Revision as of 15:21, 17 October 2018

Team:Calgary/Public Engagement/Lesson Plan - 2018.igem.org

PUBLIC ENGAGEMENT: LESSON PLAN

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

Ask students if they’ve ever heard of synthetic biology – do they know what it is?

The central dogma of molecular biology is key to understanding and defining synthetic biology
The central dogma of molecular biology refers to the transmission of genetic information held in DNA to RNA, then to proteins
First, the DNA is used as a template to create RNA by a process called transcription
RNA is used as a template to create proteins in a process called translation

DNA is a double-stranded molecule twisted in the shape of a double-helix
The information in DNA, also known as the "genetic code", is stored in the sequence of bases (Adenine, Guanine, Cytosine, and Thymine)
Adenine pairs with thymine, while cytosine pairs with guanine. Each line in the DNA diagram represents one of these "pairs"
Every individual has unique DNA code

DNA is converted to RNA by the process of transcription
RNA is a single-stranded molecule
RNA sequence is derived from the sequence of base pairs on a DNA molecule
Instead of thymine, RNA contains a uracil base
Not all DNA is converted to RNA: only certain parts of DNA that can code for proteins are converted to RNA

RNA is converted to proteins through the process of Translation
Every three bases in RNA codes for a single amino acid. For example, AUG codes for methionine
There are only four bases, but 20 different amino acids
Proteins have many functions within a cell
They can synthesize molecules, breakdown molecules

Synthetic biology can be defined as the laboratory editing of any of the processes involved in the central dogma
DNA, RNA, or proteins can be edited to make the cell do different things
Can manipulate the colour, shape, size, function, etc. of the cells
For example, if you put a gene that codes for the red fluorescent protein (RFP) in E.coli, the cell will glow red

There are many ways in which synthetic biologists can edit DNA, RNA, or Proteins
There are three common techniques that are very important for the work that scientists do in the lab
- Digestion/ligation
- PCR amplification
- Gel electrophoresis

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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:

Place a strawberry in a ziploc bag. Seal the bag and squish the strawberry in the bag until the mixture is smooth.

Measure 20 mL of the Strawberry Extraction Buffer and pour it into the ziploc bag.

Seal the bag and gently mix the contents. Try to avoid forming bubbles in the bag.

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.

Gently squeeze the sides of the filter paper to push any remaining liquid through the filter paper.

Measure 10 mL of ethanol and pour gently down the side of the cup. Let sit for 5 minutes.

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.

Fix, Cut

Repair, Mutate

Mutate, Repair

Fix, Cut

2. PCR stands for _____.

Polymerase Chain Reaction

Protein Coding Reaction

Polymerase Chain Repair

Protein Coding Reaction

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

Top, Bottom

Left, Right

Right, Left

Bottom, Top

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

RNA, DNA, Protein

Protein, RNA, DNA

DNA, RNA, Protein

DNA, Protein, RNA

5. DNA is _____, while RNA is _____.

Double-stranded, single-stranded

Double-helix, single-helix

Double-stranded, single-helix

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.

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-                     <p style="text-indent: 0px">Lorem ipsum dolor sit amet consectetur adipisicing elit. Consequuntur, totam laudantium, dolor porro
+                     <ul>
-                         laboriosam illo tenetur velit nulla corrupti quasi non eum amet quod dolores, doloremque eius ad
+                         <li>Synthetic biology can be defined as the laboratory editing of any of the processes involved in the
-                         temporibus perferendis! Lorem ipsum dolor sit, amet consectetur adipisicing elit. Sit explicabo suscipit
+                            central dogma</li>
-                         similique id expedita cum consequatur voluptatibus consectetur adipisci beatae unde, cupiditate inventore.
+                         <li>DNA, RNA, or proteins can be edited to make the cell do different things</li>
-                         Quis officiis quam porro a expedita non.</p>
+                         <li>Can manipulate the colour, shape, size, function, etc. of the cells</li>
+                         <li>For example, if you put a gene that codes for the red fluorescent protein (RFP) in E.coli, the cell
+                            will glow red</li>
+                    </ul>
                  </div>
              </div>
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                  </div>
                  <div class="col-lg-6">
-                     <p style="text-indent: 0px">Lorem ipsum dolor sit amet consectetur adipisicing elit. Consequuntur, totam laudantium, dolor porro
+                     <ul>
-                         laboriosam illo tenetur velit nulla corrupti quasi non eum amet quod dolores, doloremque eius ad
+                         <li>There are many ways in which synthetic biologists can edit DNA, RNA, or Proteins
-                         temporibus perferendis! Lorem ipsum dolor sit, amet consectetur adipisicing elit. Sit explicabo suscipit
+                         </li>
-                         similique id expedita cum consequatur voluptatibus consectetur adipisci beatae unde, cupiditate inventore.
+                         <li>There are three common techniques that are very important for the work that scientists do in the
-                         Quis officiis quam porro a expedita non.</p>
+                            lab
+                            <ul>
+                                <li>Digestion/ligation</li>
+                                <li>PCR amplification</li>
+                                <li>Gel electrophoresis</li>
+                            </ul>
+                         </li>
+                    </ul>
                  </div>
              </div>

Difference between revisions of "Team:Calgary/Public Engagement/Lesson Plan"

Revision as of 15:21, 17 October 2018

PUBLIC ENGAGEMENT: LESSON PLAN

Part A: Synthetic Biology 101

Part B: Strawberry DNA Extraction

Part C: Evaluation of Understanding

You can download the printable lesson plan here