Tuesday, 4 September 2007

S204: TMA-6 / Experimental Week 2

Back to the potatoes!

Oh yes - the potatoes have their revenge. In this combined experimental week and TMA you have to do a new experiment of your own devising on the poor potato homogenate and then write it up fully as TMA-6. This is very similar to TMA-2 except you have about twice the word limit, and you have to write much more about everything, but particularly on the biological mechanisms that you are investigating. On the plus side, this is all you have to do for this TMA!

After a few flights of fancy, I decided to follow the advice and stick to something reasonably simple. A couple of options were to vary the temperature or pH of the solution and see if there was any discernible difference in results. I figured that what they were looking for in this exercise was producing some results and analysing them. They were not looking for new contributions to science.

Its a lesson I've found rather hard to come to terms with in this and other courses. For instance the whole purpose of catalase in the potato homogenate is to break down H2O2. Now why would you have H2O2 present? It turns out this is how free radicals, those rather dangerous reactive molecules are flushed out of the system. They are converted into hydrogen peroxide to partially neutralise them. However should H2O2 come into contact with Fe ions, you suddenly have a worse problem than before as it will make very very reactive free radicals, as opposed to just reactive free radicals. If you follow this through, you find all sorts of interesting avenues, such as oxidative stress, mitochondrial errors, apoptosis signals and so on. Although some of this can go into the report, you have to curb your enthusiasm and write down only what the mark scheme is likely to be looking for. This does mean somewhat that you have to try and stick to the course materials as if you find new discoveries since they were written, or more advanced descriptions of mechanisms, no matter how right they are, they are unlikely to get you marks.

Anyway, I settle for two temperatures and attempt to see if there is a difference in reaction rate. This is actually more chemistry than biology, heat increases all reactions. The only biology that comes in is that most catalysts are rather fragile enzymes that will fall to bits if you heat them too much. So I pick two temperatures that are likely to work. A temperature of 0°C is easy to maintain with ice-cubes, a warmer temperature is more difficult. Without some sort of heating, it will tend to cool, so I pick a temperature about 10°C above room, and hope that a large enough water bath won't cool too quickly to affect things. I know catalase works in animals up to 37°C so I don't think potato catalase will fall apart at 28°C or so, so I should be OK.

It would be interesting to look at a whole range of temperatures and see where its peak rate was, and where it started to denature and so on. But ambition must be curbed, and if you've spent a few hours counting drips from mashed up potato juice, this is actually surprisingly easy to temper! Plus you can only do a t-test on two sets of results, so that's all you really need.

After about 4 hours or so, I've been through the experiments, which include a couple of pilot experiments to work out appropriate concentrations and drip rates.

The write up is much easier than the last TMA, although it takes a while to get it all formatted and the biological data into place, run the t-test software on the results and so on. Ultimately though, it is just a question of doing the time and formatting the results. None of the cold hand of fear from the last TMA! Some faith restored. I struggle to reach close to the 2000 word limit, and a certain amount of revision is required to get not too far away.

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