Protein Synthesis 

DNA has a very impactful role in our lives. If there is a mistake in the replication process, it can cause a mutation. Mutations can either be positive, neutral, or negative. Although it is rare because there are so many ways an incorrect nitrogenous base match would get “edited”, mistakes can occur in protein synthesis. Genes code for proteins which make traits. Protein synthesis is the process of how our cells can make proteins which determines how we look and allows us to function.

Protein synthesis is a process that starts with DNA. The first step is called transcription. In order for the process to start, DNA must first unwind and unzip. Transcription takes place in the nucleus of our cells because that is where our DNA is found. DNA replication is a semi-conservative process, which means that each DNA molecule has a single strand phosphate deoxyribose sugar backbone from an original DNA from which it duplicated. An enzyme called Helicase (scissor shaped cut out) starts by breaking the hydrogen bonds that hold the backbone’s double helix shape, which causes it to unwind, and Helicase is also responsible for the unzipping of the genes.

Once the DNA is unwinded and unzipped, an enzyme called RNA polymerase (heart shaped cut out) comes and bonds complementary bases to the templet strand of DNA through hydrogen bonds.

The single strand is made out of a ribose sugar (pink hexagon) phosphate backbone and when it is done its complimentary base pairing, it is called messenger RNA (mRNA). Once the mRNA is completely made, the DNA starts to return into a double helix and the mRNA separates from the DNA template strand.

The mRNA is so small that it can fit through the pores of the nucleus and it can leave and travel to the cytoplasm of the cell. This is when the next step of the process starts which is called Translation. In the cytoplasm, the mRNA finds a ribosome (red cut out) which is made of Ribosomal (rRNA). The mRNA binds to a subunit of the ribosome, and then 2 ribosome sub units bind together.

This is the initiation step in translation. The next step in translation, is elongation. On mRNA, every 3 nitrogenous bases are called codons. Each codon codes for a specific amino acid. While ribosomes hold the mRNA, in the cytoplasm there are molecules called Transfer RNA (tRNA) (green “T” shapes).

tRNA read mRNA’s codons and match anticodons that are complimentary to mRNA’s codons. tRNA gets amino acids (purple cut outs) based on what the codons say. Once the tRNA has collected the right codon, one binds to the P site and another binds to the A site on the ribosomes. Because of the binding, it initiates changes and causes the amino acids on the tRNA to detach. When multiple amino acids detach they form a chain by binding to the amino acid beside it. When the tRNA is no longer carrying an amino acid, they leave the ribosomes and the ribosomes move down the mRNA to the next codons. As the ribosomes move down, the tRNA that was originally at the A site, is now at the P site and a new tRNA comes to the A site. The elongation process starts when the mRNA codes for the start codon with the letters “AUG” and it makes an amino acid chain until it reads a stop codon with the letters “UAG”, “UAA”, or “UGA” and stops elongation.

The third step with in translation is Termination. Because the stop codon does not code for an amino acid, the ribosome is no longer needed so it disassociates into its original subunits and the amino acid chain is released. The polymer of amino acids are polypeptides, so the amino acid chain is called a polypeptide.

 

Our Model

To help build a strong understanding of protein synthesis, we used models so we could visually see each step of the process. The models accurately demonstrated how protein synthesis is done by the help of many different molecules. It accurately demonstrated the job of the Helicase enzyme, DNA and RNA polymerase, and the Ligase enzymes. It provided clarification as to exactly what their jobs were, and which direction they moved in. Our model also accurately represented each individual nucleotide. Because we had to make each nucleotide by hand, it put us directly into the perspective of the molecules that are responsible for replicating DNA and RNA. The detail with the DNA and RNA backbones was accurate. Making the deoxyribose sugar green and the ribose sugar bright pink was a good way to show that they are different sugars. Our chain of amino acids was also very accurate because we had to read the codons to get the corresponding amino acids, just like a ribosome would read the codons, and how tRNA would bring the amino acids to attach them to the chain.

With most modelling activities, there are going to be parts of the model that are not always accurate, and it is important that you recognize where the inaccuracies are. The first inaccuracy that we came across with our model, was the shape of the DNA. Because we were replicating it on a flat surface we were not able to model the unwinding part of transcription. If you didn’t have the prior knowledge that DNA is in a double helix shape, and that the backbones hydrogen bond to each other, one might not be aware that the unwinding step occurred. With our model, something else that we did not show, was where in the cell the processes were happening. When we replicated our DNA and RNA we did not show that it was all happening inside the nucleus, and we did not show when our mRNA left the nucleus through its pores. We did demonstrate the mRNA finding a ribosome, but we didn’t specify that it was now in the cytoplasm part of the cell. Some changes that could help create a more accurate representation of the process could be making our DNA out of a material that could be twisted and in a 3D form to represent the unwinding step. Another thing that could add some clarification to the process, could be showing the steps on a background of a cell instead of a whiteboard. We could have shown that the beginning steps took place in the nucleus and then changed the background to show the mRNA leaving and entering the cytoplasm in the later steps.

I think models are a very effective way to demonstrate intricate processes. All types of learners would benefit from models, but visual and kinesthetic learners would especially benefit from either just viewing, or creating a model to help understand a concept. Sometimes people can assume they understand what is happening, but until you view or build a model yourself, it is easy to overlook the details of what exactly happens. Models are a really good tool to simplify concepts into a way that can be easier to understand. If someone does not have a lot of scientific knowledge it can be confusing to try and understand scientific words, but models are a great way to break down a barrier of confusing scientific terms and they allow non scientific people to understand scientific processes such as protein synthesis.

Secondary Sources

Class One Note

AmoebaSisters. (2018, January 18). Protein synthesis (updated). YouTube. Retrieved October 12, 2022, from https://www.youtube.com/watch?v=oefAI2x2CQM