1.2.5Inquiry Process
Nucleosomes and Molecular Visualisation Software: Skills — IB Biology HL Revision Notes & Topical Questions
5 min read 4 parts Lesson 2 of 160
Part 1 of 4Histones and Nucleosome Structure
Eukaryotic nuclear DNA is far too long to fit in the nucleus unless it is packed, and histone proteins do most of the packing.
Histones
- Small, positively charged proteins that bind tightly to the negatively charged phosphate groups of DNA, forming chromatin.
Histone octamer
- A core of eight histone proteins, two copies each of four types, around which the DNA is wrapped.
DNA wrapping
- About 147 base pairs of DNA coil around the octamer for a little under two turns, forming the bead of a nucleosome.
Linker DNA
- Short stretches of DNA join one nucleosome to the next, giving the appearance of beads on a string.
Linker histone
- An extra histone that attaches near the entry and exit points of the DNA and helps to hold the nucleosome in position.
| Feature | Prokaryotic DNA | Eukaryotic nuclear DNA |
|---|---|---|
| Packaging proteins | Not associated with histones (naked) | Wound around histones to form nucleosomes |
| Form | Single circular chromosome | Several linear chromosomes |
| Compaction | Supercoiled by other proteins | Nucleosomes coil further into compact chromatin |
Part 2 of 4Why Nucleosomes Matter
Why Nucleosomes Matter
Supercoiling
- Winding DNA round histones and then coiling the strand again makes a long molecule fit inside a tiny nucleus.
Protection
- Packaged DNA is shielded from physical damage and from some enzymes that would otherwise cut it.
Cell division
- Tightly packed chromosomes can be moved apart during mitosis and meiosis without tangling or breaking.
Gene expression
- Chemical tags on histone tails can loosen or tighten the packing, which promotes or suppresses transcription of nearby genes.
Part 3 of 4Using Molecular Visualisation Software
Free programs let you view three-dimensional models of macromolecules taken from public databases.
1
Search a database such as the Protein Data Bank for the structure you want, for example a nucleosome or a haemoglobin molecule.
2
Open the entry in a viewer such as Mol* or JSmol, which draws the atoms from stored three-dimensional coordinates.
3
Rotate, zoom and recolour the model so that DNA, histones and other chains can be told apart clearly.
4
Switch between ball-and-stick, space-filling and ribbon views; ribbon views show the protein backbone and the folding pattern most clearly.
5
Relate what you see to function, for example how DNA sits in two loops around the histone core while the histone tails project outwards.
Part 4 of 4Exam Checklist & Tips
1.2.5 – Key Points for the Exam
- Chromatin The complex of DNA and histone proteins found in the eukaryotic nucleus.
- Nucleosome A unit of DNA wound around a core of eight histones.
- Histone A basic protein around which DNA is wrapped in eukaryotes.
- Supercoiling Further coiling of an already coiled DNA strand to make it more compact.
- Protein Data Bank A free online database of experimentally determined three-dimensional structures of macromolecules.
Common Mistakes
- Saying that prokaryotic DNA is wrapped around histones;
- the typical bacterial chromosome is naked, unlike eukaryotic nuclear DNA.
- Describing the histones as being inside the DNA helix rather than as a protein core that the DNA is wound around.
- Claiming a ribbon diagram shows every atom; it only simplifies the protein backbone to show folding.
- Forgetting that a molecular model is an interpretation of experimental data, not a photograph of the molecule.
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