Unit 6 Reflection

This unit was about biotechnology. We learnt about how there are many ethical questions currently surrounding the biotechnology industry, because scientists and others are concerned about the ethics and values of each person about genetic engineering. Then, we learnt how scientist recombine DNA in bacteria. They take the plasmid and insert the gene into it. Then, they place the bacteria in broth to make them grow and place them in the antibiotic that the bacteria should have resistance to. All the bacteria without this gene/plasmid will die. To learn more about this concept, we did the recombinant DNA. We simulated restriction enzymes cutting out genes and placing them into plasmids with the Recombinant DNA lab.
To read more about it  click here:  http://revavaidyabiology.blogspot.com/2016/01/recombinant-dna-lab.html
Then, we learnt about the basic process of replication of DNA and analyzation. In order to reenforce the concepts we did the pGLO lab. We inserted plasmids into DNA by mixing certain bacteria with a solution with the GFP gene and moving it from cold to hot temperatures so it would absorb it. Only those with the GFP gene would glow.

Click here to read more:  http://revavaidyabiology.blogspot.com/2016/01/pglo-lab.html . However, before this we did the gel electrophoresis lab in class to get first hand experience on analyzing DNA. Click here: http://revavaidyabiology.blogspot.com/2016/01/candy-electrophoresis-lab.html. We learned how to use a micropipette to insert the DNA samples and references into the gel wells. In this lab, we did not use DNA, but instead used commonly color dyes from candies.

I feel that I understood this unit quite well, especially because of the labs. One thing that was difficult however, were the labs, because we had to be much more precise and careful, otherwise we would not get the desired results. This unit expanded on Unit 5 which was about DNA. I want to learn more about how do we use other forms of life other than bacteria in biotech. When will we be able to alter human DNA? Will it ever be widely used? Could this play a hand in evolution?

So far in relation to my New year's goals, I have not been very successful. I planned on studying a week and a half before tests, but am only studying 3 days before, or just on the weekend and then the night before.  I started making flashcards for all tests so I will have them to study for finals. I have also not been able to finish all my homework the day it is given: however, I have been more productive during tutorials.

pGLO lab

1.

Plate	Number of Colonies	Color of colonies under room light	Color of colonies under UV  light
-pGLO LB	carpet	brownish yellow	whitish blue
-pGLO LB/amp	0	N/A	N/A
+pGLO LB/amp	150-200	brownish yellow	whitish blue
+pGLO LB/amp/ara	47	brownish yellow	glowing green

2. The bacteria gained two new traits. The bacteria in the "+pGLO/LB/amp/arab" glowed under UV light and gained resistance to ampicillin because they were able to survive in the ampicillin and grow into 47 colonies.

3. On the "+pGLO/LB/amp/arab" plate, there were around 47 colonies. There was a lot of empty space, almost 1/2 of the plate was empty. Each bacteria that transformed would have multiplied into a colony, therefore around 100 bacteria were in the 100 micro-liters, and half of them died. On the "+pGLO LB/amp" around 150 colonies were on the plate. However, since we spread the bacteria all around the plate and there are empty spaces, we must have put around 250 bacteria. On the "-pGLO/LB" there were many more bacteria than on the other plates that made it onto the plate because almost the entire plate was covered. On the "-pGLO/ LB/ amp", we do not know how many bacteria made it onto the plate because they all died on contact since they did not have the ampicillin resistance.

4. The glowing is caused by GFP or Green Fluorescent Protein.  The GFP is "turned on" in the presence of arabinose, and starts expressing its traits. So arabinose causes the cells to glow green. 

5. There are many uses of GFP for scientists. In cellular biology, GFP has been used as reporter gene, cell marker, fusion tag. This means that if the cell glows then the scientists know that whatever gene they inserted into the cell is also being expressed, because GFP is attached to that protein. In the early 1990s, molecular biologist Douglas Prasher, used GFP to design probes, a technology involving fragments of DNA to detect the presence of nucleotide sequences. GFP is also used to to make the resultant protein react to wider wavelengths and emanate different colors. 

6. Genetic engineering can be used to alter crops so that they become more resistant to pesticides and pests.  It can also be used to make bacteria mass produce insulin for diabetics. 

under normal light

All under UV light

UV light from the top

UV light from the side

Source: 

https://embryo.asu.edu/pages/green-fluorescent-protein

Candy Electrophoresis Lab

1. Our blue reference was slightly ahead of our blue sample. We had no orange dye in our samples unlike our reference. The green sample separated out into blue and yellow, which we expected because green is made of blue and yellow. The references were a bit brighter than the samples. All of them moved in the right direction.

2. Citrus Red 2 would move at the same speed as Red 40, Yellow 6 and Yellow 5  because they are all made up of three sugars. Fast green FCF and Blue 1 would move at similar speeds because they are both made up of 5 sugars and have a similar structure.

3. Dog food manufacturers put artificial food colors in dog food to modify the appearance of the dog food. They try and use the food colors to make the food look richer and, therefore, healthier. People are tricked into buying these foods because they think it is the best thing for their dog.

4. Artificial food colors may be preferable to natural food colors because, while they are unhealthy, using a smaller amount probably results in a darker and richer color. This appeals to customers and the manufacturers save money.

5. Length affects how far the colored solutions migrate because the shorter it is the easier it is to migrate faster. Structure would also affect the speed. If the structure is thin and long, then it will be much slower than a short and contained one.

6. An electric current moves the dyes through the gel. The dyes have a negative charge, and  a positive charge is put at the other end of the box and a negative charge is behind it. The dyes repel the negative charge and are attracted to the positive charge which causes them to move.

7. The gel is filled with tiny holes. The smaller the molecules are, the easier it is for them to avoid the holes and get to the other end. The bigger molecules take a more time to navigate around the holes, causing them to get left behind.

8. The DNA with the weight of 600 daltons would be the farthest from the well. Then it would be 1000, 2000, and 5000 respectively. The heavier pieces of DNA would be bigger and the lighter pieces would be heavier. The smaller pieces of DNA always travel faster than the bigger ones. (refer to question 7) 

Before the current flows

In the box

Out of the box

The color dye samples

Recombinant DNA lab

First locate the gene of interest and organism to insert the gene into, which was the insulin gene in this lab. Then, obtain a plasmid from bacteria and what is its antibiotic resistance. In this lab, our plasmid was resistant to ampicillin.
Next, find a restriction enzyme that makes one cut in the plasmid and one above and below the gene of interest so it can be taken out and inserted into the plasmid. Restriction enzymes cut DNA wherever they find a specific sequence. It cuts using "sticky ends" so that the DNA base pairs can easily bond together. We used Hin dIII because it made only one cut in the plasmid and the closest cuts above and below the insulin gene. If the enzyme had made two cuts in the plasmid, then the DNA would break apart, resembling two unattached semicircles.
Then, add ligase to stick the ends of the gene into the plasmid. After that, plate bacteria on petri dish with the antibiotic mixed. We could use ampicillin since the plasmid we chose to insert the insulin gene into was resistant to it, and only those with ampicillin resistance would survive; therefore, those would be the ones with the insulin gene. We would not use tetracycline or kanamycin because our genetically modified bacteria would be killed because they are not resistant to these antibiotics. Finally, we would transfer the bacteria to a "broth" so they will multiply quickly and then extract and purify the protein the inserted gene produced.
This process is important in our everyday lives because it provides people who cannot produce a certain protein with a way to get it into their bodies, for example diabetic patients cannot produce enough insulin, but because of recombinant DNA they can take insulin injections or pills. This process could also be used to make vaccines and make crops resistant to pesticides or enhance their flavor and nutritional content.

New Year's Goals

Last year/ semester was good, but this year/ semester should be even better!

My first goal is to receive a high A or an A+. The plan I have is as follows: consistently receive good grades on the tests and labs. To do this, I will start studying for my tests a week and a half in advance. I will read the relate and reviews, and then study in depth for 20-30 minutes each night leading up to the test.
My second goal is to manage my time much more efficiently. I will do this by completing my homework on the day it is given, and start planning for long term projects. I will also allot time to study for tests and use tutorials wisely.