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.