Unit 5 Reflection

This unit was focused on the central dogma. This is the process of changing DNA to RNA to Proteins, and eventually to an organism. The reason for this process is to create the phenotypes of organisms. Proteins make up phenotypes. The Central Dogma states that information is transferred from DNA to RNA to Proteins, and eventually to Organisms (phenotypes). Transcription is the process where DNA unzips, and RNA is made to match the spare nucleotides to make messenger RNA. The mRNA them travels out of the nucleus and over to the ribosomes, where they will be read. Once they are read, they are separated into sets of 3 amino acids, or codons. These are protein sequences that make up our phenotypes.

Although the process sounds simple enough, many things can change, either cause harmless genetic variations, or make things go horribly wrong. These are called mutations. There are many different types of mutations. The first is called substitution. This is the least harmful mutation. Substitution is when one base is accidentally switched with another base. This causes slight variations in the protein codes. The most harmful mutation is deletion. Deletion is the taking away of necessary bases from the sequence. This can lead to serious damage and loss of code.

One of my greatest strengths was the ease in which I could transcribe and translate DNA to RNA, and then convert into codons. Because of this, I really enjoyed my Protein Synthesis Lab, and was done with it rather quickly. One of my greatest weaknesses however, was my lack of ability to understand gene regulation. I don't understand how the physical transfer of information works, which leads me into my unanswered questions.

Like I said, I don't fully understand how the physical transfer of information works, nor do I understand gene regulation in full. I am also not sure about how different genes all fit into 4 different nitrogen bases.

I think I grew the most in this unit because I had to stop and slow down to make sure I understood everything to the best of my ability. This was not a small/simple unit, but rather one I had to focus on. I did not just do the vodcasts for the credit, but I did it out of my eagerness to learn. I learned to do things for my own personal gain/incentive. I did not do it for the grade.

Protein Synthesis Lab

   Protein Synthesis Lab

To make a protein, you must start with DNA and RNA. We start with DNA being copied by an enzyme in the nucleus. The copy that is produced in the RNA. RNA then leaves the nucleus and goes to the ribosomes. The RNA bonds with a ribosome to make proteins. The ribosome reads the RNA strand in a sequence of 3 amino acids at a time, which is called a codon.After the chain is read, the RNA is balled and condensed up to form a protein. 

https://upload.wikimedia.org/wikipedia/commons/thumb/5/50/Molbio-Header.svg/2000px-Molbio-Header.svg.png

The changing of bases in DNA is substitution. This is one type of Point Mutation. Substitution was almost completely harmless, We know this because the codons and the codon abbreviations did not change at all from the original transcription and translation of the DNA. Our next mutation was insertion, or the addition of an unnecessary base. This had obvious effects, as 5 amino acid sequences were changed, and so was the length of the code itself. Our last mutation was deletion, which is the subtraction of a necessary base from the DNA code. The effects of deletion from this code were catostrophic, as the sequence itself was shortened dramatically, and the sequences themselves were changed. Over half of the code was changed. Substitution was the least harmful of all mutations, while deletion was the most harmful.


https://www.researchgate.net/profile/Axel_Visel/publication/26800032/figure/fig2/AS:282055054249989@1444258573084/Figure-2-Consequences-of-deletion-and-mutation-of-the-limb-enhancer-of-sonic-hedgehoga.png

Considering the fact that deletion causes the most harm out of the 3 tested mutations, I chose deletion, but instead put the deleted base at the beginning of the code. The effects were even more harmful than when the deletion occured in the middle of the code. When the first base was deleted, the amino acid sequences stopped after the start codon. There was no continuation of the code. Where the mutation occurs greatly affects the mutation and its effect on the organism. For example, the first deletion occurred in middle of code, and this lead to a change and a shortening of code. However, the second deletion occurred at the very start of the code, which lead to only one, the start, amino acid sequence to form.


This lab, although not as visual as our other ones, showed the possible effects of mutations, both harmless and harmful, and also negative. A mutation could affect our life because it would affect the proteins that make us up. They do this by adding, subtracting, or switching around the bases in the DNA code. This leads to a wrong genetic code, which will then lead to the ribosome that connects to the RNA reading the codons wrong and ruining the proteins. This would then ruin the organism, or even kill it. Deletion syndrome, or formally known as DiGeorge Syndrome, is a deletion mutation that occurs due to the deletion of a small chunk of chromosome 22. This syndrome mostly affects children from birth to the age of two years old. Deletion syndrome leads to poor development of body parts and systems, and will later lead to such things as heart defects, poor immune system function, cleft plates, and low amounts of calcium in the blood. The disease is rather rare, and less than 200,000 people throughout the world have it. Unfortunately, there is no cure to this disease, and it is a chronic syndrome. Treatment is available, but it is often lifelong, due to its fatality.


https://upload.wikimedia.org/wikipedia/commons/9/9e/22_del_q11.2.png

DNA Extraction Lab Conclusion

In this lab, we asked the question, "How can DNA be separated from cheek cells in order to study it?" This lab was different from the rest, however. Instead of following the steps of the lab and getting the end result, we actually had to organize the procedure into the correct steps in order to achieve the desired results. We first scraped cheek cells from the inside of our cheeks. Then, we swished them around in a small amount of Gatorade, and spit the solution into a cup. After that, we poured the solution into a test tube and mixed it in with a small amount of salt, and about 9 drops of both Dawn Dish Soap and Pineapple Juice. The salt facilitated the precipitation, which allowed the ends of the DNA to move closer together. The dish soap was used to lyse the solution, or disintegrate the cell wall/membrane and get to the DNA. Finally, the Pineapple Juice acted as the enzyme which helped break down any remaining proteins, called histones, which the DNA molecule wraps itself around.  After this, we shook the test tube containing the newly made solution, and waited for about 5 minutes for the solution to mix and settle. After the 5 minutes, we added cold isopropanol alcohol in such a way that the Gatorade solution and the alcohol don't mix. This would lead to an unwanted result. The alcohol itself is non polar, while the DNA is polar, which leads to the DNA falling out or separating at the interface of the two solutions. We found that by following the procedure stated above as closely as possible, and by being especially careful while handling such solutions as the alcohol or Gatorade solution with everything mixed in can help attain the desired results.

This photo shows the procedure we organized

At first when we added the salt, soap, and juice to the Gatorade solution in the test tube and gently mixed it, the solution was a rather still translucent red. You could begin to see the cheek cells inside the solution. They looked like small white specks connected/bunched together to make thin, fibrous strands. However, after we added the alcohol, we could start to see a haze in between the two solutions. This was the slow precipitation of the DNA extraction. Soon after the white haze had formed, small chunks of DNA started to separate and become visible in the alcohol solution.

 This is the Gatorade solution and the alcohol in the test tube and the start of the precipitation process.

While our hypothesis was supported by our data, there could have been errors in my test tube and experiment especially because of the amount of solution that ended up in my test tube. From my table group's results and my own results, I can conclude that the amount of the Gatorade solution, and the alcohol which had to have a similar result, does affect the time the precipitation process takes. One table partner had used very little of both solutions, a little less than one third, and this lead to a large amount of DNA extracted from the solution in a short amount of time. However, I created an end solution that filled the test tube. This lead to an extremely slow precipitation process and the small amount of DNA extracted from the process. Another possible error could be the soap bubbles created due to the speed and intesity of the shaking of the solution before we added the alcohol. The procedure specifically states shake the test tube in such a way that minimized the creation of soap bubbles. However, no matter how we shook the test tube, bubble always formed. I cannot say that this affected our results in a negative or positive way because we all tested the tube with the same procedure of shaking the tube. Due to these errors, in future experiments I would suggest the procedure be changed for two of the steps. First, it would minimize the risk of creating soap bubbles by using a device to stir the solution gently instead of shaking it. This could lead to more accurate results. Another step that would be more helpful to change would be the amount of Gatorade solution used in the test tube. I would suggest that the procedure only states 1/3 of the test tube should be filled up in order to speed up the process and create more DNA extraction. 

 This picture shows the soap bubbles formed from the shaking of the solution. 

This lab was done to demonstrate not only the isolation process of DNA, but also the functions and characteristics of DNA, homogenization, lysis, and precipitation. From this lab, I learned more about the characteristics of DNA, like the fact that it is polar. I also learned the functions of many factors used to isolate DNA, which helps me understand how scientists can isolate DNA and study it. It also helps me understand the concept of DNA itself.