Gel Electrophoresis Virtual Lab

Gel Electrophoresis Virtual Lab Worksheet Name_Jonathan Li____________________

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 identifying where the flurorescent dye is attached which stops the synthesis on the strand.

Go through the simulation:

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

3. What is the “gel”? Filter that sorts DNA strands and made of Jell-o with small holes.

4. Write down the step of gel electrophoreses

Set up gel apparatus.

2.  Look DNA sample in gel.

3. Hook electric current and run gel.

4. Stain gel and analyze results.

5. What does the current do the DNA samples? Pass positive and negative energy through gel.

6. What kinds of strand move quickly and further down the gel?

Shorter strands

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

8. What about the strand that are the same length?

They move the same speed and are grouped together.

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

Electrphoresis box

10. What are the ingredients to make a gel? Make your Gel!

Powdered agarose, flask, Gel Mold, Gel Comb, Buffer, Microwave.

11. Load the Gel with the DNA!
12. After you load the DNA sample into the tray, what is the next step? Look at the gel box to see what is happening.

13. How do you know current is running through the gel?

By the bubbles being produced.

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

Take the gel mold out of electrophoresis box.

15. How long does this process take?

Half an hour

16. What type of light do you use to view the gel? Is it safe and what precautions would you might need to use?

UV light, which isn’t safe and you want to wear protective or safety googles.

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

If you do not know how to take a screen shot go to http://www.take-a-screenshot.org

18. Write your size estimates below:

1. Strand 1_3000 bp__________________

2. Strand 2 2000 bp____________

3. Strand 3  1500 bp___________________

19. Could you list one reason why we would run a Gel electrophoresis on someone and explain your answer.

To determine whether their DNA can be seperated at anytime esp. electric voltage, since voltage creates shock and whether DNA can resist to it, is the main reason why.

Relate and Review

Write at least 5 sentences summarizing the process of electrophoresis and relating to what you’ve learned before.

In this Gel Electrophoresis lab, we learned the process of Gel Electrophoresis, by first setting up the gel apparatus, using the electric current to move strands toward gel. Then look for the DNA sample in gel. Next, hook electric current and run gel by the  electric current moving bubbles inside. Finally,  stain the gel and estimate length of DNA strands. Gel Electrophoresis is mainly seperating the DNA fragments or strands using the electric voltage or current. This relate to Mr. Orre’s vodcast of technologies of Biotech , when he introduced Gel Electrophoresis and how it seperates DNA.

pGLO lab conclusion

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 0(carpet) white light tan - pGLO LB/amp 0 white white + pGLO LB/amp 75 white white + pGLO LB/amp/ara 250 tan/green green

2.	What two new traits do your transformed bacteria have?
	Ampicillin resistance and ability to glow by shining UV light on it.
3.	Estimate how many bacteria were in the 100 uL of bacteria that you spread on each plate. Explain your logic. About 1000 microliters of bacteria because adding 25 to each plate and the +Glo LB/amp/ara had 250 colonies which is 10 times the amount of bacteria from adding the bacteria to the plate. so 100(10) equals 1000 microliters.
4.	What is the role of arabinose in the plates?
	To express the gene of the plasmids having that sugar, in order to let bacteria glow.
5.	List and briefly explain three current uses for GFP (green fluorescent protein) in research or applied science.
	It is used to image pathogenic bacteria, an indicator to show when one glows, the other glows, and gives quantitative amount of bacterial association with mammalian cells.
6.	Give an example of another application of genetic engineering. Genetic Engineering helps create Genetically Modified Organisms in Agriculture, and in organisms, determine the functions of their certain genes.

Candy Electrophoresis Lab Conclusion

In this lab we explored how by taking the dye out of the candy can be used for gel electrophoresis. When we analyzed our results, we found that only the experimental yellow dye did not match the reference green dye, but all the experimental dyes were a different size to the reference dyes as they were smaller compared to the reference dyes. The structure of Carminic acid migrates similarly to dyes is because like the OH and O sticking out forward, the red and blue dyes are the only dyes to shoot up after gel electrophoresis and the fact that it is a double layered structure, that is why it is Carminic acid.

3.

For example, a dog food manufactures put artificial food colors(FD&C dyes)  in dog food, so that it prevents the chance of them being sick or having some bad disorder. 2 factors that control the colored solution dyes to migrate is the size and structure of the dye from the candy(M&M, Skittles, or MIke Ikes). These dyes are being moved through the gel by electric voltage so that they are able to spread the dyes out, as shown above. The component of gel electrophoresis that causes the dye's molecules to seperate by size, is when the electric current is present ,dyes spread out by their size, as shown above. Finally, if I had to deal with molecules of 600,1000, 2000, and 5000 daltons, the 600 daltons would separating the furthest, and the 1000 daltons seperating a little further than 2000 daltons, but very close to each other. Then, the 5000 daltons would be still not be seperated its' dye. From this lab, I was able to learn how the dyes in the candies (Skittles, M&Ms', and Mike Ikes) we eat, have different migration patterns under Gel Electrophoresis based, on the size and structure from looking at the candy itself.

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Extra Credit:Preventing Genetic Identify Theft

In order to make Genome Sequencing useful and valuable, the Presidential Commission for Study of Bioethics provided a report that provides recommendations of protecting the individuals in Genome Sequencing, such as having the state and federal government outlaw genome sequencing without consent and improving the database's securities that store the genetic information so that it gives new models for integrating whole genome sequence in health records. The reason that the commision made this decision is when it used to be carried by clinicians from Health Insurance Probability and Accountability act, it revealed inadequeate security for genetic protection in commercial and research arenas, leading only half of US states protecting individuals against surreptitous commercial sequencing. This can be dangerous and drop the genome sequencing cost from 2.5 billion to 1000 dollars , leading to a collapse in commercial sequencing. “In many states in the U.S., someone could legally pick up your discarded coffee cup, send a sample of your saliva out for sequencing to see if you show a predisposition for certain diseases,” Gutmann explained.(End of Pg.1). So protecting the individuals in Genome sequencing will be important to protect the value of genome data.

http://knowgenetics.org/wp-content/uploads/2012/12/kevin2.png

http://cdn.globalbiodefense.com/wp-content/uploads/2014/06/genomic_sequencing_usamriid.jpg

What is good of protecting Genome sequencing is it does not cause the value to decrease or lessen, therefore preventing crashes in the sequencing, and the system has a great chance it will not be hacked because of the state and federal government monitoring.  The risks of protecting Genome sequencing is that the state and federal government has other to worry about than Genome Sequencing, causing them to not always having time to supervise the Genome sequencing. Also what happens if some states still do not want to protect genome sequencing, they become hackers, and sooner or later, they will find some way to hack the system, therefore crashing its' value.

http://www.stateside.com/wp-content/uploads/2012/04/us-capital-300x210.jpg

Protecting Genome Sequence is better since there is a very rare chance that someone will be able to hack Genome Sequencing because of the new models in the genome database.  The states would be forced to do it ,even though they reject the idea, by the state and federal government, who are recommended to protect the system of Genome sequencing. Also, even if Genome Sequencing gets hacked, the State and Federal Government will hunt down and possibly provide refund in Genome Sequence's money value, making it trustable. “Trust is the key to amassing the large number of genomic data sets needed to make powerful life-saving discoveries,” the commission wrote in a statement. (End of Page 2). So if you want the genome data, which contains human health and medicine, to be saved, then protecting the Genome sequence is the trustable and reasonable choice.

http://dmlcompetition.net/Blog/wp-content/uploads/2014/10/trust.png

Unit 6 Reflection

In this unit we learned about Biotech and the fields that apply to it, specifically, Industrial/Environmental Biotech that includes Fermentation which uses yeast to convert sugars, Agricultural Biotech that has Classical breeding that is used to predict how many species are to produce from breeding over time, Medical Biotech including Gene therapy which replaces the gene copy that is defective, and finally Diagnostic Biotech which is used in testing to search possible genes or DNA that cause disorders. We also learned the steps of creating Recombinant DNA by first identifying the Gene of Interest, find its’ antibiotic resistance in the plasmid, then find the area of the gene that Restriction Enzymes cuts once as well as above and below region. Next, we use Ligase to mix the sticky ends of the Restriction Enzymes, and mix Recombinant plasmid with bacteria, by placing it on agar mixed with antibiotics. Then we grow transformed DNA and transfer to broth to make bacteria to express gene, with finally extracting and purifying protein once gene is produced. The last few steps from when it places Recombinant DNA on agar oto using broth to express gene to purify the protein is part of pGLO, and was used in our pGLO lab. We also learned the technologies of Biotech, with first, PCR preparing DNA for future analysis, and then using Gel Electrophoresis to separate DNA fragments based on size, and uses a ruler to determine the number of base pairs. Next, DNA  is being sequenced where it is determined by order of bases, and by having an extra Fluorescent dye attached at each sequence ends the synthesis of the strand and determined which strand goes first. Then it copies Gel Electrophoresis onto a computer to result an Electropherogram. We also had labs like the Candy Electrophoresis lab where we use the steps of Gel Electrophoresis by extracting the dye of the candy to observe what happens to the dye when it is put under the Gel Electrophoresis, and the answer to it is it seperates from the dye where smaller dyes seperate farther from than larger dyes. Also, along with Recombinant DNA, we had the Recombinant DNA lab where we identify any restriction enzymes in the plasmid near the Insulin gene and cut it once. Finally, the pGlo lab was about testing different plates when under Lorraine Broth,and/or Ampicillin, and/or Arabinose.

My strengths in the Unit are knowing the applications of Biotech,Bioethics and the technologies of Biotech. I still need to study more of the Recombinant DNA process, with the steps along with it.

By learning from this unit, I learned Biotech is used in our daily lives, and has many fields to it. The applications to Biotech is a lot, but I need to know the important ones like Engineering and doing Diagnostic testing. I am a better student than yesterday, and will study more for the upcoming test, by looking over the vodcasts more. I have did more of asking questions, which was one of my New Year's goals and thinking about others, but I still need to work on shushing others and accepting "constructive criticism.

Recombinant DNA Lab Conclusion

In the Recombinant DNA Lab, me and my partner discovered in order for Recombinant DNA to transfer with another organism’s DNA sequence, we needed to identify the restriction enzymes, specifically those that are closer to the insulin gene. If bacteria takes in our plasmid, I would chose antibiotics of ampicillin, and kanamycin, because ampicillin gives treatment probably too the most important systems of the body, urinary, that is used to pee and respiratory system to breath normally,and kanamycin is an antibiotic drawn from a strand of bacteria, so I would want an antibiotic that is used to fighting against bacteria, because it will know what to do if bacteria enters the immune system I would not use tetracycline, because it gives treatment to those who have four legs, and humans have two legs. Restriction enzymes cut DNA fragments and have a “sticky end” that allows DNA to recombine with each other.I chose Eco RI, mainly as my restriction enzyme since it was the closest to the insulin gene I found in the red enzyme. If we cut plasmids, we would have to find 2 different organisms that can use ligase to connect restriction enzymes from DNA sequences together. This relates to our daily life of whenever we get sick, we use antibiotics to resist the plasmids in the bacteria, in order to maintain our DNA sequence in order, and healthy. This Recombinant DNA process can be used to determine the genetic disorders  in someone’s DNA sequence, and what antibiotics or medicine should they take(gene therapy; Medical and Pharmaceutical Biotech).

Couldn’t take any photos,due to class time. Sorry.