Isolating DNA -- a long polymer chain

DNA, which stands for Deoxyribonucleic acid, is made up molecules known as nucleic acids. These were first identified by Swiss physician and biologist Johannes Friedrich Miescher in 1869, who called them “nuclein” because they were found in the nucleus of the cell. Every type of life form known contains nucleic acids, in the form of DNA or RNA (ribonucleic acid).

Oswald Avery received the Nobel Prize in 1943 for confirming that DNA carried genetic information. Each strand of human DNA is divided into 23 pairs of chromosones, which in turn contain hundreds or thousands of genes. Genes record information in the form of chemical codes about how to build the proteins and other molecules which make up living organisms.

DNA is one of the longest type of polymers, or chains of molecules. Strands of human DNA are 6 feet long. In 1950, scientist Rosalind Franklin used X-ray crystallography to find that DNA is made up of two long polymers, or chains of molecules, twisted into a shape called a double helix. In 1953, James Watson and Francis Crick discovered that the strands were connected by crossbars, like a ladder. They won the Nobel Prize in 1962 for uncovering DNA’s structure.


Isopropyl (rubbing) alcohol (70 or 91 percent)
Clear plastic cups
Plastic spoons
Small plate (preferably disposible)
Drinking water
Salt
Dish soap
Blue food coloring (optional)

Step 1: Chill the alcohol
Place the bottle of alcohol in the freezer to chill while preparing the next steps. (Do not leave in long enough to freeze!)


Step 2: Gather the DNA
In the plastic cup, mix ¼ teaspoon of salt in 1/4 cup of water. Swish the salt water around in your mouth for a minute, making sure it reaches the inside of your cheeks. Spit all the water back in the cup. Do not swallow! (If you prefer, you can also use Gatorade, which is sweeter.)

Cells from the inside of your cheek mix with the salt water and are carried away when you spit. Above is a photograph of cheek cells under a microscope. You can see the nucleus inside each cell.

Step 3: Release the DNA from your cheek cells
Put a drop of dish soap on the plate. Touch the spoon to the soap, and then dip it in the cup of salt water. Gently stir once or twice. Cells are contained within membranes that are made up of fats. The soap solution breaks down the fat molecules, just like soap breaks down grease on your dishes, and releases the contents of the cell.

Step 4: Add the alcohol
Remove the alcohol from the freezer. Pour about a quarter of a cup into a second plastic cup. If desired, add a drop of blue food coloring to make the alcohol easier to see. Stir until evenly mixed. Take the salt water cup and tilt to one side. Hold the cup of alcohol up so that the lip touches the tilted cup. SLOWLY pour a little alcohol down the inside of the cup so that it floats on top of the salt water without mixing. Continue until there is about an eighth of an inch of alcohol on top of the salt water.

Step 5: Watch the DNA strands appear
Wait a few minutes and you will see long strands or clumps of a sticky white substance start to come together in the alcohol layer. This is the DNA from thousands of cheek cells in the salt water. The DNA cannot dissolve in the chilled alcohol, so it precipitates out (comes out of solution as a solid).
Variation: If you want to remove the DNA to look at it through a microscope, dip a toothpick into the alcohol layer and twirl it to gather up the sticky DNA. Place on a glass microscope slide. You can also save the DNA in a small clear container with a little extra salt water. Keep tightly covered.

More information:

http://tang.skidmore.edu/pac/mtm/DNA/index.html
www.nespal.org/oziasakinslab/edout/AnimalDNAExtraction.pdf
http://www.vampirewear.com/dna.html
http://nature.ca/genome/05/051/0511/0511_m204_e.cfm
http://www.californiasciencecenter.org/Education/GroupPrograms/HomeSchool/docs/DNA.pdf

Splitting Saltwater

Last week we watched an episode of  The Joy of Science dealing with elements that have an affinity for one another, like sodium and chlorine.  In the great Theo Gray book Mad Science, he shows that combining sodium and chlorine to make your own salt results in quite a bang.I was looking for other interesting sodium-related YouTube videos when we came across one that showed a cool way to split salt into its component elements.

Above you can see our version of the experiment. What we did is explained below.

Saltwater Electrolysis

Materials:

-Salt
-One 9-volt battery
-Two spoons
-A medium-sized glass bowl

Steps:

1. Fill the bowl with warm tap water, and stir in a spoonful or so of the salt.


2. Place the two spoons in the water, being careful not to let the two spoons touch each other.

 3. Hold the ends of the two spoons to the battery connectors, one spoon on each connector.

4. Within a few seconds, you should see tiny bubbles coming off of the spoons. You will also notice what looks like smoke coming off the water.

5. After holding them in a minute or so, you should be able to see the water begin to turn murky yellow.

6. After several minutes, the water starts to turn dark green.

Here is an explanation of what's happening (from the NASA Aquarius website):

In chemistry, electrolysis is a method of separating bonded elements and compounds by passing an electric current through them. An ionic compound, in this case salt, is dissolved with an appropriate solvent, such as water, so that its ions are available in the liquid. An electrical current is applied between a pair of inert electrodes immersed in the liquid. The negatively charged electrode is called the cathode, and the positively charged one the anode. Each electrode attracts ions which are of the opposite charge. Therefore, positively charged ions (called cations) move towards the cathode, while negatively charged ions (termed anions) move toward the anode. The energy required to separate the ions, and cause them to gather at the respective electrodes, is provided by an electrical power supply. At the probes, electrons are absorbed or released by the ions, forming a collection of the desired element or compound.

One important use of electrolysis is to produce hydrogen. The reaction that occurs is 2H2O(aq) → 2H2(g) + O2(g). This has been suggested as a way of shifting society towards using hydrogen as an energy carrier for powering electric motors and internal combustion engines. Electrolysis of water can be achieved in a simple hands-on project, where electricity from a battery is passed through a cup of water (in practice a saltwater solution or other electrolyte will need to be used otherwise no result will be observed). Electrolysis of an aqueous solution of table salt (NaCl, or sodium chloride) produces aqueous sodium hydroxide and chlorine, although usually only in minute amounts. NaCl(aq) can be reliably electrolysed to produce hydrogen. Hydrogen gas will be seen to bubble up at the cathode, and chlorine gas will bubble at the anode.

According toWikipedia, this is the formula for the chemical reaction taking place:

2 NaCl + 2 H2O → Cl2 + H2 + 2 NaOH

That means, two sodium chloride molecules (which is the salt) plus two dihydrogen monoxide molecules (also known as water) becomes one chlorine molecule, one hydrogen molecule, and two molecules of sodium hydroxide (which is also known as lye). So in our experiment, the bubbles were hydrogen, the "smoke" coming off the water was chlorine gas, and the yellow color of the water was the sodium, in the form of lye.

Proving Atoms Exist with Brownian Motion

In 60 BC, the Roman poet Lucretius published a poem entitled De rerum natura, or On the Nature of Things. Its contents were mostly philosophical, focusing on themes of life, death, love, the soul, and such. However, the first two sections of the six-book poem were focused on a very different subject matter: atoms. The poem read:

“Observe what happens when sunbeams are admitted into a building and shed light on its shadowy places. You will see a multitude of tiny particles mingling in a multitude of ways . . . their dancing is an actual indication of underlying movements of matter that are hidden from our sight. It originates with the atoms which move of themselves [i.e., spontaneously]. Then those small compound bodies that are least removed from the impetus of the atoms are set in motion by the impact of their invisible blows and in turn cannon against slightly larger bodies. So the movement mounts up from the atoms and gradually emerges to the level of our senses, so that those bodies are in motion that we see in sunbeams, moved by blows that remain invisible.” 

This is a phenomenon called “Brownian Motion,” named after Botanist Robert Brown. Although it was Albert Einstein that finally described the physics behind this, it was named after Brown because of his being the first to test this theory by observing pollen grains bouncing off of water molecules. But it was ultimately Einstein who brought this to the attention of the physics community, and in doing so, proving the existence of what we now think of as atoms and molecules.

We decided to reproduce Brown’s experiment, adapting directions from Dave Walker.


What you need:

• student microscope with 200X or 400X magnification
• milk (we used 2%)
• microscope slides and coverslips
• thin needle or wire
• water (preferably distilled, although we used tap water)
• Vaseline petroleum jelly (optional)

To prepare the slide:

1. Place a very small drop of water in the middle of the slide (use a dropper).

2. Dip the needle in the milk, then dip and stir in the water drop. We picked up a drop in the eye of the needle and stirred it with the needle almost flat in the water drop.

3. Gently lower the coverslip onto the diluted milk drop.

4. Make sure no water is near the edge of the cover slip. This is important to ensure you observe Brownian motion and not liquid movement caused by evaporation).

5. Optional: To make a slide that lasts longer, seal the coverslip on with a thin line of Vaseline to minimize evaporation.

Still photo of fat molecules taken with standard microscope and point-and-shoot camera.

We tried this experiment with both our computer microscope and our standard microscope. Although we were unable to get decent pictures with either microscope, we were able to see decent results with the basic microscope.

We placed a droplet of water on a glass slide, and then, using a pin, we placed a smaller droplet of milk (we used 2% instead of whole) inside the water. We then placed a coverslip over the droplet, and sealed it with vasoline. The first few times we did this, we were unable to observe, or even locate the water droplet with our computerized microscope. However, after a few tries, we found that making adjustments to the experiment (such as not using vasoline and placing smaller droplets on the slide) were effective, allowing us to at least see the water. Switching from the computerized microscope to our lower-tech but more high-powered microscope produced much more positive results. The higher magnification allowed us to actually observe the Brownian Motion of the milk fat particles bouncing off the water molecules.



We also decided to test a simplified version of Brown’s experiment by dropping food coloring into a large bowl of water. While this was not as precise as the milk experiment, observing the cigarette smoke-like movements of the dye was more effective at demonstrating Brownian Motion. Above, you can see a video of a similar experiment, conducted by GeekMom writer Kay Holt and her son Bastian.

Other resources:

Wikipedia
Einstein Year
University of Virginia
Discover Magazine