Unit 6 Reflection

This unit was all about biotechnology. The introduction of biotechnology discussed how it is known as the study and manipulation if living things in order to benefit mankind. This large field focuses on understanding DNA, proteins, and inheritance. There is a long timeline of biotechnology.

•  It began in 4,000 BCE in the classical biotechnology time period, where dairy farmers developed in the middle east and Egyptians used yeast to bake and learned to make wine through fermentation. 
• In 3,000 BCE Peruvians selected and cultivated potatoes.
•  In 2,000 BCE Egyptians, Sumerians, and Chinese develop techniques of fermentation: brewing and cheese making. 
• In 1500 CE acidic cooking techniques led to sour kraut yogurt- 2 examples of using beneficial bacteria to flavor and preserve food. Aztecs make a cake from spirulina algae.
• In 1861 french chemist Louis Pasteur develops pasteurization: preserving food by heating it to destroy harmful microbes.
• In 1910 American biologists Thomas Hunt Morgan discovers that genes are located on chromosomes
• In 1953 James Watson and Francis Crick Describe the double helix of DNA using x-ray diffraction patterns of Rosalind Franklin and Maurice Wilkins.
• In the early 1970's Paul Berg, Stanley Cohen, and Herbert Boyer develop ways to splice DNA, introducing recombinant DNA techniques.

A big emphasis in the introduction to biotechnology was the 4 real-life applications of the science and its effect. 

• Industrial and Environmental: Fermentation- the use of bacteria or yeast in an oxygen-free environment to convert sugars into acids, gasses or alcohol. (ex: food like yogurt, cheese, beer, wine, bread etc)
• Medical and Pharmaceutical: Gene therapy-putting a healthy copy of a gene into cells of a person whose copy is defective, Germ Line gene therapy- insert the gene into germ cells(sperm/egg), Somatic gene therapy- insert the gene into specific cells w/defective expression of the gene. 
• Agricultural: Classical breeding- individuals with desired traits are bred over many generations. GMO/Transgenic organisms are the product of recombinant DNA(Foreign DNA inserted in them)
• Diagnostic: Genetic testing- search for genes or DNA segments indicating risk for various diseases or disorders.

An interesting infographic about GMOs 

We also talked about the "technologies of biotechnology" and the different steps and procedures commonly used. We talked about Polymerase Chain Reactions (PCR) first, and then we talked about Gel Electrophoresis. We had already learned about gel electrophoresis when we did our Candy Electrophoresis Lab and our virtual lab.
   The lab was long, but it was lots of fun. It really helped me understand how gel electrophoresis really works. Although some errors got in everyone's way(as mentioned in the link), I feel like I have a better understanding of why each step in the procedure was there. Also, I learned how to use a micropipette to fill the wells of the gel after extracting the colored dyes from candies.

PCR: A procedure to amplify a specific DNA region that yields millions of copies of a sequence of DNA. It is the first step in preparing DNA for many experiments like gel electrophoresis and any other form of analyzation. The process makes millions of copies of the small DNA fragment so it is easier to study.
Check out this video that explains PCR: https://www.youtube.com/watch?v=3XPAp6dgl14

Steps of PCR:

1. Denature the double stranded DNA with heat
2. Anneal the primers to single stranded DNA above and below the region of interest. *A primer is a small fragment of DNA that bonds with a specific sequence.
3. Extend primers with DNA polymerase yielding new double stranded DNA. This cycle repeats steps 1-3 usually 20-40 times. The copies from PCR occur in exponential amplification which means after 30 cycles, DNA is amplified over a billion-fold. 

Helpful diagram displaying PCR

Gel Electrophoresis is the use of electricity to separate DNA fragments based on size. Large pieces travel slower than small pieces, and the results of distance traveled by the unknown lengths are compared to those of known lengths. It has many different applications such as forensics, biochemistry, genetic diagnosis, etc.

Sequencing was also discussed in the vodcast. Sequencing by definition is determining the exact order or sequence of a given DNA strand. DNA polymerase, primers, extra bases, and fluorescent dyes are all used to create copies. These copies are one base longer and contain fluorescent dyes attached. They are then electrophoresed and analyzed with a computer. The result is an electropherogram and the colored bases represent 1 of 4 bases. Finally, the sequence of bases is recorded.

Recombinant DNA was also discussed, where DNA of one organism is inserted into the DNA of another organism. Recombinant DNA or rDNA is also known as genetic engineering. The result of rDNA is GMO's (genetically modified organisms) or transgenic organisms. The steps followed to use rDNA technology in bacteria is as follows.

1. Gene of interest: know the location and sequence of your gene(above and below it)
2. The restriction enzyme cuts DNA wherever it reads a specific sequence. It latches onto the restriction site. Each restriction enzyme leaves a sticky end at the cut, which allows DNA to bond other DNA. 
3. Plasmids: circular DNA found in prokaryotes contains a replication gene that tells the plasmid to be copied. Typically it contains genes with antibiotic resistance that are small enough to be passed through pores of the cell membrane.
4. Ligase: an enzyme that re-attaches base pairs. 

The process of transforming bacteria to mass produce a protein product:

1. Isolate the DNA by finding the gene of interest and organism to insert the gene into
2. Get the plasmid, and know what antibiotic it is naturally resistant to
3. Digest  the DNA by finding a restriction enzyme that will cut the plasmid once above and below the gene
4. Mix the digested DNA(plasmid + gene)
5. Add ligase to attach sticky ends
6. Mix recombinant plasmid with the bacteria
7. Plate bacteria on agar with the antibiotic mixed in (only those with the plasmid(antibiotic resistance) will survive)
8. Grow the transformed bacteria and transfer to broth(liquid agar) to make many bacteria expressing the gene
9. Extract and purify the protein the inserted gene produced. 

Recombinant DNA technology has an interesting history. It was discovered when Herb Boyer and Stanley Cohen met at a conference. With their combined knowledge of restriction enzymes and isolating genes, they were able to work on the toad/bacteria rDNA together in the March of 1973. They discovered how DNA could be transferred between different species, and the world of genetic engineering was born. 

Another topic was the pGLO lab, which elaborated on the previous vodcast. It was about the bacterial transformation of an e.coli bacteria, using the presence of plasmid for a fluorescent glowing reaction.  My pGLO Lab Analysis and this video do a great job of explaining the process. Without doing the virtual lab, and the pGLO lab, I would have little understanding of how the procedure occurs, and why every step does what it does.  https://www.youtube.com/watch?v=OZyFX9megs8
   I learned how to predict which bacteria would glow, grow, or have nothing at all. For example, the plate with just LB, or lysogeny broth which makes the bacteria grow, would have bacteria on the plate. The plate with LB/amp (ampicillin, the antibiotic which the plasmid is resistant to) without the plasmid would not grow. The plate with LB/amp with the plasmid, would grow. Lastly, the plate with LB/amp/ara (arabanose is the sugar that acts as a promoter of the GFP gene, controlling its expression) would grow bacteria and glow with green flouresecnt protein. 

A picture of the results of another group in the class.

The last, most unique topic explored was about bioethics, and how we should answer not only ethical but bioethical questions. I feel like it has really opened my eyes to what my morals and values are, which will help me make ethical decisions in the future. The answer to ethical questions come from your morals(your justification of what is right or wrong), and your values(what is most important based off of your unique, personal experiences). The same approach is taken when you are faced with a bioethical question. You must first clarify your values, then identify the issue. Find as many options possible, and then list the pros and cons of each decision . Rank your ideas from best to worst, and once you've come to a decision, defend it. 

After reading articles in class, I wonder about all the infinite possibilities and ideas people can come up with to apply biotech. After listening to summaries of other classmate's articles, I was intrigued by the various fields and forms biotech took. I did further research on my own article about gene editing tools used to cure genetic diseases caused by mutations which you can find on my blog: Bioethics Reading. That's why it was a bit of a struggle for me to get started on my 20-time project, because I wasn't used to such vast boundaries. Usually, there is a set goal, but I think this free- thinking has really reignited my creativity. 

Lastly, I have been checking in on my New Year Goals, and I have found that I've been improving my studying skills. I can identify the forms of studying that are best for me, much quicker for each topic, but I still struggle with time management. As for drinking more water, I have bought a new water bottle, and I have been motivated to stay hydrated. I think overall, I am making good progress for both of my goals, but there is always room for improvement. 

Works Cited:

GMO infographic. Digital image. Kids Right to Know. N.p., n.d. Web. 31 Jan. 2017. <http://www.kidsrighttoknow.com/wp-content/uploads/2010/05/What-is-a-GMO.jpg>.

Polymerase Chain Reaction - PCR. Digital image. Wikimedia. N.p., n.d. Web. 31 Jan. 2017. <https://upload.wikimedia.org/wikipedia/commons/thumb/9/96/Polymerase_chain_reaction.svg/835px-Polymerase_chain_reaction.svg.png>.