Les 4 DNA Extraction Lab

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Les 4 DNA Extraction Lab Powered By Docstoc
					Biology 40S – Lesson 5 Unit 2 Mol. Gen.                  Name                                 /15
S4B-2-02 Describe the structure of a DNA nucleotide. Include: deoxyribose sugar, phosphate group,
nitrogenous bases.
S4B-2-03 Describe the structure of the DNA molecule. Include: double helix, nucleotides, base-
pairing, gene
                 How To Extract DNA From Anything Living
  In the footsteps of Friedrich Miescher (1869)—an introduction to Molecular Genetics.

Find anything that contains DNA—onions, potato, spinach…Since DNA is the blueprint
for life, everything contains DNA. In this lab procedure you will extract DNA. Make careful
observations during the procedure—determine the function of each step. Complete the back of
this sheet. Turn in the lab in your duo-tang as instructed.

DNA source (Yellow split peas)   Measuring cup/beaker            Rubbing/Isopropyl alcohol
blender                          liquid detergent                wooden stick or other hook
1/8th tsp/1 ml salt (NaCl)       test tubes                      GOGGLES are mandatory.
ice cold water                   Source of enzymes (pineapple
Strainer                         juice or contact lens solution)

Procedure (You and your group of 3-4 people are being assessed on how you progress
through the procedure. Be sure to use proper techniques and follow steps in order):
 Your teacher will place the DNA source in a blender along with a large pinch of salt, twice as
    much ice cold water as the DNA source (eg. 100 mL of split peas with 200 mL of water).
 Blend on high 15 seconds. We will now refer to the mixture as “soup”.

Your Group’s Part: You will be preparing 3 samples out of this 100 mL batch you collect:
1. Pour the thin soup through the strainer into the measuring cup or beaker. Collect about 100
   mL of “soup.” Be sure to dump the residue into the garbage can.
2. Record the actual amount you receive using the graduation on the measuring cup or beaker
   in the space below. Add 1/6 this amount worth of detergent and swirl to mix.
   Volume of genetic “soup”
3. Let stand 10 minutes.
4. Each partner now pours the mixture into test tubes about 1/3 full.
5. Add a pinch of enzyme (about 5 drops) to each tube and stir GENTLY. If you stir too hard
   you will break up the DNA molecules—it is fragile!
6. Tilt your test tube and SLOWLY pour rubbing alcohol into the tube down the side so that it
   forms a layer on top of the soup mixture. Pour until you have the same amount of alcohol in
   the tube as pea mixture.
7. OBSERVE! Use your stir stick or hook to draw up the DNA (like spaghetti).

      After observations and the coolness of what you have done has settled, clean up your
       apparatus by pouring the soup down the sink with water.
      Your DNA can be pulled off the “hook” and discarded in the garbage can.
      Wash all glassware/plastic-ware and set it out to dry on the counter/drying rack.
      COMPLETE the back of the page.
                                                                                      /5 marks
Describe your own observations of the experiment. Include how the DNA looks, texture, etc.
Include a detailed diagram that is neatly drawn and clearly labelled. (3)

Questions: Answer these questions based on your observations of the procedure and
1. Why is salt added to the split peas? (1)

2. What is the purpose of the blender? (1)

3. Adding detergent is an important step. DNA extraction is not possible without it. What
   seems to be the role of the detergent? (1)

4. What is the role of the enzyme (contact lens solution)?(1)

5. Alcohol was added in the last step. What is its function? Why does the DNA rise to the top
   of the alcohol? (1)

6. Why can’t you see the double helix?(1)

7. Seed foods, such as peas, have more protein residue in the liquid than plant stalks.
8. What part of the cell did the DNA come from?(1)
9. Give two reasons why we would want to extract DNA from humans? (2)

                                                                                    /10 marks

   1. I don't think I'm seeing DNA. What should I be looking for?

Look closely. Your DNA may be lingering between the two layers of alcohol and pea soup. Try to help the
DNA rise to the top, alcohol layer. Dip a wooden stick into the pea soup and slowly pull upward into the
alcohol layer. Also, look very closely at the alcohol layer for tiny bubbles. Even if your yield of DNA is low,
clumps of DNA may be loosely attached to the bubbles.

   2. What can I do to increase my yield of DNA?

Allow more time for each step to complete. Make sure to let the detergent sit for at least five minutes.
If the cell and nuclear membranes are still intact, the DNA will be stuck in the bottom layer. Or, try
letting the test tube of pea mixture and alcohol sit for 30-60 minutes. You may see more DNA precipitate
into the alcohol layer over time.

Keep it cold. Using ice-cold water and ice-cold alcohol will increase your yield of DNA. The cold water
protects the DNA by slowing down enzymes that can break it apart. The cold alcohol helps the DNA
precipitate (solidify and appear) more quickly.

Make sure that you started with enough DNA. Many food sources of DNA, such as grapes, also contain
a lot of water. If the blended cell soup is too watery, there won't be enough DNA to see. To fix this, go
back to the first step and add less water. The cell soup should be opaque, meaning that you can't see
through it.

Understanding the Science behind the Protocol

   3. Why add salt? What is its purpose?

Salty water helps the DNA precipitate (solidify and appear) when alcohol is added.

   4. Why is cold water better than warm water for extracting DNA?

Cold water helps keep the DNA intact during the extraction process. How? Cooling slows down
enzymatic reactions. This protects DNA from enzymes that can destroy it.

Why would a cell contain enzymes that destroy DNA? These enzymes are present in the cell cytoplasm
(not the nucleus) to destroy the DNA of viruses that may enter our cells and make us sick. A cell's DNA is
usually protected from such enzymes (called DNases) by the nuclear membrane, but adding detergent
destroys that membrane.

   5. How is the cell wall of plant cells broken down?

It is broken down by the motion and physical force of the blender.
   6. What enzyme is found in meat tenderizer?

The two most common enzymes used in meat tenderizer are Bromelain and Papain. These two enzymes
are extracted from pineapple and papaya, respectively. They are both proteases, meaning they break
apart proteins. Enzymatic cleaning solutions for contact lenses also contain proteases to remove protein
build-up. These proteases include Subtilisin A (extracted from a bacteria) and Pancreatin (extracted from
the pancreas gland of a hog).

   7. How much pineapple juice or contact lens solution should I use to replace the meat tenderizer?

You just need a drop or two, because a little bit of enzyme will go a long way. Enzymes are fast and

   8. Why does the DNA clump together?

DNA precipitates when in the presence of alcohol, which means it doesn't dissolve in alcohol. This
causes the DNA to clump together when there is a lot of it. And, usually, cells contain a lot of it!

For example, each cell in the human body contains 46 chromosomes (or 46 DNA molecules). If you lined
up those DNA molecules end to end, a single cell would contain six feet of DNA! If the human body is
made of about 100 trillion cells, each of which contains six feet of DNA, our bodies contain more than a
billion miles of DNA!

   9. How can we confirm the white, stringy stuff is DNA?

There is a protocol that would allow you to stain nucleic acids, but the chemical used would need to be
handled by a teacher or an adult. So, for now, you'll just have to trust that the molecules precipitating in
the alcohol are nucleic acids.

   10. Isn't the white, stringy stuff actually a mix of DNA and RNA?

That's exactly right! The procedure for DNA extraction is really a procedure for nucleic acid extraction.

   11. How long will my DNA last? Will it eventually degrade and disappear?

Your DNA may last for years if you store it in alcohol in a tightly-sealed container. If it is shaken, the DNA
strands will break into smaller pieces, making the DNA harder to see. If it disappears it's likely because
enzymes are still present that are breaking apart the DNA in your sample.

Using more sophisticated chemicals in a lab, it is possible to obtain a sample of DNA that is very pure.
DNA purified in this way is actually quite stable and will remain intact for months or years.
Comparing the DNA Extracted from Different Cell Types

   12. Does chromosome number noticeably affect the mass of DNA you'll see?

Cells with more chromosomes contain relatively more DNA, but the difference will not likely be
noticeable to the eye. The amount of DNA you will see depends more on the ratio of DNA to cell volume.

For example, plant seeds yield a lot of DNA because they have very little water in the cell cytoplasm.
That is, they have a small volume. So the DNA is relatively concentrated. You don't have to use very
many seeds to get a lot of DNA!

   13. Why are peas used in this experiment? Are they the best source of DNA?

Peas are a good source of DNA because they are a seed. But, we also chose the pea for historical
reasons. Gregor Mendel, the father of genetics, did his first experiments with the pea plant.

   14. How does the experiment compare when using animal cells instead of plant cells?

The DNA molecule is structurally the same in all living things, including plants and animals. That being
said, the product obtained from this extraction protocol may look slightly different depending on
whether it was extracted from a plant or an animal. For example, you may have more contaminants
(proteins, carbohydrates) causing the DNA to appear less string-like, or the amount of DNA that
precipitates may vary.

   15. What sources might I use to extract DNA from animal cells?

Good sources for animal cells include chicken liver, calf thymus, meats and eggs (from chicken or fish).

   16. Why do peas require meat tenderizer, but wheat germ does not?

We at the GSLC have done a fair amount of testing with the split pea protocol and the wheat germ
protocol. We have found no difference in the "product" (nucleic acids) that is observable, whether using
meat tenderizer or not. So, the step was left out of the wheat germ protocol, but kept in the split pea
protocol just for fun.

Even though it's not necessary, it may be doing something we can't see. For example, perhaps by using
the meat tenderizer you get a purer sample of DNA, with less protein contaminating the sample.

Real-life Applications of the Science of DNA Extraction

   17. Can you extract human DNA using this protocol?

Yes, in theory. The same basic materials are required, but the protocol would need to be scaled down
(using smaller volumes of water, soap and alcohol). This is because you're not likely starting the protocol
with the required amountâ€”1/2 cupâ€”of human cells! That means that you will not extract an amount
of DNA large enough to visualize with the naked eye. If you wanted to see it, you would need a
centrifuge to spin down (to the bottom of the tube) the small amount of DNA present in the sample.
   18. What can be done with my extracted DNA?

This sample could be used for gel electrophoresis, for example, but all you will see is a smear. The DNA
you have extracted is genomic, meaning that you have the entire collection of DNA from each cell.
Unless you cut the DNA with restriction enzymes, it is too long and stringy to move through the pores of
the gel.

A scientist with a lab purified sample of genomic DNA might also try to sequence it or use it to perform a
PCR reaction. But, your sample is likely not pure enough for these experiments to really work.

   19. How is DNA extraction useful to scientists? When do they use such a protocol, and why is it

The extraction of DNA from a cell is often a first step for scientists who need to obtain and study a gene.
The total cell DNA is used as a pattern to make copies (called clones) of a particular gene. These copies
can then be separated away from the total cell DNA, and used to study the function of that individual

Once the gene has been studied, genomic DNA taken from a person might be used to diagnose him or
her with a genetic disease. Alternatively, genomic DNA might be used to mass produce a gene or protein
important for treating a disease. This last application requires techniques that are referred to as
recombinant DNA technology or genetic engineering.

   20. Can I use a microscope to see the DNA that I extract?

Unfortunately, a microscope will not allow you to see the double helical structure of the DNA molecule.
You'll only see a massive mess of many, many DNA molecules clumped together. In fact, the width of the
DNA double helix is approximately one billionth of a meter! This is much too small to see, even with the
most powerful microscope. Instead, a technique called X-ray crystallography can be used to produce a
picture of the DNA molecule. It was by looking at such a picture (taken by Rosalind Franklin) that James
Watson and Francis Crick were able to figure out what the DNA molecule looks like.

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