Wednesday, April 10, 2013
Essay/ Final Product
In my presentation, I will first explain different safety measures that need to be taken for scientific experimentation, and then I will explain the principles of PCRs. The interactive activity will be what was described two posts ago.
Research Essay
Since my topic is somewhat broad and covers the importance of research and basic scientific research strategies, I will need to narrow down my topic for my research essay. I think I will focus on the importance of research, and maybe use the basic research strategies as examples of how anyone can conduct research. I guess the purpose of my paper will be to show the non-scientific community that anyone can conduct the basic principles of scientific research, even if they are not experienced in the field.
Presentation
My presentation will focus on teaching the class how to perform a PCR correctly, and what precautions should be taken.
Safety: the students will have to identify the safety equipment that may be needed. Gloves are a necessity, because contamination can be a problem. Bonus points will be awarded for any student that includes the use of an "Ice bucket" in order to keep the enzymes close to their normal temperature.
The DNA sample that is being amplified will be simulated as honey.
DNA primers will be dish soap (blue).
DNA polymerase will be vegetable oil.
Excess nucleotides will be water.
When the student conducts the "experiment," the correct order will end up being the honey, dish soap, water, and then the rubbing alcohol or vegetable oil. The PCR will be conducted in clear cups. The students will then have to list the temperatures and what happens at each temperature, and choose a reasonable number of cylces (about 30).
The winner (the group that has the order, the temperatures, the descriptions, and the number of cycles correct) will receive a prize.
Safety: the students will have to identify the safety equipment that may be needed. Gloves are a necessity, because contamination can be a problem. Bonus points will be awarded for any student that includes the use of an "Ice bucket" in order to keep the enzymes close to their normal temperature.
The DNA sample that is being amplified will be simulated as honey.
DNA primers will be dish soap (blue).
DNA polymerase will be vegetable oil.
Excess nucleotides will be water.
When the student conducts the "experiment," the correct order will end up being the honey, dish soap, water, and then the rubbing alcohol or vegetable oil. The PCR will be conducted in clear cups. The students will then have to list the temperatures and what happens at each temperature, and choose a reasonable number of cylces (about 30).
The winner (the group that has the order, the temperatures, the descriptions, and the number of cycles correct) will receive a prize.
Beer's Law
Beer's Law has to do with spectrophotometers, which were discussed in the previous post. Beer's Law is given by the equation A=ebc, where A is the absorbance (A has no units), E is the molar absorptivity with the units L/(mol*cm), b is the path length (cm), and c is the concentration of the solution (mol/L).
This equation can be used not only to find the absorbance of a solution given the other three variables, but it can be applied to spectrophotemtry. The spectrophotometer could output the absorbance, and b (measure the size of the cuvette) and E (use a graph) are known, so the concentration of the solution could be found.
Beer's Law is useful in not only finding concentrations of solutions one creates. Researcher's apply Beer's Law to their research. In many cases, Beer's Law can be used to determine the concentration of plasmid, DNA, or protein in a solution, which can then be used for calculations to find out how much would need to be placed in a PCR or other experimental procedure.
This equation can be used not only to find the absorbance of a solution given the other three variables, but it can be applied to spectrophotemtry. The spectrophotometer could output the absorbance, and b (measure the size of the cuvette) and E (use a graph) are known, so the concentration of the solution could be found.
Beer's Law is useful in not only finding concentrations of solutions one creates. Researcher's apply Beer's Law to their research. In many cases, Beer's Law can be used to determine the concentration of plasmid, DNA, or protein in a solution, which can then be used for calculations to find out how much would need to be placed in a PCR or other experimental procedure.
Spectrophotometers
Spectrophotometers are used to measure the concentration of a solution.
A solution is placed in a cuvette (picture below)- about 3/4 of the cuvette is filled, and a beam of light (from inside the spectrophotometer-the cuvette is placed in the open door) is shone through the cuvette. The purpose of the beam of light is to see how much light "gets through" the solution, thus indicating the concentration of the solution.
If a solution is more concentrated, then less light will pass through, because a certain amount of light is absorbed by the solution.
The light is beamed towards the sample solution using an entrance slit, which directs the light. The light will pass through the solution and then reach a source. The source usually measures the wavelength of the light in order to convey how much light passes through.
The number given can either be absorption (the amount of light that does not pass through) or transmission (the amount of light that passes through the solution).
A solution is placed in a cuvette (picture below)- about 3/4 of the cuvette is filled, and a beam of light (from inside the spectrophotometer-the cuvette is placed in the open door) is shone through the cuvette. The purpose of the beam of light is to see how much light "gets through" the solution, thus indicating the concentration of the solution.
If a solution is more concentrated, then less light will pass through, because a certain amount of light is absorbed by the solution.
The light is beamed towards the sample solution using an entrance slit, which directs the light. The light will pass through the solution and then reach a source. The source usually measures the wavelength of the light in order to convey how much light passes through.
The number given can either be absorption (the amount of light that does not pass through) or transmission (the amount of light that passes through the solution).
Wednesday, February 6, 2013
Expansion on Presentation Ideas
This is a draft of what I think my final experiment simulation will look like:
The DNA sample that is being amplified will be simulated as honey.
DNA primers will be dish soap (blue).
DNA polymerase will be rubbing alcohol or vegetable oil.
Excess nucleotides will be water.
When the student conducts the "experiment," the correct order will end up being the honey, dish soap, water, and then the rubbing alcohol or vegetable oil. The students will then have to list the temperatures and what happens at each temperature, and choose a reasonable number of cylces.
The winner (the group that has the order, the temperatures, the descriptions, and the number of cycles correct) will receive a prize.
The DNA sample that is being amplified will be simulated as honey.
DNA primers will be dish soap (blue).
DNA polymerase will be rubbing alcohol or vegetable oil.
Excess nucleotides will be water.
When the student conducts the "experiment," the correct order will end up being the honey, dish soap, water, and then the rubbing alcohol or vegetable oil. The students will then have to list the temperatures and what happens at each temperature, and choose a reasonable number of cylces.
The winner (the group that has the order, the temperatures, the descriptions, and the number of cycles correct) will receive a prize.
Final Product?
Right now, I am unsure of what my final product or presentation would be on. I am considering having the class perform a simulation of a PCR, in order to teach the class the basic concepts behind scientific research. PCRs are integral to many types of scientific research, and it would be useful to know how to construct a prediction of the gel, and actually perform a simulation.
My idea for the simulation involves using oil as the polymerase, and different food colourings to indicate the other reagents involved in conducting PCRs.
My idea for the simulation involves using oil as the polymerase, and different food colourings to indicate the other reagents involved in conducting PCRs.
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