DNA and Protein Synthesis

  1. The Structure of DNA:
    The Basic structure of DNA consists of two sugar-phosphate backbones with complementary base pairs. They twist into a double helix shape which creates our DNAIn each nucleotide in DNA, there is a central deoxyribose sugar, a phosphate group, and a Nitrogenous base. The Nitrogenous base can either be a purine or a pyrimidine. Purines are double ring structures that are either Adenine or Guanine. Pyrimidines are single ring structures of either Cytosine or Thymine.
    The Sugar and Phosphates from each nucleotide line up to form a sugar-phosphate backbone and the nitrogenous bases are perpendicular.
    There are two strands of nucleotides that get paired together from the complementary base pairing of the nitrogenous bases. A single ring pyrimidine gets paired with a double-ringed purine, more specifically Adenine is always paired with Thymine and Guanine is always paired with Cytosine. These base pairs are bonded through hydrogen bonds, whereas the phosphate and sugars are paired through covalent bonds.

    Because of the specific base pairings, the Strands are in an antiparallel structure. One strand has a Phosphate then sugar order, and the other is sugar-phosphate. The attraction between hydrogen bonds causes it to twist into a double helix shape that we have come to know today.

  2. How did this activity help you understand DNA’s structure and what can be done to improve the accuracy of the models?

    This Activity helped me to visualize what a strand of DNA looks like, and how the base-pairing worked. Being able to see the sugar-phosphate backbones with the nitrogenous bases perpendicular. It also helped me understand DNA’s antiparallel structure and the bonds between purines and pyrimidines. One thing that I would change to improve the accuracy of the models is to add a different color pipe cleaners to represent hydrogen bonds between bases.

  3. When does DNA replication occur

    DNA replication is essential for all life and occurs in all living organisms. DNA replicates during cell division before mitosis. It happens during the interphase of the cell cycle when the DNA begins to unwind and unzip for new DNA to be created. This process was first hypothesized in 1953 and is called semi-conservative replication. The Original DNA unwinds and unzips, and each strand pairs with a daughter strand.
    Cells may divide when we grow, to repair any damage, and to replace old cells with new healthy ones

  4. Name the 3 steps involving DNA replication

    Step 1: Unwinding.
    — The DNA unwinds and unzips to break apart hydrogen bonds
    — This step is facilitated by DNA Helicase which is a wedge-like shape breaking bonds between bases.Step 2: Complimentary base pairing.

    — The Nucleotides on the single DNA strands are still attached and the bases want to make hydrogen bonds.
    — Free-floating nucleotides in the cell’s nucleus make hydrogen bonds with their complementary base pairs.
    — this step is facilitated by the DNA polymerase. The polymerase can only build from 5′ to 3′ meaning is starts on 3′ to the 5′ on the backbone. This causes the leading strand to be built continuously because it is ordered 3′ to 5′.

    –The Lagging strand is antiparallel to the leading strand meaning it is built 5′ to 3′. Since the polymerase can only read from 3′ to 5′, the polymerase on the lagging strand has to read backward. This causes the lagging strand to be built in chunks, not continuously.

    Step 3 is Joining
    — The nucleotides from the new strands of DNA bond together by ligase. Ligase glues together the sugar – phosphates to form covalent bonds between the separate nucleotides. This results in the sugar-phosphate backbone to be formed.

    — Finally, the two replicated DNA can twist to form a double helix shape again and begin to function.

  5. How did you demonstrate complementary base pairing and joining, and how was it accurate and inaccurate?

    We used blue playdoh to demonstrate the DNA polymerase attaching the hydrogen bonds of the complementary bases. One strand was attached all at once in a continuous pattern, where the other was done in fragments. This showed the different ways that the DNA polymerase reads the strands of DNA. The lagging strand is read backward so the polymerase works in fragments to attach the Hydrogen bonds. The leading strand is read forward so the polymerase can read it continuously. The joining step we demonstrated by attaching the red playdoh (ligase) to the backbone of each daughter DNA strand. The ligase is responsible for the covalent bonds in the backbones between the nucleotides. Then the DNA is complete and can form back into a double helix structure. One inaccuracy that we found when demonstrating this is the attachment of the backbone during the Complimentary Base Pairing step. In reality, only the hydrogen bonds between complementary base pairs are present. The backbone of sugar-phosphate is not yet created. That process occurs in the joining step. We couldn’t show the individual bonding between nucleotides because we didn’t have enough material or time to demonstrate it.

    Overall, this activity helped me visualize the process of DNA replication and helped me to understand how it works.

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