DNA, the molecule of life, carries the genetic information from generation to generation. Deoxyribonucleic acid, found in all living organisms, is a double helix containing millions of pairs of nucleotide bases, each base being connected to a deoxyribose sugar and a phosphate group. The four bases are adenine, guanine, thymine, and cytosine; adenine pairs with thymine and thymine pairs with guanine. In short, DNA makes us who we are. It determines everything from eye color to skin color to body type to susceptibility to certain diseases. Certain sequences of DNA that code for a specific trait are called genes. Differences in the base pairs in genes, often occurring because of mutation, are what account for diversity among organisms.
In humans, DNA is stored in the nucleus of all cells. Every cell has a complete set of DNA, but only certain genes are expressed in each cell. What DNA (genes) really does is code for certain proteins in the cell. DNA is first transcribed into messenger RNA, and this mRNA travels out of the nucleus to the ribosomes where the genetic message is read and the correct proteins are built.
In this lab we will attempt to precipitate DNA out of solution, extract it, and put in in a necklace. Visualizing the genetic molecule in this way could be very beneficial to scientist's in the real world. Isolating DNA allows biologists to study and compare between individuals or different species. The sequencing of DNA has been an extremely important development of the last twenty years and will have even more significant benefits in the future when we are more knowledgeable.
The precipitation of DNA is actually a very simple process. First, we will chew on the insides of our cheeks to loosen the cells. Then we will swish a saline solution around in our mouths to extract the cheek cells. The isotonic solution has a concentration that is favorable to the cells. In order to get to the DNA we will add a lysis buffer that breaks open the cell membrane by dissolving the phospholipids. To further isolate the DNA, we will break down the histone proteins DNA is wrapped with using an enzyme called protease. Protease will also destroy the DNAse in the cytoplasm that would otherwise dismantle our DNA. We will speed this reaction up by placing the test tubes in a hot water bath. If our DNA was in just a water solution the DNA, which is negatively charged and polar, would interact with the polar H2O molecules. The added salt binds with the DNA, making it non-polar. We complete the lab by adding cold ethanol, which has a lower freezing point than water. This allows us to get the solution to extremely low temperatures, stimulating precipitation.
Finally, we will have a beautiful necklace containing the very molecules that give us life and make us who we are.
Wednesday, September 15, 2010
Tuesday, September 7, 2010
Yogurt Lab Discussion
Because I was starting this lab with little introduction, I was a little confused throughout the experiment. Therefore, I am not that confident in the results.
In tube 1 (just milk), the milk was sour but the texture was normal. Airborne bacteria probably contaminated the milk and then divided during inoculation. The milk was spoiled, but these particular bacteria were not yogurt-ness bacteria, so the texture did not change.
In tube 2 (milk and yogurt), the substance was thicker and had a smell like yogurt. I was unsure whether this was because the milk actually turned into yogurt or because yogurt was added. However, I am assuming that the yogurt really did change the composition of the milk because the whole sample changed even though we only added a tiny amount of yogurt. The bacteria in the yogurt must have created the original yogurt, as well as altering our milk sample.
As we expected, tube 3 (yogurt, milk, and ampicillin) was absolutely unaffected by the experiment. The smell and consistency were normal, as was the pH, because all the bacteria that could have altered the milk were killed by the ampicillin.
Like tube 1, tube 6 (milk and E. coli) also resulted in a sour smell with normal consistency. The smell of this sample was overwhelmingly sour and made me want to throw up. E. coli seems to spoil milk but not turn it into yogurt.
Our pH readings may have been a little skewed, but it is clear that every tube subjected to bacteria had a lower pH than the tube with ampicillin. Tube 1 had the lowest pH (5), and tubes 2 and 6 had a pH of 6. These numbers don't seem to make sense because the milk with lowest pH should curdle as casein proteins denature. Tube 2, however, was the only one that curdled.
There were a few sources of error that may have affected the results of the experiment. First of all, if the inoculating loops touched any non-sterile surfaces, the tubes could be contaminated with outside bacteria. Also, the colors on the pH scale are so similar that someone could conclude a strip shows a pH of 5 when it is really closer to 7. Finally, we may have used the vortex for too long, which potentially could kill the bacteria by breaking open the sturdy cell walls.
Despite some confusion, I believe our results turned out fairly accurate. Most importantly, we had a great time in our first lab of the year.
In tube 1 (just milk), the milk was sour but the texture was normal. Airborne bacteria probably contaminated the milk and then divided during inoculation. The milk was spoiled, but these particular bacteria were not yogurt-ness bacteria, so the texture did not change.
In tube 2 (milk and yogurt), the substance was thicker and had a smell like yogurt. I was unsure whether this was because the milk actually turned into yogurt or because yogurt was added. However, I am assuming that the yogurt really did change the composition of the milk because the whole sample changed even though we only added a tiny amount of yogurt. The bacteria in the yogurt must have created the original yogurt, as well as altering our milk sample.
As we expected, tube 3 (yogurt, milk, and ampicillin) was absolutely unaffected by the experiment. The smell and consistency were normal, as was the pH, because all the bacteria that could have altered the milk were killed by the ampicillin.
Like tube 1, tube 6 (milk and E. coli) also resulted in a sour smell with normal consistency. The smell of this sample was overwhelmingly sour and made me want to throw up. E. coli seems to spoil milk but not turn it into yogurt.
Our pH readings may have been a little skewed, but it is clear that every tube subjected to bacteria had a lower pH than the tube with ampicillin. Tube 1 had the lowest pH (5), and tubes 2 and 6 had a pH of 6. These numbers don't seem to make sense because the milk with lowest pH should curdle as casein proteins denature. Tube 2, however, was the only one that curdled.
There were a few sources of error that may have affected the results of the experiment. First of all, if the inoculating loops touched any non-sterile surfaces, the tubes could be contaminated with outside bacteria. Also, the colors on the pH scale are so similar that someone could conclude a strip shows a pH of 5 when it is really closer to 7. Finally, we may have used the vortex for too long, which potentially could kill the bacteria by breaking open the sturdy cell walls.
Despite some confusion, I believe our results turned out fairly accurate. Most importantly, we had a great time in our first lab of the year.
Monday, September 6, 2010
Yogurt Lab Intro
It was not until a little over a hundred years ago that scientists discovered bacteria were capable of causing disease. Bacteria had been identified in sick people much earlier, but it took many years of experiments and guesswork to prove that bacteria were the actual infecting agents. German physician Robert Koch developed a series of tests to prove anthrax was caused by bacteria, but his method can be used to prove that any microbe causes a specific disease. These tests, termed "Koch's postulates," are as follows:
1. The microbe is found in organisms with the disease but is not found in healthy organisms.
2. The microbe is isolated from the diseased subject and grown in culture.
3. The cultured microbe causes disease when introduced to a healthy organism.
4. The microbe is again isolated from the host and shown to be identical to the original.
Bacteria have several characteristics that make them effective disease-causing agents. Most importantly, they are tiny prokaryotic cells much smaller than the eukaryotic cells that make up animals and other living organisms, allowing them to infiltrate a host. Also, the thick cell walls of bacteria make them very resilient.
Using milk as a model test subject, we will use apply Koch's postulates to determine whether microbes in yogurt cause milk to thicken and turn into yogurt. By adding yogurt to milk and inoculating, we will see if the milk turns into a substance similar to the original yogurt.
We will use four test tubes for our experiment: a negative control with milk only; a positive control with milk and yogurt; one with milk, yogurt, and ampicillin; and one with milk and E. coli. The tube with just milk is a control because it shows that milk will not turn into yogurt just by fermenting for a day. The tube with yogurt and ampicillin is a similar control because ampicillin kills all the bacteria in the yogurt, so the milk should not be spoiled. The E. coli tube should spoil the milk, but it won't necessarily turn the milk into yogurt. For the procedure, we will transfer the bacteria using sterile inoculating loops. Then, we will let the tubes sit in a hot water bath overnight to stimulate bacterial fission.
I predict that the positive control (milk and yogurt) is the only tube where the milk will turn into yogurt. The yogurt itself was once milk and, therefore, must have the yogurt-making bacteria in it.
1. The microbe is found in organisms with the disease but is not found in healthy organisms.
2. The microbe is isolated from the diseased subject and grown in culture.
3. The cultured microbe causes disease when introduced to a healthy organism.
4. The microbe is again isolated from the host and shown to be identical to the original.
Bacteria have several characteristics that make them effective disease-causing agents. Most importantly, they are tiny prokaryotic cells much smaller than the eukaryotic cells that make up animals and other living organisms, allowing them to infiltrate a host. Also, the thick cell walls of bacteria make them very resilient.
Using milk as a model test subject, we will use apply Koch's postulates to determine whether microbes in yogurt cause milk to thicken and turn into yogurt. By adding yogurt to milk and inoculating, we will see if the milk turns into a substance similar to the original yogurt.
We will use four test tubes for our experiment: a negative control with milk only; a positive control with milk and yogurt; one with milk, yogurt, and ampicillin; and one with milk and E. coli. The tube with just milk is a control because it shows that milk will not turn into yogurt just by fermenting for a day. The tube with yogurt and ampicillin is a similar control because ampicillin kills all the bacteria in the yogurt, so the milk should not be spoiled. The E. coli tube should spoil the milk, but it won't necessarily turn the milk into yogurt. For the procedure, we will transfer the bacteria using sterile inoculating loops. Then, we will let the tubes sit in a hot water bath overnight to stimulate bacterial fission.
I predict that the positive control (milk and yogurt) is the only tube where the milk will turn into yogurt. The yogurt itself was once milk and, therefore, must have the yogurt-making bacteria in it.
Friday, September 3, 2010
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