Protein Synthesis involves two processes: Transcription and Translation.
Transcription – The process by which the instructions for building protein are copied from DNA to RNA.
The steps of transcription are as follows: unwinding/ unzipping, complementary base pairing with DNA, and joining, (separation from DNA).
*All 3 steps below involve RNA polymerase. RNA polymerase is an enzyme that is similar to DNA helicase, (unzips strands) DNA polymerase, (scans strands) and DNA ligase (sticks strands back together) within Replication- except RNA polymerase, does all 3 jobs.
Unwinding and unzipping: The helix of DNA unwinds, meaning that the helix unravels and opens, and unzips, meaning that the hydrogen bonds between adjacent nucleotide bases are broken by the RNA polymerase. After this process, the DNA is split into two separate strands.
Figure 01. This model shows unwinding and unzipping within replication, our group did not complete the transcription model, but unwinding and unzipping within DNA replication is very similar to unwinding and unzipping within transcription. The “bird’s head” shape (DNA polymerase), the scissor shape, (DNA helicase), and the star shape, (DNA ligase), would be replaced with the heart shape (RNA polymerase).
Complimentary base pairing: Unbound nucleotides that can be found within the nucleus of cells complementary base pair with the nucleotides on the “sense” strand of DNA. Adenine pairs with Uracil and Guanine pairs with Cytosine. Uracil replaces Thymine because the DNA nucleotides are ATCG, and the RNA nucleotides are AUCG.
Figure 02. The red strand on the right side represents the copied mRNA strand, while the strand on the left side represents the sense strand.
Joining: The RNA polymerase allows covalent bonds to form between adjacent nucleotides on the newly formed RNA strand, called the mRNA. Before leaving the nucleus, the mRNA strand will be edited. The original DNA molecule will reform its double backbone helix.
Figure 03. After the mRNA strand is complete, the two backbones of DNA will reform the original double helix shape.
Translation – The process by which the mRNA strand’s instructions get synthesized at the ribosome, creating a protein.
The steps of Translation are as follows: initiation, elongation, and termination.
Initiation: The mRNA strand binds to the small subunit of the ribosome, after, the large subunit and the small subunit of the ribosome join together, forming a “Squidward” looking shape. The ribosome “reads” the mRNA strand until it reaches the “start” codon (AUG). The ribosome does not start producing the protein until it reaches the start codon.
Elongation: The ribosome holds onto the mRNA. This allows tRNA to complimentary base pair at binding sites. The binding sites at the ribosome are “P” (left) and “A”(right). The tRNA brings the start anticodon to the P site, along with the corresponding amino acid to the start codon, and then binds to the P site, beginning a polypeptide chain. This process repeats itself at site A, where another tRNA complementary to the next codon brings over a corresponding amino acid binding to the A site. The amino acid from the tRNA at the P site discharges and binds with the amino acid at the A site. The tRNA from the P site dissociates from the ribosome, and then the tRNA that was at A site moves to P site. This process repeats every codon until it reaches the “stop” codon.
Figure 05. tRNA “UAC” along with the amino acid Tyrosine is bonded to the P site of the ribosome.
Figure 06. tRNA “AAC” along with the amino acid Asparagine is bonded to the A site.
Figure 07. the tRNA “UAC” that was bonded at the P site has its amino acid move and peptide bond with the amino acid on the A site, and the tRNA dissociates from P site.
Figure 08. tRNA “AAC” moves up to P site, and another tRNA “CUC” along with another amino acid, Leucine, bonds at the A site.
Figure 09. Due to a shortage of time, we decided not to repeat until we reach the stop codon. But once the ribosome reaches the stop codon, no new amino acids are added on to the polypeptide chain.
Termination: Once the ribosome “reads” to the “stop” codon (UAA, UAG, UGA), the ribosome dissociates back to the two subunits and the polypeptide chain is let go. The “stop” codons do not have a complimentary amino acid to add to the chain, so because of that, there is no more adding to the polypeptide chain, making it ready to be released.
Figure 10. The tRNA dissociates, along with the polypeptide chain. The small subunit and the large subunit of the ribosome also dissociate.
Models:
Our protein synthesis activities used models to learn about complex microscopic processes.
The models I used to accurately reflect the process include the diagrams I used to explain Translation. These diagrams go through every significant movement within the Translation process and are easily interpreted. Because of that, I feel that it provides accurate and necessary guidance toward my explanation. However, there are significant misinterpretations that could be pointed out for the models that we made to describe transcription. The way I used an unwinding/unzipping diagram for replication to describe transcription could be misleading. Underneath the model, I explained the differences between replication and transcription, and why I had to use this model instead, but to somebody who may not know what I am talking about, it may be confusing. A way that all of my diagrams could be misleading is that the photos are 2D, stagnant, and not detailed enough. The models also do not include labels which may make it hard for someone who is clueless about the subject to interpret it.
Changes that can be made to the modeling activities to make them better represent the process are to have fewer small individual pieces, and more easy-to-interpret pieces. With smaller pieces, it could have the interpreter more confused and lost within the diagram, but with structured and full pieces, it is easier to interpret. Another way is labeling the diagrams as it is more efficient in explanation.
I think using models is an effective way to educate people about science because then the individual will have a visual representation of what they are meant to understand, but only if the model itself is displayed in an effective manner. If scientific models are overcomplicated or too simple it might not be effective for the person learning about the subject, depending on what level of knowledge they have. Overall, I feel that models are useful tools that help people understand science from a level different than just textbook knowledge, and it is especially useful for science students performing labs.
Works Cited:
A&P P5 Fall 2022 Notebook – DNA Protein Synthesis
A&P P5 Fall 2022 Notebook – Cell Functions CYU Answer Key