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DNA MODELING Laboratory
STRUCTURE OF DNA
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Learning Objectives Each student should be able to:
1. Identify and recognize the three components of DNA
2. Assemble the two strands of DNA through hydrogen bonding between base pairs
3. Explain the association of double-stranded DNA with histones and the formation of a nucleosome
4. Identify the direction of a strand of DNA
5. Explain the mechanism of DNA replication
6. Discuss the discovery of the structure of DNA
Materials required:
1. 8 Nucleotides
2. 1 Spacefilled model of DNA
3. I Nucleosome
4. Laptop computers
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EXERCISE #1: STRUCTURE OF DNA
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1. Locate the 4 nucleotides, GTCA and identify the three parts of the nucleotide in your lab report.
2. Connect the base pairs through hydrogen bonds. List the 2 base pairs and indicate how many hydrogen bonds are formed between the two base pairs in your lab report.
3. Connect the two base pairs and identify the backbone of the DNA - indicate the backbone on your lab report.
4. Using the models, identify the four nitrogenous bases of DNA on the lab report.
5. Using the models, identify the carbon atom in the sugar deoxyribose that is attached to the one of the four bases and the carbon atoms attached to the phosphates. Make sure to answer the questions on the lab report
6. Connect the four base pairs, to form a double helix. When completed show your work to Dr. McDonald who will check your lab report. Then move onto the next exercise.
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EXERCISE #2: SUPERCOILING EUKARYOTIC DNA
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1. Carefully pick up the model of the nucleosome from the lab table and answer the questions 8-10 on the lab report.
2. Follow the directions for making a picture of the nucleosome model. Click on 1AOI.pdb tab on the bottom of the screen of the computer provided. On the left hand side is a console. Ask Dr. McDonald to help you get started and then type the commands printed on the next page. Start with ‘select all’ and work down and then right through each column. Don’t forget to print your picture of a nucleosome!!!
3. Type the following commands:
select all select *A select *E
cartoon off cartoon off cartoon off
spacefill on spacefill on spacefill on
color cpk color red color red
select *I select *B select *F
spacefill off cartoon off cartoon off
cartoon on spacefill on spacefill on
color white color yellow color yellow
cartoon 1.0
select *C select *G
select *J cartoon off cartoon off
spacefill off spacefill on spacefill on
cartoon on color green color green
color white
cartoon 1.0 select *D select *H
cartoon off cartoon off
spacefill on spacefill on
color blue color blue
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EXERCISE #3: DNA REPLICATION
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1. Carefully pick up the single strand of DNA provided. Starting from top left to bottom right, record how many nucleotides (bases) are present in the model in your lab report.
2. Indicate how many are purines and how many are pyrimidines are present in the model.
3. Record the direction of the single strand of DNA in your lab report
4. If this single strand was replicated what would be the direction of the copied strand? Indicate whether it would be the leading or lagging strand?
5. Watch the video on DNA replication on the computer provided and answer question 14 in the laboratory report.
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EXERCISE #4: DETERMINING THE STRUCTURE OF DNA
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1. Read the original paper by James Watson and Francis Crick on determining the structure of DNA.
2. Answer question 15 in your lab report.
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