Comparative proteomics free essay sample

Proteomics is the study of proteins. Their functions, interactions with other proteins, cellular locations and levels at which they are expressed. The purpose of this lab was to compare the proteins present in different species of fish to be able to determine which species of fish have the closest relation. This can be determined based on which two fish species have the most proteins in common with one another. The Central Dogma of biology is a process in which a gene made of DNA is transcribed by a messenger RNA and then translated into a protein. Based on the Central Dogma of biology if two species have similar proteins, that means that they have similar DNA. At the start of this lab we did research about all the fish we would be doing the experiment on in order to create a thesis on which two of the fish would be the most similar. We will write a custom essay sample on Comparative proteomics or any similar topic specifically for you Do Not WasteYour Time HIRE WRITER Only 13.90 / page Based on the research from a database on fish (http://www. fishbase. net) I came up with the thesis that Salmon and Trout would be the most similar fish in the study. They would be the most similar because they live in the same areas, they are both freshwater fish, they both swim in the same way, they have similar diets and they have similar lifespans. So based on their similarities they would have similar proteins, and therefore similar DNA. METHODS The method used in this lab to map the proteins was the method of Polyacrylamide gel electrophoresis. This method can be used to separate the proteins present in the fish muscle and separates them on size. Due to the fact that they are separated by size, the proteins can be compared because similar proteins with stop at the same spot in the gel. So measuring the bands that show up on the gel you can determine if different fish species  have similar proteins. The first thing that is done is to extract the proteins from the muscle tissue. This is done by taking a sample of fish muscle and denaturing it using mechanical and chemical techniques. The proteins are also added to a Laemmli sample buffer in order to give each protein a negative charge so it is able to get pulled through the polyacrylamide gel. The next step is to put the gel into the electrophoresis module and to run it. It is run until the proteins have almost reached the bottom of the gel. A blue tracking dye is added to the Laemmli sample buffer in order to track the distance in which the proteins travel through the gel. If it is run for too long, the proteins will run off the bottom of the gel and it will mess up your results. Once the protein reach the bottom of the gel, the gel is stained in order to be able to see the individual bands of the different proteins. When the gel is stained, the protein distances will be able to be measured and compared. For a detailed procedure, refer to the Comparative Proteomics Kit I: Protein Profiler Module Lab Manual. RESULTS I did not get conclusive data from the gel I made. As you can see in figure 1, the bands that showed up on the gel were too cluttered to be able to measure them. So I could not compare protein bands between the fish species based on our gel. Instead, I used a default gel picture that another group did in the class to get my data. From their gel I was able to compare the different species. Table 1 shows the number of bands that were similar between the different fish species when they were compared. I was able to determine that fish species C (Tuna) F (Tilapia), A (Salmon) G (Halibut), and E (Rockfish) G (Halibut) all had two bands that were similar. I could also determine that fish species E (Rockfish) C (Tuna) and C (Tuna) G (Halibut) had no bands in common so they were the least similar. DISCUSSION This lab went very smoothly until I went to go look at my gel and found out that it was too cluttered to be able to use. I believe that that problem could have been fixed if I ran the gel longer. I think that would have spread the bands out more. I was unable to prove or disprove my thesis due to the fact that trout was not one of the samples that were tested in the gel I had to use to collect my data. But from the data collected I was able to determine that there were three groups of fish that had two bands in common, so they were the closest in relation to one another. Those groups were Salmon Halibut, Tuna Tilapia and Rockfish Halibut. If I was able to use my gel I would have been able to determine if my thesis was valid or not. So the next time I do this lab I am going to make sure that my gel is run for the proper amount of time so that I get clear usable evidence.