A) DNA fingerprinting has revolutionized how crimes are solved, and has also aided in other applications. Since described in 1985, Restriction Fragment Polymorphism (RFLP) has acted as the factotum for DNA fingerprinting/profiling, and currently Polymerase Chain Reaction (PCR) is in use. The Restriction Enzymes are vital to the functionality of DNA fingerprinting. Restriction Enzymes are obtained from E-Coli, and the enzymes act as a natural defense against viruses. Restriction Enzymes work by cutting DNA at palindromes. To compare the desired strands of DNA, it is ran on a gel. The DNA differences are the fragments of different lengths. Running DNA on a gel produces different results, because gel electrophoresis is the use of electricity on a gel, giving it both a positive and a negative end. DNA has a slightly negative charge, so the fragments run to red. In the case of DNA, the smaller fragments go farther and the larger fragments remain closer to the original well.
B) The purpose of this experiment is to match DNA from a crime scene. During the experiment, our lab table will be attempting to match the DNA of the suspects with the DNA found at the crime scene. We hope to analyze the DNA correctly and receive experience in the field of crime solving.
C) The use of Restriction Enzymes in this experiment is vital. To analyze the various sample of DNA, and to successfully determine the culprit we will be using six samples of DNA: one from the crime scene, and five other tubes which contain DNA samples from suspects 1-5. We will be pipetting the restriction enzymes into the different tubes. We will then make a gel (add correct ingredients, and mix it) and run the various samples with a dye to make the fragments visible on the gel. The smaller fragments will move farther, and the success of the lab will depend on the similarities between the crime scene DNA and the DNA from one of the five sample tubes. The Variables of this experiment will be the five DNA samples, and the control will be the DNA from the crime scene. We will attempt to visually compare and identify the controls with the variables to figure out which variable most matches the control.
D) The hypothesis cannot be produced at this time, because I have no knowledge of the suspects or the crime. However, I do predict success for my lab group and I as we use DNA fingerprinting in our special CSI lab.
Monday, October 25, 2010
Tuesday, October 12, 2010
Prolonging Life with Life Discussion
A) Throughout day one the lab, our group attempted to record the effectiveness and efficiency of cellobiase on an artificial substrate which represented cellobiose. One day two of the lab, our group measured the effectiveness and efficiency of edible mushroom in turning cellobiose into glucose. We measured the rate of conversion from the artificial substrate (acts as cellobiose) to glucose by adding a strong base. The strong base turns the artificial substrate yellow, and stops cellobiase. To measure reaction rate, we labeled five tubes and added a fixed amount of artificial substrate and cellobiase (day 1) and a fixed amount of artificial substrate and our mushroom (day 2)., and added the strong base at set points in time. This allowed our group to discover that both were approximately even when it came to efficiency. Overall, my hypothesis was correct. The cellobiose was converted into glucose efficiently by both the cellobiase and the mushroom solution on both day one and day two of the lab.
B) Possible Sources of Error:
- When adding the strong base, we could have added it at the wrong time messing up the correct coloration of yellow.
- Failed to grind the mushroom up enough, thus the majority of the enzymes remained unable to produce glucose.
- Not enough cellobiase was added, thus a slower conversion occurred and inaccurate readings were obtained by our group.
- The centrifuge was not spinning for long enough to fully separate the mushroom solution, not enough of the mushroom was added to accurately convert the artificial substrate.
- Too much cellobiase was added, so the artificial substrate was converted too rapidly for our group to notice a change after three minutes.
B) Possible Sources of Error:
- When adding the strong base, we could have added it at the wrong time messing up the correct coloration of yellow.
- Failed to grind the mushroom up enough, thus the majority of the enzymes remained unable to produce glucose.
- Not enough cellobiase was added, thus a slower conversion occurred and inaccurate readings were obtained by our group.
- The centrifuge was not spinning for long enough to fully separate the mushroom solution, not enough of the mushroom was added to accurately convert the artificial substrate.
- Too much cellobiase was added, so the artificial substrate was converted too rapidly for our group to notice a change after three minutes.
Tuesday, October 5, 2010
Prolonging Life With Life; Extending The Future By Exploring Possibile Benefits Of Biofuels
A) The current fuel system is subject to change. The global economy is dependent on petroleum, which is a polluting natural resource which is destined to run out. Although the future seems bleak for the global economy, there is hope in alternate fuels. Some of the most promising of the prospects to replace gasoline are biofuels. Biofuels are the classification for fuels derived from biomass. In the wall of plant cells lies a polymer with a lot of potential named cellulose. Cellulose cannot be broken down naturally by animals, and this is the reason why it's importance for energy has not become relevant until now. Cellulose is broken down by the cellulose enzyme which is present on the inside of Protists. Enzymes are beneficial to reactions because they speed up chemical reactions and are not consumed with the reaction, so they can be used again and again. The majority of enzymes are proteins, and have a specific 3-D structure. For a chemical reaction to take place, the active site (site of chemical reaction) binds to the substrate (the reactant of the enzyme catalyzed reaction). The process is sped up because the substrate is positioned in a way which allows the transition state of the reaction to become stabilized, and the activation energy is lowered to allow quicker reaction rate. However, the conditions of enzymes must be kept within an optimal range, (the right pH, the right temperature, and the right level of salinity). For centuries, termites have broken down cellulose and used its energy as fuel, and not until recently, scientists discovered how the termites were able to accomplish this feat. The termites have a protozoan called Trichonympha living inside their abdomen, and the trichonymphba has a bacterium named Rs-D17 that lives inside it and produces cellulase enzymes, including cellulase. Cellulase enzymes convert the cellulose into cellobiose, which is converted into two glucose molecules by the enzyme cellobiase. Biofuels work by using glucose (energy) obtained from cellulose to power their engines.
B) For our class, the purpose of this experiment is to measure the enzymatic activity of cellobiase, and to identify the optimal conditions for the enzyme. This also acts as a real world example of the possibilities behind enzymatic studies, and the relevance in the possible future. For industry, the research of Biofuels can offer an alternative energy which would be more sustainable than petroleum. The biofuels offer a new future for industry, one which could make life less polluting, more sustainable, and more reliable.
C) The lab will start with a one milliliter pipette of cellulose. Cellulose is broken down by bacteria, protists, and fungi, so we will use enzymes derived from these sources to convert cellulose into cellobiase. Cellobiase is composed of two glucose molecules, and will be the substrate of the experiment. Cellobiose will be placed in a test tube along with Cellobiase, an enzyme which breaks down cellobiose into single glucose molecules. To measure the effect of the cellobiase on the cellobiose, we will substitute the cellobiose with an artificial substrate. The artificial substrate will be composed of Glucose and P-Nitrophenol. At various time points, we will add a strong base to the test tube which kills cellobiase, and turns P-Nitrophenol yellow. This will allow documentation of the coloration of the test tube, and we will be able to drw a conclusion from this data. For extended exploration in this experiment, we will bring in mushrooms to test which mushrooms are better decomposers. We will grind up the mushrooms, and add them in place of the cellobiase (add them with the Glucose and P-Nitrophenol). This part of the experiment will give us a greater understanding of the cellobiase content in the foods that we eat, and also in some of the mushrooms that we see.
D) I believe that the cellobiase in Day 1 will make glucose disappear faster than the ground mushrooms which we will add in day 2. The controls of this experiment are the Cellobiase and the artificial substrate (Day 1), while the variables of the experiment will be the ground mushrooms and artificial substrate (Day 2). The cellobiase acts as the control, because cellobiase will definitely separate the artificial substrate at a quicker pace with its higher concentration. The ground mushroom acts as the variable in this case, because we are unaware of the cellobiase concentration within the organism, and we are charting the difference between cellobiase and the mushroom.
B) For our class, the purpose of this experiment is to measure the enzymatic activity of cellobiase, and to identify the optimal conditions for the enzyme. This also acts as a real world example of the possibilities behind enzymatic studies, and the relevance in the possible future. For industry, the research of Biofuels can offer an alternative energy which would be more sustainable than petroleum. The biofuels offer a new future for industry, one which could make life less polluting, more sustainable, and more reliable.
C) The lab will start with a one milliliter pipette of cellulose. Cellulose is broken down by bacteria, protists, and fungi, so we will use enzymes derived from these sources to convert cellulose into cellobiase. Cellobiase is composed of two glucose molecules, and will be the substrate of the experiment. Cellobiose will be placed in a test tube along with Cellobiase, an enzyme which breaks down cellobiose into single glucose molecules. To measure the effect of the cellobiase on the cellobiose, we will substitute the cellobiose with an artificial substrate. The artificial substrate will be composed of Glucose and P-Nitrophenol. At various time points, we will add a strong base to the test tube which kills cellobiase, and turns P-Nitrophenol yellow. This will allow documentation of the coloration of the test tube, and we will be able to drw a conclusion from this data. For extended exploration in this experiment, we will bring in mushrooms to test which mushrooms are better decomposers. We will grind up the mushrooms, and add them in place of the cellobiase (add them with the Glucose and P-Nitrophenol). This part of the experiment will give us a greater understanding of the cellobiase content in the foods that we eat, and also in some of the mushrooms that we see.
D) I believe that the cellobiase in Day 1 will make glucose disappear faster than the ground mushrooms which we will add in day 2. The controls of this experiment are the Cellobiase and the artificial substrate (Day 1), while the variables of the experiment will be the ground mushrooms and artificial substrate (Day 2). The cellobiase acts as the control, because cellobiase will definitely separate the artificial substrate at a quicker pace with its higher concentration. The ground mushroom acts as the variable in this case, because we are unaware of the cellobiase concentration within the organism, and we are charting the difference between cellobiase and the mushroom.
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