# Classification of the Three Domains ## Introduction to Domains - Taxonomy is the practice of biological classification - It involves placing organisms into a series of categories called **taxa** (singular: taxon) - The hierarchical classification system has different ranks - The **highest rank** is the domain

A domain is the highest taxonomic rank in the classification of life

## The Role of Cell Type in Classification - Cell type plays a major role in classifying organisms into domains - **Do not confuse** cell types with domains - they are different concepts ### Two Cell Types - **Prokaryotic cells**: lack a nucleus and membrane-bound organelles - **Eukaryotic cells**: contain a nucleus and compartmentalised structures with organelles

Cell type is important for classification, but domains represent a broader categorisation than just cell structure

## Discovery of the Three Domains - Initially, life was divided simply into prokaryotes and eukaryotes - Advances in **molecular biology**, **biochemistry**, and **cell structure** studies in the late 20th century revealed something unexpected - Scientists analysed **RNA genes**, **ribosomal RNA (rRNA)**, **protein synthesis**, **cell membranes**, and **flagella** - These analyses showed prokaryotes are **not one uniform group** - Prokaryotes can be divided into **two separate domains**

Using cell type alone to classify organisms is insufficient

### The Three Domains of Life 1. **Bacteria** (prokaryotes) 2. **Archaea** (prokaryotes) 3. **Eukarya** (eukaryotes) ## Domain Bacteria ### General Characteristics - Organisms with **prokaryotic cells** that contain no nucleus - Size varies widely: smallest are larger than the biggest known viruses; largest are smaller than the smallest single-celled eukaryotes - Cells divide by **binary fission** ### Example Organism - *Staphylococcus pneumoniae*: a bacterial species causing pneumonia in humans ## Domain Archaea ### Discovery and Habitat - Often called the **extremophile prokaryotes** - First discovered living in **extreme environments** (though not all archaea live in such places) - Think of organisms thriving in boiling hot springs in Yellowstone - Or microbes living in the ultra-salty waters of the Dead Sea

Archaea were initially classified as bacteria until unique properties distinguished them

### General Characteristics - Cells have **no nucleus** (prokaryotic) - Similar size range to bacteria - Metabolism is similar to bacteria in many ways ### Unique Features Separating Archaea from Bacteria #### 1. Membrane Lipids - Membrane lipids are **completely unique** - Not found in bacterial or eukaryotic cells - Archaea: **branched** hydrocarbon chains bonded to glycerol by **ether linkages** - Bacteria: **unbranched** hydrocarbon chains bonded to glycerol by **ester linkages** #### 2. Cell Wall Composition - Archaea: cell walls **do not contain peptidoglycan** - Bacteria: cell walls **always contain peptidoglycan** #### 3. Ribosomal Structure - Both have 70S ribosomes, but key differences exist: - The **small subunit** in archaeal ribosomes is more similar to eukaryotic ribosomes than bacterial ribosomes - **rRNA base sequences** show more similarity to eukaryotes than bacteria - **Ribosome protein structures** are more similar to eukaryotes than bacteria #### 4. DNA Transcription - DNA transcription is **more similar** to that of eukaryotes ### Example Organism - *Halobacterium salinarum*: lives in environments with extremely high salt concentrations, such as salt flats or hypersaline lakes ## Domain Eukarya ### General Characteristics - Organisms with **eukaryotic cells** containing nuclei and membrane-bound organelles - **Massive size variation**: - Smallest: single-celled organisms just a few micrometres across - Largest: multi-metre organisms like blue whales (over 30 metres long) - Cells divide by **mitosis** - Can reproduce **sexually** or **asexually** ### Example Organism - *Canis lupus* (wolves) ## Key Differences Between Archaea and Bacteria | **Feature** | **Archaea** | **Bacteria** | |-------------|-------------|--------------| | **Cell type** | Prokaryotic | Prokaryotic | | **Chromosome** | Circular | Circular | | **Cell membrane lipids** | Glycerol-ether lipids (branched chains) | Glycerol-ester lipids (unbranched chains) | | **Ribosomes** | 70S (small subunit more similar to eukaryotic ribosomes) | 70S ribosomes | | **Cell walls** | Always present (without peptidoglycan) | Always present (with peptidoglycan) | | **Histones** | Yes | No | | **Introns** | Sometimes | Rarely |

Archaea and bacteria are both prokaryotic but are as different from each other as they are from eukaryotes

## Comparing All Three Domains | **Feature** | **Archaea** | **Bacteria** | **Eukaryotes** | |-------------|-------------|--------------|----------------| | **Cell type** | Prokaryotic | Prokaryotic | Eukaryotic | | **Chromosome** | Circular | Circular | Linear chromosomes + circular mtDNA and cpDNA | | **Cell membrane lipids** | Glycerol-ether lipids | Glycerol-ester lipids | Glycerol-ester lipids | | **Ribosomes** | 70S (small subunit is more similar to eukaryotic ribosomes) | 70S ribosomes | Larger 80S ribosomes in cytosol and 70S ribosomes in mitochondria and chloroplasts | | **Cell walls** | Always present (without peptidoglycan) | Always present (with peptidoglycan) | Sometimes present (without peptidoglycan) | | **Histones** | Yes | No | Yes | | **Introns** | Sometimes | Rarely | Yes | ## Evolutionary Relationships - The three-domain system clarifies **evolutionary relationships** between organisms - Molecular evidence suggests: - Archaea and Eukarya share a **more recent common ancestor** with each other than either does with Bacteria - All three domains ultimately trace back to a **universal ancestor**

Think of the three domains as three major branches from an ancient tree of life, with Archaea and Eukarya being closer together than either is to Bacteria

## Why the Three-Domain System Matters - Provides a more **accurate reflection** of evolutionary history - Based on **molecular evidence** rather than just observable features - Recognises the **fundamental differences** within prokaryotes - Shows that **Archaea are as different from Bacteria as Bacteria are from Eukarya** ## Summary Table: Domain Characteristics | **Characteristic** | **Details** | |-------------------|-------------| | **Number of domains** | 3 | | **Domains** | Bacteria, Archaea, Eukarya | | **Prokaryotic domains** | Bacteria and Archaea | | **Eukaryotic domain** | Eukarya | | **Key distinguishing evidence** | rRNA sequences, membrane lipids, cell wall composition, ribosomal structure | | **Highest rank** | Domain |