Part A: Synthetic Biology 101

Lesson Type: Informal Lecture

Learning Objectives:

• Define synthetic biology
• Explain the processes involved in the central dogma of molecular biology
• Describe the molecular processes behind restriction digest/ligation, PCR, and gel electrophoresis

Lecture Presentation

Part B: Strawberry DNA Extraction

Lesson Type: Demonstration/Performance

Learning Objectives:

• Describe how DNA is packaged within the cell
• Explain the differences between strawberry cells and human cells
• Understand how histones are removed from DNA

Background

The adult human body contains trillions of cells - each incredibly small and impossible to see with the naked eye. Within each of those cells, there is a bundle of DNA called the nucleus which contains almost all of your genetic information. Inside each nucleus, which is 6 micrometers in diameter, are 46 chromosomes of DNA, for a total of 3 billion base pairs. Although each base pair is microscopically small, we have enough DNA in each of our cells to amount to 2 meters in length when stretched out. Inside our cells, our DNA doesn’t exist as elongated strands. Instead, the DNA in our cell is wrapped tightly around proteins called histones, allowing for large stretches of DNA to be condensed into a structure called chromatin.

Humans are a diploid organism, meaning we have two copies each of the 23 chromosomes in our cells. Strawberries, which we will be extracting DNA from today, has 8 copies of each chromosome, making it an octoploid organism. Because they have so many copies of each chromosome, its cells contain much more DNA than our cells do, making the DNA easier to see when removed from the cell.

DNA in strawberry cells can be made visible to the naked eye as long as many cells are broken open and the DNA is separated from the histones that package the DNA. First, the cells are broken apart using a detergent that disrupts the membrane layer of the cell. Then, DNA is separated from the histones via simple ionic interactions. When the cell is flooded with aqueous NaCl, the Na+ ions bind to the negatively-charged DNA molecules, and the Cl- ions bind to the positively-charged histones, separating the two. This mixture is filtered to remove excess cell debris. Lastly, a layer of alcohol is added to the mixture. DNA, which is soluble in water, is insoluble in alcohol will collect at the meeting between the water and alcohol layers.

Materials (per student):

• 2 strawberries
• 1 ziploc bag
• 20mL Strawberry Extraction Buffer
• 5 reactions of buffer can be made from
• 10mL detergent
• 90mL water
• 1.5g of NaCl
• 1 coffee filter
• 1 beaker or plastic cup
• 10mL ethanol
• 1 stir rod or toothpick

Procedure:

1. Place a strawberry in a ziploc bag. Seal the bag and squish the strawberry in the bag until the mixture is smooth.
2. Measure 20 mL of the Strawberry Extraction Buffer and pour it into the ziploc bag.
3. Seal the bag and gently mix the contents. Try to avoid forming bubbles in the bag.
4. Place a coffee filter inside a beaker or plastic cup. Pour the contents of the bag into the coffee filter. Let sit for 10 minutes.
5. Gently squeeze the sides of the filter paper to push any remaining liquid through the filter paper.
6. Measure 10 mL of ethanol and pour gently down the side of the cup. Let sit for 5 minutes.
7. Use a toothpick or stir rod to swirl in between the alcohol and water layers. Remove toothpick to see DNA!

Part C: Evaluation of Understanding

Lesson Type: Worksheet and/or Quiz

This section may be modified based at the discretion of the teacher. These sample questions can be used as a part of a stand-alone quiz for this lecture, or integrated as a part of a unit test.

Multiple Choice Questions

1. Restriction Enzymes _____ the DNA, while DNA ligases _____ the DNA.

1. Fix, Cut
2. Repair, Mutate
3. Mutate, Repair
4. Fix, Cut

2. PCR stands for _____.

1. Polymerase Chain Reaction
2. Protein Coding Reaction
3. Polymerase Chain Repair
4. Protein Coding Reaction

3. In gel electrophoresis, shorter DNA fragments appear at the ____ of the gel, while longer DNA fragments appear at the ____.

1. Top, Bottom
2. Left, Right
3. Right, Left
4. Bottom, Top

4. The Central Dogma of Molecular Biology is the process in which information flows from ____ to ____ to ____.

1. RNA, DNA, Protein
2. Protein, RNA, DNA
3. DNA, RNA, Protein
4. DNA, Protein, RNA

5. DNA is _____, while RNA is _____.

1. Double-stranded, single-stranded
2. Double-helix, single-helix
3. Double-stranded, single-helix
4. Double-helix, single-stranded

Short Answer Questions

How is DNA packaged into a small cell?

What does the addition of NaCl do to the DNA in lysed strawberry cells?

Explain the steps involved in 1 cycle of the PCR Reaction.

Answers

Multiple Choice

1.D 2.A 3.D 4.C 5.A

Short Answer

1. DNA is “packaged” by tightly winding around proteins called histones to create a structure called chromatin.

2. Positively charged Na+ ions bind to negatively charged DNA, and negatively charged Cl- binds to positively-charged histones, resulting in the separation of DNA from histones.

3. The DNA strand is denatured (separated into two strands) at 95 degrees. At 55 degrees, the PCR primers anneal to the DNA. afterwards, the DNA is heated to 72 degrees, stimulating Taq DNA polymerase activity, resulting in DNA elongation.

You can download the printable lesson plan here