Ribosome In the process of having genotypes expressed phenotypiclly, the process begins within the body with DNA. DNA is first transcribed onto an RNA template, called mRNA. After the transcription phase, there is the translation phase. Here, RNA, amino acids, and ribosomes interact to form proteins, a phenotypic expression of a gene. The mRNA template is shuttled into the cytoplasm and then binds with the bottom part of a ribosome. The mRNA contains a line of nucleotides, with every three nucleotides forming a codon. These codons are “read” by tRNA, which have anti-codons to match the codons in the mRNA. Many multiple tRNAs are floating around in the cytoplasm, with each tRNA having a certain anti-codon and a certain amino acid that it holds. The tRNA are in a clover shape, which can be seen by our model. On the top part of the ribosome, represented by the larger piece of twisted pipe cleaners in our model, there are two sites, a P site and an A site. These sites hold in place tRNA as they interact with themselves to add amino acids together to build a protein. In the P site, a tRNA sits in place, matching up its anti-codon with the codon of the mRNA. The tRNA in the P site contains the chain of amino acids in the ongoing process of protein elongation. Then another tRNA, one that matches the next codon in the mRNA, comes into the A site next to the P site. The P site tRNA connects its elongation strand of amino acids to the A site tRNA’s amino acid, with the elongation strand ending being attached to the A site tRNA. The P site tRNA then detaches from the ribosomes and exits. The A site tRNA moves over to the P site and the cycle of elongation in translation starts over until a stop codon is detected on the mRNA. In our model, we showed the beginning of the translation process just described. The codons used in the mRNA are Methionine (AUG), the start codon; Tryptophon (UGG); and Tyrosine (UAC). These are represented by the colored spheres. They bond to each other through the use of magnets. The codons and anti-codons bond through specific lock and key lengths of the building block set. One thing to note about our model is that the relative sizes are not to scale. mRNA and tRNA are truly much smaller than a ribosome. In eukaryotes the large ribosome subunit is 49 proteins long and the small ribosome subunit is 33 proteins long. The whole size of the ribosome is 4.2 megaDaltons. However, due to time constraints, our pipe cleaner ribosome model could not be made to the relative size. In noting detail, we incorporated the correct clover shape of tRNA, seen by our model. The pipe cleaners and copper wire in the tRNA do not represent anything, but instead are used for rigid support. Also being used for support are the legos and lab clamps in our model. The actual elongation process is enormous, consisting of thousands of amino acids. Here, we showed the beginning of the process to give the idea of how it works. To show that the process keeps going, the mRNA keeps going, even though there are no tRNA in our model to match up with the rest of the codons. This model is relevant to nanotechnology for multiple reasons. First, it shows the act of protein building, which is one area being studied, specifically dealing with how proteins fold and the mechanics behind it. In understanding this, scientists could apply information learned to new techniques of nanomachines, especially biological nanomachines. Beside the protein synthesis itself, this process represented by our model is relevant to nanoscience in the strict design of how the model works. It represents multiple parts coming together and interacting on the smallest scale. The ribosomes, tRNA, and mRNA collectively can be labeled as nanobuilders for their role in creating a protein. Our model shows these components and their act of creation. Also, our model shows the concept of specific bonding, which was discussed in the first half of class and again in the class read novel “Double Helix.” Our model shows the binding of anticodons to codons and how there is only one unique tRNA for a mRNA codon sequence. Again, this model has multiple connections to basic principles of nanoscience. The first process in any model building project is to decide what to build. The primary choices in our group were either to create a model of a virus and its mutant strands, or to create a model of the process of protein synthesis complete with ribosome, mrna, and Trna. After deciding that the idea of protein synthesis would better connect to the concept of nanoscience, the task of deciding how to go about building the model arose. What would we use to construct the four components of our model? How would we put them together? These questions developed at the beginning of the model building process. The use of connector model building toys were chosen to build the Trna and mrna strands. Figure 1. (left) Full photo of Trna component with complementary mrna strand and protein structure in the form of a Styrofoam ball. (rigtht) Extra mrna strand not used in presentation. The different colors and different lengths of the bonds were to correspond to the different bases and bonds that each codon and anticodon use to create proteins. Adenine was represented by yellow colored model pieces, uracil red, guanine green, and cytosine blue. The first idea for the ribosome was to make it out of play-doh. However, since the size of the Trna was considerably large, the ribosome had to be made of something that could create a larger object. It was then decided to make the ribosome out of pipecleaners. There were two parts to the ribosome, a bottom part that was wound around a lego base and the mrna that is being bonded to the Trna to provide support, and a larger top part to represent the positions that the Trna take to bond to the mrna. Figure 2. (left) Completed top half of ribosome structure. (right) Bottom half of ribosome structure wound around legos and mrna strand for support. The next problem came about as the group pondered over how to present the model to the class. The initial idea was to wheel the ribosome along with the Trna on a wheeled lego cart. The large size of the ribosome made this impossible, therefore the group decided for the presentation that the motion of the model would be dependent on group members alone. The finished amino acids that would hang off of the end of the Trna were to be made out of Styrofoam balls. After assigning what the model would be made out of, the actual building took place. In order to create the Trna, component mrna strand, and ribosome, the use of a biology book was used. As stated before, in the Trna and mrna a different colored model piece was assigned to each different base. The Trna was modeled to have the shape of the Trna demonstrated in the book. Originally there were only three different specific codons on the mrna strand, a start codon, composition codon, and stop codon. However, we soon discovered that stop codons do not require Trna. Because we had constructed three Trna structures, we added another codon to the chain in order to compensate. After the Trna and component mrna were constructed, several more codons were added onto the chain to represent what would actually happen in a cell (see Figure 1). The ribosome was built by tying the pipecleaners together and stringing them into a huge mass. The bottom half of the ribosome was wound around a lego base and the mrna being used in the bonding. Winding the pipecleaner around these two objects allowed for more support of the mrna. The top half of the ribosome was created by creating a large mass of pipecleaners and shaping them into the form of what a ribosome would look like. The pipecleaners were different colors to represent the different mrna and proteins that an actual ribosome is made out of (Figure 2). The last component of the model, the end amino acids and polypeptide chain, was made out of Styrofoam balls. These balls were covered in tape and painted red, blue, and yellow. These balls were attached to the top of the Trna by carving out a hole onto each ball and attaching it to the ball end of the model. On the sides of the Styrofoam balls are magnets that were placed into grooves cut out of the Styrofoam balls. These magnets represented the different amino acids coming together to form a polypeptide chain. Having everything built, the last step in the model process was to put the pieces together to prepare for the presentation. `We already knew that the model would have to be moved by hand, but how would we support the Trna? Unfortunately the model is not proportional, with the Trna being much larger than the ribosome. There were three options to this dilemma. The Trna could either be suspended by hanging them on a wire or string, hand held during the entire presentation, or held by clamps and a ring stand. Because the latter seemed the most plausible, it was the method chosen. Figure 3. Clamps used to hold the Trna in place. While the first two Trna would be already bonded, the last clamp was to hold the last Trna, however would be twisted out of view until it is needed in the process. The Trna were then suspended on the clamps but the problem of stability arose. The Trna strands would not stand on their own and would fold over as a result of the model pieces they were made out of. To fix this problem, wire and pipe cleaners were used to provide some sort of structured stability (Figure 4). Figure 4. Cut wire threaded through the Trna structure in order to give it more stability. In order to keep the Styrofoam balls attached to the top of the Trna strands, shish kabob sticks were taped to the top strand of the Trna to give it even more stability. Using the sticks allowed the styrofoam balls to be able to be attached and able to attach to each other through the magnets in them. Figure 5. Completed Model. As far as the connection to nanoscience, the process of translation in protein synthesis is imperative to become closer to forming proteins through the use of nanotechnology. The mrna and Trna demonstrate the specificity of the bonds used in protein synthesis. Specific bases bond to their complementary bases, (A-U, G-C). Perhaps in the future nanotechnology can produce its own ribosome to create its own proteins and amino acids.