Why rRNA Was Chosen for Analysis

1. rRNA is found in all living organisms, making it a universal molecular marker.
2. It has conserved regions that barely change over time, allowing comparison across distantly related groups.
3. It also has variable regions that accumulate mutations steadily, providing evidence for evolutionary divergence.

Discovery of the Three-Domain System

1. In 1977, microbiologist Carl Woese and colleagues compared rRNA base sequences from different prokaryotes.
2. The results revealed two fundamentally distinct groups of prokaryotes:
   1. Eubacteria (true bacteria)
   2. Archaea (a separate lineage, more closely related to eukaryotes than to bacteria).
3. This led to a paradigm shift: a new taxonomic rank above kingdoms called domains.

1. Domain Archaea

1. Prokaryotic, but distinct from bacteria.
2. Often live in extreme environments (thermophiles, halophiles, methanogens).
3. Key features:
   1. Circular chromosomes.
   2. Cell wall without peptidoglycan (unlike bacteria).
   3. Glycerol-ether lipids in cell membranes (unique).
   4. 70S ribosomes, but with a small subunit more similar to eukaryotes.
   5. Histone-like proteins present.
   6. Introns present in some genes.

2. Domain Eubacteria (Bacteria)

1. True bacteria; unicellular prokaryotes.
2. Found in almost all environments.
3. Key features:
   1. Circular chromosomes.
   2. Cell walls with peptidoglycan.
   3. Glycerol-ester membrane lipids.
   4. 70S ribosomes, distinct from archaeal and eukaryotic ribosomes.
   5. No histones, introns extremely rare.

3. Domain Eukaryota

1. Includes animals, plants, fungi, and protists.
2. Key features:
   1. Linear chromosomes within a nucleus.
   2. 80S ribosomes in the cytoplasm (70S in mitochondria and chloroplasts).
   3. Histones present.
   4. Introns common in genes.
3. Complex cells with membrane-bound organelles.

Why rRNA Was Used for Classification

1. rRNA is found in all organisms.
2. It evolves slowly, making it suitable for comparing distantly related groups.
3. Conserved regions allow alignment, while variable regions show evolutionary divergence.

Implications of the Three-Domain System

1. Created a new level of classification above kingdoms.
2. Provided a framework that reflects true evolutionary ancestry.
3. Showed that:
   1. The “prokaryotes” were not a single unified group.
   2. Archaea and Eukaryota share a more recent common ancestor than either does with Bacteria.