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# 4.3: Activities and Answer Keys

Difficulty Level: At Grade Created by: CK-12

## Activity 3-1: Precipitation and Spooling of DNA

### PLAN

Summary Students precipitate, spool, and observe the physical properties of purified DNA. They record observations, determine the importance of studying DNA, and propose a follow-up activity using the isolated DNA.

Objectives

Students:

$\checkmark$ precipitate, spool, and observe purified DNA.

$\checkmark$ record observed results using words and diagrams.

$\checkmark$ explain the importance of DNA in genetic studies.

$\checkmark$ propose a follow-up activity using the isolated DNA.

Students Materials

• Activity Report

Per team of 2-4 students

• Test tube containing $2\;\mathrm{ml}$ DNA in solution
• Test tube containing $4\;\mathrm{ml}$ alcohol
• $50\;\mathrm{ml}$ beaker containing strong salt $(\mathrm{NaCl})$ solution and an eye dropper
• Wooden skewer

Teacher Materials

• Teacher Resource
• Optional: DNA visuals, including models and/or posters Note: You can substitute glass for the stirring rod.

Estimated Time One class period

Interdisciplinary Connection

Art Make drawing of 3-D model of DNA.

Prerequisites and Background

Students should be familiar with metric units of volume.

This activity is a great way to introduce and motivate students to learn more about deoxyribonucleic acid (DNA). In this activity the DNA has been isolated from the nuclei of herring sperm cells. Isolated and purified DNA can be obtained from Sigma Company (1-800-325-3010). The catalog number for herring sperm DNA is D 6898. Salmon sperm DNA (catalog number D 1626) also works well and is less expensive. A buffer identified on the container of DNA you receive will be required to dissolve the DNA.

Herring are fish that belong to the family Clupeirdae; a commercially important food fish Clupea harengus is found in the Atlantic and Pacific oceans.

The DNA requires several days to dissolve in the buffer or water. It is important that the DNA solution be kept refrigerated until use.

When students observe the DNA in solution, they will notice that it appears colorless and viscous. This appearance is due to the phosphate on the DNA, which is negatively charged. The viscosity will be reduced with the addition of sodium chloride $(\mathrm{NaCl})$, enhancing the precipitation. In addition, DNA is not very soluble in 95-100% ethyl alcohol. Therefore, at the interface-where the DNA layer comes in contact with the alcohol layer-the DNA precipitates out of solution and can be spooled onto a clean wooden skewer.

Order DNA for delivery at least a week before use. Dissolve DNA in buffer or distilled water, and store several days in refrigerator.

Aliquot DNA and alcohol into test tubes. If alcohol is aliquotted in advance, the test tubes need to be sealed or capped to prevent evaporation.

Keep all solutions cold prior to activity.

If you are going to do the DNase extension (Resource) you will need additional materials indicated in Resource.

### IMPLEMENT

This activity precedes Activity 3 -2: Removing DNA from Thymus Cells. Though it is possible to do these activities in either order, it is recommended that the purified DNA spooling be done first so students first see purified DNA, which helps them to correctly identify the impure DNA extracted from the thymus cells.

Steps 1-2 Have students begin recording their observations on the Activity Report. You might want to demonstrate how to mix by tapping the test tube gently.

Step 3 Demonstrate how to trickle the alcohol down the inside of the test tube. Remind students to wash their hands thoroughly at the end of the activity.

Steps 4-7 Make sure students are recording their observations on the Activity Report. Make sure students wash their hands at the end of this activity.

Step 8 Consider the following method for having students save their DNA samples:

Using a clean dry forceps, carefully remove the DNA from the skewer and place it on a small piece of black construction paper. Use clear tape to cover the specimen, to keep it from drying out, and fasten in onto the paper.

### ASSESS

Use the completion of the activity and the written answers on the Activity Report to assess if students can

$\checkmark$ precipitate and spool isolated DNA.

$\checkmark$ describe the physical properties of the spooled DNA.

$\checkmark$ explain the importance of DNA in genetic studies.

$\checkmark$ propose a follow-up activity using the isolated DNA.

If students have difficulty proposing a follow-up activity using their spooled DNA, provide some guidance using the following examples:

• Observe DNA under a microscope.
• Redissolve DNA with DNase (Genentech: Pulmozyme) and discuss applications in treating cystic fibrosis (see Resource).

Have students bring in, discuss, and summarize news articles about DNA. Display articles on a “DNA Bulletin Board” for all to see.

## Activity 3-l: Precipitation and Spooling of DNA Activity Report Answer Key

• Sample answers to these questions will be provided upon request. Please send an email to teachers-requests@ck12.org to request sample answers.
1. Write a paragraph describing your observations of the DNA during the procedure. Include drawings as necessary.
2. Describe in words and a drawing the appearance of your isolated DNA.
3. Why is it important to study and learn about the structure and function of DNA?
4. Describe a follow-up activity using your isolated DNA.

DNA is frequently the subject of scientific study and sometimes a point of controversy. Watch your local newspapers and select articles about chromosomes and DNA. Write a one-paragraph summary and another paragraph about your opinion and thoughts.

What Do You Think?

Science is partly a process of answering questions that then produce more questions. What questions come to your mind from the discovery of DNA and its structure?

## Activity 3-2: Removing DNA from Thymus Cells

### PLAN

Summary Students treat fresh thymus tissue, sweetbreads, to remove its DNA. They precipitate, spool, and observe the DNA in a test tube. Students design an alternative procedure to isolate thymus DNA. They also consider different tissue sources for obtaining DNA.

Objectives

Students:

$\checkmark$ extract the DNA from the nuclei of thymus cells.

$\checkmark$ describe the physical properties of DNA.

$\checkmark$ design an alternative procedure to isolate thymus DNA.

Student Materials

• Safety goggles; Activity Report Sample of fresh thymus cells in a beaker; Sand; Liquid soap, clear; Alcohol; Cheesecloth square (several layers, $15 \times 15\;\mathrm{cm}$); Mortar and pestle; Test tube; Small funnel; Test tube rack; Wooden skewer; Forceps; Eyedropper; Permanent marking pen; Paper towels; Black construction paper, $4 \times 4\;\mathrm{cm}$; Transparent tape; Microscope, slides, and cover slips

Teacher Materials

• Serrated knife for cutting the thymus tissue
• Extra student materials, especially cheesecloth, skewers, test tubes, and fresh thymus cells (You can substitute glass for the stirring rod.)
• Methylene blue stain can be used to stain the thymus nuclei in Step 5
• Optional: DNA visuals, including models and/or posters
• Model of a cell with a large , distinct nucleus
• Picture of a human torso to show the location of the thymus gland

Purchase fresh thymus tissue, also called sweetbreads, from your local butcher. You can freeze the thymus tissue if you do not plan to use it right away.

Cut the thymus tissue into $2-\mathrm{cm}$ cubes using a clean knife.

Keep all solutions cold prior to beginning the activity.

Estimated Time One to two class periods

Interdisciplinary Connection

Art Students make a 3-D model of DNA.

Prerequisites and Background

Students should have good microscope skills. If the microscopes use mirrors and natural light, remind students not to point the mirror directly at the sun.

This activity is a great way to introduce and motivate the student to learn more about deoxyribonucleic acid (DNA).

DNA is not very soluble in 95- 100% ethyl alcohol. It is at the interface where the DNA layer comes in contact with the alcohol layer that the DNA precipitates out of solution and can be spooled onto a clean, wooden skewer, glass rod, or pipette.

### IMPLEMENT

Introduce Activity 3-2 by reminding students of safety procedures in the lab, such as safety when using microscopes and wearing goggles when working with alcohol.

Point out the location of the thymus gland on a picture of a human torso.

Set up a slide to show intact thymus cells .

Steps 1-13 Be sure students are using their Activity Report as they progress through the Procedure.

Step 4 Monitor disposal of thymus tissue and cleanup.

Step 5 This step can be done as a demonstration.

Steps 6-7 Make sure students tap only gently.

Step 8 Demonstrate how to trickle the alcohol down the inside of the test tube.

Steps 9-12 Monitor the disposal of materials and the general cleanup process. Again, make sure students are recording responses on their Activity Reports.

Step 13 Include a discussion of controls and variables.

Step 14 Remind students to wash their hands thoroughly at the end of the activity.

• Use a clear detergent.
• Any alcohol such as ethanol, isoproponol, or rubbing alcohol can be used.
• Have students evaluate how they liked designing their own experiments and if it helped them learn more about DNA.

### ASSESS

Use the completion of the activity and written responses on the Activity Report to assess if students can

$\checkmark$ identify the location of DNA in thymus cells.

$\checkmark$ describe the physical properties of DNA.

$\checkmark$ design an alternative procedure to isolate thymus DNA.

$\checkmark$ identify different tissue sources for obtaining DNA.

## Activity 3-2: Removing DNA from Thymus Cells Activity Report Answer Key

• Sample answers to these questions will be provided upon request. Please send an email to teachers-requests@ck12.org to request sample answers.
1. What is the purpose of the thymus tissue?
2. Make a drawing of your observations. You should be able to see the nuclei from the thymus cells. Be sure to label a few nuclei.
3. Which part of the cell was broken by the sand and grinding? Which part was broken by the soap?
4. Draw a labeled diagram and explain in words what happened when the alcohol was added to the test tube.
5. What is the purpose of twirling the wooden skewer?
6. Describe the appearance and texture of the DNA. In the space below, attach the paper containing your specimen. Label the DNA.
7. Describe your alternative procedure for removing thymus DNA. Include labeled diagrams as needed.
8. Explain how you would modify your original experimental design using different sources of DNA.

## Activity 3-3: Building and Using a DNA Model

### PLAN

Summary Students make paper models of DNA nucleotides and use them to construct a DNA molecule consisting of 12 nucleotide pairs. They then use this DNA model to simulate the process of DNA replication.

Objectives

Students:

$\checkmark$ build models of DNA nucleotides.

$\checkmark$ construct a model of a DNA double helix.

$\checkmark$ simulate the replication of DNA.

Student Materials

• Resource
• Activity Report
• Scissors
• 6 sets of different colored paper
• Tape

Teacher Materials

• Models and diagrams of DNA molecules and nucleotides
• Extra supply of colored paper (6 different colors)

If you are unable to get different colors of paper, you can have students color the sugars, phosphates, and nitrogen bases as follows. Or you can copy them on the indicated colors of paper.

60 deoxyribose sugars (white)

60 phosphates (orange)

15 of each of the four nitrogenous bases: adenine (red), thymine (blue), cytosine (yellow), and guanine (green)

Allow ample time to precut the template pieces.

Estimated Time One to two class periods, if template pieces have been precut

Interdisciplinary Connections

Math Relate the repeating patterns of nucleotides in DNA to other patterns in math.

Prerequisites and Background

Students should read and/or discuss the text material on DNA and replication before beginning this activity.

### IMPLEMENT

Students can work in lab teams of 2-4. As indicated in the Advance Preparation, you can have students color the sugars, phosphates, and nitrogen bases as follows.

60 deoxyribose sugars (white)

60 phosphates (orange)

15 of each of the four nitrogenous bases: adenine (red), thymine (blue), cytosine (yellow), and guanine (green).

It takes about one class period to color and cut out the templates. This can be done at home. It is important that the same color code is used for the different parts of the DNA nucleotides, or you can copy them on paper of the colors indicated above.

Instead of using the colored paper for the copies of the templates, students can color both sides of the templates with pens or crayons. It takes about one class period to color and cut out the templates. This can be done at home. It is important that the same color code is used for the different parts of the DNA nucleotides.

Introduce Activity 3-3 by demonstrating how to put together a nucleotide, and then how to combine the nucleotides into a DNA molecule.

Steps 1-3 Remind students that they can sequence the nucleotides in any way they choose, but they should use no more than seven of each nucleotide. Remind students to save extra nucleotides for simulating replication.

Step 4 Remind students to complete items 1 to 5 on their Activity Reports.

Step 5 Confirm that students can explain replication.

Step 6 Remind students to complete their Activity Reports and tell them where to store their completed model.

### ASSESS

Use the construction of the nucleotides and DNA double helix, the simulation of DNA replication, and the written answers on the Activity Report to assess if students can

$\checkmark$ build accurate models of nucleotides.

$\checkmark$ construct an accurate model of a DNA double helix.

$\checkmark$ explain the structure of DNA.

$\checkmark$ simulate the replication of DNA.

## Activity 3-3: Building and Using a DNA Model Activity Report Answer Key

• Sample answers to these questions will be provided upon request. Please send an email to teachers-requests@ck12.org to request sample answers.
1. What are the three components of a nucleotide molecule?
2. What makes up the “rungs” of the DNA ladder?
3. What makes up the sides (uprights) of the DNA ladder?
4. What are the possible combinations of nitrogen bases?
5. Make a drawing of your completed DNA model. Be sure to include labels.
6. Make a drawing of the process of replication (Steps 8 and 9).
7. How do the replicated DNA molecules compare with the original DNA molecule?

Many people have said that the discovery of DNA is the most important discovery of the 20th century. Do you agree? Why or why not? Find articles from newspapers or magazines about DNA. Use the articles to write your own article that might appear 10 years from now.

• Sample answers to these questions will be provided upon request. Please send an email to teachers-requests@ck12.org to request sample answers.
1. What is a chromosome made of?
2. What is DNA made of?
3. What is a nucleotide?
4. What is a double helix? What is its structure?
5. Which nucleotide molecules pair together?
6. What happens to DNA during cell replication?

## Activity 3-1: Teacher Resource Precipitation and Spooling of DNA

One of the major symptoms of a patient with cystic fibrosis is the thick, sticky mucus that causes recurrent lung infection. The thick mucus also blocks the airways interfering with normal breathing and blocks the secretion of digestive enzymes needed to digest food. The main cause of the mucus being thick and sticky is the presence of DNA. A new treatment for cystic fibrosis is to give patients DNAase. DNAase is an enzyme that dissolves the DNA, making the mucus less sticky and thick.

I. Demonstration

A. Place $1\;\mathrm{ml}$ of $10\;\mathrm{mg/ml}$ DNA in test tube
B. Add $50\;\mathrm{\mu l}$ of $1\;\mathrm{M}$ Tris $\mathrm{pH} \ 7.5$
C. Add $10 \;\mathrm{\mu l}$ of $1\;\mathrm{M}$ $\mathrm{MnCl}_2$
D. Flick to mix
Sample should be very viscous (may not slide along tube when slightly inverted, bubbles trapped in solution barely move).
E. Add $2\;\mathrm{\mu l}$ DNAse I
F. Flick to mix. Continue to flick and/or slightly invert tube to notice change in viscosity. You will note definite change at -20 sec.; very fluidy ~2 minutes.

II. Students' own spooled DNA.

A. Students will have spooled DNA.
B. Have students place their DNA into a sterile $15-\mathrm{ml}$ tube containing $1\;\mathrm{ml}$ of TE buffer ($10\mathrm{mM}$ Tris, $1\;\mathrm{mM}$ EDTA @ $\mathrm{pH} \ 8$) or water. Let sit overnight or until it dissolves. The solution should be quite viscous.
C. Proceed as in B-F above.

## Activity 3-1 Report: Precipitation and Spooling of DNA (Student Reproducible)

1. Write a paragraph describing your observations of the DNA during the procedure. Include drawings as necessary.

2. Describe in words and a drawing the appearance of your isolated DNA.

3. Why is it important to study and learn about the structure and function of DNA?

4. Describe a follow-up activity using your isolated DNA.

## Activity 3-2 Report: Removing DNA from Thymus Cells (Student Reproducible)

1. What is the purpose of the thymus tissue?

2. Make a drawing of your observations. You should be able to see the nuclei from the thymus cells. Be sure to label a few nuclei.

3. Which part of the cell was broken by the sand and grinding? Which part was broken by the soap?

4. Draw a labeled diagram and explain in words what happened when the alcohol was added to the test tube.

5. What is the purpose of twirling the wooden skewer?

6. Describe the appearance and texture of the DNA.

In the space below, attach the paper containing your specimen. Label the DNA.

7. Describe your alternative procedure for removing thymus DNA. Include labeled diagrams as needed.

8. Explain how you would modify your original experimental design using different sources of DNA.

## Activity 3-3 Report: Building and Using a DNA Model (Student Reproducible)

1. What are the three components of a nucleotide molecule?

2. What makes up the “rungs” of the DNA ladder?

3. What makes up the sides (uprights) of the DNA ladder?

4. What are the possible combinations of nitrogen bases?

5. Make a drawing of your completed DNA model. Be sure to include labels.

6. Make a drawing of the process of replication (Steps 8 and 9).

7. How do the replicated DNA molecules compare with the original DNA molecule?

6 , 7 , 8

Feb 23, 2012

Sep 06, 2014