Unit 5 Reflection

        In this unit, I learned about processes involved with the essential nucleic acids: DNA and RNA. I learned about how DNA has an antiparallel, double helix structure made of nucleotides. These nucleotides have nitrogenous bases, which include the purines adenine and guanine, and the pyrimidines cytosine and thymine.

Structure of DNA

They pair to make a code, which can be replicated through semi-conservative replication during interphase, or be transcribed by helicase and RNA polymerase to create mRNA used in protein synthesis. The mRNA is translated into amino acids in a ribosome, and the resulting protein is sent to use in the cell or body. However, mutations can cause significant changes in DNA that lead to radically different proteins being produce, and this can interfere with processes. Additionally, gene expression is regulated by transcription factors and repressors, keeping certain genes from being read by RNA polymerase. This controls the production of certain proteins, such as lactose, from being produced unless they are needed. In general, much of this was a review for me, but there were also times where I took longer to understand new concepts that were presented, such as how operators work in gene expression and regulation. On the other hand, the structure of DNA and protein synthesis were not too challenging to grasp, especially since I had encountered them before in science classes, though the practice was very helpful.

DNA extracted during the DNA extraction lab

        Throughout the unit, I found that I learn better when asking questions and clarifying more complex parts of the content. I discovered that for topics like gene regulation and expression, I tended to understand the material and process much better after the in-class discussion the next day. As a student, I would consider myself having improved, as I learned how to garner more information and skills from what is presented; in essence, I am not only smarter now than a month (or the duration of the unit) ago, but I have improved at improving. (Δ(Δk)?) I think the strategy of physically typing and creating a study guide is an effective one: through writing down the material, one is reviewing and remembering perhaps nuances that were forgotten over the course of a few months. Next semester, I will try to utilize this method to synthesize material better and continue to learn more. (and learn more about learning)

Protein Synthesis Lab

        In this lab, we modeled the processes involved in protein synthesis. To make a protein, on goes through transcription and translation. First of all, we copied down the DNA strand and transcribed it into mRNA, replacing thymine with uracil. This is what RNA polymerase does in the nucleus. Then, we translated the mRNA by splitting it into codons and finding the corresponding amino acid for each codon. This process, representing the tRNA's work in the ribosome, produced the primary structure of the protein.

Diagram of protein synthesis
https://commons.wikimedia.org/wiki/File:0328_Transcription-translation_Summary.jpg

        The mutations that seemed to have the greatest effect were the frameshift mutations, insertion and deletion, while the mutation that seemed to have the least effect was substitution. For the frameshift mutations, the location of the mutation was also very influential: a mutation near the beginning of the sequence would alter (shift over) almost every codon, while one at the end would change very little. This is due to frameshift mutations affecting every codon after it.

Some possible mutations in DNA
https://en.wikipedia.org/wiki/File:Chromosomes_mutations-en.svg

        I chose the frameshift mutation as what my data indicated would cause the most damage to the gene. This mutation, unlike other mutations we tested, had a chain reaction effect that rippled across and changed the frames of every codon after it. This could lead to devastating consequences, such as a stop codon in the beginning or completely different amino acids. As mentioned earlier, this effect is especially predominant if the mutation is at the beginning, as it would change everything after it.

Effect of a frameshift mutation (insertion)
https://www.flickr.com/photos/yourgenome/26855221022

        Because of the direct connection between DNA and proteins, and the influence proteins have in the body, dangerous DNA mutations can wreak havoc and create abnormalities in daily processes such as blood flow, digestion, and respiration. For example, cystic fibrosis is caused by a mutation in the CFTR gene. These mutations prevent chloride ion channels from functioning properly, and unusually thick mucus is produced, which clogs airways.

Diagram of cystic fibrosis
https://www.flickr.com/photos/yourgenome/26855222462

Human DNA Extraction Lab

        In this lab, we asked how DNA can be separated from cheek cells to study. We found that significant amounts of DNA can be extracted as a visible precipitate. The thread-like structure could be seen suspended in the isopropanol alcohol, after the layer of nonpolar alcohol was added on top of the solution with DNA. It has been proven that through homogenization, lysis, and precipitation, one can extract DNA. This is done through breaking down the membranes and nuclear material with polar liquid, lysing the membranes, emulsifying the proteins and lipids, and breaking down the histones in the DNA. Then, by adding a polar substance as a layer, the DNA will fall out of solution at the interface and become a precipitate. Our data supports this claim and is the result of such a process, using salt as a precipation facilitator, detergent as a disruptor, and pineapple juice as a catabolic protease to help break down different structures in the cell and free the DNA.

DNA precipitates into the ispropanol alcohol

        Some errors people in our lab group made led to alcohol and solution mixing, thus precluding the DNA from becoming a precipitate. In one experiment, the inversion to mix detergent with the solution was done too quickly and violently, thus leading to bubbles forming and disrupting the liquid surface. This would have kept the DNA from successfully precipitating at the interface, and could have mixed up or damaged the DNA strands in the solution. Another error was not measuring very precisely, which lead to a variety of results, some unsuccessful. We simply estimated amounts (e.g. pinch of salt), which may have led to imprecise measurement and thus a failed extraction with a certain substance being too dilute or concentrated. In a future experiment, I would suggest making sure to mix slowly, which would keep the solution from forming many bubbles. Additionally, keeping measurements precise, such as using measuring spoons and graduated cylinders, would give less variation and a higher success rate in general.

Precipitation is unsuccessful due to violent inversion

        This lab was done to demonstrate how DNA can be extracted from inside the nucleus of a cell. Moreover, I also learned how the membranes, histones, and nuclear material must all be broken down before the DNA can be extracted. This helped me understand how much protection the DNA has, due to it holding the genetic information. Not only does it never leave the nucleus (mRNA copies and leaves instead), there are many layers of membranes to keep it from being damaged by substances outside the cell. Outside of these concepts, based on my experience from this lab, I also now know how one might break down cell membranes to access, not only the DNA, but any organelle one might be studying using the techniques of homogenization, lysis, and precipitation.