1. Explain the structure of DNA — use the terms nucleotides, antiparallel strands, and complimentary base pairing.
DNA is a large polymer (ladder- like) made from nucleotide monomers. DNA is also made up of sugars, phosphate, and nitrogen bases. DNA has two phosphate- sugar backbones that have nucleotide bases facing inwards of each other. From there, the bases attach to each other through a hydrogen bonds; which are across from each other making “rungs” of the ladder. Which will will show our four bases – Two pyrimidines – called Thymine (blue bead) and Cytosine (Green bead), and two purines, called Adenine (yellow bead) and Guanine (purple bead). The pyridines are single ringed and purine are double ringed bases. Complimentary base pairing is when a purine must bond with a pyrimidine this happens so, it keeps a correct distances from the bases in the ladder and keeps them in order. Guanine (G) always bonds with Cytosine (C), and Adenine (A) always bonds with Thymine (T). Antiparallel is two stands in the DNA ladder, that get “read” in opposite directions. It would be “read” like phosphate, sugar, phosphate, sugar, on one side of the stand and on the other sugar, phosphate, sugar, phosphate. This is shown in our model.
2. How does this activity hep model the structure of DNA? What changes could we make to improve the accuracy of this model? Be detailed and constructive.
This activity was very useful and helpful, showing us how DNA looks. When we had to match up the base pairs, this helps knowing the reason for complimentary pairing, and when creating two separate opposite stands helps understanding the antiparallel shape. I believe a way that could make this model more accurate is having a better representing of the antiparallel part of the two strands. Since the beads moved along the pipecleaner , it made it easy for them to slide and end up looking the same. A solution could have been to put the letter “P” (representing Phosphate (Pink)) in the direction of the strand being read. An other way to make the model better could have been, having the bases as small beads on the pipecleaner (white) leaving lots of space in between the bases and backbone. It kind of made it look like something else was attached or there on the bases to the backbone, not the base bonding to the backbone. An idea could be to have smaller piece of the pipecleaner in four different colours, instead of beads. This way you could use a smaller piece for pyrimidines and a longer piece for purines, this would make it easier to understand the bonding between them.
One strand of DNA
Untwisted Double strand of DNA
Double helix DNA
1. When does DNA replication occur?
DNA replication occurs when cells need to divide in order to repair, replacement, and grow. An example would be when you get a cut, damage your skin, grow, and when cells die. DNA replicates because cells need to double in everything, this includes genetic information.
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 happens when DNA straightens from a double helix to a straight ladder structure. In our model above of the flat DNA strand, it then has a DNA Helicase enzyme (the watermelon candy) slides along the base pairs and breaks the hydrogen bond which splits them into two separate strands.
The second step in DNA replication is complimentary base pairing. This is when unbounded nucleotide in the nucleus move to make hydrogen bonds with their partners on single DNA strands. This happens from DNA polymerase (blue foot candies).
The last step of DNA replication is joining. This is when nucleotides on the new strand make covalent bonds with each other to make new double stranded DNA molecules. When the two strand are splitting, they get read differently, and at the same time new strands are being made; because they are antiparallel. One side gets read from bottom up, that’s the new DNA being formed; it’s a continuous unzipping of the DNA which is the leading strand (blue Bigfoot toe is pointing up on the right side). On the other side of the unzipping DNA is called the lagging strand, this is because it starts from top down therefore its read in fragments as the DNA unzips (blue Bigfoot toe is pointing down on the left side). The fragments are joined together why DNA ligase, which takes longer.
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?
The way we showed complimentary base pairing is placing thorn DNA polymerase (blue Bigfoot) on the bases, showing them being Hydrogen bonded. To show the joining stage of the nucleotides, we placed the DNA ligase (red Bigfoot) on the back bone showing the connection. I really liked this activity due to the fact it was a great way to demonstrate DNA replication as the pipecleaners are easily separated. Also, they can bend, easily showing the process of the new pipecleaner DNA being built. The difficult part was showing the lagging strand and how its read in pieces, making the DNA made in sections joined by DNA ligase. Another problem when showing the model was the pipecleaners representing the backbone had to remain whole and we had to cover up pieces of pipecleaner with extra paper.
DNA helicase unzips the nitrogen bases
DNA Polymerase forms new bonds with nitrogen bases on the leading and lagging strand, and the DNA ligase bonds the sections together on the lagging strand
Two identical DNA strands