Unit 5 Reflection

     In Unit 5, we learned about DNA.  When I learned about DNA, I learned about the central dogma of biology.  The central dogma states that information flows from DNA to RNA to proteins to an organism.  The process of making DNA to RNA is called transcription, the process of making RNA to proteins is called translation, and the process of proteins to making an organism is called the phenotype of an individual.  The central dogma explains a lot about this unit because it shows me how DNA makes proteins.  Some other things we learned about included what DNA is, semi-conservative replication, Protein Synthesis, mutations, and gene expression and regulation.  All these terms may seem very difficult, but they all are connected in a unique way.  The starting block of all these processes is DNA.  From then, we can learn about how DNA gets the instructions out into the cell.  The two main ways we learned in class were semi-conservative replication and Protein Synthesis.  These two processes are very similar but are also very different.  Semi-conservative replication is when you split the DNA and run DNA Polymerase down the DNA and add the respective nitrogen base to make two DNA molecule strand from the one original.  Protein Synthesis, however, is much more different.  DNA unzips and allows RNA Polymerase to match nucleotides to make an RNA strand.  This strand, known as the mRNA then heads to ribosome.  The ribosome reads three bases at a time, known as a codon, translates the nucleotides into amino acids.  Each codon then codes for one amino acid.  There are start codons to tell to start codon and stop codons to tell to stop coding.  Some of the main themes are DNA and how they replicate.  However, when they replicate, something can go wrong, which is known as mutations.

     This unit was short and sweet.  This unit contained a lot of information about different thing about DNA.  One thing that went well with this unit was that I learned more about myself and how I function as a student.  I enjoy memorizing a bunch of things, but one thing I am not so good at is understanding the big picture.  I need to know the big picture before concentrating on the tiny details that help make up the big picture.  Knowing the big picture helps a lot because I know what I am studying and that helps connects big topics together.  Not knowing the big picture can hurt one because they memorize a lot of facts that they do not know what for.  Understanding the big picture helps you understand what you are studying.  Some successes I learned about my studying is that if I learn all the material a little before the test, I will have enough time to let the information settle into my brain.  Digesting the information I learned can really help for me because I am not a person that is good at cramming and I also want to avoid cramming.  Some setbacks where that some of the topics were confusing so I needed spend more time understanding the topic.  I can do this by retaking CFU's and reading my relate and review.  I did not quite understand gene expression and regulation at first, but once I broke the information down the the key points and drawing a few diagrams, I could understand the big picture vividly and not get caught in all the small details.  The demands of high school biology can be a lot, but as I learn more about myself, I can keep up with the demands using time management skills I have previously learned.

     Since this is our fifth unit of biology, I have experienced a lot since the beginning of the year.  Some things I learned about from experience is that I am a visual learner.  I learn the best when I am watching a video on how the process works or looking at diagrams.  With visuals, I can get an idea of how all this is working by looking at something I can see.  I also learned a lot from labs.  Since I like to see things I am working with, I enjoy labs because they are real life examples of what is happening.  I enjoy labs because I can make something.  While making that thing, I can see it and feel the object.  The process of making that object also helps because there are reasons behind the lab procedure, which relate to concepts learned in class.  The infographic helped me a lot as well.  Infographics cannot contain too much text, so I needed to think about how to deliver the information in a concise manner for the reader.  My finished infographic helped me study the unit because I was able to view the key points necessary for that subject in a clear manner with help of some pictures.  The overall feel of the infographic was clean, so this tool helped me put information into different categories to study.

     I have some questions about DNA.  I do not understand why there are only four different nitrogen bases.  I also do not understand how there is protein language and then gene codes.  I feel that I am a better student than yesterday because I learned more about how I function as a student.  I learned over the semester that I study better when I look at visuals.  Diagrams and videos help me a lot because I can see how the thing is working.  Visuals also help me study because I like to organize information into different places, conceptually mapping inside my head.  Tackling my strengths to study help me study efficiently so I can get the most out of studying.  I cannot force to be a student that is good at reading things to study efficiently.  If I know what I am good at studying, I should stick to that method because it will be the best way to get information into my brain.  Studying in 30-45 minute chunks and then resting for five minutes is a way I study best.  Studying to too long in one sitting will not work for me because at a certain time point, I will not be effectively absorbing information.  In that five minutes, I usually walk around my house, go to the bathroom, drink or eat something, or even talk to my parents about trivial things.  After that five minutes, my brain is fresh again and I am ready to study effectively again.  Some things holding me back is that I usually not very confident in the way I study.  I tend to think that I am no studying the best way or I am not studying right.  This lack of confidence in my studying holds be back because I am not confident in how I study or if it is the right thing to do.  As I said before, I am a very good visual learner and I learned that again in the VARK Questionare.

Protein Synthesis Lab Conclusion

     There are two steps to making proteins.  The first step is transcription.  This is the process where RNA Polymerase reads and copies the DNA code, also called genes, for a protein as a mRNA copy.  In transcription, DNA unzips.  After DNA unzips, RNA Polymerase matches square nucleotides to make an RNA strand.  mRNA, or messenger RNA, is produced and leaves the nucleus and goes to the cytoplasm.  This is the beginning of the second step, translation.  Once the mRNA arrives at the ribosome, the ribosomes read mRNA three bases at a time and translates DNA language, nucleotides such as A, T, C, and G, into protein language, such as amino acids.  Each three base sequence of A, T, C, and G is known as a codon.  Each codon codes for one amino acid.  AUG is known as the start codon because it tells the ribosome to start translating.  There are also stop codons to tell the coding to stop.  As a result from this process, long chains of amino acids are made, which are known as primary structure.  Another thing is that the chain of amino acids twist and fold to combine with other chains of amino acids and become a protein.

Slonczewski, Joan L. Wikimedia Commons. Digital image. Wikimedia. Wikimedia, Web. 12 Dec. 2016. <https://commons.wikimedia.org/wiki/File:Bacterial_Protein_synthesis.png>.

     Mutations are changes in the DNA code.  There are two different types of mutations.  Substitution is where one or two base pairs are changed.  These mutations are small and very common. The second mutation is frameshift mutation.  Insertion and deletion fall under the frameshift mutation umbrella.  Insertion is when one base pair is added in a spot of the DNA code and deletion is when one base pair is deleted from the DNA code.  The mutation that has the greatest effect on proteins is substitution.  Substitution can change one or two base pairs, but those two altered base pairs can change the amino acid, which affects which kind of amino acid it is.  If you substitute a base pair near the end, it would not matter as much because only the amino acids behind the mutation will be changed.  However, if the first base pair is substituted, the start codon may not exist.  For example, if you have AUG and change it to UUG, the code will never be coded unless there is another start codon in the code.  A code could also have changed the stop codon so where the stop codon does not exist.

RazielWraith. Gene Alterations. Digital image. Gene Alterations. Gene Alterations, Web. 12 Dec. 2016. <http://comicvine.gamespot.com/genetic-alterations/4015-55878/>.

     In step seven of my Protein Synthesis Lab, I chose one mutation to see how much that mutation altered the DNA code.  I chose one of the frameshift mutations, deletion, because I wanted to see how much one deleted base pair would change the DNA code.  Instead of choosing a random base pair in the middle of the gene, I decided to change the very first base pair.  I did this because I knew that this would affect the start codon.  With this mutation, the coding of DNA did not start coding until later on in the gene where there was another start codon.  Comparing this to the other mutations, this does not just change one amino acid, this affected the whole gene because the gene did not start coding where I wanted it to start.  The location of the mutation does matter, especially in frameshift mutations because the gene would not be affected much if I changed something in the middle of the gene, but it would change a lot of I did change the start or stop coding. 

     Mutations can affect our life because if we do not get coded the correct protein, humans would have ears on their feet and eyes would appear on your hands.  In order to keep eyes off your hands and ears off your feet, genes need to be expressed correctly which is called gene expression and regulation.  An example of a mutation that affects a normal persons life is called Progeria.  Progeria is a mutation that accelerates aging.  Most children that have this disorder have a die around the age of 13 but some can live up to the age of 20 years old.  The common death of this disease is a heart attack or stroke.  This mutation occurs in around one in eight million people.  This mutation attacks the LMNA gene, which is a protein that provides support to the cell nucleus.  Some examples of progeria may include rigid skin, boldness, growth impairment, grown abnormalities, and a "sculpted" nasal tip.

HBO. Picture of a person with progeria. Digital image. Gizmozo. Gizmozo, Web. 13 Dec. 2016. <http://io9.gizmodo.com/10-unusual-genetic-mutations-in-humans-470843733>.

DNA Extraction Lab Conclusion

     In this lab, we asked the question "How can DNA be separated from cheek cells in order to study it?"  We found that making a solution composed of Gatorade, laundry detergent, salt, pineapple juice, and cold rubbing alcohol mixed with our cheek cells would cause the DNA to be separated from the nuclear membrane and the arriving near the top of our solution.  In this lab, we took some Gatorade and swished it in our mouth for 30 seconds.  After time was up, we scratched some cells off our cheeks and then spit the Gatorade mixed with the cheek cells into a cup.  We then added a salt, laundry detergent, and pineapple juice.  We placed this mixture into a test tube.  The test tube tilted so when we added the cold rubbing alcohol, the cold rubbing alcohol would be on a different layer in the test tube.  After letting the solution sitting for a little bit, we inverted the tube six times.  We then waited around five minutes to see if the DNA would rise to the top.  When we were waiting, I observed that the red Gatorade did not interfere with the cold rubbing alcohol which created two layers.  Another thing I observed while waiting was that there were tiny particles flying around in the layer of the red substance.  Near the end of the time allotted, DNA rose to the top of the mixture.  The DNA was separated from the cheek cell because of the substances our group added.  The salt facilitates the precipitation by shielding the negative phosphate ends of DNA which allows them to move closer.  The detergent is added to disintegrate the cell membranes and to emulsify the liquids and proteins of the cell.  The pineapple juice acts like the enzyme is added to further break down any proteins such as histones that DNA molecule wraps itself around.  With all this added together, this makes the DNA to come out of the nuclear membrane and then to float to the top of the substance.

     While our hypothesis was supported by our data, there could have been errors due to the time that we let the cold rubbing alcohol on a different layer from everything else.  According the the procedure our group put together, we needed to allot for the cold rubbing alcohol to sit on top of the mixture of Gatorade, detergent, salt and pineapple juice.  Our group did not successfully do this.  Our group put in the cold rubbing alcohol in the test tube and immediately started the invert the tube.  The time to we let the mixture settle was not enough for the DNA to arise from the cell.  Another problem was that the different substances we needed to put in might have been a varied a little bit.  For example, if we needed to put 5-10 drops of pineapple juice, I put five drops but my partners could have put ten of seven.  Also, there could have been a lot of air in the drops that I put in.  This means that I only put two or three drops instead of five.  The different amount of enzymes could affect how long it takes for the DNA to be separated.  This means that if I were to add a few more quality drops of pineapple juice, the DNA could have been extracted in the time frame our group allotted.  Due to these errors, in future experiments I would recommend making sure that there is enough time for the cold rubbing alcohol to settle into the other mixtures and the drops to be a good amount of quality droplets.

     This lab was done to demonstrate how it is possible for DNA to be separated from the cell.  From this lab I learned how different types of substances, such as pineapple juice, had important components which made the lab possible.  The concept that pineapple juice was the enzyme helped me understand a real example of an enzyme, not just some chemical I have no idea what it is.  I understood the purpose of the enzyme coming into this lab, but I did not have a concrete and real example of what it is.  Understanding that the pineapple juice acted like an enzyme helps me understand the concept of different thing such as enzymes.   Learning about the basic function and structure of the DNA really helps because we learned it in Biology class.  Biology class taught me how the different components added into the mixture had their own benefit into helping the DNA emerge out of the cell.   Based on my experience from this lab, I could make my own experiment about what kind of DNA out of different types of cells.  If I wanted to do this at home, I could gather up my materials and perform the experiment correctly because not only know the procedure, but I know background information about how DNA acts and works.  Knowing the background information I learned in my Biology class helps a lot because I know what is going on instead of just doing the experiment because I was told so.