Blog Post 1: DNA, Replication

DNA REPLICATION

  1. Explain the structure of DNA – Use the terms nucleotides,  Anti-parallel strands and complimentary base paring.
    DNA (Deoxyribosenucleic acid) is a large polymer that consists 4 nucleotides, each of them made up of a phosphate group, a sugar group (deoxyribose), and also a nitrogenous base:
    PYRIMIDINE: Adenine and Guanine (Single ringed)
    PURINE: Thymine and Cytosine (Double ringed)

    DNA Backbone

    DNA Structure and Base Pairing

    The two backbones of DNA are formed through the bonding of the sugar-phosphate pieces of adjacent nucleotides. The complimentary bases faces inwards and are formed through Hydrogen bonds between the base pairs. The bases attaches together always with the same partner; complimentary base pairing (Adenine -> Thymine & Guanine -> Cytosine). The base pairs then form two long strands that spiral, creating a double helix shape. The two DNA strands are anti-parallel, they lie parallel to one another and but read in opposite directions.

    Double Helix

    forms a Double Helix

    2. How does this activity help model the structure of DNA? What changes could we make to improve the accuracy of this model? Be detailed and constructive. 
    This activity helped model the basic structure of DNA through the use of pipe-cleaners and beads to show its different parts. The pipe-cleaners were used to show the backbones as well for the Hydrogen bonds that were formed. The beads were used to represent the four complimentary bases and also the number of rings each base contained. We used two beads to show the double rings in the Purine bases and we used one bead to show the single ring in Pyrimidines. The different bead colours used for the bases helped make a clear visual on how complimentary base pairing worked.
    The model we made also demonstrated how the strands are anti-parallel to one another.
    Some changes that could be made to this modelling activity to make it more accurate would be to have more accurate measurements included in order to show the spacing between everything on the DNA strands. Also, the activity does not accurately demonstrate the number of hydrogen bonds that are formed between the base pairs.
    3. When does DNA Replication occur?
    DNA replication occurs prior to cell division. It is a  semi-conservative process as each new molecule must contain one backbone from the original DNA strand, allowing each molecule to have the same instructions to make new proteins.
    4. Name and describe the 3 steps involved in DNA replication. Why does the process
    There are 3 stages that occur in DNA replication: Unwinding, Complimentary Base Pairing, and Joining.

    DNA Helicase ‘unzips’ the DNA molecule

    STEP 1: UNWINDING
    The DNA’s double helix shape begins to unwind, the enzyme known as the helicase “breaks” the hydrogen bonds that are holding the complimentary base pairs together. The separation of two single strands of DNA creates a shape referred to as the replication fork.

    DNA Polymerase begins working on the strands

    STEP 2: COMPLIMENTARY BASE PAIRING
    Nucleotides presents in the nucleus move and form a Hydrogen bond with “partners” on the template strands of DNA. This process is facilitated by DNA polymerase. One strand is in the 3′ to 5′ direction (towards the replication fork), this is the leading strand. The other strand is in the 5’to 3′ direction (which is away from the replication fork),this is the lagging strand. The replication that occurs on the leading strand is continuous. A primer binds to the end of the leading strand ad acts as a starting point for DNA synthesis. DNA polymerase binds to the leading strand and ‘walks’ along it, adding new complimentary bases to the strand along the way in a 5′ to 3′ direction. Replication that occurs on the lagging strand is discontinuous. A number of RNA primers bind to the lagging strand at various points. Parts of DNA (Okazaki fragments), are then added to the lagging strand at various points. The reason the lagging strands replication is discontinuous is due to the fact that the Okazaki fragments needs to join up later.

    STEP 3: JOINING
    Covalent bonds form between nucleotides on the new strand. The leading strand will remain continuous as the DNA “unzips”. On the lagging strand, fragments will begin to form as the DNA “unzips”. The fragments will be glued together by DNA ligase. As a result, two daughter strands are formed.

    Daughter Strands

    5. The model today wasn’t a great fit for the process we were exploring. What did you do to model the complimentary base pairing and joining of adjacent nucleotides steps of DNA replication. In what ways was this activity well suited to showing this process? In what ways was it inaccurate?
    The way we modeled the complementary base pairing, we paired some of the ‘free’ nucleotides to the complimentary base on the template strand. To model the joining of adjacent nucleotides, we attached the newly based pairs to one of the backbones. The activity provided a good visual on how the leading and lagging strands are read. It also showed how the bases were attache to the leading strand. Although, there were some inaccuracy in the usage of the candies as the candies were only placed in the areas where it was thought to be placed and function. We did not get to see how they interacted and worked. It was easy to comprehend how DNA Polymerase interacted with the leading strand but was harder to grasp and show for the lagging strand.

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