DNA in Prokaryotes and Eukaryotes

Q1 — Marking criteria (8 marks)

• 1 mark — Defines chromatin as eukaryotic DNA associated with proteins (histones) in a less condensed form.
• 1 mark — Identifies that eukaryotic DNA is multiple linear chromosomes inside a membrane-bound nucleus.
• 1 mark — Uses the stimulus numbers (~2 m of DNA fits into a ~6 µm nucleus, a ~300 000× compaction) to quantify the compaction problem.
• 1 mark — Identifies that the prokaryote also has a compaction problem (~1.6 mm of DNA into a ~1 µm nucleoid) but at a much smaller scale, organised by supercoiling of a single circular molecule.
• 1 mark — Explains that chromatin is not just compressing DNA — it must also allow DNA to become less condensed locally so genes can be read.
• 1 mark — Explains how multiple linear chromosomes allow large eukaryotic genomes to be managed (independent inheritance, region-specific regulation).
• 1 mark — Maintains correct lesson terminology throughout (chromatin / nucleus / nucleoid / linear / circular used precisely, no confusion between nucleoid and nucleus).
• 1 mark — Reaches a clear overall judgement that the eukaryotic packaging problem is biologically more demanding, justified with data from the stimulus.

Sample Band 6 response

Chromatin is the term for eukaryotic DNA when it is associated with packaging proteins (histones) in a less condensed form. This DNA-protein complex is the basic way that eukaryotic cells solve the problem of fitting their entire genome inside the nucleus.

The stimulus data make the scale of that problem explicit. A single human cell contains about 2 metres of DNA — but its nucleus is only 6 µm across. That is roughly a 300 000-fold compaction, with the additional constraint that the DNA is split across 46 separate linear chromosomes rather than one continuous loop. Eukaryotic cells solve this by wrapping the DNA around histones to form nucleosomes, then folding those nucleosomes into chromatin fibres, which condense further into the chromosomes visible during cell division.

E. coli faces the same kind of problem but at a much smaller scale: ~1.6 mm of circular DNA inside a ~1 µm nucleoid. There is no nucleus, no histone-based chromatin, and only one main chromosome — supercoiling and nucleoid-associated proteins are enough. The eukaryote's challenge is therefore biologically harder because the compaction ratio is two orders of magnitude greater and the DNA is fragmented across many separate molecules that must each be replicated, segregated and read.

However, compaction alone is not sufficient — eukaryotic DNA must also remain accessible. If chromatin were permanently maximally condensed, genes could never be transcribed. Chromatin solves this by existing in dynamic, more-condensed and less-condensed states, so the cell can locally "unpack" regions of DNA where genes are needed and re-pack regions that are not in use.

Organising the eukaryotic genome into multiple linear chromosomes inside a nucleus also lets each chromosome be inherited independently, replicated in parallel, and regulated with chromosome- or region-specific patterns. Combined, the nucleus + chromatin + linear chromosome architecture is what makes the eukaryotic packaging solution work — and it is genuinely more sophisticated than the prokaryote's, even though both ultimately compact DNA into a small volume.

Q2 — Marking criteria (8 marks)

• 1 mark — Defines plasmid as a small circular DNA molecule separate from the main bacterial chromosome.
• 1 mark — Defines vector as a DNA molecule used to carry an inserted gene into a host cell, and links it explicitly to plasmids in biotechnology.
• 1 mark — Uses the small size of pBR322 (~4 361 bp) and its circular form to explain why it is technically easy to manipulate (e.g. cut, insert, sequence).
• 1 mark — Uses pBR322's location (cytoplasm) and independent replication to explain why it can be propagated in bacteria without disrupting the host chromosome.
• 1 mark — Identifies that human chromosome 1 is ~57 000× larger than pBR322, linear (not circular), and locked inside a nucleus — making it impractical to extract intact and unsuitable for routine cloning.
• 1 mark — Identifies that human chromosomes do not replicate independently and are tightly regulated within S-phase, so they cannot be "passed around" the way plasmids can.
• 1 mark — Reaches a justified evaluative judgement that structural features of plasmids (size, circular form, independent replication, separability from main chromosome) — not "prokaryotic DNA in general" — are what make them useful as vectors.
• 1 mark — Uses precise lesson terminology throughout (plasmid, vector, circular DNA, linear chromosome, nucleus, nucleoid) and avoids the oversimplification that "prokaryotic DNA is better".

Sample Band 6 response

A plasmid is a small, circular DNA molecule found in many prokaryotes that is separate from the main bacterial chromosome and can replicate independently. A vector is a DNA molecule used in biotechnology to carry an inserted gene into a host cell — plasmids are the most widely used vectors precisely because they were already that kind of "carrier" in nature.

The data on pBR322 explain why. At ~4 361 base pairs, the plasmid is small enough to be extracted intact from E. coli, cut at known restriction sites, ligated with foreign DNA, and reintroduced into bacteria — all routine lab operations. Its circular form means it has no free ends to degrade or to ligate incorrectly. Because it sits in the cytoplasm and replicates independently of the main chromosome, copies multiply along with the bacterium without disrupting host gene expression. These three features alone — small, circular, independently replicating — are what make pBR322 a workhorse vector.

Human chromosome 1, by contrast, fails on every one of those features. It is ~249 million base pairs long — roughly 57 000 times the size of pBR322 — so it cannot realistically be isolated intact, let alone cut and re-ligated. It is linear, so its ends require specialised protection (telomeres). It is locked inside the nucleus and packaged with histones as chromatin, and it does not replicate independently; replication is tightly regulated during S-phase. None of those properties make it useful as a routine biotechnology vector.

Therefore the claim is largely defensible but needs sharpening: it is not "prokaryotic DNA in general" that powered biotechnology, but specifically the plasmid form — a small, circular, independently replicating, easily-extracted DNA molecule. Bacterial main chromosomes are also circular and prokaryotic, yet they are not routinely used as cloning vectors either. So the right judgement is: the structural features of plasmids (size, circularity, independent replication, separation from the main chromosome) — features that have no exact equivalent on eukaryotic chromosomes — are what made prokaryotic DNA organisation the foundation of modern biotechnology.