Setting the Stage for 20 Time

     In my Biology course, we are starting a project called 20 Time.  Also known as Inquiry Hour or a passion project, I will spend roughly 20% of my time in class or every other Monday working on what I am interesting in and passionate about.  In my 20 Time project, I will ask the question "How will different nap lengths benefit how well one can study?"  By studying, I mean the different aspects of studying such as memory, understanding new concepts, accuracy in subjects such as math, and many other factors that are used in a useful studying session.  Using the scientific method of inquiry, I plan to design an experiment testing different lengths of power naps to identify what would be ideal for the most efficient studying.

     I chose this specific project because I question what the most efficient and effective way to study is and how to achieve this.  I also love sleeping and I am sure everybody values their sleep.  Not many teenagers get the recommended 9-10 hours of sleep daily.  It turns out that the average teenagers get around two hours less than what experts recommend.  In order to compensate for the missed sleep time, I wonder what length of a nap could help boost both how you feel emotionally as well as how to study more efficiently.  This project will answer the question I asked above through a series of experiments and trials.  After running various tests, I will analyze the data and observations I have gathered in the experimental phase and come up with my best answer to my question given the data I received in my experiment.

     My goal in my 20 Time project is to find how to attain a high quality studying session by taking various naps.  Through my course of this 20 Time project, I hope to find the sweet spot for the amount of time each nap should be to have the best studying time afterwards.  By collecting data, I could measure how much progress I have made my determining if I have hit my jackpot yet or not.  If not, I will continue to find the best time and duration.  Moving forward, I plan to use the steps of the scientific method I have learned in class and design my own experiment.  I will gather information, form a hypothesis, construct and run an experiment, and collect data and analyze.  I will repeat the experimental steps if needed.

Unit 6 Reflection

     This unit was called biotechnology.  Biotechnology is the manipulation of living organisms in order to benefit mankind.  Biotechnology is very broad, but in this unit, we focused on the question, "What is the purpose of biotechnology?"  Biotechnology generally focuses on topics such as DNA, proteins, and inheritance.  Throughout this unit, we learned various subjects of biotechnology such as sequencing, PCR, and gel electrophoresis.  Watching the nightly vodcasts, I learned a lot of detailed facts about these various subjects, but there is a bigger scope than just memorizing the facts about the subjects.  Sequencing, for example, can be applied into the bigger world rather than just a biology class.  Sequencing can find the exact order of the DNA.  This is impressive and also can be used in the outside world.  Sequencing can be used for forensics to see who committed the crime with the given DNA sample.  Another example is PCR, which stands for polymerase chain reaction.  This is the process that amplifies a certain DNA segment into making millions and millions of copies.  Again, PCR can be used in the outside world in cloning.  If a scientist wanted to clone something, he or she would use the process of PCR.  Gel electrophoresis can also be used in the real world.  Gel electrophoresis can be used to identify criminals that ran away from the scene.  The forensic scientist would scoop up a DNA sample and can try and find the culprit.  The DNA would be put into the tiny wells into the agar gel to run the gel electrophoresis and analyze the data like in my previous blog post about gel electrophoresis.  These subjects are just a few of the many topics I learned this unit.

     This unit was short and sweet.  Some strengths in this unit for me was that I just came off a nice long vacation after the stressful finals week.  My family and I went out of town to visit family and this was a nice break from the constant stress of school.  My brain was allowed to be relaxed and decompress, which made my mind fresh for this unit.  I also had a clearer idea of how to study and tackle various assignments such as vodcasts, tests, and lab reflections.  Some setbacks, however, included the constant studying I wanted to accomplish.  I wanted to constantly study after each vodcast, but I was not able to do so.  A success I would like to share is the use of note cards for studying for the big unit test.  I convert all my vodcast notes into note cards and this is a neat way to study in short chunks separated by a few minute breaks in between.

     In this unit, we did the Candy Electrophoresis Lab and the pGLO lab.  In the gel electrophoresis lab, I learned about how to get the DNA.  In this lab, we did the candy with dye.  The dye acted like the DNA.  The different DNA would run against the control DNA, and I learned that the results were never exact.  Some were pretty close, but not all of them were 100% perfectly this color or length.  More information about how I analyzed the lab can be found using this link:  http://leibiologyblog.blogspot.com/.  The other experiment we did in the biotechnology unit was the pGLO lab.  In this lab, we tried to use different possibilities to try and see which DNA would glow.  In this unit, I learned the reason for each substance that we used.  For example, the calcium chloride would be used for loosing the membrane and the arabinose would make the bacteria glow.  With all these chemicals, I was able to find out what each substance did to the final result.  My analysis can be found with the same link which is: http://leibiologyblog.blogspot.com/. 

     As always, there is never enough to learn about a various topic.  Biotechnology is so broad that we barely covered the fundamentals.  I wonder about the real world of biotechnology and how it can be implemented to benefit our society to make things easier.  For example, the movie GATTACA.  GATTACA was a dystopian society where everybody was perfect genetically.  I want to prevent things like that, but also use biotechnology to benefit our society.

     In the beginning of the year, we wrote a New Years Resolution.  My goals were to maintain my grades fairly high.  So far after around three to four weeks, my grades are still maintaining a high percentage.  The hardest part of the semester is definitely the first month.  This period of time is the hardest of all because the grades fluctuate a lot.  If you get a 5/10 on your first assignment, you will have a D as a grade.  Right now, I am still around where I would like to be grade wise.  There are a few steps, however, I could start doing.  The first thing for biology is to study proactively.  This means after each vodcast relate and review and CFU, I need to study the material so I could come in prepared with all my questions that needed to be answered.  This way, I do not need to cram the last minute.

pGLO Lab Analysis

pGLO Observations , Data Recording & Analysis

1.

Obtain your team plates.  Observe your set of  “+pGLO” plates under room light and with UV light.  Record numbers of colonies and color of colonies. Fill in the table below. Plate Number of Colonies Color of colonies under room light Color of colonies under   UV light - pGLO LB 0 grey-white grey-white - pGLO LB/amp 0 Clear (nothing) Clear (nothing) + pGLO LB/amp 49 grey-white grey-white + pGLO LB/amp/ara 64 Glowing green Glowing green

2.	What two new traits do your transformed bacteria have? The first trait that I observed was that the transformed bacteria started to glow,  The second trait that I saw that the transformed bacteria were not only growing, but the bacteria were both green and glowing.
3.	Estimate how many bacteria were in the 100 uL of bacteria that you spread on each plate. Explain your logic. I think that there are too many bacteria to count in the 100 uL of bacteria.  Bacteria are microscopic and with that, it is hard to tell how many single bacterium there are.
4.	What is the role of arabinose in the plates? The role of arabinose is to provide a way to control expression of the GFP gene.
5.	List and briefly explain three current uses for GFP (green fluorescent protein) in research or applied science. The first application of GFP is US Company Yorktown Technologies sold florescent green zebra fish in order to detect pollution in waterways. The second application of GFP is that a Japanese-American team created florescent green cats as a proof of concept to use cats as a model organism for disease. The third application of GFP is that a South Korean Team bred red glowing dogs which allowed scientists to study the genes that cause humans diseases such as blindness.
6.	Give an example of another application of genetic engineering. Genetic engineering can be used to design various things.  An example of genetic engineering would be to mass produce human growth hormones in the field of medicine.  Genetic engineering can mass produce other various things such as vaccines and insulin.

Candy Electrophoresis Lab

1.  Two of our group's dyes did not look normal.  The first dye was our green dye.  Instead of having one dye in one place, there was a blue dye and a yellow dye at two different spots.  The blue dye was in the same place as the sample and the yellow dye was in the same place as the sample as well.  Our group's brown dye looked a little off.  Instead of showing one distinct spot of where the dye is, there is a faded spot of where the dye might have ended.  The space between the final spot and the starting spot had a trail of red colored dye.  These two dyes that had errors could be another kind of dye other than the four that our group observed.

2.  I think that the carminic acid would be the brown dye because the structure of the carminic acid seemed stretched out just like our brown dye.  The betanin (beetroot red) would be the red dye because the color of the dye is red and red is in the name of the dye.  The fast green FCF would be the green dye because the name says green, so the dye is probably going to be a green-like color.  Lastly, the citrus red 2 would be the yellow dye because I think of yellow as a red-like color but not exactly red.

3.  I think the main reason manufacturers put artificial food coloring in dog food to make the food look more appealing to the dog eating the food.  Also, enhancing the color of the dog food makes the dog owner attracted to how good the product looks.

4.  The main reason artificial food colors are preferred over natural colors is because of the appearance.  The overall look of the food really influences how much the person eating feels.  For example, eating a brown apple is much worse than eating a ripe red apple.

5.  The two factors that control the distance the solutions migrate are if the pieces are larger or smaller and the amount of electricity the gel is receiving.  Larger solutions tend to travel slower and less and smaller solutions tend to travel longer.

6.  The electrical current causes the solutions to move through the gel.

7.  The components of the electrophoresis system to separate by size are the gel lanes and the amount of voltage running into the gel because it determines how fast the short size solutions are going and how slow the large are.

8.  The 600 Dalton DNA solution would move the farthest, the 1000 Dalton DNA solution would move the second farthest, the 1200 Dalton DNA solution would move the third farthest, and the 5000 Dalton DNA solution would move the least.  The 600 Dalton DNA solution would move the farthest because it is the lightest and the 5000 Dalton DNA solution would move the least because it is the heaviest.

New Year Goals

     New year, new me.  Each year, I try to become better at what I do.  I can achieve this by setting a few goals to get my year on track and onto a productive year.  My two SMART goals of 2017 are to get 95% or higher in each unit test for this class and to get 95% or higher on all my course grades.  This may seem almost impossible at first, but with a few simple steps, I could set myself on track to achieve these goals.

     My first goal is to get 95% or higher on all unit tests in this class.  This goal can be accomplished with a few easy steps.  My first step is to first get the big picture.  I need to understand what the unit will be about before diving into the great detail.  Before every unit, I will look at the unit and see what the unit is about and what the different vodcasts are about.  Doing this, I can better understand what I am learning about.  Then, I will learn the material vodcast by vodcast.  After each vodcast, I will do the usual CFU's and Relate and Reviews.  In addition to my normal routine, I will study each vodcast before that and the vodcast I just learned.  Actively reviewing will help me keep the information fresh in my head so I will be ready for the unit tests.  Next, after I learn all my vodcasts, it is time for me to review everything.  By now, I will have all the vodcast information onto notecards.  I will already have learned the information and the information should not be new to me.  The last week before the test should be all review.  One week before the test, I should be only reviewing, not learning the concept.  I will be reviewing and identifying any concepts that I am having trouble with and seek for help by looking myself, asking friends, and lastly asking my teacher.  These steps should point me to where I want to be.  After each test is graded and I do not get a score I like, I need to reflect on this and change something for the new unit.  After the unit, I should also review the previous units I have learned as well as the unit I have just learned to keep the information in my head for the final.

     My second goal is to get 95% or higher on all my classes.  In the previous semester, I struggled to get the grades I wanted.  With my experience from my first semester of high school, I can utilize the information I learned about getting good grades to the next semester.  Each course is different in terms of how easy I find it or what the material is about, but I need to find a way for each class to maintain a high grade.  I can maintain a high grade in each course with a few simple steps.  The first step is to pay attention to everything the teacher says of hands out.  Paying attention to the teacher because they tell you what they want and if I do not listen, I will not know what they want.  The second step is to work thoroughly.  For each assignment and project, I need to not just slap work together, but to put extra time and effort to show the teacher that I deserve my grade.  Executing these steps consistently through the course of the semester should bring me the grades I think I should earn.

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>.