cdkelly's blog

These three projects compounded with the weekly draft posts and perfect paragraphs changed the way that I look at writing in a scientific setting. I have had plenty of writing courses prior to this one, but I believe that I was able to gain experience that is relevant to my career aspirations from this course. The methods project taught me the importance of writing clear and concise methods. Whereas the proposal project showed me how to write in such a way to persuade people that my project is worth attempting. Finally, the project at the end of the semester introduced me to independent research and improved my research-poster making skills. Overall, this course demonstrated to me the importance of writing in the sciences and I firmly believe that I came out a better scientific writer.

The proposal project was an interesting project for me because we worked as a group and tackled different parts of the project. Initially, I came up with a rough idea for a research project involving spiders and then acquired a team of two other students from the class. We then streamlined the proposed project and did research on previous studies on a similar topic; keeping in mind that we were writing this to convince people to join our project. I will say that the original draft was pretty rough, but after reviewing the comments on it, I believe that we turned it into a solid proposal. As far as group work went for this course, I would say that this portion went the best for all of us. We all managed to contribute equally to the paper and the presentation. This then lead to a large number of students deciding to work with us for the final project in the course. In retrospect, this project introduced me to a skill that I didn’t previously have and laid a great foundation for my future proposal writing.

When I initially heard of the methods project at the beginning of the course, I thought that it was going to be a lot of work. And while I found this to be true, I also learned a number of valuable skills that I didn’t have prior. For instance, the construction of the figure using Inkscape. In the past I would construct all of my figures and graphical elements for reports in Microsoft Paint, but after finishing the methods project I felt much more comfortable using the more advanced Inkscape. In addition, the actual process of writing everything that I did explicitly made me appreciate how detailed a methods section needs to be. If you are expecting repeatability for your experiment, then it it imperative that you include all of the relevant details. This was demonstrated by having another student in the class attempt to recreate my figure based only on the methods that I wrote. In my case, my figure was recreated with few errors, but there still were some areas that could have used more clarity in my methods section. It was really neat to see what the other person came up with, as well as comparing my replicate to the original. Overall, this project taught me a great deal about methods writing and will most certainly help me with writing scientific papers down the road.

Like eukaryotic DNA, prokaryotic DNA (plasmids) must segregate during replication. This idea is interesting because of the structural differences between eukaryotic DNA and plasmids. Plasmids are essentially circular pieces of DNA the attach at both ends. A plasmid is generally condensed, similar to how a rubber band twists up. The potential energy stored in the condensed plasmid configuration can be used to propagate certain interactions. Since our eukaryotic cells utilize microtubules in chromosomal segregation, I wonder how microtubules interact with plasmids; their structure is different, so I imagine their segregation is similarly different when compared to eukaryotic DNA.

It's interesting that Okazaki fragment is able to not get lost in the process of DNA replication and become oriented perfectly in the newly synthesized DNA strand. There must be a series of cellular machines that keep this in the realm of possibility. However, I would assume that a good amount of the DNA errors that do occur are related to the Okazaki fragment, since the process is considerably more complex than synthesis of the leading strand (at least conceptually).  

This is really an amazing mechanism that happens within our bodies and within all other eukaryotic organisms. I wonder how the DNA polymerase is able to make the conformation shift to compare the newly synthesize strand to the original. Perhaps a ligand or even a phosphate group binding leads to the action of DNA polymerase. Also, this is far from the only proofreading mechanism that exists for DNA replication, which explains the incredible accuracy exhibited by the complex over the huge magnitude of DNA replicated.

Since this reaction requires a considerable amount of free energy to occur, it must be couple with a different process in the cell in order to be thermodynamically possible. Endothermic reactions like this need to be paired with an exothermic reaction to make the product formation favorable. All reactions need to have a negative change in free energy, the process of making that happen is called metabolic coupling.

I've read elsewhere that DNA polymerase is actually a series of enzyme subunits working together as a complex rather than a single enzyme. This makes sense when you think about it though. Considering that an enzyme typically corresponds with one reaction, there must be many involved to achieve DNA replication. DNA is a complex molecule and thus it would require a number of reactions and organization to achieve true replication.



 

Another function of helicase is to prevent the DNA in the process of replication from getting two wrapped up. Similar to how a rubber band is changed when both ends are twisted. When DNA is put into such a conformation it is unable to be copied due to the torsional strain on the molecule. Thus, it is critical that helicase performs this action as well as simultaneously working to separate the two strands of DNA.

This property must be due to a conformational shift in the tubulin that causes it to lose some affinity for its binding partner in polymerization. This is an excellent mechanism to utilize for dynamic instability because it is not too complex and can occur quickly within the cell. In addition, the cap is an important part of this process because it prevents the microtubule to completely degrade.

One of the most fascinating qualities of Tau protein is its incredible stability. Even in its regular form, Tau protein can withstand the heat of boiling and not denature. When the protein begins forming aggregates, it becomes even more difficult to denature and researchers believe that this property contributes to the mechanism by which tau build-up kills other cells in its vicinity. It takes up excess space and essentially suffocates the cell.

While I realize that microtubules are involved in the process of motility in cells, I always thought that actin filaments were the primary driver. As described here, the microtubule push outward onto the cell membrane and cause the cell to move. Perhaps microtubules are more involved in the directionality of the movement, rather than specifically generating the force necessary for the cell to move. That would leave actin as the protein with the purpose of generating the force required.

This concept is one of the most interesting jobs of microtubules in my opinion. Especially because no one fully understands how they influence gene regulation. I've heard that microtubules in the cytoskeleton form in a specific way once the cell differentiates and results in certain regions of the DNA to be unreadable. Therefore, each cell type will have a specific set of protein that it is able to transcribe and translate. The DNA that a given cell has access to after differentiation is dictated by the microtubule cytoskeleton and accounts for the proteins that give each cell type its specific identity.

This is really interesting because of the differences between eukaryotic DNA segregation and plasmid segregation. Plasmids a essentially circular pieces of DNA the attach at both ends. The plasmid is generally condensed, very similar to how a rubber band twists up. The potential energy stored in the condensed plasmid configuration can be used to propagate certain interactions. Since our cells utilize microtubules in chromosomal segregation, I wonder how microtubules interact with plasmids; their structure is very different, so I imagine their segregation is similarly different when compared to DNA.

The amino acid chemistry of Beta-tubulin must make it more conducive to the propagation of microtubule growth. Since it is a GTPase, perhaps it has a higher affinity for GTP and consequently more likely to bind to another tubulin protofilament than the alpha or minus end. It's interesting because there is still addition to the microtubule from the minus end, just not as much as the plus end.

I wonder what benefit the alpha-beta seam found in many microtubules does. If it is a regularly occurring molecular orientation utilized by cells, then there must be a purpose for it. Perhaps it enhances the flexibility of the microtubule, either positively or negatively, as a way to regulate its function. For example, sometimes microtubules need to be more rigid than normal, and sometimes the opposite is true.

An example of an intricate three-dimensional shape taken by RNA is the ribosome. Although it is more than just RNA, a large part of its structure is made of it. There are other structural and functional proteins involved, but it’s interesting to think about. The ribosome reads mRNA, a more specialized RNA molecule, and translates it to an amino acid chain.

This idea relates back to the difference in hydrogen bonding between nucleotide pairs. Because the AT pair has only two hydrogen bonds and CG has three, it requires more energy to break apart a strand of DNA that has a majority of CG pairs. Thus, it requires more heat to denature DNA of this nature and less heat to denature a majority AT strand of DNA.

I know that the interior of the microtubule is not believed to have serve a function, but I just think that its strange that it's entirely hollow. Just based on the tubulin composition, I would assume that there is some type of electrostatic interaction that exists on the interior of the microtubule, like hydrogen bonds of ionic interactions. Another idea is that perhaps the reagents needed for GTP hydrolysis of the microtubule are able to flow through in interior and increase the rate, affecting dynamic instability. Of course, it could just be as simple as we suspect.

The different pairs of nucleotides have their own properties that allow different functions. For example the pair AT uses 2 hydrogen bonds to bridge the two nucleotides together. Whereas the CG pair uses three hydrogen bonds. Thus, in areas of higher CG presence the DNA is more tightly coiled. Also, the tightness of the DNA coil can affect the ability of certain binding partners to fulfill their role because of steric strain.

I wonder what the presence of the oxygen on the sugar portion of DNA does to the structure and function. Perhaps it affects the way that thymine binds to the backbone. In this was it could maybe form more stable bonds with uracil. In addition, it’s possible that the presence of the oxygen on the RNA sugar could contribute to some of the other functions of RNA, like its ability to interact with different cellular machinery.

The mechanisms of the enzyme that moves this process along is probably similar to the way that amino acid chains are polymerized. Although in that case it is a peptide bond and in this example it is a phosphodiester bond, I imagine the processes are still similar. I believe that the enzyme that functions to establish the phosphodiester bonds in DNA is DNA ligase, which does exactly as its name implies.