Unit 5 Reflection

In this unit, called "Walking the Dogma" we took a closer look at DNA, the genetic code that is in each and every one of our cells. In the previous unit, we learned that our DNA codes for genetic traits, but we didn't know the specifics of how it did that. DNA stands for deoxyribonucleic acid; it is a double-helix and it is composed of nucleotides. Nucleotides are composed of a 5-carbon sugar (in this case deoxyribose), a nitrogenous base (either Adenine (A), Thymine (T), Cytosine (C), or Guanine (G)), and a phosphate group. The structure of DNA resembles a ladder; the backbone is composed of a phosphate group and a sugar, and the rungs are composed of nitrogenous bases. The double-ringed bases, called purines, bond with the single-ringed bases, called pyrimidines. Adenine and Guanine are purines, while Cytosine and Guanine are pyrimidines. I felt that this part of DNA structure was definitely one of my strengths.

We also learned that DNA is antiparallel meaning that one side runs from 5' to 3' and the other side runs from 3' to 5'. The phosphate group from one nucleotide bonds with the carbon from another. I understand the basic principle of this, but I think that the details of the bonding is a weak point for me.

When we studied the cell cycle, we learned that DNA replicates itself in interphase. In semi-conservative replication, when DNA is unzipped, there are two identical strands, each half of the original. An enzyme called helicase breaks the hydrogen bonds that the nitrogenous bases have with each other. Then another enzyme called DNA Polymerase adds the matching nucleotides to each strand. I feel that I have a clear understanding of this topic. One of the main topics that we studied this unit was protein synthesis. At a 10,000 ft level, the Central Dogma of biology states that genetic information flows from DNA to RNA (transcription) to proteins (translation) to our traits. RNA has uracil instead of thymine, and is single-stranded. It is in some ways similar to a temporary copy of DNA. I felt I was able to understand this process fairly well.

The graphic illustrates the process of how DNA is copied. 

Most of the time, DNA is copied correctly and humans are given the correct proteins that they need to functions. However, sometimes mutations--changes in the DNA, can arise. One type of mutation is a substitution, when one base pair is substituted for another. At its worst, it can change one amino acid, however, sometimes it causes no change at all, resulting in a silent mutation. Another type of mutation is a frameshift mutation, either when a base pair is inserted or deleted, and it cause all the amino acids afterwards to change.

One of the topics that I initially found to be challenging but that I understand now was the ways that genes are regulated. Every cell has the same DNA, and that certain genes have to be turned on or off depending on what type of cell it is.

I have learned much more about DNA and how it is copied and how proteins are made from this unit. From the VARK Questionnaire we took last time, I learnt that I am multimodal, but visual was my highest score. I tried to redraw and memorize diagrams which helped me. Also, I feel that when I try to label unlabeled diagrams for Do Now's in class, I retain the information a lot better.

Protein Synthesis Lab Analysis/Conclusion

In order for the body to make proteins, first the DNA must be transcribed into RNA in the nucleus. It is then converted into messenger RNA (mRNA) and sent out of the nucleus to a ribosome. Instead of thymine (T) though, RNA, single stranded, has the base pair uracil (U). The RNA Polymerase pairs the corresponding nucleotides when it is transcribing DNA into RNA. In the ribosome, the RNA is translated from nucleotide "language" into amino acid "language." The RNA is read three letters at a time, called a codon. Each codon codes for an amino acid. These amino acids are joined together to form a protein.

In the lab we experimented with different kinds of mutations that could potentially occur while DNA is being transcribed into RNA. One example of a mutation we tried is a substitution, where one base pair is substituted for another. This mutation had the littlest effect on the final protein. In the worst possible cases it could change just one amino acid, in many cases it could have no effect. The frameshift mutations had a much greater effect, particularly insertion. Almost all of the amino acids were changed when a base pair was inserted, therefore changing the protein entirely. The mutation is worse if a base pair is inserted at the beginning, because more amino acids are changed. 

I chose an insertion when we were asked to choose our own mutation that would make the greatest difference, therefore the greatest damage to the protein. I chose to insert a G directly after the start codon. Inserting a base pair at the beginning made a huge difference to the protein, because it changed all amino acids in the protein except for Met. My mutation changed the protein the most out of all the ones I tried in the lab. This was because the mutation occurred at the earliest time possible. An insertion also changes the amino acids completely. 

An example of a mutation that occurs in humans is Tay-Sachs disease. It is very rare but depending on the onset can be deadly. The autosomal recessive genetic disorder destroys nerve cells in the brain. Gangliosides are fatty substances which are necessary for development of the brain. Normally, gangliosides are broken down, but people who have Tay-Sachs disease lack the enzyme that breaks them down. This destroys the functioning of the nerve cells. There is a mutation on the Hex A gene that causes Tay-Sachs. 

Human DNA Extraction Lab Conclusion

In this lab, we asked how DNA can be separated from cheek cells in order for it to be seen and studied? We found that in order to extract DNA from cheek cells, three steps must be followed: homogenization, lysis, and precipitation. We accomplished this by homogenizing the cell's tissue with polar liquid. This breaks down the cell membrane and nuclear membrane of the cheek cell. We scraped off some of our cheek cells with our teeth, then swiveled it around in our mouths for 30 seconds. Afterwards we added soap, which was involved in lysis (the disintegration of the cell membrane). We used pineapple juice to break down histones found in DNA that the DNA wraps itself around. This is because pineapple juice, like a few other liquids, has catabolic proteases, enzymes, that help to break down the histones. Then we poured cold isopropanol alchohol onto the test tube and due to the nonpolarity and the polarity of the DNA the DNA became a precipitate and rose to the top of the isopropanol alchohol layer. This data support our claim because in order for DNA inside the nucleus to be seen, first the cell membranes, plasma membranes, and nuclear material must be broken down.

While our hypothesis was supported by our data, there could have been possible errors due to gargling the Gatorade for less than exactly 30 seconds. This would have affected the experiment in that all of the cheek cells would not have been caught in the solution. Also when we left the test tubes in the rack for observation, we did not time the 5 minutes exactly and this may have not allowed the solution to settle enough. I think our group should have used timers for both the gargling of Gatorade and the test tube 5 minute observation to make the experiment more accurate.

This lab was done to demonstrate our understanding of DNA and the process of extracting DNA out of a cell. From this lab I was able to understand how DNA is located in the cell, and that all the membranes that must be broken down differently in order to see the DNA. Based on my experience in this lab, I can apply this same process to extracting DNA from any cells and understand how the process works.