Category Archives: Grade 12

DNA and Protein Synthesis

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– This was a 2 day project that we did to refresh ourselves on the basis of DNA and Protein Synthesis.

Replication

1.Explain the structure of DNA – use the terms nucleotide, anti parallel strands, and complimentary base pairing.

The structure of DNA is a polymer comprised of nucleotides which is a compound of a nitrogen base (Usually referred to as Adenine, Thymine, Cytosine, and Guanine for DNA), and a five-carbon sugar which is bonded to one or more phosphate groups. The nitrogenous bases are always hydrogen bonded through their complementary base pairing which, in terms of DNA is Adenine-Thymine and Cytosine-Guanine. Similarly, through the complementary bases, an antiparallel strand of DNA gets bonded to the template DNA creating a double helix shape.

2.When does DNA replication occur?

DNA replication is the process of which the DNA makes identical copies of itself, as its structure is a mechanism for reproducing itself. DNA Replication occurs when the cell divides, more specifically before the mitosis phase of cell division.

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

In DNA replication, each strand of DNA can be a template to force a new stand of DNA through complementary base pairing. The steps in DNA replication are as follows: 1) The unzipping phase where the DNA double helix unwinds and the hydrogen bonds that hold the two strands together separate (break). 2) Complimentary base pairing is crucial, as new nucleotide move into the separated DNA strand to form a new and complete DNA. These nucleotide are always floating within the nucleoplasm. 3) Adjacent nucleotide bonding, where sugar-phosphate bonds form between the adjacent nucleotide of the new strand to compete the molecule. Afterwards, the new molecule winds into the double helix. Thus completing the replication.The lagging strand is organized continuously, by which is synthesized by adding nucleotides to the 5′ end. The leading strand is organized in short fragments that are ultimately stitched together. The leading strand is organized particularly by adding nucleotides to the 3′ end of the strand, which continues to grow.

 

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

In the replication modelling activity, to show the complementary base pairing we first formed the template DNA strand with paper cut-outs of the nucleotides, phosphate group, and sugar group while showing covalent bonds by solid lines and hydrogen bonds through dotted lines. Afterward, we had drawn the complementary bases of the template strand bonded through H-bonds (dotted lines) the comp bases are also accompanied by a sugar group and phosphorous group to form an antiparallel strand of DNA to the template DNA. Afterward, we used paper cut-outs of scissors to represent the helicase used in unzipping the DNA. Then, we showed two strands of DNA that start forming adjacent nucleotide bonds with a pointy circle to represent the polymerase and stars to represent the ligase. Doing this is an excellent way to visualize the idea of a single template DNA being replicated and turning into two new identical strands of DNA. Though this method can’t express aspects such as the double helix structure of the DNA

Transcription

1. How is mRNA different than DNA?

In its essence, mRNA is a copy of a DNA template strand that carries genetic information (code), from the nucleus into the cytoplasm and to the Ribosome. mRNA is a single strand molecule that is is structurally distinctive, as well as the fact that it has Uracil in replacement of Adenine. mRNA carries the genetic code for amino acids to create proteins. On the other hand, DNA is double stranded molecules of deoxyribose sugars and phosphate molecules, while RNA has ribose sugar. Furthermore, DNA is distinctive in its “double helix” shape before transcription is initiated, in which it “unwinds and “unzips” the double stranded molecules for transcription.

2. Describe the process of transcription

The process of transcription is the production of RNA from DNA. Transcription follows a sequence of steps that allow for a successful “mirror” replication following complimentary base pairs (with the exception of adenine replaced with Uracil). First, a section of DNA “unwinds” and “unzips,” exposing a set of bases for the second step: complementary base pairing along one of the two strands of DNA. Thirdly, adjacent RNA nucleotide forms sugar phosphate bonds. Fourthly, the RNA strand is released from DNA and follows the fifth step, which DNA molecule “rewinds,” and returns to its original shape of a double helix. Finally, once RNA is produced, mRNA strand is often processed, by which certain sections called introns are cut out and a “poly A” tail is added to the 3′ end, and a cap is added to the 5′ end. From there, the RNA leaves the nucleus and goes into the cytoplasm.

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

In the paper model of RNA transcription, it had effectively shown how the mRNA is created based on the template DNA, though a few downsides to this method is that as the nitrogenous bases were just written on paper, it is impossible to show the differences between adenine, uracil, cytosine, and guanine. Furthermore, through the methods we used in the RNA transcription model, we weren’t able to show the effects of genetic mutations.

Translation

1. Describe the process of translation

Translation is the process that converts mRNA to actual proteins, which occurs outside of the nucleus, within the cytoplasm and on the surface of the ribosome. It is known that the order of bases in DNA, which is processed into RNA, determines the amino acid sequence necessary to produce the polypeptide chain that creates the protein. The process of translation can be categorized in three sub processes. Translation begins with initiation, where the mRNA and its start codon of AUG attaches to the ribosome, specifically at the R site. The AUG codon always initiates translation and it is the code for producing amino acid Methionine, or (MET) for short. The sequence of producing amino acids relies on 3 bases called the anti-codon that is complementary to the mRNA codon. Next, Elongation occurs where more and more amino acids are added to create a chain of amino acids (polypeptide). As Elongation occurs to lengthen the polypeptide chain, the final step of translation occurs: Termination. Termination ends translation, where a special codon called the “stop” codon is read. These stop codons can be UAA, UAG, or UGA. The stop codon does not produce an amino acid, but rather signals to stop the translation. In Termination, a protein called release factor binds directly to the stop codon in the A site, thus separating the chain from the last tRNA.

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

The modelling of the translation was a good way to show how the mRNA goes through the rRNA and how tRNA with its anticodons pairs with the codons on the mRNA and form a polypeptide chain. Some parts of the model that are inaccurate is that it couldn’t properly express that the rRNA are two subunits formed into one.

Desmos Art Functions Card 2022

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Desmos project link: https://www.desmos.com/calculator/0w5izfplxr

Please Note: When loading my demos project, demos show some parts of the colouring as blank. However, I have coloured everywhere I liked, simply zoom in to see. It must be a loading issue.

Please Note: I decided to make something original for this demos project, as mentioned briefly in the paragraph below, I have graphed the map of Iran, and graphed the northern and southern borders to replicate the outline of the Iran imperial flag. Additionally, I graphed another photo of the lion in the imperial flag.

Reference photo of the Iran map along with the northern and southern border outline:

Source: https://lizardpoint.com/geography/iran-quiz.php

Reference photo of the imperial lion emblem:

Source: https://www.pinterest.ca/pin/611504455634467461/

This Desmos Arts Function project for Pre-Calculus 12 is a midterm project that our class was assigned to do in 2022 to 2023 to draw any image of our choosing: what I chose to do was to draw the map of Iran and to make this drawing my own by drawing the flag colours in a sequence of the outlines of the northern and southern provinces, as well as showing the imperial lion emblem from the Pahlavi Dynasty flag. When drawing the outline of Iran’s map, I had to consider the heavy details of the great natural barrier (western provinces bordering Iraq), the border with the Persian Gulf, as well as the border with the Caucasus. To ensure that the map was as accurate as possible, I decided to rely on complex graphs with good use of transformations: rational functions, cubic functions, square root functions, exponential functions, semi-circle functions, and more are such graphs I decided to rely heavily on addition to the other graphs that were required in the criteria. I figured out what equations to use when I looked at a particular section of Iran or a border of the provinces. These borders are complex in shape and thus would require graphs such as a rational function to make up 3 other simple equations. When I began the project, I faced numerous challenges when considering the amount of detail that I should or should not put the effort into. I found out quickly that more attention to detail requires much more time to perfect. The great natural barrier of the map is seen to be the most detailed and I would say that it took me over 4 hours to complete. Additionally, trial and error were my enemies in this project as I was trying to find the perfect equation that had the perfect curve to it (with respect to the transformations used). Thus, my primary challenge was to decide which equation was most useful when graphing the borders of my map. One of the biggest ‘aha’ moments I had was while I created the northern and southern province outlines with the use of rational functions. As seen in my project, there were lots of grooves, ups, and downs. Thus, to make use of the rational functions, I decided to use them for this specific piece in my project. However, I discovered that I had issues transforming rational functions. It began with me not even knowing how to create the equation to transform it according to the criteria. What I later learned, and used, was that I would have to create the custom rational function, then transform it using separate functions in accordance with the specified rules of transforming. Learning this made me more efficient in the accuracy and general quality of my project. To learn this method, I had help from my peers who had similar experiences as I did. Though I did not rely on the internet guidance, I did have one-on-one discussions to figure out equations and transformations. While creating my project, I used one primary strategy to replicate my photo, but put less stress on the attention to detail that is heavily required for the specific image that I have chosen. I decided that I would simplify areas that required heavy detail and keep true to the original shape and form of the borders. Furthermore, I would use a similar equation to replicate the same curves of the map. But, again, not paying attention to every angle for as long as it looks fairly similar. Using this strategy resulted in my overall efficiency and the satisfactory replication of the Iran map. Overall, I have learned how to apply transformations to all sorts of equations and functions that vary in difficulty and complexity. This project has allowed me to understand specific transformations to create a specific image that combines other functions and equations. Furthermore, I understand the variable and value changes of inverses, stretches, and transformations, which now allows me to be more specific with my graphing.