A. DNA Model

1. DNA is a polymer made of nucleotides monomers. DNA has two backbones which are created by sugar-phosphate portions of the adjacent nucleotides bonding together by covalent bonds. The sugar part is represented by the sections of the blue pipe-cleaner; the phosphate group is represented by the pink bead. The backbones form a double helix shape and are antiparallel: if one runs from 5′ to 3′ (the first strand being built), the other one runs from 3′ to 5′. The nitrogenous bases face into the “ladder”, forming the “rungs” by H-bonding with suitable complimentary base: Adenine (yellow) with Thymine (blue), Guanine (purple) with Cytosine (green).
2. This activity provides a visual image of a section of DNA. It demonstrates the double helix shape, the antiparallel backbones, and the complimentary base pairing. The model could be more accurate if specific measurements of the length of the minor and major grooves, of the width between the two strands are given based on the actual ratio of the real DNA. With these number, a more accurate model could be achieved.

B. DNA Replication

 

1. DNA replication occurs prior to cell division.
2. – Step 1: Unwinding and unzipping. DNA untwists and becomes a straight ladder shape. Then it unzips with the help from DNA helicase (watermelon candy). Step 2: Complimentary base pairing. DNA polymerase (blue candies) attaches new nucleotides to the template strand by H-bonding following complimentary base pairing rule. The directions of the DNA polymerase on the two strands are opposite: the DNA polymerase on the leading strand goes in the direction of the DNA helicase, while the DNA polymerase on the lagging strand goes in the opposite direction (the two blue candy pointing in the opposite directions). Step 3: Joining. The leading strand is continuous as the DNA unzips. The lagging strand has fragments as the DNA unzips, which is glued together by DNA ligase (the red candy) Then the two new DNA twist to form the double helix shape.
3. The process occurs differently on the leading strand and the lagging strand because DNA polymerase could only read in one direction: from 3′ to 5′ (from sugar to phosphate). The leading strand is from 3′ to 5′; therefore, the DNA polymerase works toward the twisted part of the DNA (the left strand in the picture. On the other hand, the lagging strand is from 5′ to 3′; thus, the DNA polymerase have to work outwards, away from the twisted part of the DNA (the right strand in the picture), creating fragments.
4. At the complimentary base pairing step, we connected the complimentary base the template strand before we put the blue candies on top of them to represent DNA polymerase. We didn’t do anything at the joining of the adjacent nucleotides step, except for putting a red candy on top of a section to show that the DNA ligase is connecting two fragments (but there was actually no fragment). This activity is suitable for showing the untwisting and unzipping of the DNA, the difference in the direction of the DNA polymerase on the two strands. However, it didn’t demonstrate the exact process of how the free nucleotides are connected with the suitable “partner” on the template strands, and how the fragments of the new backbone on the lagging strand is connected. It wasn’t able to accurately present to continuous process of DNA replication, when DNA helicase, DNA polymerase, and DNA ligase working together.