DNAgo: The Building Blocks of DNA

  • DNAgo: The Building Blocks of DNA
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    Hits the standard: HS-LS1-1. Construct an explanation based on evidence for how the structure of DNA determines the structure of proteins which carry out the essential functions of life through systems of specialized cells.
    Lesson Brief: The DNAgo model is an intuitive model of how DNA is assembled from component molecules to encode genetic information. It serves several purposes. It shows how the 4 base pairs and the double helix scaffold are not molecularly complex by having the 5 different atoms involved labeled. The DNAgo model is more intuitive than a traditional ball-and-stick molecular model because the 6 individual molecules are shown as complete sub-units with the bonds between these represented. This allows students to form an intuitive mental model of how DNA encodes information.

    The model may be used to show students the 6 different sub-units in DNA. These can then be assembled into the helix scaffold before showing how the monomers bond to the scaffold and are paired with their matching monomers (i.e., arginine with thymine, cytosine with guanine).

    Background: The genetic information encoded within DNA is conveyed through the sequence of 4 monomers: arginine, cytosine, guanine, and thymine. These bases are held in sequence upon a double helix that is formed of alternating phosphate and deoxyribose sugar molecules. Spanning between the two helices that form the DNA scaffold, arginine pairs with thymine and cytosine pairs with guanine. This pairing allows the DNA to be replicated. The sequence of base pairs along a section of the DNA, called a gene, determines the nature of the protein that is created from that sequence.

    Activity: Print the DNAgo model. In the slicer software specify to print the molecules flat and the chemical bonds upright. Use adhesive to attach the bonds (Figure 1) to the molecules— cyanoacrylate glue works well if the ends are sanded smooth first.
    For each set of 2 base pairs you will need:
    ● 4 phosphate
    ● 4 deoxyribose
    ● 15 male bonds
    ● 15 female bonds
    ● 1 of each of the 4 nucleotide bases

    Analysis: After showing the assembly of DNA (Figure 2) and explaining how this encodes information for replication or protein-building, you may include some math if you wish.
    Q: With the number of base pairs in your DNA segment, how many different genes could you have to build different proteins? [Answer: 4^(number of base pairs)]
    Q: If there are 20 different amino acids build (and combined into proteins) what is the minimum size of sequence of base pairs that encodes amino acids? [Answer: 3]
    Q: Plot the number of different genes possible (y) versus the number of base pairs in a gene (x) for several sizes of genes.

    Figure 1: Example of assembly of one sub-unit. Female bonds are 6 mm in diameter and male bonds are 5 mm in diameter to facilitate matching these.

    Figure 2: Assembled segment of DNA with 2 base pairs. Note that scaffold of phosphate and deoxyribose has alternating sub-units and direction is reversed on opposite side.

  • Tested the visibility of the atom labels after spray-painting to ensure they still stood out. They become much more visible! The image below shows a deoxyribose sugar molecule with (left) and without spray paint (right). I hit the one on the left with grey primer followed by a light touch of white primer. I used this two coat method because I was trying to get the color close to the stone look of the other molecules.

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