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| Agar plate for use in DNA transformation |
PCR is a fundamental procedure: a denatured template strand has primers annealed to it, and then DNA polymerase is used to extend the primers in several cycles. Soon, millions of copies of the strand of DNA can be produced. This DNA can be analyzed and sequenced through gel electrophoresis: the setup of electrodes around a gel box with different DNA samples causes shorter DNA strands to move faster through the pores of agarose gel, pulled by the backbone's negative charge. In order to test the composition of various dyes found in candy, we used this process in the gel electrophoresis lab. The test allowed us to see how the chemical structure of different dyes made them run differently in the gel, and how different dyes were sometimes mixed to produce a wider variety of colors.
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| Gel electrophoresis in action |
In addition, fluorescent dyes can be attached to increasingly longer copies in a PCR reaction to yield a sequence of different dyes that correlate with base pairs. After gel electrophoresis, the base pairs can be analyzed, and an electropherogram can be produced. Another technique involve creating transgenic organisms using restriction enzymes and ligase. The enzyme cuts the strand at a restriction site, creating sticky ends, and the spliced piece is attached to another strand using ligase. We were exposed to the results of this technique in the pGLO lab, in which we introduced engineered plasmids into bacteria to make them produce GFP and glow in black light. A setback here was that due to imprecision at some point in our experiment (see the page for more detail), our plasmids were unable to become integrated into our bacteria, rendering the end result a failure. Nevertheless, as we witnessed the success of other groups, it showed how revolutionary this technology was, in changing the very DNA of bacteria to make it undergo different processes.
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| Recombinant DNA manipulation in action |
However, these extensive processes allow humans to manipulate organisms and inheritance in an unprecedented, highly intrusive manner. Bioethics is a specific branch of biology dedicated to determining the ethics of using new technologies based on values and morals. The questions posed are endless, and include dilemmas such as if stem cells from embryos should be used to treat diseases, as well as if life should be extended and human capabilities enhanced.
Overall, the unit was very unique in that it expanded from the usual biological theory and introduced tangible applications of manipulating biological molecules and processes. An observation I might make about my performance in this unit, in comparison with previous ones, is that as the procedures grew more complex, I felt more detached and intimidated by all of the advanced techniques involved. However, it was truly the labs that brought me back to the reality of how it could be done easily, even with limited equipment. Rather than being lost in the causes and effects of how everything worked, I became more concerned with the actual organisms and molecules we analyzed and worked with. I believe this really is what sets this unit apart from all of the others (so far), and what at the same time tied everything together.
To check back on my goals from the new year, I would say I have improved at least somewhat in better connecting the different subjects in summaries (relate and reviews, textbook notes, reflection, etc.) and in my mind. Perhaps it is the unit topic, but I can now more coherently visualize what processes and concepts affect one another. In the coming unit(s), I will also try to follow up on my goal of finding further information on each topic to broaden my understanding; of course, I will also continue to make more connections in writing and otherwise. In general, I look forward to either returning to the comfortable world of abstract mechanisms and learning more about the natural processes on Earth (ecology perhaps?), or wandering further in this new frontier of applied technology.
