Prokaryotic Cell Structure: Inside and Out Revision Notes | A Level AQA Biology

1. Why Prokaryotes Matter: The Oldest Life on Earth

Bacteria have been on Earth for around 3.5 billion years — long before any nucleus ever appeared. Understanding their structure is not just academic; it is the reason antibiotics work, and the reason some bacteria resist them.

Prokaryotes are defined by what they lack as much as by what they have. Every feature you learn here connects directly to how these cells survive, reproduce, and respond to drugs. That makes this one of the most clinically relevant topics in the entire A Level specification.

2. Size: The First and Most Fundamental Difference

Prokaryotic cells are significantly smaller than eukaryotic cells. A typical bacterium measures roughly 1–10 micrometres (µm) in diameter, whereas a typical eukaryotic cell — such as a human liver cell — is closer to 10–100 µm. That is roughly a tenfold difference in linear dimension, which translates to a thousandfold difference in volume.

This size difference has real consequences. A smaller cell has a higher surface area to volume ratio, which means substances can diffuse in and out more rapidly relative to the cell's needs. Prokaryotes do not need the elaborate internal transport systems that eukaryotes rely on — their small size makes diffusion efficient enough on its own.

3. No Nucleus — But the DNA Is Still There

Here is the feature that defines the entire domain: prokaryotes have no nucleus. There is no nuclear envelope, no nucleolus, and no membrane separating the genetic material from the rest of the cell.

Instead, the genetic material exists as a single circular DNA molecule that sits freely in the cytoplasm in a region called the nucleoid. Crucially, this DNA is not associated with proteins — specifically, it is not wrapped around histone proteins the way eukaryotic DNA is. This is an important distinction that examiners test directly.

Because transcription and translation both occur in the cytoplasm — with no nuclear membrane to cross — prokaryotes can begin translating an mRNA strand while it is still being transcribed. This is called coupled transcription-translation, and it is one reason bacteria can respond to environmental changes so rapidly.

4. A Cytoplasm Without Compartments

Picture the inside of a prokaryotic cell as one open space. There are no internal membranes dividing the cytoplasm into compartments — no mitochondria, no endoplasmic reticulum, no Golgi apparatus, no chloroplasts. The cytoplasm lacks membrane-bound organelles entirely.

This does not mean prokaryotes are simple in a dismissive sense — they carry out all the essential biochemical reactions of life. Respiration, for example, occurs at the cell surface membrane rather than in mitochondria. The enzymes and molecules needed for these reactions are dissolved or suspended directly in the cytoplasm.

Some prokaryotes do contain small circular DNA molecules called plasmids in addition to their main chromosome. Plasmids are separate from the main circular DNA and often carry genes for antibiotic resistance. They replicate independently and can be transferred between cells — a process with enormous implications for the spread of antibiotic resistance.

5. Smaller Ribosomes: The 70S Difference

Prokaryotic cells do contain ribosomes — they need them to synthesise proteins, just as all living cells do. However, prokaryotic ribosomes are smaller than those found in eukaryotic cells. Prokaryotic ribosomes are described as 70S, while eukaryotic ribosomes are 80S. The 'S' stands for Svedberg units, a measure of how quickly a particle sediments during centrifugation — it reflects both size and shape.

This size difference is clinically significant. Many antibiotics — including streptomycin and erythromycin — work by binding specifically to the 70S ribosome and blocking protein synthesis in bacteria. Because human cells contain 80S ribosomes, these antibiotics do not bind to our ribosomes, which is why they can kill bacteria without (in theory) harming the host. This is the principle of selective toxicity.

One subtlety worth noting: mitochondria and chloroplasts in eukaryotic cells also contain 70S ribosomes. This is one piece of evidence supporting the endosymbiotic theory — the idea that these organelles were once free-living prokaryotes. At A Level, you are not required to evaluate this theory in depth, but it is worth knowing as context.

6. The Cell Wall: Murein and Why It Matters

Surrounding the cell surface membrane of most prokaryotes is a cell wall. This wall provides structural support, maintains cell shape, and prevents the cell from bursting due to osmotic pressure. So far, this sounds similar to the cell walls of plants or fungi — but the chemistry is completely different.

The prokaryotic cell wall contains murein, also known as peptidoglycan. AQA classifies murein as a glycoprotein, but you should be aware that its structure is different from glycoproteins found in cell membranes. Murein consists of polysaccharide chains cross-linked by short peptides, forming a rigid, mesh-like layer that encases the cell. No eukaryotic cell wall contains murein: plant cell walls are made of cellulose, and fungal cell walls are made of chitin.

The antibiotic penicillin works by inhibiting the enzymes that form the peptide cross-links in murein. Without these cross-links, the cell wall weakens and the bacterium lyses — it bursts — due to osmotic pressure. Because human cells have no cell wall and no murein at all, penicillin has no equivalent target in our cells, making it selectively toxic to bacteria.

Gram staining — a technique used to classify bacteria — also depends on murein. Gram-positive bacteria have a thick murein layer that retains the crystal violet stain, appearing purple. Gram-negative bacteria have a thinner murein layer surrounded by an outer membrane, and they appear pink after counterstaining. This distinction matters clinically because different antibiotics target different cell wall structures.

7. Additional Prokaryotic Structures

Beyond the core features required by the specification, prokaryotic cells often possess additional structures that extend their capabilities. These are worth knowing for application questions, where you may be asked to suggest the function of an unfamiliar feature.

• Capsule: A layer of polysaccharide outside the cell wall in some bacteria. It protects against phagocytosis by the host immune system and helps bacteria adhere to surfaces.
• Flagellum (plural: flagella): A protein filament used for locomotion. Prokaryotic flagella rotate like a propeller, driven by a molecular motor in the cell membrane.
• Pili (singular: pilus): Short protein projections on the cell surface. They help bacteria attach to host cells and to each other during conjugation (transfer of plasmid DNA).
• Plasmids: Small, circular DNA molecules separate from the main chromosome. They replicate independently and often carry genes for antibiotic resistance.

These additional structures are not always present in every prokaryote — they vary between species and even between strains of the same species. When an exam question asks you to 'suggest' a function, draw on the principle that each structure has a survival advantage in a particular environment.

8. Exam Technique: Scoring Full Marks on Prokaryote Questions

AQA questions on prokaryotic cell structure tend to use the command words 'describe', 'explain', and 'compare'. Each demands a different type of response, and confusing them is one of the most common reasons students lose marks.

Worked example: Answering a 'Compare' Question on Prokaryotic and Eukaryotic Cells

Compare the structure of a prokaryotic cell with that of a eukaryotic cell. [4 marks]

1. Command word: 'Compare' — A compare answer must include both similarities AND differences. Stating only differences will not gain full marks. Each valid comparative point scores one mark.
2. Prokaryotic cells lack a membrane-bound nucleus; eukaryotic cells have a nucleus enclosed by a nuclear envelope. [B1] — A complete comparative point names the feature and states what each cell type does. Saying only 'prokaryotes have no nucleus' without mentioning eukaryotes is a description, not a comparison.
3. Prokaryotic cells have 70S ribosomes; eukaryotic cells have 80S ribosomes. [B1] — Ribosome size is a high-value point because it is specific and testable. Vague statements like 'prokaryotes are simpler' score nothing.
4. Prokaryotic cells have a cell wall containing murein; eukaryotic cell walls (where present) do not contain murein — plant cell walls contain cellulose. [B1] — Naming murein specifically is essential. Saying 'different cell wall material' without naming murein is unlikely to score.
5. Both prokaryotic and eukaryotic cells have a cell surface membrane and ribosomes, though the ribosome size differs. [B1] — Including a similarity demonstrates genuine comparative thinking. It also acts as a safety net if one of your differences is marked incorrect.

Answer: A full-mark response identifies at least four valid comparative points, each naming the feature and stating the situation in both cell types. Naming murein, 70S vs 80S ribosomes, and the absence of membrane-bound organelles are the highest-value points for this topic.

Across this lesson, every structural feature of the prokaryotic cell — the absence of a nucleus, the single circular DNA molecule free in the cytoplasm, the 70S ribosomes, the murein-containing cell wall, and the lack of membrane-bound organelles — maps directly onto an AQA specification requirement. Knowing not just what each feature is, but why it differs from eukaryotes and what consequence that difference has, is what separates a grade 6 answer from a grade 9 answer.