DNA and Protein Synthesis

1. Explain the structure of DNA – Use the terms nucleotides,  Anti-parallel strands and complimentary base paring. 

DNA is a large polymer made of nucleotide monomers with 2 “backbones” in a double helix shape.(As seen in the picture.) The backbone is composed of sugar-phosphate represented by the blue pipe cleaner and pink beads. The nucleotides, which are the white pipe cleaners holding the different coloured beads, face each other and are bonded through  hydrogen bonding with their partner. There is two different types of nucleotides, purines and pyramids. Purines contain adenine and Guanine, and Pyramides contain thymine and cytosine. Adenine will always bond with thymine and guanine will always bond with cytosine. In the picture, adenine is represented by the yellow beads, guanine is represented by the purple beads, thymine is represented by the blue beads and cytosine is represented by the blue beads. The two strands are antiparallel, meaning they are read in opposite directions

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. 

It represents the final product well but doesn’t accurately show the steps in which DNA takes to form and replicate

3. When does DNA replication occur? 

During mitosis in the synthesis phase of the daily life cycle of the cell. DNA replication occurs before the cell divides because each new cell needs to contain the same information from the parent cell. These include, cells structure, organelle and genetic information.

4. Name and describe the three steps involved in DNA replication. Why does this process occur  differently on the leading and lagging strands? 

First, the DNA  will unwind from its double helix into a “ladder” shape. (Picture #1) Then it will “unzip”, meaning the hydrogen bonds between the pairs will break. (Picture #2) DNA helicase causes the unwinding and separating, represented by the watermelon candy.  Now the two back bones have separated.

Second, there are always free flowing nucleotides in the nuclear with DNA, these nucleotides will move into place with the complimentary base and form a hydrogen bond with their partner. This process is facilitated by DNA polymerase, represented by the blue big foot.

Finally, the nucleotides on the new strand/backbone form covalent bonds. However, since the backbones are oriented in opposite directions, there is a leading and lagging strand. The leading strand has DNA ligase (The red big foot) continuously attaching the new strand of DNA, however the lagging strand starts where the separation is and moves outwards and then comes back to the new separation.   The results are two DNA molecules that are identical to each other. (Picutre #2)

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? 

During the complimentary base pairing my partners and I just placed the appropriate nucleotide beside its partner, and then to show the joining during replication, we used the blue big foot to represent the DNA polymerase to move the nucleotides togethers and the red big foot to join them together on the leading and lagging strands to the appropriate nucleotide. The activity did a good job at displaying the nucleotides coming together however it was difficult to show how DNA ligase joins the nucleotides together. Because joining nucleotides is different on the leading and lagging strands, we had to be careful showing which was the big foot was pointing. Because DNA has to be read from the 3′ carbon, one big foot would continuously move along which is the leading strand starting at the sugar, but the lagging strand starts where the molecule has unzipped and moves out and then back in to glue the fragments together. This is a difficult process that is hard to show in this activity.

How is mRNA different than DNA? 

1. It is single stranded and short. 2. Contains sugar ribose instead of sugar phosphate. 3. Instead of thymine, has uracil, which bonds with DNA adenine.

Describe the process of transcription. 

A specific section of NDA unwinds, exposing one gene only. This happens when running low on protein. The picture shows a section, however in the rest of the activity we undid the whole DNA molecule to allow mRNA to work.

Along 1 strand, complimentary RNA bases bond, through hydrogen bonds. (Uracil, which is shown with the brown bead, will bond with DNA’s adenine.) Now, only 1 strand of DNA has the instructions for which RNA nucleotides will bond to, this is the sense strand.

Adjacent nucleotides form covalent bonds and build RNA backbone, through RNA polymerase (Represented by the fuzzy peach), the enzyme in which initiates this process.

RNA is released and moves out of the nuclear to the mitochondria. DNA then reforms into the double helix.

How did today’s activity do a good job of modelling the process of RNA transcription? In what ways was our model inaccurate? 

It showed the basis of the steps of transcription, but was not detailed enough. First of all, when one section of DNA is supposed to unwind exposing one gene, was not showed accurately as we undid our entire DNA molecule. We assumed our molecule was one gene but it doesn’t accurately show how many genes are contained in one molecule of DNA. As well, RNA must be refined in the nucleus before being released, which this activity did not show. Adding on to that, this activity was good at showing the basic structure of DNA, but didn’t show the whole picture of why DNA is structured like it is, and how transcription, as well as translation works.