DNA Chips: Using Microarrays to Study Genes Related to Disease

Introduction

a) Background:

Scientists are able to view DNA from different samples to see certain genes that cause disease. This can be helpful in targeting base pairs in DNA. Hopefully in the future scientists will be able to fix certain genetic diseases using this technology. Through the lab, we will be able to transform genes using cDNA to make them a color. The shade and tint of the color refers to which cell sample it is from, and whether or not the gene is muted or not.

b) Process:

For this lab we had 6 gene samples, and using a pipette set at 20 microliters, we placed all 6 samples onto a small slide. Then, we used a pipette to place 20 microliters of cDNA. The cDNA made the gene samples change color. 

c) Results:

Some of the genes were light pink, which means that they were present in the cancerous lung cell. The other colored genes were blue, which means that they are present in both the cancerous and normal cells. The gene 4, which is hemoglobin, was actually clear after cDNA was used, so this means that it was not present in either sample.

Using Gel Electrophoresis and Restriction Enzymes to Solve the Mystery

Introduction
a) Background:
In this lab we used restriction enzymes. Restrictions come from bacteria and have a defense against viruses. They are like "molecular scissors" because they cut the DNA at palindromes, and this results in fragments of different lengths. Agarose Gel electrophoresis separates the DNA fragments according to their size. The slightly negatively charged DNA is drawn towards the positive pole of the gel slab. A current passes through the agarose gel, and smaller DNA fragments travel farther than the larger ones. This process is called DNA typing, DNA profiling, or DNA fingerprinting.

b) Purpose:
The purpose of this lab is to cut DNA fragments and use Gel electrophoresis to undercover the DNA profile. By comparing the DNA fragments, is is possible to trace criminals, identify certain foods, set free innocent people from jail and identify human bones. Also, you can determine the relatedness between humans and ancient peoples, test families' DNA, identify harmful organsims that cause diseases, and undergo paternity testing. There are many other uses of DNA profiling as well.

c) Process:
There is an acronym for the process: RFLP. R stands for "restriction" because the restriction enzymes are necessary to cut the DNA. F stands for "fragment" because the DNA is cut into different sized fragments. L stands for "length" because the fragments are all different lengths. P stands for "polymorphism" because the fragments all reach different locations on the gel electrophoresis. In our lab, we are going to use a pipet to transfer DNA samples to micro test tubes. Enzyme milk goes on the bottom of these tubes. We mix the components of the tubes carefully. The tubes should be incubated overnight, and after the period of incubation, the tubes are placed in a refrigerator. Loading dye is added to each tube, and then the DNA samples are placed into the electrophoresis device and agarose gel.

d) Hypothesis/Controls/Variables:
It is hard to hypothesize who the criminal is because there is no way to tell until our results from the electrophoresis are visible. The controls for this lab are the criminal's DNA. The variables are the suspects DNA. The Loading Dye is also a control. It is placed in every vile with DNA.

Discussion/Results:
It turns out that suspect 3, Chloe Krey, is the guilty person. Our gel electrophoresis results were very clear and it was easy to compare them to the actual set. We did not puncture the gel except for in the practice slot. Overall, I think that we did a great job. It helps that everyone at my table used gel electrophoresis in biology, so we already knew the proper technique.

Using Enzymes to Create Alternative Fuels

Introduction
a) Background:
In this lab we are attempting to create biofuels. Enzymes are key elements in this lab. Enzymes are normally proteins and they speed up the rate of chemical reactions. They are able to speed up reactions by positioning the substrate in a position so that the transition state of the reaction is stabilized. Cellulose is a common sugar used by organisms that produce cellulases, a type of enzyme. Cellulases start the transformation of cellulose into glucose. In creating biofuels, cellulases are important to change cellulose from plant walls into sugars. The sugar is then changed into ethanol through microbial fermentation. Cellulose is the main component of plant cell walls, and cellulose consists of a long chain of glucose molecules.


b) Purpose:
Research companies would complete this lab to identify the most efficient ways to create biofuels. They want to develop new fuels in a way that will not disrupt the carbon cycle and will be able to fit into systems that are already in place. This lab is helpful for our class because we will gain hands-on experience to gain an understanding of the enzymatic reaction process.


c) Process:
Day 1
We are transforming cellulose (from the plant cell wall) into cellobiose. We use an enzyme to catalyze this reaction. Microbes are able to break down cellulose. Microbes consist of bacteria, protists, and fungi. Then, an artificial substrate is created and enzymes break it down into glucose and P-Nitrophenol. At certain times, we will add a strong base to kill the enzyme and turn the P-Nitrophenol yellow. We add the strong base into small tubes, and then add the artificial substrate and cellobiase to the large tube. At certain times, we added a substance from the large beaker and put it into the small beaker. The more product that forms, the darker the yellow tint will become because the strong base adds color.
Day 2
We use a mortar and pestle to grind up a mushroom. We add extract (mushroom juice) to the reaction, and the mushroom juice carries enzymes that speed up the reaction. We will test different kinds of mushrooms and try to identify the most efficient ways to create biofuels.


d) Hypothesis/Controls/Variables:
My hypothesis is that larger mushrooms will carry stronger enzymes and will create more efficient biofuels. The controls in this lab are the cellulose and artificial substrate. The variables are the mushroom enzymes and strong base.


Discussion:
During this lab, my group put the solution in at incorrect time slots, so that was our source of error. From doing this lab I learned more about enzymes and their role in reactions. I also learned about how biofuels can be created and that in the future they will be a positive option because the fossil fuel supply could deplete. 

The Essence of Life in a Vile: DNA Cheek Cell Extraction Lab

Introduction:


a) Background:
In this lab, we extracted a cell from inside of our cheek and extracted its DNA. DNA, Deoxyribose Nucleic Acid, carries genetic information and determines one's features. It holds the information that is necessary for cells to carry out functions. DNA can be called a "biological blueprint" because it holds the information that creates the organism. DNA's structure is a double helix with 4 bases. Each base connects with a phosphate group and a sugar, forming the backbones of the DNA. DNA holds all of the information regarding your genes.


b) Purpose:
The purpose of this lab was to precipitate DNA. Precipitating DNA will allow us to compare DNA of different organisms, to map and sequence it, and to use it for other experiments, such as cloning. DNA in the precipitated form can help scientists in many areas. It can also text for diseases, show certain traits, and help determine one's identity in a crime scene. 


c) Procedure:
First, we loosened our cheek cells. We used a saline solution, also called "iso tonic" that was 0.9% salt water, and this solution helped to ensure that the cheek cells were in the right concentration. We then added a lysis buffer, which would burst the cells open by dissolving the cell membranes). The cell membrane consists of fats, and the lysis buffer dissolves phospholipids. The cell membrane is hydrophobic, so it needs detergent to break it apart. Next, we added protease. Protease is an enzyme that breaks down protein. It left the DNA intact, and we were able to extract the DNA alone. After adding the enzyme, we placed the vile into a hot water bath. The hot water speeds up the reaction and helps to break up the cell membrane. After placing it in the heat for 10 minutes, we added cold ethanol to help with the precipitation process. DNA has a negative charge and the phosphates are also negative and have to be on the outside of the structure. When dropped into water, DNA dissolves, so to precipitate it, we add salt. NA+ neutralizes the charge and makes DNA nonpolar, so that it does not break up in the water and it stays intact. 


Summary/Results/Possible Sources of Error:


I was able to extract my DNA and place it into a small vile. The vile was attached to a necklace. While doing the lab, I learned about the process to precipitate DNA. The process was straightforward and easy to follow, and I understand the reason why we did all of the steps. The lab results could have been skewed because it was possible for one to put the vile in the hot water for not enough time. This would cause the reaction to take place more slowly and the cell membrane would have trouble breaking up. Also, if I did not add salt, the DNA would have dissolved. 

Yo, Its Yogurt!: Using Bacteria to Transform Milk Into Yogurt

Introduction:


a) Background
In this lab we are using bactaeria to change milk into yogurt. Bacteria is actually the most successful life form on the entire planet! There is even evidence that bacteria might exist on other planets, like mars. Bacteria are prokaryotes, which are creatures with single-cells. They are so tiny that one inch would be filled eith up to 50,000 bacteria. Normally people think that bacteria are harmful and cause disease, but only a small portion of bacteria are dangerous. Bacteria is also the cause of milk spoilage. However, not all bacteria has negative effects. E.Coli is a type of bacteria that is actually beneficial and necessary for bodies to function correctly. There are a few different types of bacteria, such as coccus, bacillus, and spirillum. 


b) Purpose
Bacteria has many purposes. It is used to make yogurt from milk by breaking down lactose into pyruvic acid, and creating lactic acid using enzymes. Bacteria also demonstrate's Koch's postulates and show that a microorganism can cause a certain disease. 


c) Procedure
In this lab, we are going to create yogurt from milk. In order to do this we must pasteurize milk by heating it up and quickly cooling it down. Pasteurization kills bad spoilage bacteria. Next, add some yogurt (fage yogurt for this lab. Then mix the yogurt and the milk together and store it for 24 hours. The next day you will have yogurt! The milk sugar (lactose) created lactic acid. The change in pH created a milk protein known as casein and that was denatured. It changed from liquid to solid form. Lowering the pH kills all spoilage bacteria so it does not go rancid easily.


d) Controls/Variables/Prediction
The controls in this lab are Milk, and Milk and Yogurt. The Variables are Yogurt and ampicillin, and E. Coli. My prediction is that E. Coli helps to prevent the yogurt from spoiling. Also, as some sources of error for this lab, one could add the incorrect amount of ampicillin. Ampicillin is an antibiotic, so if there is not enough of it, the bacteria could cause the milk to spoil. 




Summary/Results/Possible Sources of Error:


In this lab, I learned how to apply Koch's Postulates. We had 4 tubes containing milk, milk & yogurt, yogurt & ampicillin, and E Coli. The first two tubes were the controls and the second two were the variables in the experiment. We inoculated milk with yogurt and the yogurt+amp. We added E Coli into the tube containing E Coli. By adding bacteria from yogurt to milk showed Koch's 3rd postulate, the cultured microorganism should cause disease when introduced into a healthy organism. All bacteria doesn't turn milk into yogurt, as proven when adding E Coli. Adding ampicillin, an antibiotic, into one of the tubes acted as a control so that we knew what is the yogurt bacteria. As possible sources of error, I could have added too much or too little ampicillin into the test tube. Adding too little could have made the yogurt go rancid, and adding too much could have killed too much bacteria and not created milk. We could have also not pasteurized the milk correctly, so some spoilage bacteria could have been left over. So as a summary, Tube 1 with milk alone resulted with white, liquid milk with a pH of 6. Nothing reacted with the milk except the bacteria that was pre-existent. Tube 2 with yogurt and milk created thick, white yogurt with a tart/sour smell and a pH of 4. The bacteria in yogurt reacted with the milk to create yogurt. The pH changed and changed the state of the solution to a solid. Tube 3 with yogurt and ampicillin resulted in a liquid, white milk with a pH of 7. The ampicillin killed the yogurt bacteria so it was changed back into liquid form. Finally, tube 4 with E Coli created a murky white liquid that smelled like sour milk and had a pH of 8. Although a type of bacteria, E Coli did not create yogurt. The control yogurt cup had a pH of 4.