Author: Leige

In Anatomy and Physiology 12 we were assigned to create a process of transcription and translation model using cut-out shapes that represent the nucleotides, sugar-phosphates, DNA helicase, DNA polymerase, and RNA polymerase. My group and I had to analyze and understand what was happening during the processes and by showing what we have learned one of our group members took pictures of each step that have occurred. As an end result the images that are being shown below are for a thorough and indepth explanation of protein synthesis.

Structural Differences between RNA and DNA:

RNA is distinguished from DNA by the use of ribose sugar instead of deoxyribose. In contrast to DNA which is millions of nucleotides long, while mRNA is about 1000 nucletides long, therefore, has a shorter length so it is able to leave the cells nucleus. Due to the fact that it only contains one strand rather than two, it is a single backbone. It does not resemble a double helix because mRNA replaces thymine with uracil which are both pyrimadines and all adenines on DNA are paired with uracil on RNA.

Protein Synthesis:

During protein synthesis, amino acids are combined together in coded combinations to form polypeptide chains. Transcription contains the process of converting DNA into mRNA, and translation involves the process of converting the code of mRNA into polypeptides.

Transcription:

Unzipping/unwinding:

In the first step of transcription, the DNA molecule unwinds from its double helix shape and strands unzip. The hydrogen-bonds holding the nitrogen bases together breaks by the enzyme DNA helicase which is shown below by the scissors snipping the bases apart causing the unwinding.

Complimentary base pairing

The complementary strand of one DNA backbone strand is formed by a sugar-phosphate backbone that includes the sugar ribose. It will have complementary base pairing, which means that the mRNA strands end up becoming a complimentary bases of the sense strand. The RNA polymerase joins the RNA nucleotides with particular bases on the DNA strand to form the mRNA molecule, which has the base Uracil (representing the light green polygon) instead of the base Thymine (Yellow hexagon) but Guanine (Robin’s egg blue polygon) will still pair with Cytosine (Beige hexagon). The complementary strand of the leading strand which is created by the mRNA, must next be translated into a protein molecule. This procedure can be caused by the help of the enzyme RNA Polymerase (represented as the yellow heart) which is in charge of pairing the bases together. The RNA Polymerase links the backbone and the nucleotides by forming H-bonds between the nucleotides.

Separation:

When the RNA polymerase has completed translating the DNA’s message onto the mRNA, the mRNA will separate from the DNA strand (pink hexagon) and the DNA strand as shown below will assemble with its nonsense strand to reform the shape of a double helix. During the process any changes will occur like removing any extra bases to ensure that all bases are correct. Now that DNA is in its original double helix, mRNA can leave the nucleus and enter the cytoplasm.

 

Translation

The transcription must be completed first, followed by the translation. RNA polymerase will translate DNA messages into mRNA, making it possible for ribosomes to read them.

Initiation:

In the first step, the mRNA bonds to the small ribosome subunit, and then the large ribosome subunit binds to both subunits. The red cutout has two openings, one for the P-site and one for the A-site, which are the two subunits that bind together. The mRNA’s codon AUG which is the primary amino acid Methionine instructs the ribosome to begin the process.

Elongation:

The “P” site marks the beginning of the start codon, a three-letter sequence (triplet codon) on the mRNA strand that deliver the protein. A transfer RNA reads the codon at the “P” site by bringing an amino acid and its anticodon. On the “A” site, an amino acid and tRNA containing an anticodon are added. The tRNA carries the amino acid to the ribosome, where it is translated into a polypeptide. Following the release of the amino acid from the “P” site of the tRNA due to this binding, the empty tRNA will leave the ribosome and then shifts to fill the “P” site. Elongation continues until the rRna reaches a stop codon.

Termination

The “P” site amino acid binds to the “A” site amino acid as a new tRNA fills the “A” site, this process continues until the ribosomes reads a stop codon of either UAA, UAG, or UGA. The stop codon also known as the termination process is the last step since the stop codon does not match an amino acid, the polypeptide chain is released. No new amino acid is added and the ribosome separates into its two subunits, therefore, the final polypeptide of amino acids is complete.

 

Analyzing the models:

In what ways did your model accurately reflect the process?

Since this activity demonstrated how DNA is replicated from the leading strand and that mRNA is the final product of transcription, it accurately portrayed the transcription of mRNA. By using cut-out forms to recreate the processes, we were able to gain a deeper understanding of protein synthesis firsthand. As a result, all the different components are more easily understood than if they were simply described in long text. All stages of translation were accurately represented in this activity. We were able to visualize how things moved with the model cut-outs. Compared to transcription, translation was a lot easier to understand and assemble the model since the translation process involves converting the code of mRNA into polypeptides which was easier to do since all we had to do was make sure the correct base pairs were added and we had to know what happens during the “P” and “A” site as well as what happens at the very end which is termination.

In what ways did your model misrepresent the process? 

My groups model could be misrepresented because the structure is flat rather than 3D to interpret the double helix shapes. While working in 2D was helpful in certain ways, working in 3D would be a lot better and the visual would reflect the original model of the transcription and translation process.  Another misinterpret is this activity was it does not show how mRNA has a shorter length than DNA that’s why it is able to leave the cells nucleus and this process does not really show what the DNA strand does that is not being copied.

What changes could be made to the modelling activities to make them better represent the actual process? 

The cut-out shapes that were used in the model made it easier to see how components moved because if a person were just to look at a model without knowing the steps that took place, that led to what is being seen then confusion can arise. Having demonstrated the formation process of the “P” and “A” sites of the ribosome would have greatly improved understanding. Additionally, several ribosomes are required for each mRNA during translation, which were missing during this activity but I also understand that the more added steps we do the more the process can become complicated and that’s when confusion start to happen on what exactly happens at a certain stage. As a result of the model experiment, demonstrating the ribosome units in a complete sequence can show what exactly happens and what the polypetides on the mRNA looks like before it dissociates.

Reflection:

I think this is a very effective way to educate the public about scientific concepts. Many people enjoy learning by seeing the model visually or doing hands on work. By doing the process step by step just like what we did for the models it can make it seem less complicated and indepth as it should be by going through the steps. The modeling process allows a person to walk through the steps that they are trying to interpret/ remodel in a way that they can see it in real life rather than on screen. By putting the steps together it’s a lot more easier and eventually by recapping what is happening during the process a person can remember and eventually learn how to make connections of what is happening. To educated the people I feel like having a legend and instruction to follow would definitely help people in figuring out where to start off, especially since the scientific terms can be complex. It will make doing the process less hard if a legend of what is included like the Ribosome, DNA polymerase and helicase provides context of what each structure does during the process.