Nucleosomes & Molecular Visualisation Software: Skills (HL) (HL IB Biology)

• Unlike most prokaryotic DNA which is referred to as ‘naked’, eukaryotic nuclear DNA is associated with proteins called histones (to form chromatin)
• Histones package the DNA into structures called nucleosomes
  • The nucleosome consists of a strand of DNA coiled around a core of eight histone proteins (octamer) to form a bead-like structure
  • DNA takes two turns around the histone core and is held in place by an additional histone protein which is attached to linker DNA
  • The DNA molecule continues to be wound around a series of nucleosomes to form what looks like a ‘string of beads’
• Nucleosomes help to supercoil the DNA, resulting in a compact structure which saves space within the nucleus
  • Nucleosomes also help to protect DNA and facilitate movement of chromosomes during cell division
  • An analogy for supercoiling is twisting an elastic band repeatedly until it forms additional coils
• Nucleosomes can be tagged with proteins to promote or suppress transcription

Nucleosome structure diagram

Histones diagram

• Molecular visualisation software can be used to help understand molecular structures
  • Macromolecules like protein, DNA, RNA and complex carbohydrates can be visualised as 3-D structures
• This allows researchers to analyse macromolecules and/or study interactions between them
  • Primary sequence information can be related to structure and function
  • This helps to relate how structure might relate to chemical or biological behaviour
• Macromolecules can be represented in many different ways including ball and stick atom models or simplified ribbon representations that show the protein backbone
• Most molecular visualisation software is freely available on the Internet or can be accessed through many bioinformatics repositories such as the Protein Data Bank (PDB)

Analysing the association between protein and DNA within a nucleosome

• Visit the Protein Data Bank (PDB) site and search for: 6T79 structure of human nucleosome (do not put the search term in quotes)
• Select the “3D view” to view the protein structure in Mol*
  • The 3-D structure of the nucleosome can be viewed
  • The DNA double helix can be clearly seen surrounding the histone proteins
  • Rotate or zoom into the image to visualise the different components
  • The DNA can be seen to make two loops around the histone octamer core
• Look carefully - the tails of each histone protein can be seen projected from the nucleosome core
  • These can be chemically modified to help regulate gene expression
• Try changing different settings in the viewer or select a different viewer such as JSmol

Human nucleosome diagram

Structure of human nucleosome showing the association between DNA (in 2 loops around the edge) and histones (central region)