Unit 6 Reflection

Unit 6 Reflection

This unit was about Biotechnology, including bioethics, which is the study of decision making about moral because of advances in biological tech,  and recombinant DNA, which is the inserting of one organism's DNA into another. We also learned about the four applications of biotechnology, which are Medical/Pharmaceutical, Industrial/Environmental, Agricultural, and Diagnostic. In addition to that, we learned about the process of gel electrophoresis, which separates DNA based on strand size,   PCR, which amplifies a specific region of DNA, and bacterial transformation, which is when something (like a plasmid) is transferred to another bacteria. 

Bioethics were a little hard for me, because sometimes I was split between whether a technology was right or wrong and I couldn't decide. Recombinant DNA, PCR, Gel Electrophoresis, and Bacterial Transformation were all easy to understand and demonstrate.  My group was very successful on both the candy electrophoresis lab and the pGLO lab. We had a large number of glowing bacteria and the result of our gel electrophoresis lab was very clear. 

In this unit we did a Recombinant DNA Lab, an Electrophoresis Virtual Lab, a Candy Electrophoresis Lab, and a pGLO Lab. From each of these labs, I learned one of the themes from unit 6.  The Recombinant DNA Lab taught me how to make Recombinant DNA, the two Electrophoresis labs taught me how to set up and analyze a Gel Electrophoresis, and the pGLO lab taught me the process of bacterial transformation. 

I would like to learn more about the benefits of bacterial transformation and other things its used for besides mass-producing insulin.  I have no unanswered questions from this unit. I wonder about genetic engineering in the future, and just how life changing it will prove to be. 

My goals for the new year were to become more neat, and to become better at balancing school and sports. I have definitely made progress towards my neatness goal, as my notebook is very clean and my handwriting is legible throughout, unlike my previous one from last semester. I have yet to find a perfect schedule for me to finish homework earlier after my sports, but have definitely become more on task and focused while doing my work at home. My next steps for my goals are to make sure that I  fill in my table of contents right after I do an assignment, and to create a physical schedule to follow which accounts for all the different parts of my day. 

Electrophoresis Virtual Lab

Electrophoresis Virtual Lab

Link:
http://learn.genetics.utah.edu/content/labs/gel/


Make a prediction:
1. How do you think you could figure out the lengths of the strands in the tube of DNA?
 By using Gel Electrophoresis, which we learned about previously in our vodcast.
Go through the simulation:

2. What is the process called in which we measure the DNA microscopically? 
It is called Gel Electrophoresis.

3. What is the “gel”?
It like a Jello sponge with super small holes in it. It sorts the DNA strands.

4. Write down the step of gel electrophoresis
a. Make/set up gel.
b. Place DNA samples into the wells at the end of the gel.
c. Add an electrical current and run the gel.
d. Stain the DNA strands and analyze the results.

5. What does the current do the DNA samples?
The current makes the samples move towards the positive part of the gel.

6. What kinds of strand move quickly and further down the gel? 
The smaller strands move quicker.

7. What kinds of strand move slower and lag behind?

The bigger strands move slower.

8. What about the strand that are the same length?
Strands that are the same length move the same distance and speed.

9. What helps us see the DNA strand in the gel? 
Staining the DNA strands helps us see them.

10. What are the ingredients to make a gel? 
Make your Gel!
Powdered Agarose, buffer, flask, microwave, gel mold, and gel comb

11. Load the Gel with the DNA!

12. After you load the DNA sample into the tray,what is the next step?
The next step is to add an electrical current

13. How do you know current is running through the gel?
You know current is running through the gel because air bubbles will be coming up from the electrodes on either side of the gel.

14. After the gel is done,what must you do to it before you can analyze your results? 
You must stain it before you can analyze it.

15. How long does this process take? 
This process takes about 30 minutes.

16. What type of light do you use to view the gel? Is it safe and what precautions would you might need to use?
You use UV light. It can hurt your eyes, so it is necessary to wear goggles.

1. Take a screenshot of your gel and paste below.

18. Write your size estimates below:
a. Strand1_______6000_______
b. Strand2______3500_________
c. Strand3______1500__________ 

19. Could you list one reason why we would run a Gel electrophoresis on someone and explain your answer.
We could run Gel electrophoresis on someone to run a paternity test based on DNA fingerprinting. If the parents are the child’s biological parents, then the gel electrophoresis on his DNA will be a combination of theirs.

Relate and Review
Write at least 5 sentences summarizing the process of electrophoresis and relating to what you’ve learned before.
To figure out the lengths of pieces of DNA, we use gel electrophoresis. This process consists of four steps. First, we make the gel out of Powdered Agarose and a buffer, and set up the gel with the current. Second, we place our DNA samples inside the wells at one side of the gel (near the side with the negative current). Third, we add the electrical current to run the gel. Finally, we stain and analyze the strands. We can use this process for paternity testing, and much more. 

pGLO Observations , Data Recording & Analysis

pGLO Observations , Data Recording & Analysis

1.

Obtain your team plates.  Observe your set of  “+pGLO” plates under room light and with UV light.  Record numbers of colonies and color of colonies. Fill in the table below. Plate Number of Colonies Color of colonies under room light Color of colonies under   UV light - pGLO LB carpet gray gray - pGLO LB/amp 0 gray gray + pGLO LB/amp 104 gray gray + pGLO LB/amp/ara 1/2 carpet/ 64 gray green (glowing)

2.	What two new traits do your transformed bacteria have?
	My transformed bacteria glow in the dark and are resistant to ampicillin.
3.	Estimate how many bacteria were in the 100 uL of bacteria that you spread on each plate. Explain your logic.
	I think about 90 bacteria, because E. coli are about 1-2 micro liters each, and there were 100 micro liters.
4.	What is the role of arabinose in the plates?
	The arabinose made the bacteria glow by inhibiting the promoter and allowing the DNA polymerase to read the GFP Gene.
5.	List and briefly explain three current uses for GFP (green fluorescent protein) in research or applied science.
	Three current uses for GFP are to study cancer in mice, to remove malaria gene in mosquitoes, and to study the spread of HIV in cells.
6.	Give an example of another application of genetic engineering.

Crops that are resistant to herbicide.

Candy Electrophoresis Lab Analysis

Candy Electrophoresis Lab Analysis

1. When we analyzed the results of our gel, we found that none of our sample dyes contained different dyes than in the four reference dyes.  However, the dye band from our blue M &Ms was bigger than the Blue 1 reference dye. Also our green Mike & Ike band was much smaller than the yellow 6 reference dye. Our brown M&M had a multicolor band, with both red and blue. None of our dyes moved in the wrong direction. 

2. The Blue 1 reference dye would migrate similarly to the carminic acid, because they have similar structural characteristics.  The Red 40 reference dye would migrate similarly to the Betanin, because they both are bonded in similar patterns. The Blue 1 reference dye would migrate similarly to the Fast green FCF, because they are very very similar in their structure. The Red 40 reference dye would migrate similarly to the citrus red 2 because their structural characteristics are alike in many ways. 

 3. Dog food Manufacturers might put artificial colors in dog food to make the food look more appealing to the dog owners. 

5. The two factors which control the distance the colored dye solutions migrate are charge and size.

6. The electrical current helps move the dyes through the gel. 

7.  The small holes in the gel allow the smaller DNA strands to move quicker through tot he end with the positive charge. The bigger strands have a harder time going through. 

8. I expect the molecule which weighs 600 daltons to go the farthest, and then 1000, then 2000 (probably covering half the distance of the 1000) and then the 5000 very very far behind. 

Recombinant DNA Lab Analysis

Recombinant DNA Lab Analysis

In this lab, we made "recombinant DNA" models out of paper. Recombinant DNA is created through a process called transformation. First, a "gene of interest" is located, finding the location and sequence of the gene and its surrounding sequences. In our case, this gene was called the insulin gene. During transformation,  Enzymes called Restriction Enzymes cut the DNA when it reaches a specific sequence of bases. Different enzymes cut at different sequences. We used an enzyme called Eco RI, because it cut our plasmid once and our DNA twice, close to the gene of interest. This is important because it allows us to splice in the insulin gene to the plasmid. If we used an enzyme which cut the plasmid in two places, then the plasmid would be split into two pieces and we wouldn't be able to put in the gene. When it cuts it, it leaves a "sticky end," which helps the DNA bond with other DNA or plasmids. Plasmids are rings of DNA most commonly found in prokaryotes. Usually they have genes in them which give antibiotic resistance. Our plasmid contained a gene for resistance to both Tetracycline (used to treat acne and skin infections) and Kanamycin (treats serious bacterial infections). Ligase, an enzyme which puts base pairs back together, bonds the cut plasmid and DNA. Then the recombinant plasmid and bacteria are mixed, and the non-resistant bacteria are weeded out by adding whichever antibiotic the recombinant plasmids are resistant to.  For example, we would add in either Tetracycline or Kanamycin, because if the bacteria have taken in our plasmid, which has resistance to both, than it will survive. If it doesn't, it won't. We wouldn't use an enzyme such as ampicillin, because our plasmids are not resistant to it.  After the mixing, the gene is extracted and purified. This process is important in our everyday life because it allows us to mass produce necessary items such as insulin and more. This process could be used for herbicide or pesticide resistant crops or to clone organisms as well.

This picture is of our "recombinant plasmid" and the different restriction enzymes.

New Year Goals: 2016

New Year Goals: 2016

My first goal for the semester is to have neater, more thorough work in Biology.  I often rushed on assignments in first semester, and had terrible penmanship throughout. This worked against me in the long run, when I went back to study my completed notes and labs, I couldn't read them. I will achieve this by taking more time on my notes and being more careful when writing my lab reflections and relate and reviews.

My second goal for the semester is to to become better at balancing my schoolwork and extracurricular activities. To do this, I will focus more on my work my working in my room at my desk, and I will bring my smaller work with me in the car. I will make a schedule and plan my time according to practices and free time.