IB Biology HLDNA, RNA & the Genetic CodePaper 1 & 2Skills~8 min read
Nucleosomes & Visualisation Software
Two metres of DNA has to fit inside a nucleus far too small to see. The solution is to wrap it around protein spools — and those spools turn out to do much more than just save space.
📘 What you need to know
Most prokaryotic DNA is described as ‘naked’. Eukaryotic nuclear DNA is associated with proteins called histones, forming chromatin.
Histones package DNA into structures called nucleosomes.
A nucleosome is DNA coiled around a core of eight histone proteins (an octamer), forming a bead-like structure.
DNA makes two turns around the core, held in place by an additional histone protein attached to linker DNA.
A series of nucleosomes looks like a ‘string of beads’.
Nucleosomes supercoil the DNA, saving space, protecting it, and helping chromosome movement during cell division.
Nucleosomes can be tagged with proteins to promote or suppress transcription.
Molecular visualisation software lets researchers view macromolecules in 3D, for example from the Protein Data Bank (PDB).
Packaging DNA with histones
Most prokaryotic DNA is referred to as ‘naked’ — it floats freely with no packaging proteins. Eukaryotic nuclear DNA is different: it is associated with proteins called histones, and the DNA plus histones together are called chromatin.
Histones package DNA into repeating units called nucleosomes. Each nucleosome works like a tiny spool:
The core is made of eight histone proteins — an octamer.
A strand of DNA coils around that core, making two turns.
An additional histone protein, attached to the linker DNA, holds the coil in place.
The DNA continues on to the next nucleosome, so the whole molecule looks like a ‘string of beads’.
The beads are the nucleosomes; the string between them is the linker DNA.
What nucleosomes do
Packaging is only the first job. Nucleosomes help to supercoil the DNA, producing a compact structure that saves space within the nucleus, and they do three more useful things:
Function
Why it matters
Supercoiling and compaction
Saves space so that a huge length of DNA fits inside the nucleus
Protection
DNA wrapped around histones is physically shielded from damage
Movement of chromosomes
Compact chromosomes can be moved cleanly during cell division
Regulating transcription
Nucleosomes can be tagged with proteins that promote or suppress transcription of nearby genes
🧠
Picture supercoiling like this
Take an elastic band and twist it, and keep twisting. It does not just get tighter — it starts folding back on itself and forming extra coils, becoming a small dense knot. That is supercoiling, and it is how a very long molecule ends up occupying very little room.
The clever bit. Packaging and gene control turn out to be the same system. If DNA is wound tightly onto nucleosomes, the enzymes that transcribe it cannot reach it. Tagging nucleosomes with proteins loosens or tightens that packing, which is one way cells switch genes on and off.
Skills: molecular visualisation software
Molecular visualisation software is used to help understand molecular structures. Macromolecules such as proteins, DNA, RNA and complex carbohydrates can be viewed as 3D structures rather than flat textbook diagrams.
This lets researchers:
Analyse macromolecules and study the interactions between them.
Relate primary sequence information to structure and function.
See how structure relates to chemical or biological behaviour.
Macromolecules can be displayed in several ways, including ball and stick atom models or simplified ribbon representations that show the protein backbone. Most of this software is freely available on the internet, or accessible through bioinformatics repositories such as the Protein Data Bank (PDB).
Try it: viewing a human nucleosome
Step
What to do
1
Visit the Protein Data Bank (PDB) site and search for: 6T79 structure of human nucleosome (do not put the search term in quotes)
2
Select the “3D view” to open the structure in Mol*
3
Rotate and zoom. The DNA double helix can be seen surrounding the histone proteins, making two loops around the octamer core
4
Look closely for the tails of each histone protein projecting out from the core — these can be chemically modified to help regulate gene expression
5
Try changing the display settings, or open the same structure in a different viewer such as JSmol
This is a skills point, so you will not be asked to recall the PDB code in an exam. What you may be asked is to interpret an image of a nucleosome — so make sure you can point to the DNA, the histone core and the two loops on any diagram you are shown.
Worked examples
WE 1
Describe the structure of a nucleosome
Describe the structure of a nucleosome. (3 marks)
Point 1: the core
A nucleosome has a core of eight histone proteins, known as an octamer.
Point 2: the DNA
DNA is coiled around this core, making two turns, which gives a bead-like structure.
Point 3: how it is held
An additional histone protein, attached to the linker DNA, holds the DNA in place, and the linker DNA continues on to the next nucleosome.
Eight histones + two turns of DNA + a ninth histone holding it in placethe numbers eight and two are both worth marks — do not just say “several”
WE 2
Explain the functions of nucleosomes
Outline the roles of nucleosomes in eukaryotic cells. (4 marks)
Point 1: packaging
Nucleosomes supercoil the DNA, producing a compact structure that saves space in the nucleus.
Point 2: protection
Wrapping the DNA around histone proteins helps to protect it from damage.
Point 3: cell division
Compact packaging helps chromosomes to be moved during cell division.
Point 4: gene regulationNucleosomes can be tagged with proteins to promote or suppress transcription of nearby genes.
Package, protect, move, and regulatefour marks means four separate roles — do not spend all your words on packaging
💡 Exam tips
Learn the numbers: eight histones in the core, two turns of DNA, plus one extra histone on the linker DNA.
Use the exact terms histone, chromatin, nucleosome, octamer and linker DNA.
Remember the prokaryote contrast — prokaryotic DNA is ‘naked’, with no histones.
Do not stop at “saves space”. Protection, chromosome movement and transcription control are all separate marks.
Be able to label a nucleosome diagram: histone core, DNA double helix, linker DNA, histone tails.
⚠ Common mistakes
Saying a nucleosome is a type of organelle. It is a DNA–protein structure, not a cell compartment.
Confusing nucleosome with nucleolus or nucleoid. Three different words, three different things.
Writing that DNA wraps once around the histones. It makes two turns.
Saying prokaryotes have nucleosomes. Most prokaryotic DNA is naked.
Forgetting the gene regulation role. Nucleosomes are not only packaging.
Calling histones enzymes. They are structural and regulatory proteins.
Up next: The Hershey–Chase Experiment — the elegant experiment that finally proved DNA, not protein, is the molecule of heredity.
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