[Ice_cool]

I need to set up a control for each experiment I am doing. I was wondering if a control has to be set up at the optimum conditions for my experiment. E.g. for an enzyme (catalase), its optimum temp is 37 degrees and at pH 7. However, if I set up this expt just at room temperature and with nothing affecting it, then can this be my control?

[sdekivit]

what is the experiment you're doing about ?

[mike]

If you know the optimum conditions why not set the control to the optimum conditions and run one of the "variable" experiments at room temperature? Are you trying to come up with new optimum conditions? Or are you running the control without one of the reactants?

[Yggdrasil]

Your control should definitely be run in the same conditions as your experiment.  For example, if your control is a solution of hydrogen peroxide without catalase while your experiment is a solution of hydrogen peroxide with catalase, you would obtain different results for your control if you ran it at 25 C instead of 37 C, since the rate of hydrogen peroxide decomposition depends on temperature.

[mike]

Your control should definitely be run in the same conditions as your experiment.

Unless your experiment is to alter the conditions

[Ice_cool]

thank you for the replies  

Please bear with me as I try to explain what I do

Ok, my experiment is concerning the breakdown of hydrogen peroxide by the enzyme catalase, contained in liver. I am investigating different factors which could affect the rate of the reaction. I have varios sets of experiments which correspond to the factors. e.g.

1) Effect of different temperatures
2) Effect of different pH's
3) Effect of different concentrations of hydrogen peroxide
4) Effect of different heavy metal solutions (transition metal solutions)

(This is not a complete list, but I think it is enough for you to get a rough idea of what is going on)

Within these experiments I have 5 or 6 different experiments.

E.g. for...

1) I have 3 degrees, 20 degrees (room temp), 36 degrees, 37 degrees, 38....60...etc

So do I need a control for the above? I thought NO because it is a range of variables - that will make a LINE GRAPH

For 2) and 3) I thought similarly


But for 4) it is a number of different solutions (thus making a BAR GRAPH) so would a control for this just be: the usual experiment but WITHOUT any other solutions? As I think a control must only differ in one variable (i.e. if I add lead iodide, etc to the hydrogen peroxide in one expt, my control would be the same but with that solution ommitted)

So...for 1), 2) and 3) my control would just be the experiment for which the optimum is at? e.g. for 1) the control is the expt at 37 degrees celsius. Is this true? If so, do I need to call it aa control, or do I only do that for sets of experiments such as 4)?


I apologise for asking sp many questions and I realise that answering them across a forum is difficult. But is the last paragraph true for what I said?


thank you very much  

[sdekivit]

i would take my blanco as a solution containing catalase, but no H2O2. Now you know any extra activity measured is due to adding the H2O2. This is for the experiments about the effect of temperature, pH and concentration H2O2

For heavy metals, you need to change only 1 variable: the metal added. Thus the blanco is the reaction of H2O2 by catalase in just water for example, thus without any heavy metal in it.

You must choose the blanco containing everything, except the thing you want to measure.

[Yggdrasil]

For (1) I would run two sets of reactions at each temperature.  One would have the peroxide but no catalase and the other would have peroxide with catalase.  The reaason is that temperature will affect the rate of peroxide decomposition even in the absence of catalase.

For (2), I would do the same.  I'm not sure if pH will affect peroxide decomposition, but it doesn't hurt to control for it anyway.  The same goes with (3) since the rates of peroxide decomposition in each flask will be different.

For (4) I would definitely run controls without catalase.  Various heavy metals (e.g. some manganese compounds) can catalyze the decomposition of peroxide themselves.  If you do not run the reaction in the absence of catalase to check for this, you will not know if the increased rate of peroxide decomposition is due to the metal enhancing the activity of the enzyme or the metal catalyzing the reaction itself.

[Ice_cool]

thank you everyone for the useful information    :balloon:


btw, catalase is a quaternary protein isn't it?

[Yggdrasil]

Yes, catalase is a multimeric protein consisting of four identical subunits.  Catalase is an interesting multimeric proteins because the four subunits are interlocking which makes it a very stable enzyme (presumably, so that it can survive prolonged exposure to peroxides).

[Ice_cool]

Yes, catalase is a multimeric protein consisting of four identical subunits.  Catalase is an interesting multimeric proteins because the four subunits are interlocking which makes it a very stable enzyme (presumably, so that it can survive prolonged exposure to peroxides).

that was very useful Yggdrasil. Thank you  :thumbup:

[Yggdrasil]

If you're really interested in the structural organization of catalase you can check out the PDB (Protein Data Bank) entry for catalase which has multiple structures of catalase enzymes from different sources:

http://www.rcsb.org/pdb/molecules/pdb57_1.html

[Ice_cool]

hey yggdrasil, that link (http://www.rcsb.org/pdb/molecules/pdb57_1.html) doesn't work anymore! Do you know what the new url could be? I am approaching the end of this project and I am doing a write up!

[Yggdrasil]

Yeah, the PDB just changed the layout of the website, so I suppose that's why the link no longer works.  Here's the new address:

http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb57_1.html

[Ice_cool]

thank you