Unit 6 Reflection

        Unit 6 was all about the different aspects of biotech, including bioethics, what biotech is used for, and the technologies and equipment that are used in the field of biotech. Biotech involves using microorganisms to benefit humans. Genetic engineering is also a huge part of biotech. There are 4 main applications of biotechnology. For example, one application is agricultural, which would include things like genetically modified crops. Bioethics is also a part of biotechnology. Bioethics is determining what uses of the technology is moral or correct.

      This unit was generally easy for me to understand. The only concept that was slightly more confusing for me was recombinant DNA, but after going through it, I started to grasp the concept more. I think the labs we did this unit were much more successful and clean than the labs that we did last semester.
   

      For this unit, we did two labs in class and a virtual lab online. The virtual lab taught us about the process of gel electrophoresis, which we then did as an actual lab with the candy electrophoresis lab where we separated different candy dyes by size. The other lab we did was the pGLO lab. In this lab we transformed bacteria using a plasmid called pGLO, and we were able to grow bacteria that glowed under a blacklight. From the labs I learned that although the concepts and processes we learned in the vodcast may seem complicated, but they are not very difficult to execute even in a classroom setting.

       I am interested in learning about how the technologies we learned about are being used currently. I also would like to learn about what other technologies exist besides the ones that we learned about during this unit. 

      In my new years goals post I mentioned that I wanted to try and actually understand the topics we learn rather than blindly memorize them. I think I practiced that a lot during this unit, especially when learning about bioethics and having the world cafe discussions in class, as I actually formed opinions for myself, and the labs also really helped me understand the topics.

pGLO Lab

      Our transformed bacteria (with the pGLO plasmid) have resistance to the antibiotic ampicillin, and can glow under a UV light with the presence of arabinose. In the 100 uL of bacteria we used to spread on each plate, I estimate that there is a large number of individual bacteria like 50 million or even more. Since bacteria are very small and microscopic, a lot can fit into a very small amount of space. The arabinose in the plates acts as a trigger for the plasmid. According to the vodcast, the presence of arabinose triggers the GFP in the plasmid that makes the bacteria glow. 

      The protein GFP has many used and applications in applied science and research, and these are three according to livescience.com and addgene.org. The glowing protein can be used to track cells like cancer cells. It can also be used to track the spread and progress of an HIV infection. It can also be used to monitor gene expression, if it is put under the control of a specific promoter. Another application of genetic engineering is in the agriculture and food industry. Many of the foods we eat are genetically modified (GMO). For example, crops such as corn can be modified to be resistant to pests or diseases that usually affect the crops. 

Candy Electrophoresis Lab

      When we analyzed the results of our gel, there were a few minor differences between our dyes and the reference dyes. The reference dyes generally stayed in one clump and stayed in the same shape. Our own dyes dispersed and spread out a little bit more. Our red and yellow dye even left a bit of a trail as it moved forwards. None of the dyes moved in the wrong direction however, so I believe that they are all negatively charged.

      Out of the 4 dye structures that were pictured, I believe that Fast Green FCF is most similar to the dyes we examined in class. It seem to be negatively charged, as were the dyes we used in class, and all the rest of the dye structures pictured are not negatively charged.

       I believe that dog food manufactures put artificial food colors in dog foods as a marketing strategy. Since the owners want the best food for their dogs, they will most likely choose a dog food that looks more appealing, and one that has nice colors in it would look much better than the natural color of the food. Also in my own diet, I think a lot of the food that I eat has artificial food dye in it. I enjoy eating candy which usually has dye in it, and the snacks I sometimes eat, like chips, also are colored artificially.

      The distance that the dye traveled was controlled by different factors. The main factor is the size of the dye molecules and fragments. The smaller the size, the faster and farther the dye would go. The amount of time also contributed to how far the dye went. If we had left the electrophoresis machine on for longer, the dye would have traveled further. The electrical current flowing from negative to positive helped the dyes moved through the gel. The small holes in the electrophoresis gel allowed the dye to separate by size. The bigger the molecule, the longer it will take to get through the holes, which is why smaller molecules get through the gel faster.

      If we had DNA with molecular weights of 600, 1000, 2000, and 5000 daltons, I would expect the 600 and the 1000 molecules to go much further than the 2000, and especially the 5000. Because they have smaller weights, they can get through the gel much faster than the molecules with larger weights. 

New Years Goals

      This semester, I have the goal to get more sleep to help me perform better during the school day. I will do as much homework as possible during tutorial and lunch during the school day, so I will have less to do when I get home. I will also avoid procrastinating until the last minute, to save me more time in the long run. I will also limit the distractions I get while doing my homework,which are quite frequent, like putting my phone somewhere else so I am not tempted by text messages and social media notifications. I believe that if I do these things, I will wake up in the morning feeling more ready and have enough energy to focus at school. 

     In this class, I have the goal of learning and absorbing the information rather than just memorizing facts. I will do this by asking more questions to try and grasp concepts that I'm confused about. I will also listen more and think more during the vodcast rather than just trying to fill in the notes and. I will also devote more time to studying (not just before a test) as I usually take minimal time to study. I believe that if I achieve this goal, I will perform better on tests and quizzes, and I won't just forget everything by the time I reach AP Bio.

Unit 5 Reflection

      This unit was about how information flows from DNA to RNA and then to proteins. We learned how DNA codes for all of our traits and the process of protein synthesis and how ribosomes read RNA, which gives us the phenotypes we have, and even mutations, of which there are two types, point and frameshift. The processes involved in this "central dogma" of biology include protein synthesis, which is a two part process of transcription and translation where DNA is copied and the nitrogen bases are read, semi-conservative DNA replication, where the two new strands contain half of the original strand, and DNA regulation, which determines which genes are expressed and which aren't.

http://thebiologyprimer.com/transcription-rna-processing-and-translation/

       In my opinion, the majority of the concepts in this unit was easy to understand. I really understood the process of protein synthesis and how amino acids are made. I also know the different kinds of mutations fairly well, as the protein synthesis lab really helped me understand what exactly happens to the DNA and the resulting protein. Some concepts were a little more vague at first to me, like the gene regulation and expression in. Now I understand the process of gene regulation in prokaryotic cells, but I still need to review how it works in eukaryotic cells. I want to learn more in detail about protein synthesis and why the nitrogen bases in DNA pair up the way that they do. 

      I think that I am understanding the concepts even more than I did last unit. I am definitely putting in more effort into trying to understand what we learn, rather than just blindly memorizing facts like I used to do. According to the VARK questionnaire that I took last unit, I learn best by reading and writing, so I took the approach of reading over my notes and writing my own notes on what I think that I need to study for the test. I remember things better if I physically write them with my own hands, so that is how I've started to prepare for the final exam. I think in the future I still need to work on my time management in terms of studying, as I usually try and cram in the last few days before a test.

Protein Synthesis Lab

      In this lab we asked the question, "how does the body produce proteins?". Protein synthesis has two stages, transcription and translation. Transcription happens first in the nucleus. First, a copy of a section of DNA is made, called RNA, and the base thymine is replaced with uracil. Then the RNA moves to the cytoplasm, where translation happens. In the cytoplasm, a ribosome reads three base pairs at a time, this is called a codon. Each codon codes for a different amino acid. The amino acids bond together to form a long chain, which become a protein.

http://www.yourgenome.org/facts/what-is-a-mutation

      A mutation is any change in the sequence of the DNA. There are point mutations and frameshift mutations. A substitution is a point mutation that substitutes one base pair for another. For frameshift mutations, insertion is where an extra base pair is inserted, and deletion is where a base pair is removed. From the experience with the lab, the frameshift mutations seemed to have a greater effect than substitution. With substitution, only one of the amino acids is changed, but with insertion and deletion, the whole sequence is shifted, which can completely change the codons and they amino acids produced. Also if the mutation is earlier in the sequence, then it has a greater effect, as the rest of the sequence after the mutation is shifted, resulting in more change. However if a mutation happens later in the code, than it only effects the DNA after, which is a smaller amount.

http://study.com/academy/lesson/insertion-mutation-diseases-examples-quiz.html

      When I chose my mutation, I chose to do a substitution to see if it could have a huge effect like a frameshift mutation. I changed the DNA at the very beginning, resulting in the absence of a start codon, so there was no protein. I think having the mutation towards the beginning of the code has a higher chance of making a bigger change to the amino acid sequence.

      Mutations are very common and they can have little to no effect, or they could have a very dangerous or even fatal effect. Mutations effect the amino acids in proteins, so they could possible alter how your body functions, and cause diseases etc. Hutchinson-Gilford Progeria Syndrome is a very rare disorder caused by a mutation on the LMNA gene which produces the Lamin A protein. Progeria caused rapid aging in children, and children usually die of heart disease at around age 14. Symptoms can include aged skin, loss of body hair, stiff joints, and more. 

https://www.sciencenews.org/article/family-takes-progeria-%E2%80%98life-according-sam%E2%80%99

DNA Extraction Lab

      In this lab we asked the question: How can DNA be separated from cheek cells in order to study it? We found that we can extract DNA through a three step procedure of homogenization, lysis, and precipitation. We collected the cells with gatorade and added salt. We then added soap to lyse, or rupture, the cell membrane so all the contents of the cells released into the gatorade. We then added pineapple juice, which is a protease that breaks down the histones (proteins) that the DNA wraps itself around. Lastly we added a nonpolar liquid, alcohol, which made the polar DNA separate from the gatorade solution, successfully extracting DNA from our cheek cells.

     

      While our observations supported our hypothesis, there could be possible errors due to failure of properly inverted the test tube to mix the contents. If the tube was inverted too quickly, then air bubbles could have formed, and according the information about DNA extraction, air bubbles can get caught in the double helix structure. In the procedures I recommend saying to invert the tube slowly. Failure to add the alcohol in could also cause errors. If the alcohol was added too quickly, than it would mix with the gatorade, which would not allow for the DNA to separate out into a polar solution. I recommend to hold the test tube at as much of as angle as possible and to pour the alcohol very carefully and slowly.

      This lab was done to demonstrate the process of DNA extraction and what happens to the DNA through this process. From this lab I learned how to extract DNA with materials that anyone has access to. Based on my experience from this lab, if I ever entered a field like genetics or forensic science, I could use this procedure to extract DNA from important or useful sources.

A clump of DNA