DNA Precipitation: Capturing Life's Blueprints in a Bottle

Introduction
a) Background- What is DNA? Deoxyribonucleic acid or DNA is a molecule found in almost all cell types and living things. Its purpose is to carry genetic information and is responsible for everything that makes an individual unique. It also has the information for cells to perform all of their functions necessary to survive. Each person has a person combination of DNA, half from your mother and half from your father. DNA at the molecular level is a molecule shaped like a double helix that spirals and has rungs like a ladder, called bases. The bases are adenine, guanine, thymine, and cytosine, and each base functions in a code. Each of the bases are also connected to a sugar and a phosphate, creating nucleotides. When bases are pairing, adenine and thymine always pair and guanine and cytosine also pair. The four bases of DNA make codes that are comprehended by cells called genes, which make proteins that are the basis for almost all the inner workings of the body. The human body has more than 40,000 genes the come together for form the genome. Not all the genes in a cell are used. In the body, all the cells contain the same chromosomes, where the DNA information is located, but different cells read different genes from the chromosomes. It is important to remember that among humans, we share 99.9% identical DNA sequences and it is less that 0.1% sequence variation that distinguishes us from those around us, making humans not so different from one another. DNA does not directly make proteins. The templates for protein synthesis are ribonucleic acid or RNA and messenger RNA or mRNA. It is the job of mRNA to carry the information from the DNA to the ribosomes in a cell the create the protein. The proteins made give cells their traits.
b) Purpose- The purpose of this lab is to extract our own DNA from cheek cells we collect. We extract DNA to get a better look at what DNA looks like and to make it easier to study. This practice can be applied in the real world by scientists who precipitate DNA to study it, map it, compare it, sequence it, clone it, and have other uses for it as well.
c) Process- In order to extract our own DNA, we must first loosen our cheek cells by gently chewing the inside of our cheeks for about 30 seconds. After loosening the cells, we we swished a saline solution (0.9% saltwater) and spit the saline solution containing the skin cells back into the cup which we then transfered into a labeled 15 ml test tube containing 3 ml of water. After we added we added 2 ml of lysis buffer to the tube which breaks open and dissolves the cell membrane which is made of fats and the buffer serves as a detergent to remove the cell membrane. Then we gently invented the tube five times. Next we added 100 ml of protease to the tube to break up protein as well as DNAse which is a protein that kills DNA. The protease contains a salt solution as well, and by adding Na+, we neutralize the DNA and make it both hydrophobic and non polar. After we invert the tube a few times more. Then we place the test tube in a warm water bath at about 50 degrees Celsius to speed up the reaction and break open the cell membrane. Finally we add 5 ml of cold ethanol at a 45 degree angle to ensure that the DNA will not dissolve again. After 5 minutes, we slowly invert the tube five more times to aggregate. Finally, after the DNA is visible, we extracted it and placed it in a necklace. 


Discussion
Although this lab was very informative, we did not have to prove a hypothesis or prove a postulate. However, there were many possible sources of error in the lab. First, we could have not swished the saline solution vigorously enough, therefore not extracting enough cells. When shaking the tubes to aggregate the DNA, we could have inverted the tube too vigorously and could have damaged the DNA precipitation. 

Does bacteria taste good? : Making Yogurt to Prove Koch's Postulates

Introduction

During the 1800's, it was the common belief that diseases could only be transmitted through contact with an infected person. It wasn't until German scientist Robert Koch published his postulate which proved that a certain microbe could cause a certain disease. His first postulate stated that the microorganism would be able to be found in all organisms suffering from the disease but not in healthy organisms. The next postulate stated that the microorganism must be separated and grown in a pure culture. That cultured microorganism should cause the same disease when given to a healthy organism. Finally, the microorganism should be isolated again from to the experimental diseased host and proven to be identical to the original disease-causing microorganism. Because it is considered to be unethical to introduce diseases to humans, we will instead use milk to represent a healthy individual in this lab. We will then prove or disprove the hypothesis that microbes in yogurt are the cause of the "yougurtness disease", or when milk becomes thick and turn into yogurt. We must remember that the majority of the bacteria in yogurt are "probiotic" or bacteria that is beneficial. 

To give a little background on bacteria, it is important to note that bacteria has more bacteria on earth than any other life form, making bacteria the most successful species on Earth. Bacteria is classified in the domain of Eukarya and more specifically is a prokaryote as it only consists of one cell, does not have a nucleus, and can not be seen without a microscope. We should also remember that only a small number of bacteria actually cause disease, and the creation of antibiotics has reduced the risk of harmful bacteria. Humans have overused antibiotics though, causing some bacteria to become resistant to antibiotics. Bacteria increase by splitting in half many times logarithmically, which is why it can grow so fast. In order for bacteria to survive, it breaks down sugars using the process of fermentation. Some bacteria also require oxygen in order to survive, and these bacteria are called anaerobes. When yogurt is formed, the yogurt bacteria break down lactose and turn it into pyruvic acid, and then into lactic acid. Lactic acid lowers the pH of milk causing it to curdle and allowing yogurt to stay fresh which still being digestible for people. 

In order to make yogurt, you add specific types of bacteria to milk, and allow it ferment in a controlled environment. By doing so, the casein in milk tangles into a solid mass in the denaturation process. This process is due to the increase acidity, which can also allow harmful bacteria to grow. Yogurt in the United States must contain Streptococcis thermophilus and Lactobacillus bulgaricus in order to be sold in stores. In order for a product to be considered yogurt, live bacteria must be present in the product. It is this live yogurt that can be used to inoculate a new batch of yogurt.


Procedure
In order to prove Koch's third postulate, we had to make yogurt. First, we took four test tubes and filled them with a small amount of milk. In test tube 1, our negative control, we added nothing to the tube. In test tube 2, our positive control, we added yogurt to the tube. In test tube 3, we added yogurt and ampicllian (an anti bacteria). In test tube 4, we added E. Coli to the milk. After preparing our test tubes, we placed the tubes in an incubator at 37 degrees Celsius for 24 hours. The following day, we removed the tubes from the incubator and made observation about what happened after the tubes were incubated.


Results/Observations
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Discussion
After removing the test tubes from the incubator, we noticed many changes in each of the tube. In tube 1, the negative control, the milk curdled overnight and became thick and white. It smelt like fresh milk and had a pH of 6. In tube 2, the milk had also curdled and was a white color, but instead of smelling like fresh milk, it had a tart smell and a pH of 4. The pH was lowered because of lactic acid, a biproduct of the yogurt added to the milk. Lactic acid lowers the pH of milk, making it acidic. In tube 3, the milk remained liquid and was a cloudy white color and had a fresh milk smell with a pH of 7. Although we added yogurt which should have made the milk turn into a thick, white mass after incubation, we also added ampicillin, which ended up killing the yogurt bacteria and leaving the milk. In tube 4, the milk turned into a cloudy liquid and smelt like old milk. It also had a pH of 8. The E. Coli breaks the sugar in the milk down into succinic acid, ethanol, acetic acid, formic acid, and lactic acid, but does not allow the milk to curdle. Although our lab worked, there were many possible sources for error. For example, if we had contaminated any of our tubes, perhaps but using the same loop for getting yogurt and E. Coli, we would have had different results. We also had to make sure to remember that there is bacteria and molds all around us, and if we had touched a contaminant and then touched the tube, there was a chance of contamination.