state that Archaea and Bacteria are prokaryotes and that there are differences between them, limited to differences in membrane lipids, ribosomal RNA and composition of cell walls

Classification – Prokaryotes

Learning Objectives

  • State that Archaea and Bacteria are prokaryotes.

  • Identify the three main biochemical features that separate Archaea from Bacteria:

    • Membrane‑lipid composition

    • 16S ribosomal RNA (rRNA) sequence

    • Composition of the cell wall

  • Recognise why viruses are not classified as cells.

What is a Prokaryote?

  • Cell lacks a membrane‑bound nucleus and other membrane‑bound organelles (mitochondria, chloroplasts, ER, Golgi).

  • Genetic material: a single, circular chromosome located in the nucleoid region.

  • May contain extra‑chromosomal DNA called plasmids.

  • Plasma membrane follows the fluid‑mosaic model – a phospholipid bilayer with embedded proteins that permit diffusion, facilitated diffusion and active transport.

  • Typical size: 0.5–5 µm in diameter.

Prokaryotes vs. Eukaryotes (Quick Comparison)

FeatureProkaryotes (Archaea & Bacteria)Eukaryotes (Plants, Animals, Fungi, Protists)
NucleusAbsent – DNA free in nucleoidPresent – DNA enclosed by nuclear membrane
Membrane‑bound organellesNonePresent (mitochondria, chloroplasts, ER, Golgi, lysosomes, etc.)
Ribosome size70 S (30 S + 50 S)80 S (40 S + 60 S)
DNA organisationSingle circular chromosome; may have plasmidsLinear chromosomes; DNA wrapped around histones
Cell‑wall materialVaries – see table belowPlants – cellulose; Fungi – chitin; Animals – none

Microscopy in Cell Studies (Practical Tip)

Preparing a wet‑mount for prokaryotes

1. Place a drop of sterile water on a clean microscope slide.

2. Using a sterile inoculating loop, transfer a small amount of the bacterial/archaeal culture onto the drop.

3. Gently lower a cover‑slip to avoid air bubbles.

4. Start with the lowest objective (4×) and work up to 100× oil‑immersion.

5. Calculate total magnification: objective × eyepiece (e.g., 100× × 10× = 1000×).

6. Use an eyepiece graticule to measure cell size (0.5–5 µm typical for prokaryotes).

Key Organelles of Eukaryotic Cells (Brief Reference)

OrganelleStructurePrimary Function
NucleusDouble membrane with poresStores DNA, controls transcription
MitochondrionDouble membrane, inner folds (cristae)Cellular respiration – ATP production
ChloroplastDouble membrane, thylakoid stacksPhotosynthesis (plants & algae)
Endoplasmic Reticulum (ER)Network of membrane‑bound tubulesProtein (rough ER) or lipid (smooth ER) synthesis
Golgi apparatusStacked cisternaeModification, sorting and packaging of proteins
Ribosome70 S (prokaryotes) or 80 S (eukaryotes)Protein synthesis
VacuoleLarge membrane‑bound sac (plants)Storage of water, ions, metabolites
Cell wallCellulose (plants), chitin (fungi), peptidoglycan (bacteria)Provides structural support

Viruses – Non‑cellular Entities

Learning outcome: State that viruses are non‑cellular structures consisting of a nucleic‑acid core surrounded by a protein capsid (and, in many cases, a lipid envelope), and that they lack a plasma membrane, cytoplasm and ribosomes.

Prokaryotic Cell Structure (AS Syllabus Requirements)

  • Size: 0.5–5 µm in diameter (visible only with a light microscope at high magnification).

  • DNA: Single circular chromosome; may carry one or more plasmids.

  • Ribosomes: 70 S (30 S + 50 S) – smaller than eukaryotic 80 S ribosomes.

  • Cell wall:

    • Bacteria: Thick layer of peptidoglycan (murein) – the defining feature of the bacterial cell wall.

    • Archaea: No true peptidoglycan; wall may consist of pseudo‑peptidoglycan, polysaccharides, glycoprotein S‑layers or be absent.

  • Plasma membrane: Fluid‑mosaic bilayer; composition of lipids differs between the two domains (see below).

Biochemical Differences Between Archaea and Bacteria

FeatureArchaeaBacteria
Membrane lipidsEther‑linked isoprenoid chains (branched); glycerol‑1‑phosphate backbone.Ester‑linked fatty‑acid chains (unbranched); glycerol‑3‑phosphate backbone.
16S rRNA sequenceDistinct sequence; clusters with eukaryotes in phylogenetic trees.Distinct sequence; clusters with other bacteria.
Cell‑wall compositionOften pseudo‑peptidoglycan or protein S‑layer; no true peptidoglycan (murein).Peptidoglycan (murein) layer – a defining feature.

Why These Differences Matter

  • They demonstrate that Archaea and Bacteria represent separate evolutionary lineages despite superficial similarity.

  • Biochemical traits dictate ecological niches (e.g., many archaea thrive in extreme temperature, salinity or acidity).

  • The traits are the basis for laboratory identification:

    • Gram staining distinguishes bacteria with thick peptidoglycan (Gram‑positive) from those with a thin layer (Gram‑negative); archaea usually give a variable result.

    • Lipid extraction and thin‑layer chromatography reveal ether vs. ester linkages.

    • 16S rRNA sequencing is the gold‑standard for phylogenetic classification.

Link to Practical Tests (AS Syllabus)

Biochemical tests that can be related to prokaryotic features

• Benedict’s test: Detects reducing sugars; useful for identifying fermentative bacteria.

• Iodine test: Detects starch – many plant‑derived media contain starch; absence of starch in bacterial colonies is typical.

• Emulsion test: Detects lipids; can be used to show the presence of unusual ether‑linked lipids in archaeal extracts.

• Biuret test: Detects proteins; confirms the proteinaceous nature of viral capsids or S‑layer proteins in archaea.

Suggested Classroom Resources

  • Diagram: A side‑by‑side schematic of an archaeal and a bacterial cell envelope, highlighting ether vs. ester lipids, ribosome location and cell‑wall structure.

  • Electron micrograph: Typical transmission‑electron image of a prokaryotic cell. Caption: “Label the plasma membrane, nucleoid region, ribosomes and, where present, the cell‑wall layer.”

  • Phylogenetic tree hand‑out: Shows clustering of 16S rRNA sequences for representative archaea, bacteria and eukaryotes.

  • Practical worksheet: Steps for Gram staining, lipid extraction and a basic 16S rRNA PCR protocol (outline only – for classroom demonstration).