DNA extraction

Explain in your own words what extracting DNA from a eukaryotic cell means, and name two simple materials from which cells can be obtained for the practical (for example, cheek cells or a fruit). Why should the material be thoroughly mashed before starting?

In the DNA extraction practical, washing-up liquid, salt and very cold alcohol are used. Explain the role of each reagent: which cellular structures the detergent dissolves, what the salt is used for, and what happens to the DNA when it comes into contact with the alcohol.

Look at the diagram of the test tube at the end of the DNA extraction practical. Identify what the labels ?1, ?2 and ?3 indicate (the alcohol layer, the aqueous extract with the dissolved DNA, and the DNA strands appearing at the interface), and explain why DNA concentrates precisely in that area.

In the tube, the DNA goes from being dissolved in the extract to forming a precipitate of strands when the alcohol is added. Explain whether the DNA molecule has changed chemically in this process or only its physical state has changed, and compare it with what happens to salt when it precipitates in water.

At the end of the practical, a white cloudy layer formed by strands appears at the interface between the extract and the alcohol. Describe what is observed and explain what this material actually is — it is not a single molecule or the DNA of a single cell — and why it is visible to the naked eye when a single DNA molecule is not.

These steps of the DNA extraction practical are out of order: add the very cold alcohol down the side of the tube without shaking; mash the material; prepare the mixture of water, salt and detergent; filter the mixture; collect the DNA strands with a rod. Put them in order and justify why each step should be in that position.

Design an experiment to find out from which fruit, among banana, kiwi and strawberry, the most DNA is obtained using the same protocol. State which variables you would keep constant so that the comparison is fair and which one you would measure to compare the results.

A human cell contains about $6\ \text{pg}$ of DNA ($6 \cdot 10^{-12}\ \text{g}$). Estimate how many cells would be needed to obtain $1\ \text{mg}$ of DNA and reason why the practical requires mashing a good amount of material.

The DNA obtained with the school protocol is not pure: it precipitates along with proteins (histones) and lipids. One team proposes adding fresh pineapple juice (rich in bromelain, a protease enzyme) to the filtrate before adding the alcohol. Another team proposes heating the filtrate to $100\ ^\circ\text{C}$ for $15$ minutes to eliminate protein impurities.

Evaluate both proposals: justify which of the two is appropriate by explaining the action of the protease on the histones, and predict the counterproductive effect that boiling the sample would have on the DNA molecule.

In a forensic investigation, a tiny biological sample is collected (a hair with a root containing barely a few dozen cells). A student claims: "We can use the homemade strawberry protocol: we crush it, add dish soap, salt, and alcohol, and then read the genes with a magnifying glass." Refute their claim by identifying three insurmountable limitations of this school method and justify which advanced techniques (such as PCR amplification or enzymatic purification) are essential in a real laboratory to analyze the sample.

To identify a suspect, a laboratory cuts DNA samples with enzymes and subjects the fragments to agarose gel electrophoresis:

1. a) If DNA has a net negative charge due to its phosphate groups, deduce with reasoning towards which electric pole (positive or negative) the fragments will migrate when the current is turned on.
2. b) If a sample contains DNA fragments of $300$ base pairs and others of $2500$ base pairs, predict which ones will end up furthest from the loading well in the gel matrix and justify the physical reason.
3. c) Interpret what it would mean if the suspect's banding pattern matches the sample found at the crime scene exactly in position and number.