Finally -- a lab activity for my chem class

After doing the DNA extraction activity (which I initially thought would be totally useless to me), I found enough in it to make it very useful as a lab during the chapter on mixtures and solutions.  I can use it to illustrate "like dissolves like", polarity, ion attraction and repulsion, the terms hydrophilic and hydrophobic, and model building.

Here's the lab:

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Using DNA Testing in a

Chemistry Class

          Teacher note:  Our textbook doesn’t properly address the terms hydrophilic and hydrophobic.  Further, when it does address emulsions, it glosses over the theory involved.  It covers how soap works in one page.    With so little coverage the students assume there is minimal importance attributable to the concepts involved.  This “experiment” is designed to correct that misconception.

          

While it may be more fitting to do this in an intro bio course, I see no reason why it can’t be used in an intro chem course – w/ a slight shift in emphasis and extension.  Instead of being an exercise in the study of DNA, it becomes useful in the understanding of extraction technique, polarity, solubility, precipitation, and emulsions v. solutions.

 

This lab is developed from one used in the Inquiry Institute at Bryn Mawr. It was created by Wil Franklin.  The original can still be found on the serendip website: /exchange/suminst/iii2008/strawberryextraction

 

 I want to extend the activity by including centrifuging as well as redissolving and reprecipitating of the DNA.  So, the key becomes the guiding questions posed in the student instructions and placed at the end of the lab exercise.

 

To make the Extraction buffer:

            100 ml shampoo without conditioner or dishwashing liquid

            900 ml distilled water

            15 grams NaCl

 

 

Student Lab Sheet . . .

is on the next page.

Using DNA Testing in a

Chemistry Class

                  Objectives:  The student should be able to:

        Develop lab techniques.

        Acquire rudimentary knowledge of how DNA is extracted, separated,

and dissolved so as to be able to be further analyzed.

        See the actual effects of hydrophilic v. hydrophobic chemical activity.

 

            Materials:  Thawed frozen strawberries and/or corn, extraction buffer, gauze pad filters or cheesecloth, funnel, cold ethanol, 10 mL graduated cylinder, small test tubes, Beral thin stem pipets, centrifuge, distilled water, high quality zip-lock baggies, 100 mL beaker, 0.1 M HCl, 0.1 M NaOH, NaCl crystals.

 

            Safety Precautions:  Don’t drink the alcohol.  It is denatured.  Avoid getting the HCl and NaOH on your skin.  Normal lab safety procedures should be followed.  All the liquids may be safely disposed of down the drain.  Solid waste should be placed in the receptacle by the door.

 

            Background:  At this point we all believe that all living things contain DNA in their cells.  But have you ever really seen any DNA?  Today you will!  We are going to get the DNA out of strawberry or corn cells.  You will free the DNA, then separate it from the rest of the material,

 

            Procedures:  Working in groups (for supervision), but each individual will do their own.

1. Place 1 strawberry in the plastic bag.  Remove air and seal.
2. Mash strawberry for 2 minutes.
3. Add ~10 ml DNA Extraction buffer (Pre-measured).  Remove air and seal.
4. Mash for 1 minute.
5. Pour solution through cheesecloth filter into paper cup.  Squeeze filter to maximize yield.
6. Pour ~2 ml of this solution back into the 15 ml tube.  It will be very red.
7. Pour ~ 4 ml (2X the volume of strawberry solution) of cold ethanol (found on freeze door in 50 ml tubes) so that it lies on top of the strawberry solution. (NOTE: can use 1X volume of room temperature isopropanol, rubbing alcohol, as a substitute)
8. If the tube just sits, there will be DNA at the interface with bubbles in it.  If you gently rock the tube, more will come out of solution and eventually float to the top. (NOTE: if the DNA doesn’t come out of solution, add a little more salt)

              Why’s: (Underlying Reasoning)

            Strawberries?   8 times the amount of DNA of normal cells

            Why frozen?     Water expands as it freezes, thus breaking open

                                     the cells of the strawberry. 

            Detergent?        To disrupt cell membranes to liberate the DNA

            Salt?                 To shield the negative charges on DNA

                                     to allow precipitation

            Alcohol?           To cause DNA to precipitate

 

 

Questions:

I’ve given you some reasoning on the bottom of the last page.  With that as a starting point, extend that logic to answer the following questions and to try the 2 activities.  (HINT:  It will help to consider the concepts we are covering in the current chapter in the text.)

 

1. Why does it facilitate the extraction process to use frozen and thawed samples rather than fresh?

 

2. Why did we choose to use strawberries or corn?

 

3. Why does the detergent function to disrupt the cell membranes?

 

 

4. Why do we use salt in the extraction  process? 

 

 

5. Why does DNA precipitate in alcohol? 

 

 

Extention Activity:

6. We can re-dissolve the DNA?  Explain how you would do this and why your method should work.

    Try it and explain your results.

 

7. Now that you’ve re-dissolved it, re-precipitate it.  Explain the logic of your approach first.

    Then do it and “journal” the result, being sure to explain why it worked . . . or didn’t.

 

 

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