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Alberto Assignment 2


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Summaries for the labs 3-6

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Alberto Assignment 2

  1. 1. Spring Semester 2011-12 University of Puerto Rico - Cayey RISE Program Instructions for Laboratory Writing Assignments1. For each assignment you should write a summary paragraph of 8-10 sentences and a range from 160 -170 words.2. A template for each assignment is attached. Once you complete the template email it to Dr. Elena Gonzalez; she will grade it using the rubric below and return it to you. Within the next two days, you will email it to me with the corrections incorporated. In your summary include a reference to each one of the criteria in the rubric below.3. Email subject should include: Your register number; first name; Assignment # and hand-in date. Example: 1. Osvaldo Assignment 2 March __ Rubric for Assessing Laboratory Summaries Name Alberto F. Cintrón Colón Grade Date March 9, 2012 Points Assignment Number 2 30 Points Total A. PURPOSE LAB TECHNIQUE 1 2 3 4 5 Refers to purpose and objectives * of the lab techniques B. BIOLOGICAL COMPETENCE Demonstrates knowledge of * laboratory procedures Reports findings adequately * C. ENGLISH COMPETENCE Uses correct grammar, syntax, * spelling, and punctuation Demonstrates clarity and * coherence D. CRITICAL THINKING Identifies applications and or * implications of the study in concluding 27/30
  2. 2. University of Puerto Rico - Cayey RISE ProgramTemplate for Laboratory Summaries of Assignment 2 Biol. 4997-Biomedical TechniquesDue date March 9, 2012Reg.# 2 Name Alberto F. Cintrón Colón Date: March 9, 2012Paragraph 3. Column Chromatography and SDS-Page+ This workshop was given by Dr. Vibha Bansal. We discussed what were proteins, and we also isolatedproteins from a chicken egg. In the theory part of the workshop, Dr. Bansal taught us the importance ofisolating proteins, which are used for structure studies, therapeutics, dietary supplements, and catalysts.The egg white was used to isolate proteins. The protein that we wanted to isolate from the egg white waslysozyme. We first made an extract egg white solution which contained 0.025M of Tris buffer pH 8.2(tomaintain the pH within a relatively narrow range), egg white solution, again 0.025M of Tris buffer pH 8.2,and Carbonate buffer pH 10.5. Secondly, we did an ion-exchange chromatography, which is the separationof proteins based on charge interactions, in order to separate the lysozymes. Finally, we did a SodiumDodecyl Sulfate- PolyAcrylamide Gel Electrophoresis (SDS PAGE). This technique is used to separateproteins according to their size including weight and length. After the SDS is finished, we stained the gelused for the proteins in order to make them visible. The workshop given by Dr. Bansal was very helpful,because we got to develop our electrophoresis skills even better, a very important technique for a futuregraduate school in the field of genetics.Paragraph 5. Workshop MSU-Introduction to Neurobiology+ The title of the workshop given by MSU on Feb.20, 2012 was Bridge to Neuroscience. The subjects thatwere taught were structures of neurons, axonal transport, and the electrical signals in neurons. What wedid first was created two groups, and each group made a neuron, and each person represented a structureinside the neuron by doing the function that each part of the neuron carries out. The structures representedwere dendrites, axon, and axon terminals. In my case, I got to be the first segment of the axon hillock andmy function was to be the first one to receive the electrical message from the dendrites, and pass it to therest of the axon. In the end, we learned how the neurons send messages to other neurons, and that theyare responsible for the transfer of information in the nervous system. Axonal transport is the processresponsible for movement of different materials that can be carried between the cell body and the nerveterminal; it is achieved thanks to microtubules, which are cytoskeleton components that are useful for bothstructure and intracellular transport. The next point we discussed was electrical signals in neurons; welearned that nerve cells can propagate and generate electrical signals through ionic movements betweenthe cell membrane. Some of the ions are potassium, sodium, and chloride. After we finished discussing thetheory, we did 5 experiments, studied 4 cases, and dissected a sheep’s brain. The first experiment was totest if taste, smell, and vision were linked to each other. What we did was taste candy with a combinationof different senses, and found they are linked the more senses the better the perception of taste. Thesecond experiment was to test if the sensations of touch were the same throughout the body. Thirdly, wetested the motor reflexes by hitting the knee in either the left or right leg. The fourth experiment was to testmotor reactions by throwing the ruler, so that our partner could catch. Furthermore, we took our bloodpressure after different scenarios, drinking an energy drink, being relaxed, and doing exercise forcomparison purposes. After the experimentation, we also discussed case studies. The cases that weexamined were from different patients, and we had to identify their neurological disorder. Finally, wedissected a sheep brain and identified each part of the brain. This workshop was a brilliant experience.Thanks to it I got to refresh general biology concepts, like the neurons, and the brain, but also I got to learnnew things like how to identify the differences in mammal brains. All of the knowledge learned is useful inorder to help improve what we already know about our brain and its function.Paragraph 6. Protein – Protein Interactions+ The protein-protein interactions workshop was given by Dr. Maldonado. Here we learned about proteinsstructures, what were pharmacophores and they’re models as well as drug discovery strategy. First, wediscussed the theory and then the class was divided into groups. My team’s job was to do the identification
  3. 3. of the pharmacophore, which is the group of atoms in the molecule of a drug responsible for the drug’saction. Next we had to generate a model. The first part of our team’s assignment was the Benzene ClusterPreparation. What we did in this part was to use the PyMOL program in order to search for the benzenemolecules, which are a hydrophobic molecule due to their Carbon-Hydrogen bonds. After we found thebenzene molecules, we selected the receptor sequence of each benzene molecule and saved it in order touse it in the next part. In part 2, we created the pharmacophore model using the program LigandScout. Inthis program we used the “generate a model” option and used the previously saved information from part 1.After we inserted the necessary information to view the model, we took a 2D picture of each benzenemolecule with the amino acids that was interacting with respectively. Also, we took a 3D picture of eachbenzene with the amino acids that they were interacting with, and the location where the benzene was inthe protein. Finally, we used the “combine all features” option and we got the final pharmacophore modelwhich is composed of all 4 benzenes in the protein. The final segment in the workshop was to have eachgroup present their procedure and results. This workshop is of much help for the future in a career ofscience, especially pharmacology, because we learned necessary information and techniques related towhere the active regions in a protein could be, and we also learned that pharmacophore models areimportant because they help us understand the interaction between a receptor and a ligand (ion ormolecule).