DNA and Protein Synthesis – Structure & Replication

DNA Structure:

1. Explain the structure of DNA – use the terms nucleotides, antiparallel strands, and complimentary base pairing.

DNA is made up of sugars, phosphates, and nitrogen bases. It is a large, ladder-like polymer made from nucleotide monomers. It has two phosphate-sugar backbones with the nucleotide bases facing inwards from each. The bases attached to each strand form hydrogen bonds with the bases across from it to make the “rungs” of the ladder. There are four different bases – two purines, called Adenine (yellow beads) and Guanine (purple beads), and two pyrimidines – called Thymine (bl

ue beads) and Cytosine (green beads). Purines are double ringed bases while pyrimidines are single ringed. This means that when they bond, a purine must bond with a pyrimidine in order to keep the correct distance from the bases in the ladder. This is called complimentary base pairing. Adenine always bonds with Thymine, and Guanine always bonds with Cytosine. The two strands in the DNA ladder are considered antiparallel, as they are “read” in opposite directions. While one strand may be read as phosphate, sugar, phosphate, sugar, the other strand would read sugar, phosphate, sugar, phosphate. All of these were demonstrated in our pipecleaner models. We reversed the order of the pink phosphate bead, base, and blue pipecleaner sugar from the other backbone.

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 to understand how DNA looks. Having to match up the base pairs helped to visualize the reason for complimentary base pairing, and by creating the two separate opposite strands helped to understand the antiparallel shape. To improve the accuracy of the model, I think there should be a better way to represent the antiparallel part of the two strands. Because the beads move along the pipecleaner, it is easy for them to slide and end up looking the same. If we possibly wrote a “P” on the pink phosphate beads in the direction the strand is read in, it may be easier to tell. As well, having the bases be represented by small beads on the white pipecleaner leaves a lot of space between the bases and the backbones. This almost makes it appear like something else is attaching the bases to the backbone, not the bases bonding to the backbones themselves. I think if we used small pieces of pipecleaners in 4 different colours instead of beads, using shorter pieces for pyrimidines and longer for purines, it may make it easier to understand the bonding.

 

DNA Replication:

1. When does DNA replication occur?

DNA replication occurs when cells need to divide in order for growth, repair, or replacement. Examples are when a person gets a cut in the skin, when people grow, and when cells die. DNA replicates because the cells need to double in everything, including their genetic information, when dividing.

2. Name and describe the 3 steps involved in DNA replication. Why does the process occur differently on the “leading” and “lagging” strands?

The first step in DNA replication is unwinding. This is when the DNA straightens from a double helix to a straight ladder structure. In our picture, we show a flat DNA strand to show this. Then, the DNA Helicase enzyme (watermelon candy in photo) slides along the base-pairs and breaks the hydrogen bonds to split the DNA into 2 separate strands.

The second step is complimentary base pairing. This is when unbonded nucleotides in the nucleus move and form hydrogen bonds with their partners on the single DNA strand. This is facilitated by the DNA Polymerase and is represented by the blue bigfoot candies in the photos.

The last step is joining. In this step, the nucleotides on the new strand form covalent bonds with each other to form a new, double stranded DNA molecule.

When the two strands are splitting, they are read differently as the new strands form because they are antiparallel. On the end of strand that is read from the bottom up, the new DNA that forms is continuous with the unzipping of the DNA. This is called the leading strand, and in the photo, it is on the left side. The other strand of the unzipped DNA is called the lagging strand. This is because it is read from the top down and must therefore read the DNA in fragments as the DNA unzips. These fragments are then joined together by the DNA ligase, which causes it to take longer. In the photo, the lagging strand is on the right. The ligase is represented by the red bigfoot candy.

3. 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?

To model the complimentary base pairing, we placed the DNA polymerase (blue candy) onto the bases, showing them being Hydrogen bonded. To show the joining of the nucleotides, we placed the DNA ligase (red candy) on the backbone to show the connecting. This activity was a good fit to demonstrate DNA replication as the pipecleaners are easy to separate. And, as they can bend, it is easy to show the process of the new pipecleaner DNA being built. The activity was not a great fit for showing the lagging strand. The lagging strand is read in pieces as the bases are revealed, therefore the new DNA is made in sections and then joined by the ligase. However, the pipecleaners did not work well for this as the pipecleaner representing the backbone strand had to remain whole. We had to cover up pieces of the blue pipecleaner with strips of paper to represent these splits. We also had to cover up the extra pipecleaners on the leading and lagging strands with paper during the photo when it is half-way duplicated, so that they stayed whole as well.