DNA model 

Here is a double backbone DNA strand. The cyan circles represent the phosphate groups, the green pentagon is the sugar group, the yellow is Thymine, the beige is Cytosine, the baby blue is adenine, the blue is guanine, and the dashed line is the hydrogen bond that holds together the complementary pairing.

Explain The Structure Of DNA

DNA has two strands of the sugar-phosphate on each side called deoxyribose. These strands are anti-parallel, the leading strand is 5′ and the complementary 3′. There are nucleotides that are hydrogen bonded to the sugar-phosphate strand. These bases are bonded to their complementary base, the only other nucleotide they can bond with, Adenine with Thymine and Cytosine with Guanine, they are paired together by hydrogen bonds. The hydrogen bonds have a slight charge, causing an attraction between other bonds, forming the twist in the double helix shape.

DNA replication 

The DNA helicase (the yellow scissors) untwist and unzip the DNA

Then the DNA polymerase synthesizes and starts the complementary base pairs. It works upwards on the 5′ strand and down on the 3′ strand.

The DNA polymerase is attaching the compliment base as DNA ligase comes in and glues fragments together.

Soon after the replication is done and you are left with two identical DNA strands

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

The three steps are: unwinding and unzipping, complementary base pairing, and joining. DNA Helicase unwinds and unzips the DNA, causing the hydrogen bonds to be unbonded and the nucleotide pairs to be separated. DNA Polymerase brings the paired nucleotide for the lone nucleotides. After all of this, DNA Ligase “glues” everything together and there are two identical DNA strands left. The nucleotides need to follow the 3′ to 5′ pattern because the DNA is anti-parallel, there is a “leading” and “lagging” strand. For this reason, the polymerase needs to go two different ways to add the nucleotides  The leading is easy and the polymerase follows the helicase. The polymerase on the lagging strand starts from the top and must go back and forth as the new DNA is formed. This results in a lot of pairing being attached later or being fixed by the ligase.

Today’s modelling activity was intended to show the steps involved in DNA replication. What did you do to the model the complementary base pairing and joining of adjacent nucleuses steps? In what ways was the activity well suited to showing the process? In what ways was it inaccurate? 

I would say this process was good in the aspect that because everything was 1D it was simple and easy to understand. Other than that I do not feel like it was the best process. For this reason, it doesn’t show the true form of DNA, DNA is supposed to be 3D and because we couldn’t see it in its natural form I feel like we arent getting the chance to understand fully what is happening.

RNA Transcription

The mRNA forms and the DNA separates

The strand (5′) is transcripted in the process that the 5-carbon sugar backbone, ribose, is created with the help of the RNA polymerase that attaches the compliment base.

the mRNA detaches from the transcript

In the end, the DNA reforms and the single-strand RNA has the instructions and can leave the nucleus.

How is mRNA different from DNA? 

The differences are that RNA has a 5-carbon sugar called Ribose as its backbone, whereas DNA has a 5-carbon sugar called Deoxyribose. Also, in DNA Adenine pairs with Thymine. In RNA, Uracil is Adenine’s complimentary base pair. Finally, DNA is a double strand and very long. mRNA is shorter, only reads certain sections, and is single-stranded, all of this allowing it to be able to leave the nucleus.

Describe the process of transcription. 

DNA unwinds and unzips, the leading strand has nucleotides of RNA form with it. Uracil will pair with Adenine as it is forming the RNA. This causes hydrogen bonds to form. The RNA polymerase enzyme forms this bond and the backbone. Once this strand is created, they split off again resulting in the reattachment of a DNA strand and a single backbone mRNA.

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

Again this activity is good for its simplicity of it. However, I feel like it needs to be 3D to get a fuller understanding. For this reason, it feels like it is jumping to different places and everything looks the same. Therefore I feel like it would be better if it was 3D.

RNA Transcription and Translation

Here is the process of transcription, the RNA Polymerase transcribes the DNA message to the mRNA strand.

After the RNA Polymerase is done, there is a DNA strand as well as a single-strand mRNA that has the DNA’s message and is ready to leave the nucleus.

The process of Initiation begins. The mRNA goes through the ribosome (the red thing) as it starts reading the codon. The first codon starts at the P-site. It begins with a tRNA bringing in the correct amino acid to the codon and filling the P-site.

The codon in the A-site gets filled with the tRNA and its respective amino acid.

At this point the process of elongation begins as the amino acid from the P-site attaches itself to the amino acid at the A-site. The tRNA leaves the P-site. Ribosomes prefer their P-site being filled, so it will shift down the mRNA to have the codon in the P-site.

A new codon will come and fill the A-site

The Ribosome moves over. This process continues until the ribosome reaches the STOP codon.

At the STOP codon, the ribosome will release the mRNA, the tRNA, and the polypeptide chain. This is termination. The final result is a small portion of a protein.

Describe the process of translation: initiation, elongation, and termination

Initiation is the first step of translation, a messenger RNA  leaves the nucleus after transcribing DNA’s message and gets attached to a ribosome. This ribosome has two subunits that bind together, P and A sites, the first site is the P-site and the second one is the A-site. The start codon is found and begins at the P-site. The codon gets read in the P-site with a transfer RNA that brings the anticodon and the amino acid. After the A-site gets filled with a tRNA with the anticodon and the amino acid. The second step is elongation begins, the amino acid in the P-site attaches itself to the amino acid in the A-site and the P-site loses its tRNA. The ribosome moves to fill the P-site with what was originally in the A-site. A new tRNA fills the A-site and the amino acid of the P-site attaches itself to the A-site amino acid. This process will continue until the ribosome reads the stop codon, this is the third step, the termination stage. The stop codon does not have a matching amino acid so the chain of polypeptides is let go.

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

I feel like this part of the activity was represented accurately through out all the stages of translation. All the diffrent shapes/cutouts help me imagine or even invisualize how everything worked during the translation process. I dont think in any way the model was inaccurate.