Unit 5 Reflection

     This unit focused on four main concepts: DNA replication, protein synthesis, mutations, and gene expression/regulation. DNA has to be replicated identically because all cells have the same DNA. It has to unzip and fill in the bases missing in the base pairs. This is done by the DNA Polymerase, and now there are two identical strands of DNA. Protein synthesis is the process of making a protein. RNA is heavily involved in this process. The synthesis starts with transcription. DNA is unzipped again and this time, the RNA Polymerase copies the gene to mRNA (messengerRNA). Thymine is replaced with uracil, and after this is over, the mRNA goes to a ribosome. Now, translation can begin. The ribosome, or rRNA, reads the mRNA three bases at a time. These three bases are called a codon. One codon translates to one amino acid, and the animo acids formed are chained together by the ribosome. The chain folds and becomes a protein. This whole process can also be referred to as "walking the dogma". Mutations can be harmful or helpful to organisms and there are different types. Point mutations only affect one or two bases at a time. Substitution switches one base for another. Framshift mutations, like insertion and deletion, can add or subtract one or two bases in a sequence. Also, inversion and translocation involves DNA or chromosomes breaking and bonding with itself or other chromosomes. Finally, gene expression is the process of DNA being used to produce a phenotype. Gene expression has to be regulated, otherwise, ears would grow from your stomach, or eyes could grow on the top of your head. In prokaryotes, a operon, with a promoter, operator, and other parts, is used to regulate the expression of genes. Eukaryotic regulation uses proteins (called transcription factors) to control transcription. After that, the DNA is separated into exons, used DNA, and introns, unused DNA. DNA can wrap around proteins called histones to form nucleosomes.

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https://upload.wikimedia.org/wikipedia/commons/0/0c/Lac-operon.jpeg

     My strengths were completing the vodcasts on time and basically understanding the concepts by the time I got to class. During class, I was able to completely understand the concepts with Do Nows, recapping the vodcast, and labs. I think that I can do better on labs and not make mistakes I can avoid. During the DNA extraction lab, for example, I was not able to extract DNA, probably because of an error I had made during the process. Also, I should do my textbook notes early and not procrastinate on them until the last minute.
     I am a better student than I was before because I have gotten better at managing the class over time. I can now follow along with the vodcast and pause less often. It is now easier for me to write Relate and Reviews, and I realize that they help a lot, especially now studying for the final. I believe that I am a good student because I do my work, understand the concepts taught to me, and be efficient and thorough with my work. I took the VARK questionnaire, and it said that I have a multimodal learning preference, and I wasn't sure what to do with that result. In conclusion, I am getting through the class, but I can always get better than I am now.

Protein Synthesis Lab

     The process of making a protein has two main steps. DNA is replicated by an enzyme, but the copy is RNA, specifically called mRNA. The mRNA is different from the DNA because it contains uracil (U) instead of thymine (T). The mRNA then leaves the nucleus to get to a ribosome. At the ribosome, the mRNA is translated into amino acids (which make up proteins) by separating three bases at a times. One three base combination is called a codon, and each codon creates a specific amino acid. As they are made, the amino acids are chained together to make a protein.

https://upload.wikimedia.org/wikipedia/commons/thumb/5/5b/Central_dogma_of_molecular_biology.svg/1259px-Central_dogma_of_molecular_biology.svg.png 

     All mutations can have an effect on a gene, but some specific mutations can make a big difference in the DNA sequence. Deletion or insertion (both frameshift mutations) at the beginning of a sequence seem to affect the whole sequence the most because it changes all of the amino acids after it. Also, it can even cause the translating not to start at all. The mutation that has the least effect was substitution because it only changes one amino acid out of the whole chain. 

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     I chose deletion for my own mutation because I thought that it would cause the most change (damage) to the chain of amino acids. It changed many of the amino acids after it. By placing this mutation at the beginning of the sequence, it changed all the amino acids as a result. Because of this change in all of the amino acids, the protein would probably not do what it is supposed to do, and it wouldn't function correctly.

     Progeria causes accelerated aging. It is caused by a mutation in the LMNA gene, a protein which provides support to the nucleus of a cell. Most people who have progeria die by the age of 13, due to age-related health problems. Progeria interests scientists who are trying to connect certain genes with aging.

(LMNA Gene)

https://upload.wikimedia.org/wikipedia/commons/1/16/Protein_LMNA_PDB_1ifr.png 

Human DNA Extraction Lab

     In this lab, we asked the question, "Can DNA be separated from cheek cells, and if so at what point do you predict you will be able to see the DNA?". We found that you could, if you follow the process correctly, after a process called lysis and during precipitation. I was not able to extract DNA possibly because of an error during the experiment, but others did extract their own DNA. The DNA came out as a precipitate into a layer of cold alcohol. This occurred because the alcohol is nonpolar and the DNA is polar. This data supports my claim because this occurs after lysis, during precipitation. Lysis is the disintegration of a cell by rupture of the cell membrane.
     Our data contradicts the expected results because DNA was not extracted. This could have been because while the isopropanol alcohol was poured into the solution too quickly and not from the right angle. Also, during the stage of homogenization (preparation of a suspension of cell constituents from tissue by physical treatment by a liquid, the liquid being Gatorade), too much Gatorade or detergent (used for lysis) could have been measured in too large or small quantities, which could have changed the process or made it not work. One recommendation that I have is to measure quantities carefully and accurately. Another is that all actions done in the lab, like pouring alcohol, should be done in the proper way.
     This lab was done to demonstrate how DNA is extracted and when you extract it. From this lab, I learned about homogenization, lysis, and precipitation, which helps me understand the concept of DNA extraction and the structure of DNA. Based on my experience in this lab, if my or someone else's DNA is needed in a situation, I understand how to extract it from human cells.