pGLO Lab

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 Opaque white white + pGLO LB/amp Around 50 Opaque white white + pGLO LB/amp/ara Around 75 Opaque white Glowing green

2.	What two new traits do your transformed bacteria have?
	Our new bacteria grew/multiplied in colonies and can glow when under the UV light.  The new bacteria are also now resistant to ampicillin.
3.	Estimate how many bacteria were in the 100 uL of bacteria that you spread on each plate. Explain your logic. In the 100 uL of bacteria, I estimate that there were about 50-80 bacteria. This is because a colony is one bacteria that split up to form more, so if you count the colonies then you will get an estimate on how many bacteria there are.
4.	What is the role of arabinose in the plates? The role of arabinose in the plates is to make the bacteria is to make the bacteria glow when the UV light is shined on them.  It glows because arabinose makes the plasmid produce GFP and shine under UV light.
5.	List and briefly explain three current uses for GFP (green fluorescent protein) in research or applied science. 3 current uses for GFP in research or applied science is they can be applied to cancer cells, so doctors can track and observe the cancer cells for developing a cure or just for research. The second reason that I found is scientists attach GFP to insulin producing cells for diabetic research. Another way GFP is used is to track the spread of diseases like HIV.
6.	Give an example of another application of genetic engineering. An application of genetic engineering is in the food industry. A lot of our foods are GMOs or Genetically Modified. Farmers change the makeup of crops to make them more visually pleasing and last longer and more preventative to diseases.

Candy Electrophoresis Lab

1. When I analyzed the results of my gel electrophoresis lab, my results were that nothing had really moved except for the red and blue dye. The red dye band and the blue dye band's width was the same as it's reference band.  However the red dye traveled father than the blue dye which signifies that the red dye is smaller than the blue.

2.  The dye bentanin would probably move towards the blue dye because both of those are bigger than other dyes which means that they would probably come together. Likewise, Citrus Red 2 might move towards Red 40 because they are also similar in size.

3.  Dog food manufacturers put artificial food colors in dog food in order to make the food more appealing, and to make dog owners feel like they want that for the their pet. The more fresh it looks (by adding dye) the more pet owners feel like that is  what they should be feeding their dogs.

5. The factors that control how far a dye migrates is what size the dye is : smaller dyes move father than larger dyes and also the positive pull on the particles determine how far they move. In gel electrophoresis, the reason they move is because there is a positive electrical current pulling it, so that electrical current is a factor to how much the particles move.

6. The force that helps move dyes through the gel is the electrical current. The particles being pulled have a negative charge and there is a positive charge on the other side which is pulling the particles toward it.

7. The smaller particles or dyes move faster  and farther than the longer and larger particles of dye of dye. This is because the positive electric current pulls the smaller ones farther than the larger ones.

8. I would expect the molecules with a mass of 600 to move the furthest then the 1000 then the 2000 and lastly the 5000 to move not that far from its starting place. 

SMART goals

My goal for this class is to make sure I watch the vodcast entirely without skimming or not paying attention. I want to do this so I get a better grasp of the information, so I will not come to class unprepared to have a discussion of what I just learned. Another part of my goal is to not be afraid to watch the vodcast one more time if it is on a concept I do not fully understand. In order to make sure I don't get distracted mid-vodcast, I will try to remember to wear headphones every time I listen do a vodcast to cancel out distractions around me.

My second goal is to not procrastinate, because in first semester that was a big issue for me. I want to learn how to manage my time more effectively. By doing so, I will have more time to take up more extracurriculars or anything I want to do. The way I can achieve this goal is by coming home and going straight to studying rather than watching things on YouTube and Netflix which often leads me to procrastinating for hours.  Doing both of these will definitely help me work to my ultimate goal which is to be a better student in second semester than I was in first semester.  

Unit 5 Reflection

In this Unit, we learned about the central dogma of biology, how protein is made, and about mutations. The central dogma of biology is that DNA becomes RNA which becomes proteins which eventually become a organism. But in order to make the protein it has to go through the process of transcription and translation. Transcription is the process of RNA polymerase reading and copying DNA code into a temporary mRNA copy. This mRNA then travels to the cytoplasm to be translated. Once the mRNA arrives at the ribosome, the ribosome reads the mRNA in pairs of 3 or codons to correspond to an amino acid. Once the whole sequence has been translated, there is a string of amino acids left, or a protein. However, during this process bases in the sequence can be changed, which is what we call a mutation. Some types of mutation are insertion, deletion, and substitution. Insertion means inserting another base into the sequence, deleting means deleting a base, and substitution means substituting a base pair for another base pair. 

In this unit some of my weaknesses were fully grasping the concept of translation to create a protein. It took me a while to understand why that process was needed and how to exactly translate the DNA sequence itself. However some of my strengths were learning about mutations because that was a concept I could pick up really quickly. But, for translating DNA I was able to understand it much more because of the protein synthesis lab we did. In that lab we practiced translating DNA and thoroughly understood the process of protein synthesis.

After this Unit, I think I have grown as a learner. I would classify a good learner as one that learns from his or her mistakes and grows because of it. I think I would fall into that group. In the beginning of the year, I did not have the correct strategies to learn. I would wander off during vodcasts and not really pay attention and that had bad outcomes for me. However now I actively listen and my grades have reflected that. Overall this Unit has taught me a lot and has made me a better student. 

Protein Synthesis Lab

In this lab we asked the question, How does the body produce proteins? Through this experiment we got a thorough understanding on the process of making proteins. First, a section of our DNA is copied by an enzyme which produces mRNA. Then, once the mRNA is produced it leaves the nucleus and travels to the cytoplasm. That process is called translation. The next process is transcription where the mRNA bonds with a ribosome. The ribosome then reads the sequence of the bases on the RNA 3 at a time, or in codons. Each codon corresponds with an amino acid, and to determine which amino acid goes with each codon, the codon is read by RNA polymerase. Once it is determined which amino acid goes with each codon, all the amino acids are bonded together making a protein.

However, during this process bases could be changed around which is called a mutation. There are many types of mutations such as insertion, deletion, and substitution. Insertion is when an extra base is added anywhere in the sequence. Deletion is when a base in the sequence is deleted. Finally, substitution is when a base in the sequence is substituted for something else. In the lab, we tested out the effect of these mutations in the gene, and what we have found is that insertion and deletion generally causes the most damage especially if the change happens in the beginning of the sequence. The reason it had more effect if the mutation is in the beginning of the sequence is because that one change can alter everything after it, but if the change was at the very end of the sequence there is not much to alter after it. Also substitution didn't have as big of an effect because it only changes the codon that it is part of.

In step 7 of the lab we got to choose our own mutation. The mutation I chose was the deletion of the very first base. This had a much more dramatic effect than any of the mutations I had experimented with before. This is because since the base changed was the first one, not only did it change all the codons after that, but it also caused the fourth codon to be one that coded for stop so the sequence was only 4 amino acids long. This clearly shows that where the mutation occurs has a big effect. Since my mutation was in the very beginning of the sequence, it cause a lot of damage.

This relates to my life, because there could be mutations in my body that could possibly give me a disease. Mutations can be beneficial, but they can also be detrimental. For an example, a disease caused by a mutation is Tay-Sachs. This disease occurs when there is a defective gene on chromosome 15,  causing nerve cells in the brain and spinal cord to die.

DNA Extraction Lab

In this lab we asked the question: How can DNA be separated from cheek cells in order to study it? We thought that if DNA can be separated from a solution in the form of precipitate, then when alcohol is added DNA will unwind. To test our hypothesis we first began by homogenizing our cheek cells with polar liquid, in other words we began by scraping our cheek cells and swishing it in our mouth with Gatorade. Next we added salt, and soap which lyses or breaks down the cheek cells. Then we added pineapple juice which acted as an enzyme to break down any if the proteins that the DNA was wrapped around. Finally we added cold alcohol to the mixture and let it sit for 5 minutes. When we observed it after those 5 minutes were up we saw precipitate beginning to the top of the solution. This precipitate was the DNA that had been extracted from our cheek cells. This supports my hypothesis because after alcohol was added, precipitate started to form at the top of the solution.

While our hypothesis was supported by our data, there could have been errors due to not following the instruction very carefully. One example of an error we made is adding the wrong amount of Gatorade. This is because since we didn't have a measurement of how much Gatorade we were supposed to drink, some people had more Gatorade in their solution than others. This could have effected the ratio of Gatorade to other things like pineapple juice and resulted in little to no precipitate produced. A way to eliminate this error is by having a set measurement of Gatorade so everyone ends up having the same amount. Another possible error is not doing the lab in the right order. This is because for this lab all the steps were out of order and we had to put it back in the right order. It is very possible that we may have put it back together in the wrong order. For this error the only way of eliminating it would be to give us the instructions already in the right order or when we put it together to tell us whether it is correct or not.

This lab was done to demonstrate how DNA is separated for studying purposes and that DNA can be found everywhere in your body including places like your cheek cells. From this lab I learned the process of extracting DNA and all of the new vocabulary that is associated with it such as lysis and homogenization.  Based on my experience from this lab, I now know how to extract DNA from cells if that is every required of me in the future. 

Unit 4 Reflection

In Unit 4, we did an experiment called the coin sex lab. In this lab we tried to answer the question, can probability be used to predict what our offspring will be? We used coins to simulate the different genotypes of both the parents, and flipped the coins to determine the genotype of their offspring. We used the coins to display many different genotypes such as whether the offspring would be a girl or boy, have bipolar disorder, and what color hair and eye they would have. The experiment that tested what hair and eye color the offspring will have is called a dihybrid cross. In this cross, instead of using 2 coins (one for each parent) we used 4. This simulated the two different genes (hair and eye color) for each parent. Our results from this cross was that 14 out of 16 had brown hair and brown eyes and 2 had blonde hair and brown eyes. This result was far from what we had expected ; we had expected a ratio of 9:3:3:1 which means that in our results we were missing 2 phenotypes! This definitely shows that there is a limit to predicting our offspring's traits. We can always guess the probability of how likely a trait will occur but we can not predict if that trait will actually happen. This experiment relates to my life because this helps me understand why I have traits that the rest of my family does not.

 The coin sex lab was part of the Unit, Why is Sex so Great? In this unit we learned about the basics  genetics and about reproduction. We learned about the very basics, meiosis and mitosis, asexual and sexual reproduction, Mendel's Laws, dominance, and different patterns of inheritance. One of the most challenging parts of this Unit for me was understanding Mendel's Laws. Some of the laws such as the law of segregation and independent assortment were very complex and challenging for me to understand. Also the more difficult parts of genetics that we touched on such as epistasis and polygenetic were not easy for me to grasp either. However making the infographic and the coin sex lab made it easier for me to visualize what I was learning about and definitely made the topics easier to understand. The infographic was almost like a review on the whole Unit so not only did it help me to revise topics for the test but all the research I did for the infographic definitely helped me get a deeper understanding on concepts I needed help with.

From this Unit I have learned that in order to really understand any of the topics it is essential to actively listen to the vodcast. However I have also learned that listening is not always enough and it is important to take my own time to review difficult concepts. Overall in this Unit I have learned a lot about the basics of genetics and how I can be a better student for the future.