Spring Semester 2011-12                                          University of Puerto Rico - Cayey                        ...
RISE ProgramTemplate for Laboratory Summaries of Assignment 2Biol. 4997-BiomedicalTechniquesDue dateMarch 9, 2012Reg.# 15 ...
Vinadocking and ranking by binding energy. We did the last part of the whole drug discovery process inwhich weverified if ...
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Lab assignment 2 revised

  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 summaryparagraph 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 Grade Date Points Assignment Number 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 oflaboratory 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 concluding29/30 Excellent work!University of Puerto Rico - Cayey
  2. 2. RISE ProgramTemplate for Laboratory Summaries of Assignment 2Biol. 4997-BiomedicalTechniquesDue dateMarch 9, 2012Reg.# 15 Name Juan Carlos Torres Sánchez Date: March 9, 2012Paragraph 3. Column Chromatography and SDS-Page+This two dayworkshop consisted in isolating proteins. Many scientists isolate proteins for different purposes,such as catalysts, therapeutics, dietary supplements, and structure studies. First, we prepared an extract fromegg white, in which we gathered the proteins. Then, we isolated lysosome from that extract using ion-exchange chromatography. Ion exchange chromatography is a process in which binding and separation ofproteins is based on charge interactions. Our main goal is to isolate lysosome from the rest of the proteinsfound in the egg white.Tomake sure that our protein has been purified or not, we did an SDS-PolyAcrylamide Gel Electrophoresis. This type of electrophoresis technique is used to separate proteinsaccording to their size: smaller proteins will migrate faster and further than larger proteins through the gel.This technique needs charge so that the proteins will run from the negative side to the positive side; this iscalled running the gel. After we ran the protein the whole way, we stained the gel with coomassie blue. Nextwe distained it, and the bands appeared. Our results demonstrated two bands. Those bands could mean twothings, that we isolated the protein completely and two chains of the same protein were showed or that wehave two different proteins.Paragraph 5. Workshop MSU-Introduction to Neurobiology+Neuroscience, the study of the nervous system, advances the understanding of human thought, emotion, andbehavior. Neuroscientists use tools ranging from computers to special dyes to examine molecules, nervecells, networks, brain systems, and behavior. From these studies, they learn how the nervous systemdevelops and functions normally and what goes wrong in neurological disorders. We made six experimentsand made a sheep brain dissection in this workshop. Five of the experiments consisted in learning how thenervous system in our body works. One of the experiments we did was the spike box experiment. We firstcut a cockroach leg and put in the spike box; then we added the two electrodes to the leg and heard a poppingsound, which means that I heard my first neuron. Finally, we made a sheep brain dissection and identified allthe parts of the brain. We compared them to the human brain. The study of neuroscience can help in thediscovery for treatment for many diseases such as ALS, Parkinson and Alzheimer’s disease. Many drugs andprocedures have been made to treat these diseases, for example, there is riluzolefor ALS, which increases thelife expectancy of the patient.Paragraph 6. Protein – Protein Interactions+Structure based drug-design is the process of finding new drugs or medication based on the knowledge of the3-D structure of a biological target. In Silico means that the procedure is done through the computer. Thisprocess involves the design or discovery of small molecules that are complementary in shape and charge tothe bio-molecular target resulting in binding to and inhibition of this macromolecule. In Silico methods canhelp in identifying drug targets via bioinformatics tools. They can also be used to analyze the targetstructures for possible binding/ active sites, generate candidate molecules, check for their drug likeness, dockthese molecules with the target, rank them according to their binding affinities, and further optimize themolecules to improve binding characteristics. The objective of this workshop was to learn how In Silico drugdiscovery and development work. The group was divided into four groups, in which the whole process, sinceit is a long one, was divided into four. The objective of my group was to do the secondary screening:
  3. 3. Vinadocking and ranking by binding energy. We did the last part of the whole drug discovery process inwhich weverified if the drug wediscovered for a specific protein has the same or different binding sites asother drugs previously known. This study can be applied to future science work in finding new drugs andmedications such as Imatinib, a drug used to treat cancer.