Unit 6 Reflection

In this unit we learned about biotechnology and genetic modification. Biotechnology is divided into four fields: agricultural, industrial, medical, and forensics. Because humans can now modify organisms in so many ways, we also learned how to make ethical decisions on biotechnological topics. To make an ethical decision, you must first understand the choices and list pros and cons. Then find a decision that fits your morals most. The core of this unit was with recombinant DNA, electrophoresis, PCR, and DNA sequencing. Recombinant DNA is when genetic material is taken from different organisms and inserted into the DNA of a target organism. Electrophoresis allows scientists to separate DNA based on strand length. Polymerase Chain Reaction creates many copies of a strand of DNA, giving scientists the ability to examine the strands much more closely. To sequence genes, there are many possible techniques. One of them involves fluorescent dyes binding to bases depending on what base it is. Computer programs then examine the pattern of fluorescent dyes, telling the scientists what the genetic code is.

This unit had some very interesting information, although while writing this reflection I did need to go back and check on some stuff in the vodcasts. This means that I need to study from the bioethics and technologies of biotechnology vodcasts to prepare for the test.

One thing I really loved in this unit was the labs. Unlike other labs I have done in school where the results are predictable and uninteresting, the candy electrophoresis lab and pGLO lab had amazing results. In the electrophoresis lab all of our dyes matched the standard ones, but another group that extracted a green dye saw it separate into its blue and yellow parts (http://rpbioloblog.blogspot.com/2016/01/candy-electrophoresis-lab-conclusion.html). Our plate of fluorescent bacteria from the pGLO lab had one of the highest colony counts in the class and it was cool seeing the E. Coli glowing in one petri dish but not in others. (http://rpbioloblog.blogspot.com/2016/01/pglo-lab-conclusion.html)

I would love to experiment with other traits and inserting them into E. Coli bacteria. I wonder whether adding too many extra genes for protein creation will cause the bacteria to be unable to complete its basic life processes. In other words, will adding enough genes kill the bacterium.

I have failed to keep up to one of my new years goals while I have partially followed the other. At the start of the new year, I pledged to work on my textbook notes throughout the unit so I wouldn't have too much work on the day before it is due (aka today). I did not go through with this promise, probably due to the fact that I did not remind myself enough. Now on, I will set a weekly reminder on my phone to work on my textbook notes. I also said I will study 3 times a week for math to get at least 90%. Although I do not have specific study sessions, whenever I do my math homework I also go over all of my notes from that day and from the rest of the module.

Recombinant DNA where we used restriction enzymes to insert the insulin gene into a plasmid

http://rpbioloblog.blogspot.com/2016/01/recombinant-dna-lab.html

Candy electrophoresis lab where we extracted dye from candies to compare them to 4 standard dyes by using electrophoresis

http://rpbioloblog.blogspot.com/2016/01/candy-electrophoresis-lab-conclusion.html

pGLO lab where we made E. Coli bacteria absorb plasmids containing the GFP gene.

http://rpbioloblog.blogspot.com/2016/01/pglo-lab-conclusion.html

pGLO Lab Conclusion

1.

2. Our new bacteria have ampicillin resistance and they glow under ultraviolet light.

3. Since we have around 200 bacteria in our amp/ara/LB plate, and 150 in our amp/ara plate, and all of these took in the GFP gene, there must be at least 350 bacteria that took in the GFP gene. If the absorption rate is around 1 in 3, then there were probably around 1000 bacteria in the 100 microliter solution.

4. The purpose of arabinose is to activate the GFP gene and serve as a method of controlling the glow. If the arabinose is not present, bacteria will not produce GFP even if they have the gene.

5. GFP can be used to track the spread of bacteria with a certain trait. They are also an easy way to indicate whether an organism is genetically modified or not. GFP can be used to track the movements of certain cancers like osteosarcoma in dogs.

6. Another use of genetic engineering is to increase crop yield without spending large periods of time on breeding the perfect plant. Genetic engineering may be extremely important in the future with humanity's rising population and need for quick access to food.

The amp/ara/LB plate with bacteria fluorescing under UV light

Candy Electrophoresis Lab Conclusion

Although none of our dyes traveled in the wrong direction or mixed colors, there were some minor differences between the reference dyes and the ones we were testing. For example, our red and orange were darker than the reference colors, whereas the reference dyes for blue and yellow were darker than ours. However, I think this can be attributed to the amount of dye we extracted from the candy. I did not find any major variance between the distance traveled by reference and test.

I think that citrus red 2 will migrate similar to the blue 1, carminic acid will go about as far as our red 40, fast green FCF should go about as far as yellow 6, and betanin will be about the same distance as yellow 5. This is my hypothesis because although they aren't the same colors and size of molecules, the order of dyes that we tested, yellow 5, yellow 6, red, blue will correspond to betanin, fast green FCF, carminic acid, and citrus red 2. In other words, although the chemicals won't go as far as the dyes (due to their size), they should order up in the way specified above.

Dog food manufacturers probably put food coloring in the dog food to entice the dogs to eat it. Most dog food does not consist of things that a dog would naturally be fed, so to get the dog to eat up, they need to use artificial flavoring, coloring and smells.

In my food I found the artificial dyes red 40, yellow 5, yellow 6, and blue 1. I also found 2 natural dyes in cereal: annato extract color, and turmeric extract color. I found most of these dyes in cereals and sauces. It surprised me that I found the exact same dyes that we tested in the lab. I then searched the dyes up and learned that they are four of the seven permitted food colorings in the US.

The 2 factors that control the distance the dye travels is the dye's size, and how long you leave the gel in the electrophoresis box. In addition, I also think that the overall charge of the dye must also play a part in the direction it travels.

The force that moves the dye through the gel is the electromagnetic force. It is propagated through the current, caused by the voltage difference from the red cathode to the black one.

The reason why smaller dyes travel farther than large molecules of dye is because of the porous nature of the gel. Because the dye is inserted into the wells, they travel through the gel rather than on top. Thus, smaller dye molecules find it easier to navigate the cave-like environment found inside the gel.

Because DNA molecules of this size are so much larger than the dyes, I expect them not to travel as far. For this reason, it is necessary to leave the electrophoresis going for longer to see a difference in the distance traveled by each molecule of DNA.

After only a couple minutes of electrophoresis

The entire apparatus

The gel as removed. References are red-blue on left, test dyes are red-blue on right.

Recombinant DNA Lab

Process: To produce recombinant DNA, you first need a plasmid that has some antibiotic resistance. Our plasmid was resistant to ampicillin. This plasmid is cut open by a restriction enzyme which also cuts the insulin gene out of another piece of DNA. For us finding an enzyme that did all of this was quite tedious, and unfortunately, the one that worked was the last one to try.This insulin gene that was chopped out and some of its surrounding code are inserted into the plasmid and stuck together by using the enzyme ligase. This plasmid with the insulin gene and antibiotic resistance is then inserted into a bacteria. This bacteria then replicates and passes the antibiotic resistance on to all of its offspring. Ampicillin can then be added to the petri dish to kill off all the bacteria that don't have antibiotic resistance, thus leaving only the bacteria that produce insulin.

1. In my petri dish I would only use antibiotics that I know the plasmid carried resistance for. Otherwise, I might kill off the bacteria that have the insulin gene too. I also won't use antibiotics that all the bacteria in the species are resistant too, because that wouldn't refine the types of bacteria in the dish.

2. Restriction enzymes are enzymes that cut open DNA when they read a certain sequence. They work by cutting in patterns that create "sticky ends". I used HIND III because it cut extremely close to the insulin gene on both sides, as well as cut open my plasmid in one place.

3. If my enzyme cut the plasmid in 2 locations, then once the insulin gene is inserted in, I would be left with a string of DNA rather than a loop. However, I think that if ligase is introduced, the plasmid will reconnect to itself and everything would proceed as normal.

4. This process is important in our daily lives, because bacteria are extremely useful factories for protein. Although right now the only well-known use for bacteria-produced protein is insulin, I am sure in the future, we will be using bacteria as factories for all types of materials.

5. This process could eventually actually be used for bacteria to convert things like plastic and feces into usable fuel or other goods. For example, we would first have to engineer an enzyme for the digestion of plastics. We may then have to convert this into a genetic code. The code could be produced by various DNA "printer" technologies that are being innovated today. This gene will then be spliced by a restriction enzyme that also splices open a plasmid. The process will then be repeated except with an enzyme for the construction of propane or another fuel. Once all the necessary plasmids are inserted into bacteria, we could essentially feed the colony our plastic waste, and fill our cars or propane tanks out of the other side.

The plasmid with insulin gene and ampicillin resistance

New Year's Goals

In the second semester of biology this year, I want to make sure I turn in all of my textbook notes and turn in my lab conclusions on time. These are the only things that I lost points on last semester, but they still had a major effect on my grade. To ensure that the textbook notes are completed on time, I will start working on them at the start of the unit rather than waiting till the last minute. Also, instead of completing the majority of my lab conclusions at home, I will use my computer time in class more wisely.

Last semester I did much better than I expected in math, but my grade could still be better. This semester I want to ensure I get at least ninety percent in Algebra 2 Honors. I will study three times a week after school every week rather than just studying on the last two nights before a test or quiz. I may also try studying with friends I have in the class.