pGLO Lab Questions

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 tan tan - pGLO LB/amp carpet tan tan + pGLO LB/amp 130 tan tan + pGLO LB/amp/ara 150 tan green Comments: The -pGLO LB and the -pGLO LB/amp plates were switched when labeled.

2.	What two new traits do your transformed bacteria have?
	The resistance to the ampicillin and the bacteria could glow under UV light.
3.	Estimate how many bacteria were in the 100 uL of bacteria that you spread on each plate. Explain your logic.
	If you use the carpet for reference, I think that there are about a thousand to ten thousand bacteria. The reason that I think this is because the carpet is very spread out along the plate, so there will be a lot of bacteria.
4.	What is the role of arabinose in the plates?
	The arabinose, which is a sugar, had the effect of making the bacteria glow under the UV light. That is why, when you look at the plate with the arabinose with the ampicillin, LB and the pGLO and compare it to the exact same plate without the arabinose, you see that the one with arabinose will glow.
5.	List and briefly explain three current uses for GFP (green fluorescent protein) in research or applied science.
	The GFP is used because of its ability to generate a glowing color. GFP is used as a active indicator for protease action because then the scientists would know that it is working. Another reason why GFP is used is because it can glow inside an organism so the scientists could see what goes on inside the organisms cell. The third use is GFP is used for Biosensors, which allows you to analyze different conditions, like pH levels.
6.	Give an example of another application of genetic engineering.

In medicine, genetic engineering has been used to mass produce human growth hormones, insulin, monoclonal antibodies, vaccines and many more.

Candy Electrophoresis Lab Questions

When we did the green dye, there was an interesting discovery that we found. We discovered that when the green dye migrated, it separated into a blue and yellowish dye, in the same band.

The citrus red 2 dye is similar to the dyes in the lab because the structure of the citrus red 2 dye is similar to the structure of the red 40 dye that we used in the lab. Since the structure and the size of the two dyes are similar, then that means that the distance that it moves would be about the same.

The reason that some dog food manufacturers is because that the different colors could attract the dogs to eat the food. Another reason for this is that the food coloring in the dog food could make the food look more appetizing for the dog.

The reason that the people might use artificial colors over food colors because they can become brighter or more colorful without the use of a lot of the dye. The artificial color is cost effective and that is why manufacturers use artificial.

The two things that control the distance that the dye travels is size of the pieces along with the structure of the dye. These two control the distance because if the piece is smaller, then it travels farther.

The force that helps the dye move through the gel is the electricity that is running through the gel. (Negative and Positive charges)

The holes in the gel allow the molecules to separated by size. The way that this works is the smaller the molecule, the faster it can navigate through the dye and the farther they go.

The DNA molecules with those weights will separate through the holes, but some will just take longer to migrate.

Recombinant DNA Lab Analysis

In this lab, we simulated the process of producing recombinant DNA and how the enzymes were used to cut the plasmid and the DNA. There were many enzymes that we had to look through to see if the enzyme cut once in the plasmid and twice in the actual DNA. The way that we determined the plasmid was cutting out 4 strips and discarding two. The plasmid that we ended up with was resistant to tetracycline. We used this because the bacteria could survive and be produced. The other antibiotics that the plasmid were not resistant to, kanamycin and ampicillin, were not used to mass produce the bacteria. Restriction enzymes basically cut the DNA when it reads a specific sequence. We used the enzyme Hpa 2 because that enzyme could cut the DNA in two places, one above and the other below the insulin, and also the plasmid. If the plasmid was cut into two places, then the ligase could not reattach the base pairs because there are two so it could get confused. This is important because we could use this technology to make medicines or other things that could help humans in different aspects. This process is used to create fruits with delayed ripening so that it could have a longer life on the shelf of a store.

New Year's Goals

One of my SMART goals is that I will actually try and understand everything that is being taught this semester instead of just passively learning about it and then stressing out about the test the day before. That is my goal for this semester in biology. The way that I will be doing this is whenever there is a new assignment that is not due the next class, I will be working on it proactively so that I do not do it all the night before. My other goal that is not related to biology is that I will become more organized in my time management. The way that I will do this is by making a calendar of everything that I have to do so that I can look at what I have to do on the same paper.

Unit 5 Reflection

This unit was all about DNA, protein synthesis, the types of mutations and genetic regulation. We learned a lot about DNA, but some things that were key is that DNA has 4 bases of A,T,C,G and that the structure is a double helix. Protein Synthesis is the process for the production of proteins. The first step in protein synthesis is when the RNA polymerase copies the DNA into a RNA strand. This process is called transcription. Then the mRNA leaves the nucleus to try and find a ribosome. The ribosome reads the mRNA at a rate of 3 letters, which is called a codon. The codons are translating into the language of amino acids. The amino acids code for a protein. This is called translation. That chain of amino acids that is made is then called a protein. The types of mutations are point mutations and also frameshift mutations. Point mutations, which include substitution, happen in one area of the gene sequence. Frameshift mutations, which include insertion and deletion, shift the gene sequence for the reader. Gene regulation is when the genes prevents itself from being copied by the RNA polymerase. My strengths for this unit is understanding protein synthesis because I have learned this process before and it Mr. Orre's lessons really helped reinforce the process in my mind. One weakness that I have is understanding gene regulation. The reason for this was I was confused while watching the vodcast, but now I have a better understanding after Mr. Orre's diagram. I am a better student than before the unit because I learned about protein synthesis, mutations and also gene regulation in more detail. Now I can tell people how the processes work. Some things that I want to learn more about is the detail in gene regulation for eukaryotes. I wonder about how detailed gene regulation can get.

Protein Synthesis Lab

Protein Synthesis has three steps. First of all, there is transcription. During transcription, the DNA is replicated into an mRNA strand. Then the mRNA strand leaves the nucleus and enters the cytoplasm. In the cytoplasm, the mRNA arrives in the ribosome. The ribosome reads the mRNA 3 bases at a time, which is called a codon. It translates the mRNA strand into a language that the protein can understand, and that language is called amino acids. The end result is a chain of amino acids and this chain folds and twists until it becomes a protein.

Based on the experiment, I can conclude that mutations are very random in a sense that they might have a large effect or maybe no effect at all on the organism. The mutations that seemed to have the greatest effect on the gene sequence and the protein is deletion. When I simulated deletion, the DNA sequence changed significantly. In the DNA sequence without any mutations, the protein had a long chain of amino acids. However, when there was a deletion of a base pair, the mutation formed a stop codon very early in the sequence. This made the protein very short. Other mutations that I simulated were insertion and substitution. Insertion made a difference big enough in the sequence to change the protein. When I simulated substitution, the protein did not change at all. This proves that the effect mutations have is completely random. Mutations do have a difference in the impact of where they are placed. The protein will have a bigger difference if the mutation is in the beginning instead of later on in the sequence.

In step 7, we got to choose our own mutation. I chose to do deletion and deleted the first and third base of the entire sequence. The reason that I chose to do deletion was because it made the biggest impact and I wanted to test how far a mutation can change the protein. After I finished translating from the RNA strand to the amino acid language, I found out that with my mutation, the protein never had the start codon, so the protein never started to be made. Yes it definitely does make a difference if you put the mutation in the beginning than in the end. The reason for this is if the mutation is at the beginning, there is a higher chance that there will be a mutation that will make an impact on the protein.

One mutation that causes a disease that we have not learnt in class this year is a disease called Hypertrichosis. Hypertrichosis, also known as "werewolf syndrome", is a very rare disease and is a disease that is formed by a mutation in chromosome 8. The chance of getting this disease is one in a billion and only 50 cases have been reported. This disease creates a lot of hair on the face, ears and the shoulders.

DNA Extraction Lab Conclusion

In this lab, we asked the question, "How can DNA be separated from cheek cells in order to study it?" We found that DNA could be separated from the cheek cells by alcohol through a simple procedure. First of all, we have to scrape the sides of our cheek with our cheeks. Then we had to put a little but of gatorade in our mouth and then we swished the fluid for 30 seconds. Then we spit it back into the cup. After that, we had to add 10 drops of pineapple juice, which served as the enzyme for the experiment, 10 drops of dish soap and lastly a little bit of salt. Then we put the liquid in a test tube and inverted it 6 times. After that, we added some cold rubbing alcohol, which made the DNA visible. The reason that the DNA became visible was because of a few key steps. One key step was the salt that was added. This facilitated the precipitation of the DNA with caused the DNA to become a solid. Also, the soap water helped lyse the cell membranes. The pineapple juice helped break down the histones of the DNA. Lastly, the alcohol, which is non polar, and the DNA, which is polar, were put together so that the DNA would come out of the solution and become visible. This evidence does support our claim because the procedure showed that the DNA separated.

One error that could have occurred was during the part when you added the alcohol. The alcohol could have mixed with the solution if you were not careful when putting the alcohol in. This could have effected the final result because then the DNA would not become visible. Another error that could have occurred was the amount of pineapple juice that was put into the gatorade. This could have made an effect because if there was too little enzyme that was put in, then the DNA would not precipitate enough to become fully visible and separated. This would also change the end result because then the DNA would not be fully visible. Some recommendations that I have for this lab in the future is that there should be more precise measurements because 10 drops is not very specific. Another recommendation is that there should be an easier way to make sure that the alcohol and the DNA do not mix rather than just tilting the test tube and pouring in the alcohol.

The purpose of this lab was done to figure out if DNA was indeed able to be separated from cheek cells. This lab relates to enzymes and how they work to separate DNA. Based on my experience from this lab, I could apply the knowledge that I learnt and apply it to separating DNA not only from our mouth but from different parts of our body.