DNA and RNA Structure in 3D – from Nucleotide to Nucleosome
BiologyGeneticsAges 17–18
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Sign in to playA rotatable 3D model of DNA: nucleotides (phosphate, sugar, base) join by phosphodiester bonds into 5′→3′ strands, and two antiparallel strands form a right-handed double helix with A–T (2 hydrogen bonds) and G–C (3 hydrogen bonds) pairs, major and minor grooves, 10.5 bp per turn and a 2 nm width. Students edit the sequence and watch a Chargaff base-count table, compare DNA with RNA, prokaryotic with eukaryotic chromosomes, and explore nucleosomes and chromatin fibres, plus a simulated Photo 51 and the Hershey–Chase experiment. A 2D diagram view is included.
Lesson: Structure of DNA and RNA; nucleotides, complementary base pairing and Chargaff's rules; prokaryotic and eukaryotic chromosomes; nucleosomes
What it shows
DNA is a polymer of nucleotides, each made of a phosphate, a deoxyribose sugar and a nitrogenous base. Condensation reactions link nucleotides by phosphodiester bonds into a strand with a 5′ and a 3′ end. Two antiparallel strands coil into a right-handed double helix held by hydrogen bonds between complementary bases: A with T (two bonds) and G with C (three). Each pair joins a purine to a pyrimidine, so the helix is 2 nm wide, rising 0.34 nm per pair with about 10.5 pairs per turn. In eukaryotes, about 147 bp wrap round each histone octamer to form a nucleosome.
How to use
On Double helix, type a sequence or click a base pair to change it, then compare the rows of the base-count table to test Chargaff's rules. On Nucleotides, add bases one at a time and count bonds and water molecules. Use DNA vs RNA and Chromosomes to compare structures. On Nucleosome, set Linker DNA, press Record result and compare rows. Under History, try the Photo 51 sliders and step through Hershey–Chase with Next step.
Parameters you can change
- Screen DNA double helix, Nucleotides and a single strand, DNA compared with RNA, Prokaryotic and eukaryotic chromosomes, Nucleosome and chromatin fibres, History of the discovery
- View 3D (rotatable), 2D (flat diagram)
- Sequence of strand 1 (5′→3′, A, T, G, C only; 4–40 nucleotides)
- Base pairs per helical turn 10.5 (DNA in solution, 3.6 nm per turn), 10 (rounded value, 3.4 nm per turn)
- Show hydrogen bonds
- Packing level on the Nucleosome screen (1 = one nucleosome, 2 = 10 nm fibre, 3 = 30 nm fibre) 1–3
- Length of linker DNA between nucleosomes 10–90 bp
- Histone H1 present
- Eukaryotic chromosome compared with E. coli Human chromosome 1, Human chromosome 21, Yeast chromosome IV
- Number of plasmids in the bacterial cell 0–5
- History section X-ray diffraction (Photo 51), Hershey–Chase experiment
- Radioactive label (Hershey–Chase experiment) ³²P (labels DNA), ³⁵S (labels protein)
Questions to explore
- If a DNA sample contains 30% adenine, what percentage of its bases are guanine?
- Why does DNA rich in G–C pairs need a higher temperature to separate its strands?
- How does the number of nucleosomes per 10,000 bp change when the linker DNA gets longer?
