Unit 6 Reflection

     This unit was about was about biotechnology and its purpose. Biotechnology is the study of living things in order to benefit mankind. The four applications of biotechnology are industrial/environmental (converting sugars into acids through the process of fermentation), medical/pharmaceutical (putting in a healthy copy of a gene into cells of a defective gene through gene therapy), agricultural (genetic modified organisms or GMO), and diagnostic (searching for genes or DNA segments indicating risk for diseases through the process of genetic testing).

     The polymerase chain reaction, also known as PCR, is a procedure used to amplify a specific DNA region. Gel electrophoresis uses electricity to separate DNA fragments based on size. Sequencing is a process that determines the exact order of a given DNA strand.
     Recombinate DNA Technology (rDNA) inserts DNA of one organism into DNA of another organism. This process is often described as genetic engineering. 
     Bioethics is the study of decision making as it applies to moral decisions that have to be made because of advances in biology, medicine, or technology.       I really enjoyed this unit because it was very hands on and had a lot of interesting labs. My favorite lab was the pGLO lab because the result was really interesting. 

This is a picture of the container that had LB, AMP, and ARA.

This is a picture of the gel electrophoresis lab with the gels loaded.

     I learned that when arabanose sugar is added to the bacteria E.coli, the bacteria glows green under UV light. The arabonose sugar is the trigger that makes the bacteria glow. The glowing florescent protein (GFP) is extracted from jellyfish.
     I really struggled to understand the last vodcast, the pGLO prelab vodcast. I was not really sure what the outcome of each of the plates were when i was watching the vodcast. After re-watching the vodcast, and doing the lab, I was able to understand the effects of arabanose sugar and its function.
     I wonder about the many jobs in the biotech world. I think some day in the near future, the world will be very advanced in biotech and become too advanced.

My new years goals were:

• Smart Goal #1:

I will start studying at least 5 days before every test I take, and take notes when I am studying. To make sure I achieve this goal, I will set reminders on my phone. Since I like to procrastinate a lot I will have to pretend that the test is the next day so I can actually study.

• Smart Goal #2:

I will try my best in everything I do, and during lectures in class I will actively listen and make sure that I ask questions when I don't understand something. While I am actively listening, I will take notes and review the topics that I learned in class while completing my homework.

     So far, I have achieved smart goal 1 and 2. I have been taking notes while i was studying, and I completed my textbooks early in the unit. Also, I have been paying attention in class and participating. I think that I set good and reasonable goals that will challenge me to do my best throughout this semester.

pGLO Lab

Plate	Number of Colonies	Color of colonies under room light	Color of colonies under   UV light
- pGLO LB	0	none	none
- pGLO LB/amp	none	none	none
+ pGLO LB/amp	2	white/clear	white/clear
+ pGLO LB/amp/ara	At least 4	white/clear	bright green

          2. The two new traits that the transformed bacteria have are: the ability to glow under UV light and ampicillin resistance.

          3.  I think there were millions of bacteria in the 100 uL of bacteria that was spread on each plate because bacteria are very small in size, many bacteria could be found in a little amount of E.coli.

          4. The rold of arabinose in the plates was to activate the gene that makes the bacteria glow green when UV light is present.

         5.  a)GFP can be used to dye cancer cells and shbow images of them

              b) GFP can show if the bacteria took a new gene properly

              c) GFP can show if someone had a drug overdose

         

         6. Genetic engineering can be used to create genetically modified crops. Corn, papaya, cotton, and soy are all at a high risk for being genetically modified. Crops are genetically modified to increase the resistance against a disease in a crop.

Candy Electrophoresis Lab

1. The reference blue dye was way behind and the actual blue dye from the candy. All the reference dye fell off because during the experiment, our class went to an assembly. We did not come back from the assembly in time. I did not see any dyes that were a different color than any of the reference bands.  There were no dyes that moved in the wrong direction.

2. The "fast green FCF" looked like the Blue 1 that I examined in the lab. They had similar chemical compositions, and their structures also looked very alike. The "citrus red 2" looks very similar to the Red 40 that I used in the lab. Although these dyes did not have the same composition, their structures were still similar.

3. I think that dog food manufactures such as Beneful and Snausages Breakfast Bites have food dyes in their product becuase dogs prefer more colorful food. If the food did not have a good taste, but it was colored like a dog treat, I think a dog would get tricked by the color of the food and still eat it.

4. I think that an artificial food color would be preferable to a natural food color because artificial food colors have more sugar, and therefore taste better than a natural food color.

5. The two factors that control the distance the colored dye solutions migrate are the charge of the dye and the length. If the DNA segment is longer, then it will travel slower. If the DNA segment is shorter, it will travel quicker.

6. Electricity is the force that helps the dyes move through the gel. Once the dyes are put in the gel, I turned on the electrical force.

7. The gel causes the molecules to separate by size because it takes the longer DNA more time to go through the gel. The shorter DNA has an easier time getting through the gel because it has to go through small sections of the gel.

8. The DNA of molecules with molecular weights of 600, 1000, 2000, and 5000 daltons would separate from lightest to heaviest. This means that the DNA with the molecular weight of 600 would go through the gel first, followed by the 1000 and 2000 weights. The 5000 weight would finish last because it weighs the most, making it the slowest.

New Year Goals

• Smart Goal #1:

I will start studying at least 5 days before every test I take, and take notes when I am studying. To make sure I achieve this goal, I will set reminders on my phone. Since I like to procrastinate a lot I will have to pretend that the test is the next day so I can actually study.

• Smart Goal #2:

I will try my best in everything I do, and during lectures in class I will actively listen and make sure that I ask questions when I don't understand something. While I am actively listening, I will take notes and review the topics that I learned in class while completing my homework.

Unit 5 Reflection

Unit 5 was about genetic code, DNA replication, making proteins, mutations, and gene expression and regulation. DNA is a double helix made up of two strands twisted around each other like a twisted ladder. DNA is made up of nucleotides. Nucleotides are made up of 3 parts: a nitrogen base (A, T, C, G), a phosphate group, and a sugar (deoxyribose). Phosphate and sugar make up the sides of the ladder and the bases are the steps. DNA is anti-parallel. This means that each nucleotide covalently bonds with another. Nitrogen bases come in two types: double rings called purines(adenine and guanine), and single rings called pyrimidines (thymine and cytosine). Adenine always pairs with thymine, and Cytosine always pairs with guanine. Code is a system of words or symbols that are substituted for other words.

Semi-conservable replication is the process of creating two identical strands of DNA from one original strand. Two strands end up with half of the original strand. First, enzyme unzips DNA by breaking down hydrogen bonds that hold nitrogen bases together. Then, DNA polymerase add matching nucleotides to each strand. The result is two identical strands of DNA molecules that form are identical to the original DNA molecule.

The central dogma of biology is that information flows from DNA to RNA to proteins. Proteins make up out traits (phenotypes). RNA is single-stranded, has a ribose,contains uracil, and is a temporary copy of DNA. RNA delivers a copy to the ribosomes, and the ribosome uses this RNA copy to make proteins. Transcription is a process in the nucleus where RNA polymerase reads and copies the DNA code (gene) for a protein as mRNA. In the process of transcription, DNA unzips, RNA polymerase matches spare nucleotides to make an RNA strand,and mRNA is produced and leaves the nucleus for the cytoplasm. Translation is a process that takes place in the cytoplasm. First mRNA arrives at the ribosome. Then, the ribosome reads mRNA three bases at a time and transcribes the DNA language into amino acids. Each three-base sequence is known as a codon. Each codon codes for one amino acid.

A mutation is a change in DNA code (genes.) The effect can be none and sometimes it can be fatal. Mutagen is anything that causes a mutation. Mutations can happen naturally too. Point mutations are a change in one or two base pairs. These types of mutations are very small and common. A substitution is a change in which one nucleotide is substituted for another. The two types of frameshift mutations are insertion and deletion. Insertion is a mutation where one extra base pair is put in code. Deletion is a mutation in which one base pair is left out of the code. Inversion is a mutation where DNA breaks off and bonds in reverse order. Translocation is the part of a chromosome that breaks off and bonds with another. Mutations cause changes in DNA which cause changes in life. Proteins are essential to life.

This is a picture of an RNA strand being translated to an amino acid.

Gene expression is the process of a gene being used to produce a gene product or phenotype. Gene regulation is a mechanism used by cells to increase or decrease the expression of a gene. Every cell in your body has the same DNA but not all cells look the same. Cells look different because each type of cell expresses or turns on genes specific to those cells. Environment can affect how and when genes are expressed. Gene regulation is the process where cells do not want to waste energy or overexpress genes so they have many steps that are used to control gene expression. A promoter is the location on DNA where RNA polymerase attaches. An operon is a series of genes used to control the expression of a single gene. The operator is a “switch” or segment of DNA at the start of a gene that prevents or allows RNA polymerase from attaching and reading the gene. Eukaryotic regulation is much more complicated than bacterial regulation. EXons are EXpressed and introns are sequences that are cut out. Histones are proteins that allow DNA to coil. Nucleosomes are DNA that is wrapped twice around like a histone. Genes whose promoters are wrapped up in nucleosomes are not expressed. Different enzymes are involved in breaking histones free or binding them up to control gene expression. This is passed to future cells during development.
I really liked learning about making proteins and DNA. I had a difficult time on the protein synthesis lab because I did not understand how to convert a DNA strand to an RNA strand. After going back and watching the vodcast, I understood how to convert DNA to RNA. I also struggled in understanding the last vodcast. The vodcast was about gene expression and requlation. I didn't know the different parts of the operon. After doing the do now in class, I had a better visual understanding of an operon.

This is a picture from the protein synthesis lab that was difficult.

Protein Synthesis Lab

   
    There are many steps required to make a protein. First, RNA polymerase reads and copies the DNA code or gene for a protein as an mRNA copy through the process of transcription. Transcription happens in the nucleus. In the process of transcription, DNA unzips. Then, RNA polymerase matches spare nucleotides to make an RNA strand. mRNA is produced and leaves the nucleus for the cytoplasm. After transcription happens, the mRNA arrives at the ribosome. In the process of translation, the ribosome reads RNA three bases at a time and translates DNA language into protein language. Each three-base sequence is called a codon. Each codon codes for one amino acid.

A mutation is a change in DNA code. An insertion is a mutation in which an extra base pair is put in code. A deletion is a mutation where a base pair is left out of the code. The mutation substitution happens when one nucleotide is substituted for another. In my opinion, substitution affected the protein the least because it only changed one nucleotide. A deletion affected the protein the most when it was added in the beginning because it changed every nucleotide after it was added. It does matter where the mutation occurs when it is a deletion or insertion because all the code after the added or deleted nucleotide is affected.

   

 In step 7, I chose to do a deletion. I think that a deletion affects the DNA code the most. It does matter where the mutation occurs. I put my deletion in the beginning, so all my code was affected.

http://bit.ly/2hnDHVv
This is a picture of a child with Progeria.
Mutations can have a big impact on a person's life. They can create genetic disorders. Progeria causes accelerated aging. Most children who have progeria die at the age of 13. Their death is causes by a stroke or heart attack. Progeria is caused by a mutation that is located on the LMNA gene which is a protein. This protein gives support to the cell nucleus. 

   

Human DNA Extraction Lab

In this lab, we asked the question how can DNA be separated from cheek cells in order to study it? We found that it is possible to separate DNA from cheek cells. My hypothesis stated that if DNA can be seoarated fromm cheek cells, then DNA would be visible after precipitation. First, we swished Gatorade in our mouth for 30 seconds. Then, we added enzymes to speed up the process. The enzymes that were added were: salt and dishwasher soap to the solution. Since the DNA was still insoluble, we added rubbing alcohol to the solution. When we added the rubbing alcohol, the DNA percipitated from the Gatorade. In this lab, the rubbing alcohol was a protease because it catalyzed the splitting of the interior peptide bonds in a protein. The DNA rising from the gatorade was a catabolic process, which gave rise to substances of decreasing complexity. I could see the DNA after the DNA was percipitated. This data supports our claim because we could extract DNA from cheek cells, and I predicted that the DNA would be visible after precipitation.
     While our hypothesis was supported by our data, because there was no procedure in this lab, there could have been errors. In the beginning of the lab, we were given a piece of paper with the procedure. However, this paper did not have the steps of the lab in the right order. We had a tough time putting the procedure in order, and we had a big discussion at our table about which step was first. Another error was that someone at our table poured too much Gatorade into my cup. Because of this, I had a hard time swishing all the Gatorade in my mouth. If I had less Gatorade, I probably could have gotten more cheek cells. Due to these errors, I would recommend having an accurate procedure.
     This lab was done to demonstrate DNA replication and extraction. From this lab, I learned that DNA can be extracted from cheek cells, which helps me understand the concept of DNA extraction. Based on my experience from this lab, I now know how complicated DNA is and I was able to see what my DNA looks like.