Giant DNA Modelling + Supercoiling

Introduction
Public summary: 

Play with replicating DNA

Useful information
Kit List: 

Giant DNA Model
Paper DNA print out.
There's also a DNA model in Exploring Genes which may be useful.
Pieces of coloured gas tube and elastic bands (supercoiling)

Packing Away: 

Has a box with pipe cleaner chromatin
[In future maybe merge exploring genes into this box and take chromatin out to live with brain model (as pipe cleaners)]

Explanation
Explanation: 

This experiment takes the Giant DNA model which already existed and will create some more strands to allow replication, if you can explain how DNA is replicated please do. The model is Giant and does take up a lot of space (think like 3m x 3m of space minimum to perform a replication).

DNA is a chemical which encodes genetic information, these units/words of genetic information are genes. Genes are units made of DNA and are (mostly) instructions for making proteins.
There are 46 DNA molecules per human cell nucleus (23 chromosomes, two of each pair, one from each parent). The Helix is about 20 x 10^-10m wide, about 2m of DNA per human cell. The helix here is about 10^-1m wide so it's a billion times wider!
Shape is double helix, as two strands wrap around each other. The structure of double helix discovered partly from work in Cambridge (Francis Crick & James Watson in 1953, with help from Maurice Wilkins and Rosalind Franklin in London)
Our model is straightened out, when it looks like a ladder sides. The sides are the same everywhere but the information (steps on ladder) come at varying distance.
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Colours of steps: there are only 4. 4 letters in the DNA alphabet. Only certain pairs allowed. This enables one strand to act as a template for ANOTHER. As DNA makes a template for itself, can make two identical Molecules. Since DNA can replicate exactly, enables one cell to divide into two daughter cells with identical genetic material. This is how all our body cells can have the same DNA!

DNA is made up of four bases. Adenine and Guanine are purines (fused rings) and Cytosine, Thymine (DNA only) and Uracil (RNA only) are Pyrimidines (simple rings). They're commonly refered to by the first letter. These form base pairs and stack to form deoxyriboneucliac acid (DNA) and ribonucleic acid (RNA). T and U only differ in that T has an additional methyl group. A pairs with T and C with G. Purine-Pyrimidine pairs bonded along amine and carbonyl groups. Phosphates connect successive rings of adjacent bases, these ribose or deoxyribose structures provide the backbone

There are also several paper print outs so people can make their own DNA spirals.

The first step in replication is unzipping the spiral, an enzyme called helicase breaks the hydregeon bonds holding complementary bases.
This creates a 'Y' Shape called the replication fork.
One strand is the leading strand (oriented in the 3' to 5' direction) and the other is the lagging strand (in the 5' to 3' direction) these are replicated differently.

Leading strand is replicated continuously. A short piece of RNA, called a primer, (produced by an enzyme called primase) comes along and binds to the end of the leading strand. The primer acts as the starting point for DNA synthesis. DNA polymerase binds to the leading strand and then ‘walks’ along it, adding new complementary nucleotide bases (A, C, G and T) to the strand of DNA (in the 5' to 3' direction so into the fork)

The lagging strand is replicated discontinuously. Lots of RNA primers are made by the primase enzyme and bind at various points chunks of DNA are then added (Okazaki fragments) in the 5' to 3' direction so away from the fork. these fragments will need joining together later.

Once all the bases are matched up an enzyme called exonuclease strips away the RNA primers and the gaps are filled by complementary bases. It's then proofread to make sure there is no mistakes. You'll notice that in the two strands half of each is old and half new, we say DNA is semi-conservative for this reason.

You can do this replication using the model. One child is Helicase, they walk down the spiral separating it. Pick one side to be the leading strand and one person can go down and match up complementary bases following helicase, threading a rope through as they go. On the other strand someone should randomly form small segments of DNA in free location threading a small piece of rope through each section. Finally someone goes along and ties all these bits together.

Supercoiling (PLUS?)
There's some painted hosepipes around which demo this and it's a really important part of how DNA fits into cells (and I think explains the whole 5' to 3' thingy which I don't get). It sort of half fits as an extension to this experiment as we question how such a giant amount of information can fit into cells which we know are tiny! It seems easy, but remember we can't tangle it or it's going to be a pain to replicate it.

Other supercoiling things that can be done are with elastic bands. Cut one in half and then hold the ends, hold it taught and twist. Then still holding the ends bring them together. You've just supercoiled! When you bring together the elastic tries to unwind however it can't as you've got hold of the ends. Instead it 'writhes' in space. The formua Lk=Tw+Wr describes the process, Lk is the linking number, Tw the twist or amount of rotation around the centre line and Wr the writhe or difficulty in straitening.

Risk Assessment
Date risk assesment last checked: 
Thu, 13/12/2018
Risk assesment checked by: 
Tdwebster
Date risk assesment double checked: 
Sun, 03/02/2019
Risk assesment double-checked by: 
Conor Cafolla
Risk Assessment: 
Hazard Risk Likelihood Severity Overall Mitigation Likelihood Severity Overall
DNA model People may get fingers trapped when joining DNA or splintered. 3 2 6 Be careful and sand edges so not splintery.
Warn children bases 'snap' together
In case of injury, call first aider.
2 1 2
Magnets Magnets crash and smash into tiny sharp shards. 2 2 4 Make sure magnets are cushioned. Sweep shards away immediately. Call a first aider in the event of an injury. 1 1 1
Ropes Ropes may tangle and strangle. 2 4 8 No running while holding model, supervise children. Call a first aider in the event of an accident. 2 3 6
Paper Paper cuts. 4 1 4 Advise caution and warn children of dangers. Call a first aider in the event of a severe cut. 4 1 1
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