Unit 6 Reflection

     Since we got back from winter break, we have been learning about biotechnology. The content in this unit was related to what we had learned in previous units, and it helped me remember some of the previous information.
     The first vodcast was an introduction to biology. We learned about biotech, the study and manipulation of living organisms in order to benefit mankind. There are four main applications of biotech. Industrial and environmental biotech include using fermentation to make food such as yogurt and alcohol, and biofuels, using cells to break down cellulose to produce alcohol for fuel. Medical and Pharmaceutical biotech include gene therapy, which is putting a healthy copy of a gene into someone who has a mutated copy. Biotech is also used in agriculture, where is can be used to produce genetically modified organisms. Finally, biotech is used in diagnostics such as gene testing, where fragments of DNA are searched for risk of genetic disorders.
     The next vodcast was about bioethics. We learned about values, which are what we see important or morally correct.We learned about modern examples of bioethics, the study of how morals influence or decisions as related to biology.An example is whether food should be genetically modified. Finally, we learned what to do in a bioethics debate.
     The following vodcast was about recombinant DNA. Recombinant DNA is the process of inserting the DNA of an organism into the DNA of another organism. First, you need to find the gene of interest. Next, you need a restriction enzyme, an enzyme that cuts DNA wherever it reads a specific sequence. Each DNA has a sticky end that allows other DNA to bond. A plasmid that contains the replication gene is pasted by ligase, an enzyme that reattaches base pairs. After, the bacteria is grown an agar which has an antibiotic that the bacteria containing the plasmid is naturally resistant to. The bacteria is grown, and only the bacteria with the plasmid survive because they are the only bacteria that are resistant to the antibiotic. Finally, the protein is extracted and purified.
     Another vodcast was about the technologies of biotech. In this vodcast, we learned about 3 different types of biotech. The first technology was Polymerase Chain Reaction, PCR. It allows a sequence of DNA to be copied over and over again. First, a double stranded DNA is heated to denature it. Primers attach to the single stranded DNA and DNA polymerase copies it, making new double stranded DNA. The process is repeated. Another example of biotech technology is Gel electrophoresis, It uses electricity to seperate DNA by size. Larger pieces travel slower and smaller pieces travel faster. The technology is sequencing. It determines the exact sequence of a DNA strand.
Each copy is one base pair longer. Each base contains a fluorescent dye. The DNA is run through a gel electrophoresis, and the sequence is read.
     The last vodcast was about pGLO. We did this in preperation for a lab. You can learn about it here. We learned that pGLO makes an organism glow in dark. If arabinose and resistance to ampecillin are there, the bacteria will glow in the dark.
     This unit went pretty well. There were no major projects, but I still stayed on track with everything. Now that Mr. Orre does not accept late work, I will have to be on top of things even more. I even managed to finish some assignments ahead of time. Procastinating does not help.
     We did many labs in this unit. We did a lab on Recombinant DNA, Electrophoresis,and pGLO. These labs helped me remember the ideas behind the technologies. I also learned basic lab skills in the labs. Teamwork was key in the labs, as they were kind of complex. Overall, the labs were very fun and helpful.
     Biotech has proven to be a very interesting topic to me. I am interested in more of the current issues of biotech. I am also intrested in bioethics. To me, biotech is the perfect way to apply science to the real world. Using its power can really help the world.
   At the beginning of the school year, I made two new years goals, studying better for tests, and taking better notes. I have already started studying for the upcoming test. I am actively studying for tests and hope that I will do well. Since Mr. Orre no longer gives us fill in the blank notes, it was imperative that I learned to take good notes. I think that I did a good job overall. I was able to get the general idea of each vodcast down without pausing it to much.

At first, PCR was difficult for me to understand. This helped me. 

This image shows me the power of biotech

pGLO Lab

In class today, we made e coli turn fluorescent green in the dark! We put a starter e coli and transformation solution into 4 micro centrifuges. We put the pGLO plasmid into only two of them. We heat shocked the centrifuges so that the bacteria would absorb the plasmid. We finally put them onto agar and incubated them for 48 hours. The results were very interesting

Plate	Number of Colonies	Color of colonies under room light	Color of colonies under UV light
-pGLO LB	carpet	grey	grey
-pGLO LB/amp	none	none	none
+pGLO LB/amp	104	grey	grey
+pGLO LB/amp/ara	64 + some carpet	grey	neon green

Our transformed bacteria glowed neon green and had resistance to ampecillin,an antibiotic.

We spread 100 microliters of bacteria onto each agar plate. In the 100 microliters, there was about 90 e coli in the solution E coli is about 1 to 2 microliters in length. It is very packed in, so the number must be closer to 100.

In the one plate of bacteria that glowed, we put arabinose. The arabinose sugar activated the pGLO gene and allowed for it to be expressed.

There are many uses for this technology. A few examples include studying cancer in mice, removing the malaria gene from mosquitoes, and studying the spread of HIV. Cancer cells can be easily watched when they have the Green Fluorescent Protein. Scientists created a gene that destroyed the GFP gene in a mosquitoes' testicles. The next step is to create a gene that will destroy the gene critical for malaria transmission. Researchers were able to see how HIV spreads from one cell to another by placing the GFP gene in an infected T-cell.

pGLO is only one application of genetic engineering. Another is crop resistance to parasites. If one variation of corn is resistant to a parasite, it is more likely to survive. Farmers genetically engineer their corn to make it resistant to certain parasites.

Our plates

Candy Electrophoresis Lab

1.)There were no colors that did not match the reference bands
2.)Fast Green FCR and Red 40 are most likely to move like the colors we saw in the lab because they have a similar chemical structure to the reference dyes.
3.) Dog food companies put artificial colors in dog food to make it look more appealing. Humans are more likely to buy dog food that looks nice and that has bold colors. They think that this food will be better for their dogs. This is ironic, because many artificial colors have unknown side affects on dogs and humans.
4.) Most Commonly Used Food Colors with Natural Alternatives

FD&C Dye	Color	Natural Alternative	Source for Natural Alternative
Blue 1	Blue	Spirulina Extract	Cyanobacteria
Blue 2	Blue	blueberry juice	blueberries
Green 3	Green	Spinach juice	Spinach
Red 3	Red	Beet Juice	Beets
Red 40	Red	Purple Sweet Potato juice	Purple Sweet Potato
Yellow 5	Yellow	turmeric	turmeric
Yellow 6	Yellow	paprika	paprika
Citrus Red 2	Orange	Beta-Carotene	Carrots

Artificial colors are used rather than natural alternatives because they are cheaper and easier to obtain.
5.) The 2 factors that control the distance that the colored dye travels are the size of the DNA in the dye and
6.) The fact that DNA is charged negatively propels it. When electricity is turned on, DNA will go towards the positive side.
7.) The fact that the longer the DNA is, the slower it moves, separates DNA by size.
8.) If DNA with a weight of 600, 1000, 2000, and 5000 daltons were put into a gel electrophoresis, I would expect that the 600 would travel furthest, with 100 not to far behind. 2000 would be further back, and 5000 would be in last.

Our Gel

Thinking Like A Biotechnician: Recombinant DNA Lab Analysis

Recombinant DNA

     In this lab, we simulated to process of making Recombinant DNA. Recombinant DNA is the process of inserting the DNA of an organism into the DNA of another organism. First, we identified the gene of interest, which for us was the insulin gene. Then we made a plasmid. A plasmid is a small piece of circular DNA in bacteria. A plasmid is naturally resistant to a certain antibiotic, which for us was tetracycline. Next we used a restriction enzyme. A restriction enzyme cuts DNA wherever it reads a specific sequence. We made sure that the restriction enzyme only cut the plasmid once and the DNA sequence twice. We did this so that there were not to pieces of plasmid and that there was less DNA from the DNA sequence. Once the DNA was cut, we added ligase. Ligase is an enzyme that reattaches the base pairs back together. Finally, we put the bacteria into a petri dish and added the antibiotic tetracycline. We did this to isolate the bacteria that had the insulin gene. The host bacteria produces the gene product, insulin.
     We had a choice of using the antibiotics, tetracycline, kanamycin, and ampicillin. We could only use tetracycline because the DNA segment that had the insulin gene was only resistant to tetracycline. Restriction enzymes cut DNA wherever it reads a specific sequence. We used the restriction enzyme Hpa II because it only cut the plasmid once and the DNA segment twice. If we used an enzyme that cut the plasmid twice, then the plasmid would be in two pieces. This process is important in our everyday life because there are many everyday uses for this technology. Recombinant DNA has allowed scientists to create genetically modified organisms (GMOs), which we commonly eat everyday. This technology has other uses, such as gene therapy, which help people who suffer from genetic diseases. Recombinant DNA technology is still in use today. For example, recently, a new vaccine was made that utilizes a Salmonella bacteria that is genetically modified and has recombinant DNA. There are many uses of Recombinant DNA technology, and we are just scrapping the surface.

New Years's Goals

     The second semester of school has just started. With the start of the new year, I have some goals in mind that I hope to achieve. The first goal is that I will study better for tests. In the first semester, I did not have a good plan for studying for tests. I will make a plan for studying for test. Instead of just looking over my notes, I will do more active studying. I will make study guides like I did for the final. I will know that I will achieve my goal when I consistently receive As on my tests. I hope that I will achieve this goal by the end of the school year.
     Another goal that I hope to achieve is to better manage my time. At home, I have a lot of distractions such as books and electronics. For the most part, I try to do my homework before I relax. But sometimes I succumb to the pressure and dive into a book before starting my homework. I will do my homework everyday before doing other things. I know when I have achieved this goal when I consistently do my homework without being distracted every day. I hope to reach this goal by the end of the school year.