GENETICS LESSON III: DNA and Molecular Biology

Key Concepts:
Double-stranded DNA
Base pairing
Base sequence
Genetic Code

Materials needed:

• Introduction:
  DNA model
  
• Each station should have:
  Saline/Soap Solution: (200 ml distilled water, 3 tsp salt, 3 tsp clear liquid soap)
  Dixie cups
  Wooden coffee stirrers
  Falcon tubes (14 ml) #352059
  Eppindorf tubes
  tube racks
  Bottled water
  Hemp or string
  power supply
  yellow tips
  pipetman
  gel and gel box with buffer
  food coloring of various colors
  
• Materials to share:
  Isopropanol or rubbing alcohol in 50 ml tube placed in Styrofoam container with ice
  50X TAE buffer
  extra gels

Introduction

DNA has the information which determines many of our characteristics.Hold up model of DNA to begin discussion of what is DNA. Point out basic features and ask children “what is the structure”. The building blocks of DNA are deoxyribonucleotides. Deoxyribonucleotides are sugar molecules (deoxyribose) connected to a phosphate group and a base. Thousands of deoxyribonucleotides are joined end-to-end to make up the backbone of the DNA molecule. Two backbones coil around each other in a double helix, with the sugar phosphate part on the outside of the helix and the bases on the inside.

There are 4 different bases (see appendix, page 24) which make up the DNA. There are two double-ringed purines; adenine (A) and guanine (G), and the single-ringed pyrmidines; thymine (T) and cytosine (C). In the DNA helix, the bases from opposite strands pair with each other. Base-pairing has two rules: guanine always pairs with cytosine and adenine always pairs with thymine. Each base pairs with its opposite and is held precisely in position by hydrogen bonds. The order of bases along a DNA strand determines the sequence of the DNA and of a gene.

(optional) In the early 19050s people were debating if proteins or DNA was the hereditary molecule. Proteins appeared more complex because they had 20 different building blocks wheras DNA only had 4. But scientists found that DNA could be used to transfer genetic information but not protein so this established DNA as the hereditary molecule.

Class Activity: Have one student read the sequence on the DNA model and write it on board. Ask students for sequence on the other strand. Then have a student read the complementary sequence on the DNA model and see if it matches. To illustrate how differences in a DNA sequence can alter what a gene encodes, write out a hypothetical sequence for a tongue rolling gene, big R. Write out a similar sequence but change one of the bases as an example of the alternative allele, r. Tell students how the change in the DNA sequence between the two forms of the tongue rolling gene lead to a difference in genotype which then affects the phenotype, i.e. ability to roll the tongue..

If you look at a sequence of DNA ATCGTTCAAA etc. how do you read it and make sense of it? It turns out that there is a code that is used to "read" the DNA. You will learn about this code in high school. Knowing the code, you will know what protein can be made from a gene. Human DNA has the information for making at least 30,000 proteins.

Remember when you learned how to read, you first learn letters, then you put the letters together into words, then sentences, then a paragraph, and then a book. The sequence pattern of the 4 bases, ATGG creates the DNA information. There is a genetic code which is used to understand what the sequence means. You will learn about this in high school

This lesson will be run a little bit differently. Each volunteer will be responsible for one group for the entire period after the introduction.

Sequence of Activities: Each group will load DNA gels with food coloring, then while the gels are running extract DNA from cheek cells. While the DNA is precipitating, look at the gel, and then examine white strands of DNA. Finally have all students participate in "who stole the cookie" activity with theTA while the volunteers assemble the DNA bracelets to be distributed at the end.

1. Loading Agarose Gels (Appendix, Page 25)
Discuss how there are enzymes that recognize specific DNA sequences (ATCGGC) and will cut DNA that has that sequence (or site). If a piece of DNA has one such site, it will be cut into two pieces by the enzyme. If the piece of DNA has two sites, how many fragments would you get after cutting with the enzyme? In order to determine number of sites, we take piece of DNA, cut with enzyme, place DNA in an agarose gel and run a current through the gel in order to separate pieces of different sizes. The ability of DNA to cut by a DNA cutting enzyme tells us something about the sequence of that DNA.

Activity: Explain that the gel is the consistency of jello. Students can touch gel by touching lightly. Demonstrate pipet use. Have the students each practice with water. Demonstrate loading into a well. Point out that the tip will go through the bottom of the well if not careful. Let each student load the agarose gel. (One well each, then second turns if time and space permit.)

While the gel is running, discuss the principle of size separation by electrophoresis. A good analogy is big and little dogs running through the bushes. Little dog gets farther because it squeezes through small spaces. Use the handout when necessary.

Discuss principle of electrophoresis, separating DNA using an electrical current. Because DNA is negatively charged (due to phosphates), DNA will run towards positive cathode.

Prepare some agarose gels in advance to show students because we usually run out of time with first group.

2. DNA bracelet
A simple extraction technique is used to isolate DNA from cheek cells. The cells are collected with water after scraping the inside of the cheek with a wooden stirrer. A soap and saline solution is added to the tube containing the water. The soap breaks open the cells to release the DNA and the salt neutralizes the negatively charged DNA allowing it to aggregate and precipitate. When alcohol is added, the DNA precipitates from the solution and appears as white stringy strands in the aqueous layer just above the alcohol.

Details for DNA Bracelet activity

• Before the kids come in
  (i) label test tubes 1-30 and fill them with 1ml of soap solution
  (ii) label eppendorf tubes 1-30 with the same numbers
  (iii) Cut string long enough to make a bracelet
  (iv) 30 dixie cups filled with 6 ml of water
  
• Have kids scrape inside cheek. The better job done, the more DNA is collected.
  
• Have student put the water from Dixie cup in their mouth and swirl. Then slowly relinquish the “mouthwash” solution back into cup. Pinch edge of cup on one side for pouring. Then hand them the tubes with soap solution and ask them to pour the liquid into the tube.
  
• After pouring solution into test tube, have the students put the cap on TIGHTLY!
  
• Have the students gently rock/invert the tubes to mix.
  
• BEFORE you come around with ice-cold isopropanol, make sure students hear that they shouldn’t shake the tubes once you add it.
  
• Ask them to take off the tops, hold tube at an angle, then you add about 1 ml of isopropanol along the side of the tube with transfer pipette from 50 ml blue capped tube.
  
• Have students hold their tubes upright or put the tubes back in the rack.

While the tubes are sitting for about 3 minutes to allow DNA to precipitate, talk about precipitation, and tell them that they will be seeing their DNA in the upper water layer (alcohol at bottom). Can show them an example prepared ahead of time.

Examine DNA gel while DNA precipitating.

After children observe DNA, have them place tubes in rack and tell them to remember their numbers.

Children continue with “Who Stole Cookie” activity and the teachers and volunteers pick up DNA with transfer pipette and transfer to eppindorf tube with same number. Close tubes with piece of string/hemp between cap and tube so stays attached. Hand out to children and teacher can help tie bracelet.

• Who stole the cookies?
  Follow activity as described in supplementary material.

After activity, you can ask students: How is DNA sequence information used in our society. (paternity testing, criminology, etc)

Options
1. "Mix up at the hospital"
2. Discuss careers in bioscience.

Materials needed:

Introduction
DNA is the macromolecule that contains the blueprints for life. Hold up model of DNA to begin discussion of what is DNA. The building blocks of DNA are deoxyribonucleotides. Deoxyribonucleotides are sugar molecules (deoxyribose) connected to a phosphate group and a base. Thousands of deoxyribonucleotides are joined end-to-end to make up the backbone of the DNA molecule. Two backbones coil around each other in a double helix, with the sugar phosphate part on the outside of the helix and the bases on the inside.

There are 4 different bases (see appendix, page 24). There are two double-ringed purines; adenine (A) and guanine (G), and the single-ringed pyrmidines; thymine (T) and cytosine (C). In the DNA helix, the bases from opposite strands pair with each other. Base-pairing has two rules: guanine always pairs with cytosine and adenine always pairs with thymine. Each base pairs with its opposite and is held precisely in position by hydrogen bonds. The order of bases along a DNA strand determines the sequence of the DNA and of a gene.

Activity:
Have one student read the sequence on the DNA model and write it on board. Ask students for sequence on the other strand. Then have a student read the complementary sequence on the DNA model and see if it matches. To illustrate how differences in a DNA sequence can alter what a gene encodes, write out a hypothetical sequence for a tongue rolling gene, big R. Write out a similar sequence but change one of the bases as an example of the alternative allele, r. Tell students how the change in the DNA sequence between the two forms of the tongue rolling gene lead to a difference in genotype which then affects the phenotype, i.e. ability to roll the tongue. The sequence of DNA is usually constant from generation to generation being duplicated and passed to new daughter cells after mitosis or meiosis. However, sometimes mutations can occur which cause a change in the DNA sequence. Sometimes the change can have a deleterious (bad) affect.

If you look at a sequence of DNA ATCGTTCAAA etc. how do you read it and make sense of it? It turns out that there is a code that is used to "read" the DNA. You will learn about this code in high school. Knowing the code, you will know what protein can be made from a gene. Human DNA has the information for making at least 30,000 proteins.

You can ask students: How is DNA sequence information used in our society. (paternity testing, criminology, etc) [If extra time, can discuss sequence differences between people (1 change for every 1000 bases) or between people and chimpanzees 15 changes for every 1000 bases]

1. Loading Agarose Gels (Appendix, Page 25)
Discuss how there are enzymes that recognize specific DNA sequences (ATCGGC) and will cut DNA that has that sequence (or site). If a piece of DNA has one such site, it will be cut into two pieces by the enzyme. If the piece of DNA has two sites, how many fragments would you get after cutting with the enzyme? In order to determine number of sites, we take piece of DNA, cut with enzyme, place DNA in an agarose gel and run a current through the gel in order to separate pieces of different sizes. The ability of DNA to cut by a DNA cutting enzyme tells us something about the sequence of that DNA.

Activity:
First, demonstrate pipet use. Have the students each practice with water. Demonstrate loading into a well. Point out that the tip will go through the bottom of the well if not careful. Let each student load the agarose gel. (One well each, then second turns if time and space permit.)

While the gel is running, discuss the principle of size separation by electrophoresis. A good analogy is big and little dogs running through the bushes. Little dog gets farther because it squeezes through small spaces. Use the handout when necessary. Because DNA is negatively charged (due to phosphates), DNA will run towards positive cathode.

Prepare some agarose gels in advance to show to students because we usually run out of time with first group.

2. Looking at Agarose Gels
One group at time, look at a previously run and stained agarose gels under handheld UV light. Explain that this is how their agarose gel would look in a few hours. Ask them to point to bigger and smaller molecular weight bands.

Optional Discussion while gel is running:

1. Handout (maternity suit, mix up at the hospital, or cookie theif -- see appendix) or make your own up. (Use their names, or famous people, and make up a funny scenario.)
2. Discuss careers in bioscience. (doctor, nurse, research, genetic counseling, health educator, public policy, teaching, veterinary science, forensics, etc.)

Trouble-shooting Ideas

1. Start the introduction by asking the students to remember that last week ‘we talked about our genes and how they were located on chromosomes inside the nucleus of every cell of our body. Today, we are going to be discussing the material that genes are composed of, DNA, deoxyribonucleic acid.’
2. Before allowing the students to load the agarose gels, explain the shape of the well by drawing it on a piece of paper. Have the students practice picking up water into the pipet and ‘load’ the water into the paper well.
3. Explain that the gel is the consistency of jello. Students can touch gel by touching lightly. Some of the students are very rough with the gel and may poke holes.
4. Do not show the students how to ‘fire’ the pipet tips of the pipetman. Stress the importance of not putting fingers into the gel box while it is running.