Monday, February 13, 2017
Saratoga High School Garden
In short, 20 time is spending 20% of your time on something you are passionate, in the form of a project or anything else you can think of. It is meant to be creative and self motivated. The essential question I am asking is could there be a garden at Saratoga High. For my project, I am researching, and if possible, I want to see what needs to be done to create a rooftop garden, or any garden, at Saratoga High. I have always liked gardening, and I know that there are many benefits to having a garden at a school. SHS does not have a garden, so implementing a garden could help many people. My goals are to have either a garden at the school, or have the administration or staff strongly considering a garden by the end of the year. I will measure my progress by researching and answering all of my obstacles and questions that need to be answered to get this built. In the future, I hope to use class time to figure out logistics involving the garden, and contacting administration in hopes they will support this project.
Tuesday, January 31, 2017
Unit 6 Reflection
This unit was about biotechnology, its uses, and the ethical questions it raises. We learned how DNA can be recombined and inserted into a new organism through a plasmid. By inserting a gene into a plasmid and inserting the plasmid into bacteria, the bacteria will treat the new gene as its own and produce whatever protein it codes for. After introducing the plasmid to bacteria, they place the bacteria in food to make them grow and then put them into the antibiotic the plasmid provides resistance too. This ensures that all bacteria without the plasmid will die.
To learn how to analyze DNA and how to measure the lengths of the strands of DNA we did the gel electrophoresis lab. http://nakulbiology.blogspot.com/2017/01/candy-electrophoresis-lab.html We cut out DNA using restriction enzymes and tested their lengths by running them through a gel.
The pGLO lab incorporated all the things we had learned about biotech. We had several different samples of bacteria and treated each with different things. After the lab, as expected, the bacteria with the pGLO gene inserted, the ampicillin resistance, and the arabinose glowed under UV light. http://nakulbiology.blogspot.com/2017/01/pglo-lab.html
I understood this unit pretty well. It was not very long and the hands on labs helped me in my understanding. While reading the concepts of the labs I was confused, but after doing the lab it made perfect sense to me why everything happened as it did. Seeing the concepts in action really helped me see what was going on. I wonder how biotech will play a role in society in the future. Will altering multi-cellular organisms be common? Will we ever alter human DNA or clone a human?
I think I have done a good job on my New Years resolutions. I finished my chapter notes early so I wasn't stressed or piled up with work. Also, I finished most of my homework assignments early or on time. I could still improve by preparing for tests sooner instead of procrastinating my studying.
To learn how to analyze DNA and how to measure the lengths of the strands of DNA we did the gel electrophoresis lab. http://nakulbiology.blogspot.com/2017/01/candy-electrophoresis-lab.html We cut out DNA using restriction enzymes and tested their lengths by running them through a gel.
The pGLO lab incorporated all the things we had learned about biotech. We had several different samples of bacteria and treated each with different things. After the lab, as expected, the bacteria with the pGLO gene inserted, the ampicillin resistance, and the arabinose glowed under UV light. http://nakulbiology.blogspot.com/2017/01/pglo-lab.html
I understood this unit pretty well. It was not very long and the hands on labs helped me in my understanding. While reading the concepts of the labs I was confused, but after doing the lab it made perfect sense to me why everything happened as it did. Seeing the concepts in action really helped me see what was going on. I wonder how biotech will play a role in society in the future. Will altering multi-cellular organisms be common? Will we ever alter human DNA or clone a human?
I think I have done a good job on my New Years resolutions. I finished my chapter notes early so I wasn't stressed or piled up with work. Also, I finished most of my homework assignments early or on time. I could still improve by preparing for tests sooner instead of procrastinating my studying.
Saturday, January 28, 2017
pGLO Lab
1.
Plate
|
Number of Colonies
|
Color of colonies under room light
|
Color of colonies under UV light
|
-pGLO LB
|
covered
|
brownish yellow
|
whitish blue
|
-pGLO LB/amp
|
0
|
N/A
|
N/A
|
+pGLO LB/amp
|
100~
|
brownish yellow
|
whitish blue
|
+pGLO LB/amp/ara
|
22
|
brownish yellow
|
glowing green
|
2. The bacteria from the +pGLO LB/amp/ara plate gained two new traits. The transformed bacteria are resistance to ampicillin and the ability to glow under UV light. They did not die in the presence of ampicillin, and glowed under the light.
3. Each transformed bacteria must have multiplied into a colony, so about 100 bacteria were transformed in the +pGLO LB/amp. The bacteria that did not pick up the plasmid would have been killed by the ampicillin. Probably half of the bacteria died in the plate, so probably over 250 bacteria were present in the 100 micro-liters.
4. The purpose of arabinose is to "turn on" the GFP or Green Fluorescent Protein. This causes the bacteria to glow green under UV light.
5. There are several uses for GFP for biologists. It can be used as a marker when inserting a gene into a cell. If the cell glows, it means the other gene inserted is also being expressed. The protein has also been altered to react to different wavelengths and express several different colors.
6. Another practical application of genetic engineering is in food production weather it be animals or crops. Genetic engineering can make an animal or plant stronger, bigger, or more resistant to disease.
Source: https://embryo.asu.edu/pages/green-fluorescent-protein
Wednesday, January 18, 2017
Candy Electrophoresis Lab
I this lab, we asked the question of can molecules in food dye be separated in gel electrophoresis. We found that the dyes did separate, by observing the different groups of dye after electrophoresis. We learned from our textbook and the vodcasts, that smaller molecules of DNA travel faster and farther in electrophoresis, and larger molecules travel slower. The data is consistent with these scientific principles, because the dyes with the larger molecules did not travel as far as the smaller moleculed dyes.
1. In our experiment the bands were about the same size as the reference dyes. In some cases, our dyes were different colors than the reference dyes so they did not match up. None of the dyes moved towards the negative charge.
2. Of the dyes listed, betanin and citrus red 2 would move like our red dye, but citrus red 2 would move faster because it is a smaller molecule. Also, fast green FCF would move similarly to our green dye because it is similar in size.
3. Dog food manufacturers would put artificial colors in the food to make it more visually appealing and consumers are more likely to buy a food that is colorful and nice looking than a food looking unappealing and bland looking.
5. The factors that control how far the dyes go are time and size of molecule. The longer the electrophoresis is on for, the farther the dyes will travel. Also, the smaller molecules will travel faster, and therefore farther in the allowed time.
6. The force that allows the dyes to move through the gel is electricity. When the current runs though the gel, the molecules are repelled by the negative charge, because they are also negatively charged, and attracted to the positive charge, which propels them through the gel.
7. The gel is the component that separates the molecules by size. If it was a liquid for example, all the molecules would travel at the same speed, but the gel makes it harder for larger molecules to travel, separating out the sizes.
8. DNA molecules with different weights would separate out in different groups. The DNA with the molecular weight of 600 daltons would form a band ahead of the rest. Following would be the 1000, 2000, and 5000 in that order.
1. In our experiment the bands were about the same size as the reference dyes. In some cases, our dyes were different colors than the reference dyes so they did not match up. None of the dyes moved towards the negative charge.
2. Of the dyes listed, betanin and citrus red 2 would move like our red dye, but citrus red 2 would move faster because it is a smaller molecule. Also, fast green FCF would move similarly to our green dye because it is similar in size.
3. Dog food manufacturers would put artificial colors in the food to make it more visually appealing and consumers are more likely to buy a food that is colorful and nice looking than a food looking unappealing and bland looking.
5. The factors that control how far the dyes go are time and size of molecule. The longer the electrophoresis is on for, the farther the dyes will travel. Also, the smaller molecules will travel faster, and therefore farther in the allowed time.
6. The force that allows the dyes to move through the gel is electricity. When the current runs though the gel, the molecules are repelled by the negative charge, because they are also negatively charged, and attracted to the positive charge, which propels them through the gel.
7. The gel is the component that separates the molecules by size. If it was a liquid for example, all the molecules would travel at the same speed, but the gel makes it harder for larger molecules to travel, separating out the sizes.
8. DNA molecules with different weights would separate out in different groups. The DNA with the molecular weight of 600 daltons would form a band ahead of the rest. Following would be the 1000, 2000, and 5000 in that order.
Monday, January 9, 2017
New Years Goals
1. This semester I will be more organized in my work.
I often struggle to find things and get things done efficiently because my things are not in one organized place and are often strewn across many places. Having things in one place will make it easier to finish work on time and study. Also, a schedule will allow me to organize my time better.
2. I will finish textbook notes earlier.
I have sometimes done this and sometimes not. By finishing the textbook notes earlier, it will allow me to learn better and be less stressed about completing them. When I procrastinated and put off the notes, I did not learn from them because I was more focused on finishing then obtaining the information.
I often struggle to find things and get things done efficiently because my things are not in one organized place and are often strewn across many places. Having things in one place will make it easier to finish work on time and study. Also, a schedule will allow me to organize my time better.
2. I will finish textbook notes earlier.
I have sometimes done this and sometimes not. By finishing the textbook notes earlier, it will allow me to learn better and be less stressed about completing them. When I procrastinated and put off the notes, I did not learn from them because I was more focused on finishing then obtaining the information.
Wednesday, December 14, 2016
Unit 5 Reflection
Unit 5 was all about DNA, RNA, and their functions. DNA is a double helix structure that has nucleotides that code for proteins. The nitrogen bases are Adenine, Thymine, Guanine, and cytosine. A and T pair up while G and C pair up.
When RNA needs to be made, an enzyme called RNA polymerase unzips the DNA and pairs a nucleotide with each strand of DNA. In RNA, the base Thymine is replaced with Uracil (U). This single stranded mRNA breaks off and travels through the cytoplasm to a ribosome. In the ribosome, the RNA is read three base pairs at a time. Each three bases codes for a codon and each codon represents an amino acid. The amino acids keep adding on to the polypeptide until a stop codon is reached.
A mutation is a change in the genome. Mutations can either be harmful, give benefits, or have no affect at all. A point mutation is a mutation that changes on or two bases. A substitution is swapping one base out for another. A frameshift mutation is a deletion or insertion of a base and changes every codon that comes after the mutation.
Another concept is gene regulation and expression. In any given cell, only a fraction of the DNA is used to express a phenotype. In prokaryotic cells, a repressor is attached to the operator that prevents the RNA polymerase from reading the DNA, but the repressor detaches when lactose is present allowing the gene to be expressed. However, this process is much more complex in human cells.
This unit was not to difficult, as I found the process of making a protein and mutations fairly straightforward. The concept of gene regulation was difficult to understand and it was very complex. This unit helped me understand the last two units better, as they were also about genetics. Making the study guide helped me learn, because if forced me to answer questions and told me what I knew and did not know. This unit has helped me grow as a student, because it made me have to try harder to learn things I did not understand. A question I have about this unit is how the mRNA travels through the cytoplasm to the ribosome without getting lost.
When RNA needs to be made, an enzyme called RNA polymerase unzips the DNA and pairs a nucleotide with each strand of DNA. In RNA, the base Thymine is replaced with Uracil (U). This single stranded mRNA breaks off and travels through the cytoplasm to a ribosome. In the ribosome, the RNA is read three base pairs at a time. Each three bases codes for a codon and each codon represents an amino acid. The amino acids keep adding on to the polypeptide until a stop codon is reached.
A mutation is a change in the genome. Mutations can either be harmful, give benefits, or have no affect at all. A point mutation is a mutation that changes on or two bases. A substitution is swapping one base out for another. A frameshift mutation is a deletion or insertion of a base and changes every codon that comes after the mutation.
Another concept is gene regulation and expression. In any given cell, only a fraction of the DNA is used to express a phenotype. In prokaryotic cells, a repressor is attached to the operator that prevents the RNA polymerase from reading the DNA, but the repressor detaches when lactose is present allowing the gene to be expressed. However, this process is much more complex in human cells.
This unit was not to difficult, as I found the process of making a protein and mutations fairly straightforward. The concept of gene regulation was difficult to understand and it was very complex. This unit helped me understand the last two units better, as they were also about genetics. Making the study guide helped me learn, because if forced me to answer questions and told me what I knew and did not know. This unit has helped me grow as a student, because it made me have to try harder to learn things I did not understand. A question I have about this unit is how the mRNA travels through the cytoplasm to the ribosome without getting lost.
https://commons.wikimedia.org/wiki/File:0323_DNA_Replication.jpg
Monday, December 12, 2016
Protein Synthesis
The creation of a protein is a several step process. It starts with an enzyme unzipping the DNA. Another enzyme then goes along the DNA and reads the sequence and puts a the matching base pair with each base. Instead of matching A with T, it replaces the T with a U. The completed RNA then detaches from the DNA and travels to a ribosome. The mRNA is read and every 3 bases represents a codon. Each codon represents an amino acid. The ribosome goes down the line and reads every codon until it reaches a stop codon. The amino acids then break off and the protein is complete.
Mutations can either change a gene dramatically or not at all. A simple substitution in the DNA either causes one or two codons to change or sometimes, none at all. A frameshift mutation such as an insertion or deletion can cause big changes and change every codon after it. A frameshift mutation at the beginning of a sequence would cause more damage than at the end, because a frameshift causes every codon after it to change. If it occurred at the end, only a few would change.
When I chose the mutation I would like to do on a DNA strand, I chose an insertion. I chose this because it would allow me to stop the translation right after it started. It caused the most change out of all mutations because it didn't allow for any amino acids to be coded for except the start codon. It mattered where th mutation occurred, because it occurred right after the start codon. If it had been towards the end, the amino acids that came before would have still been coded for.
Having a mutation could result in several things. A mutation could result in death, a disease, or nothing at all. We all have many proteins in our body that carry out essential functions such as carrying oxygen in the blood. An alteration to one of these important proteins could have some major consequences. For example, Parkinson disease in often caused by a mutation in one of several genes. It causes loss of control of muscles. Some mutations can guarantee that an individual will develop Parkinson, and another mutation increases an individuals risk of getting the disease.
Works Cited:
Mutations can either change a gene dramatically or not at all. A simple substitution in the DNA either causes one or two codons to change or sometimes, none at all. A frameshift mutation such as an insertion or deletion can cause big changes and change every codon after it. A frameshift mutation at the beginning of a sequence would cause more damage than at the end, because a frameshift causes every codon after it to change. If it occurred at the end, only a few would change.
When I chose the mutation I would like to do on a DNA strand, I chose an insertion. I chose this because it would allow me to stop the translation right after it started. It caused the most change out of all mutations because it didn't allow for any amino acids to be coded for except the start codon. It mattered where th mutation occurred, because it occurred right after the start codon. If it had been towards the end, the amino acids that came before would have still been coded for.
Having a mutation could result in several things. A mutation could result in death, a disease, or nothing at all. We all have many proteins in our body that carry out essential functions such as carrying oxygen in the blood. An alteration to one of these important proteins could have some major consequences. For example, Parkinson disease in often caused by a mutation in one of several genes. It causes loss of control of muscles. Some mutations can guarantee that an individual will develop Parkinson, and another mutation increases an individuals risk of getting the disease.
Works Cited:
Eisen, Jonathan. “Fact Sheet: DNA-RNA-Protein.” MicroBEnet: the Microbiology of the Built Environment Network., Alfred P. Sloan Foundation, 29 Oct. 2013, www.microbe.net/simple-guides/fact-sheet-dna-rna-protein/.
“What Kinds of Gene Mutations Are Possible? - Genetics Home Reference.” U.S. National Library of Medicine, National Institutes of Health, 6 Dec. 2016, ghr.nlm.nih.gov/primer/mutationsanddisorders/possiblemutations.
“Animal Genetics.” Print Page, web2.mendelu.cz/af_291_projekty2/vseo/print.php?page=315&typ=html.
http://web2.mendelu.cz/af_291_projekty2/vseo/print.php?page=315&typ=html
“National Institutes of Health.” National Institutes of Health, U.S. Department of Health and Human Services, 21 July 216ADAD, www.niehs.nih.gov/health/topics/conditions/parkinson/.
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