DNA Organisation: Prokaryotes vs. Eukaryotes Revision Notes | A Level AQA Biology

1. Why DNA Organisation Matters

Every living cell carries a DNA instruction manual, but the way that manual is packaged differs dramatically between cell types. A bacterium and a human liver cell both use DNA to make proteins — yet their DNA looks almost nothing alike at the structural level.

Understanding these differences is not just background knowledge. AQA examiners regularly ask you to compare prokaryotic and eukaryotic DNA, and the marks hinge on precise language: circular vs linear, associated vs not associated with protein, short vs very long. Get those words right and the marks follow.

2. Prokaryotic DNA: Small, Circular, Naked

Picture a bacterial cell — no nucleus, no membrane-bound organelles, just cytoplasm and a cell surface membrane. The DNA sits directly in the cytoplasm in a region called the nucleoid. It is a single, relatively short, circular molecule.

Crucially, prokaryotic DNA is not associated with proteins. There are no histones wrapping around it. The molecule is sometimes described as 'naked' DNA for this reason. Many bacteria also carry additional, much smaller circular DNA molecules called plasmids, though these are separate from the main chromosomal DNA.

The circular shape is not arbitrary. Without a free end, circular DNA is less vulnerable to degradation by exonucleases (enzymes that chew DNA from its ends). It also replicates efficiently from a single origin of replication.

3. Eukaryotic Nuclear DNA: Long, Linear, and Histone-Associated

Now zoom into the nucleus of a human cell. The DNA here is on a completely different scale — each molecule is very long and linear rather than circular. If you stretched out all the DNA from a single human nucleus end to end, it would extend roughly two metres. Fitting that into a nucleus just a few micrometres across requires extraordinary packaging.

That packaging is provided by histone proteins. The DNA double helix winds around clusters of eight histone proteins, forming structures called nucleosomes. These nucleosomes then coil and fold further, compacting the DNA enormously. A single DNA molecule together with its associated histone proteins forms one chromosome.

Notice that the contrast is threefold: shape, length, and protein association. Examiners expect all three when they ask you to compare. Missing even one of these features typically costs a mark.

4. The Organelle Exception: Mitochondria and Chloroplasts

Here is where the story gets genuinely interesting. Eukaryotic cells contain mitochondria, and plant cells also contain chloroplasts. Both of these organelles carry their own DNA — and that DNA looks nothing like the nuclear DNA of the eukaryotic cell it sits inside.

Mitochondrial and chloroplast DNA is short, circular, and not associated with proteins — exactly like prokaryotic DNA. This is strong evidence for the endosymbiotic theory, which proposes that mitochondria and chloroplasts evolved from free-living prokaryotes that were engulfed by ancestral eukaryotic cells. Their DNA retained the prokaryotic character of their ancestors.

The same applies to chloroplasts. Whether you are asked about mitochondria in an animal cell or chloroplasts in a leaf cell, the answer is the same: short, circular, not associated with protein. This mirrors the prokaryotic pattern precisely.

5. Coding and Non-Coding DNA in Eukaryotes

You might assume that all the DNA in a eukaryotic nucleus codes for proteins. In reality, a large proportion of nuclear DNA does not code for polypeptides at all. This non-coding DNA takes two main forms: non-coding sequences between genes, and non-coding sequences within genes.

Between genes, there are non-coding multiple repeats of base sequences. These are short sequences of bases repeated many times in tandem. They do not code for amino acids. Their precise functions are still an active area of research, but they are important in forensic DNA profiling because the number of repeats varies between individuals.

Within a gene, the picture is more nuanced. Not every part of a gene codes for an amino acid sequence. The coding sections are called exons, and they are separated by one or more non-coding sections called introns. Both exons and introns are transcribed into a primary mRNA transcript, but the introns are then spliced out before the mRNA leaves the nucleus, leaving only the exon sequences to be translated into a polypeptide.

Think of a gene as a sentence with words (exons) and filler noise (introns) mixed together. The cell transcribes the whole thing, then edits out the noise before sending the message to the ribosome. Only the words — the exons — carry the protein-coding information.

Worked example: Tracing the Journey from Gene to Polypeptide: Exons and Introns

A eukaryotic gene contains the sequence: Exon 1 — Intron A — Exon 2 — Intron B — Exon 3. Describe, in order, what happens to this sequence from transcription to the final polypeptide.

1. RNA polymerase reads the template strand and produces a primary mRNA transcript containing: Exon 1 — Intron A — Exon 2 — Intron B — Exon 3 — Both exons and introns are transcribed. The primary transcript is sometimes called pre-mRNA. This step occurs in the nucleus.
2. Intron A and Intron B are recognised and removed. The remaining exon sequences are joined: Exon 1 — Exon 2 — Exon 3 — Splicing is carried out by a complex called the spliceosome. Only the intron sequences are removed; the exon sequences are ligated (joined) together to form the mature mRNA.
3. The mature mRNA (containing only exon sequences) passes through nuclear pores into the cytoplasm. — Because introns have been removed, the mRNA now carries only the coding information needed to specify the polypeptide's amino acid sequence.
4. Ribosomes read the mature mRNA codon by codon. Each codon (triplet of bases from the exon sequences) specifies one amino acid, building the polypeptide chain. — Only the exon-derived sequences contribute to the final polypeptide. The intron sequences, having been removed, play no direct role in translation.

Answer: The whole gene (exons + introns) is transcribed into a primary mRNA transcript. Introns are then spliced out, leaving a mature mRNA containing only the exon sequences. This mature mRNA is translated at ribosomes to produce the polypeptide.

6. Exam Technique: Getting Every Mark

Questions on this topic tend to use the command words compare, describe, and explain. Each demands a different response structure, and mixing them up is a reliable way to drop marks.

When a question says compare prokaryotic and eukaryotic DNA, you must address both sides for each feature. Writing only about prokaryotes, or only about eukaryotes, will not earn comparison marks. Use paired statements: 'Prokaryotic DNA is circular, whereas eukaryotic nuclear DNA is linear.'

When a question says explain why introns do not affect the amino acid sequence of the polypeptide, you need a causal chain: introns are transcribed into the primary mRNA transcript, but they are removed by splicing before translation, so they do not contribute codons to the mature mRNA that is read by ribosomes.