Unit 5 Reflection

DNA Extraction Lab

   This unit was about genetic code and how it is regulated, expressed and in rare cases mutated. In the DNA Extraction Lab I learned how to extract DNA. This involved the process of first extracting the cheek cells, then adding salt, detergent, and a catalyst pineapple juice, and finally a layer of alcohol on top to extract. In the process of this lab I learned more about the structure of DNA and how it wraps around histones inside the nucleus. In the Protein Synthesis Lab I learned how proteins where created. This involved the process of the RNA polymerase zipping down the DNA and making a strand of messenger RNA in the process. The RNA can be thought of as a temporary copy for the DNA. Then, the RNA goes out the nucleus through the pores and travels to the ribosomes where it attaches and each 3 bases on the RNA are one codon which codes for one amino acid. Once the amino acids have built up and the ribosome reads a stop codon on the RNA, the amino acids are released and fold up into a protein. Some of these concepts, where quite confusing at first because they are complicated and hard to understand. But over time I came to learn and understand the concepts of this Unit, and now I understand them very well. I want to learn more about these concepts because they are very interesting and I could learn more on this topic.

Protein Synthesis Lab

   Over this unit and over the last semester I have also grown as a student. To be a good student means that you can learn better and make connections better in the things you learn, rather than just memorizing the facts. Since finals is coming up I made a study guide for the semester. Although this was an assigned assignment I wanted to make the most of it so I would be better able to understand some of the topics that I still do not understand from this semester. Since I am a visual learner I decided to make my study guide mostly containing visuals. I think these visuals will help my studying a lot because they are not only just facts written down but they show how everything connects, which is necessary for any practical application of this knowledge in the future. Before I would just study what I had to study to get a good grade, however studying in a way that connects all the concepts would not only help me more now, but also help a lot in the future when I am learning science. Also as a student I have learned to pay attention to the details more. When our group was doing the DNA Extraction Lab we had at first put the instructions in the wrong order. But after I double checked it I found that we where supposed to layer the alcohol on last after it was shaken so that it would have a layer and not be mixed into the solution. If I had not double checked these instructions, we would not have been able to successfully extract the DNA in this lab.

Semester 1 Study Guide

Protein Synthesis Lab

   In order to make a protein, first the RNA must be made by the RNA polymerase using the DNA as blueprint. The single stranded messenger RNA then goes out of the nucleus through the pores in the nuclear membrane. The RNA then goes to the Ribosomes where it attaches and starts to create the protein. Each sequence of 3 nitrogen bases on the RNA is a codon which codes for 1 amino acid in a protein. The process of creating a protein is started by a start codon in the RNA and ended by a stop codon in the RNA. Once the RNA is finished with being read, the stop codon releases the amino acids and they fold up into a protein.

https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/ribosomes-and-protein-synthesis-110/the-protein-synthesis-machinery-449-11674/

   The mutations that have the greatest effect on changing bases are the insertion and deletion mutations. These are known as frame shift mutations and they have a great effect because they shift every base over creating a major problem and very different amino acids. The mutations that seemed to have the least effect on proteins where substitution mutations because they only changed one amino acid in the sequence. Mutations can have very different effects depending on where the mutation occurs.  If an insertion or deletion happens near the end of a sequence it might not have as great of an effect as if it where near the beginning, as long as it does not interfere with the stop codon. Even substitution mutations can have great effects if they are in a spot where they create a new codon that is greatly different then the original codon and could have major effects.

http://academic.pgcc.edu/~kroberts/Lecture/Chapter%207/mutation.html

   In step 5 I chose a mutation that would insert T after AT. The resulting amino acid sequence was Met-Stop. This created a stop codon right after the start codon making the protein very small. In this example I used an insertion, however the same result could be made by a substitution of T with the nitrogen base after AT. This shows how the location of  mutation can effect the result of a mutation. If I where to do a substitution in a different place it would likely have not had as great of an effect.

  Albinism is a genetic disorder caused by a mutation in the TYR gene. The TYR gene is the gene that produces the pigment melanin in humans. With this mutation people are not able to produce pigment in their skin and eyes. This changes the phenotype of a person to having no pigment in their skin, hair and eyes.
https://www.dnalc.org/view/15932-what-is-albinism-.html

http://slideplayer.com/slide/5699007/

DNA Extraction Lab

   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 seperated from cheek cells by first using Gatorade to extract the cheek cells. Then adding salt, detergent, and pineapple juice to go through the processes. Then we would layer a layer of alcohol on top of the solution. After we preformed the experiment I found that the DNA from the cheek cell floated up to the top of the alcohol layer in my sample. This DNA was a tangled strands of most likely many strands of DNA. This experiment worked because the salt facilitated precipitation by shielding the ends of the negative phosphates, allowing them to move closer together.  Then the soap emulsifyed the protiens and lipids in the cell, this disrupted the polarity in the cell membrance causing the cell to release all of it's contents. The pineapple juice acting as a Catabolic protease then further broke down histones which are proteins that DNA wraps around. The alcohol which is nonpolar then caused the DNA to precipitate where the solution touches the alcohol.

   Our data contradicts the expected results because not everyone had a good sample of DNA that precipitated to the top of the alcohol even though I did get a good sample. This happened even when people did the procedure correctly. The most likely cause of this is because not everyone swabbed their mouth enough to get a large enough sample of the cheek cells. However I did swab a bit excessively, so I had a good sample. We could help eliminate these errors by having everyone swab excessively as I had done, the sample may look a bit disgusting, but that is because it if filled with cheek cells which are absolutely necessary for the extraction process. We could also use a stronger solution to extract the cheek cells than Gatorade, however it might not taste as well.

   This lab was done to demonstrate how to extract DNA from human cheek cells. From this lab I learned the process of DNA extraction, which helps me understand the concept of how DNA condenses for mitosis and when geneticists condence DNA to study it. Based on my experience I now know how to condense and extract DNA from cheek cells.