Experiment 1 Testing For Proteins Answers

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  To each test tube, add 10 drops of the materials to be tested. Add 8 drops of iodine to each tube and tap to mix 4. Obtain 7 test tubes and number 2. To each test tube, add 2 ml of the materials listed in Table 2 3. Add 6 drops of Buret reagent to...
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  Contributors Introduction You may wish to read about Carbohydrates before you begin this part of the lab. Read up to the "Lipids" section, then push the "back" button on your browser to return here. Cleaning Up It is important to keep the lab in the...
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• Testing For Biological Molecules
  Fill each of the test tubes 1 through 6 to the 3 cm mark with Benedicts reagent and put the tubes in a boiling water bath for 5 minutes. Record your results in your notebook. A change in color indicates the presence of reducing sugars. Below: The test solutions and Benedict's reagent are boiled in a water bath for five minutes. Click on the image to view an enlargement. Press the "Back" button to return. Below: Results of several solutions tested with the Benedict's test Starch Iodine solution IKI reacts with starch to produce a dark purple or black color.
  Link: http://www3.geosc.psu.edu/~dmb53/DaveSTELLA/Carbon/carbon_intro.htm
  
• Biuret Test
  Use a wax marker to mark two test tubes 1 cm from the bottom. Fill one of the tubes to the 1 cm mark with water and fill the other to the 1 cm mark with starch solution. Be sure to stir the starch before filling your tube. Add two drops of IKI solution to each tube and note the color change. Below left: starch solution and IKI - Iodine turns dark in the presence of starch. Below right: distilled water and IKI Place a small slice of potato on a piece of paper towel in your work area. Put a drop of IKI solution on the potato. Note the color after several minutes and record your observation in your notebook. Place a small slice of onion on a paper towel and then add a drop of IKI to the onion. Record your observation in your notebook. Put a thin slice of potato on a slide and stain it with IKI. The potato should be sliced as thin as possible; thinner than paper is best.
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• Biuret Test-Principle, Requirements, Reagents, Preparation, Procedure And Result
  If you cannot get it thin enough, press down on the cover glass to crush the specimen. Draw a potato cell from the slide that you prepared in the previous step. Label the cell wall and starch granules. Which macromolecule are the dark granules within the potato cells composed of? What caused the iodine to turn dark? Try to get a piece that is thinner than paper; the thinner it is, the better the image will be. Draw an onion cell. Does onion store food as starch? The numerous starch granules seen in potatoes are absent. Lipids Read about lipids in the class notes before you begin this part of the lab. Read up to the "Proteins" section, then push the "back" button to return here. Emulsification Lipids are nonpolar and therefore do not dissolve in water. Emulsifiers are molecules have both polar and nonpolar parts and thus are capable of dissolving in or interacting with both lipids and water. When emulsifiers are mixed with lipids and water, they may act to suspend small droplets of the lipid in water.
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• Carbohydrates, Lipids, Proteins
  Add one drop of a liquid hand soap to one of the test tubes. Cap each test tube with your thumb and shake them vigorously. Observe each of the tubes immediately after shaking. Put the tubes in a rack and observe them after 1 minute, 5 minutes, and 30 minutes. Record your observations. Below: The tube on the right contains oil and water. The one on the left contains oil, water, and a detergent.
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• Service Unavailable In EU Region
  Both tubes were shaken to mix the oil and water. The oil can be seen floating on the water in the tube on the right. The tube on the left shows that the oil droplets remain mixed with the water longer before separating. Below left: oil and water X 40 - Note the large fat droplet on the upper, right half of the photograph. The smaller bubbles scattered throughout the photograph are air bubbles due to vigorous shaking. Below right: oil, water and detergent emulsifier X 40 - The large oil droplets have been broken up into smaller droplets after shaking. Proteins Read about Proteins before you begin this part of the lab. Read up to the "Nucleic Acids" section, then push the "back" button to return here. A deep violet color indicates the presence of proteins and a light pink color indicates the presence of peptides.
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• Experimentation In Scientific Research
  It allows acedemic users to automatically generate high-quality model predictions of 3D structure and biological function of protein molecules from their amino acid sequences. When user submits an amino acid sequence, the server first tries to retrieve template proteins of similar folds or super-secondary structures from the PDB library by LOMETS , a locally installed meta-threading approach. In the second step, the continuous fragments excised from the PDB templates are reassembled into full-length models by replica-exchange Monte Carlo simulations with the threading unaligned regions mainly loops built by ab initio modeling.
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• Lab 3: Biological Molecules
  The purpose of the second iteration is to remove the steric clash as well as to refine the global topology of the cluster centroids. The decoys generated in the second simulations are then clustered and the lowest energy structures are selected. Figure 1. For predicting the biological function of the protein the last column at Figure 1 , the I-TASSER server matches the predicted 3D models to the proteins in 3 independent libraries which consist of proteins of known enzyme classification EC number, gene ontology GO vocabulary, and ligand-binding sites. The final results of function predictions are deduced from the consensus of top structural matches with the function scores calculated based on the confidence score of the I-TASSER structural models, the structural similarity between model and templates as evaluated by TM-score , and the sequence identity in the structurally aligned regions.
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• Biology Experiments
  CASP or Critical Assessment of Techniques for Protein Structure Prediction is a community-wide experiment for testing the state-of-the-art of protein structure predictions which takes place every two years since The experiment often referred as a competition is strictly blind because the structures of testing proteins are unknown to the predictors. Figure 2. Figure 3. LOMETS is a meta-server threading approach containing multiple threading programs, where each program can generate tens of thousands of templates. I-TASSER only uses the templates of the highest significance in the threading alignments, which are measured by the Z-score the difference between the raw and average scores in the unit of standard deviation. Usually, one or two template of the highest Z-score is selected from each threading program, where the threading programs are sorted by the average performance in the large-scale benchmark test experiments.
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• Biology Experiments. Educational Experimental Work To Download By D G Mackean
  In Monte Carlo theory, the largest clusters correspond to the states of the largest partition function or lowest free energy and therefore have the highest confidence. The confidence of each model is quantitatively measured by C-score see below. Since the top 5 models are ranked by the cluster size, it is possible that the lower-rank models have a higher C-score. Although the first model has a higher C-score and a better quality in most cases, it is not unusual that the lower-rank models have a better quality than the higher-rank models. This is usually an indication that the models have a good quality because of the converged simulations. What are 'Proteins structurally close to the target in the PDB'?
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• How To Conduct A Science Experiment: 13 Steps (with Pictures)
  This section reports the top 10 proteins from the PDB which have the closest structural similarity i. Due to the structural similarity, these proteins often have similar function to the target. However, users are encouraged to use the data in 'Predicted function using COACH' to infer the biological function of the target protein, since COACH has been extensively trained to derive function from multi-source of sequence and structure features which has on average a much higher accuracy than the function annotations derived only from the global structure comparison.
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• Amino Acids And Proteins Questions
  What is C-score? It is calculated based on the significance of threading template alignments and the convergence parameters of the structure assembly simulations. C-score is typically in the range of [-5,2], where a C-score of higher value signifies a model with a high confidence and vice-versa. What is TM-score? TM-score is a recently proposed scale for measuring the structural similarity between two structures see Zhang and Skolnick, Scoring function for automated assessment of protein structure template quality, Proteins, Because RMSD is an average distance of all residue pairs in two structures, a local error e.
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• KROK 1 2015 ANSWERS EXPLAINED
  In TM-score, however, the small distance is weighted stronger than the big distance which makes the score insensitive to the local modeling error. TM-score or RMSD is a known standard for measuring structural similarity between two structures which are usually used to measure the accuracy of structure modeling when the native structure is known, while C-score is a metric that I-TASSER developed to estimate the confidence of the modeling. In case where the native structure is not known, it becomes necessary to predict the quality of the modeling prediction, i.
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• Test For Proteins | Principle, Preparation, Summary & Result
  To answer this question, we tried predicted the TM-score and RMSD of the predicted models relative the native structures based on the C-score. Correlation coefficient of C-score of the first model with TM-score to the native structure is 0. However, the C-score is listed for all models just for a reference. Why some lower-rank models have higher C-score? We have found that the cluster size is more robust than C-score for ranking the predicted models. Nevertheless, the C-score has a strong correlation with the quality of the final models, which has been used to quantitatively estimate the RMSD and TM-score of the final models relative to the native structure. Unfortunately, such strong correlation only occurs for the first predicted model from the largest cluster. Thus, the C-scores of the lower-rank models i. In other word, even though the lower-rank models may have a higher C-score than the first model in some cases, the first model is on average the most reliable and should be considered if without special reasons e.
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• Biuret Test - Principle, Preparation And Procedure
  How to use known information e. If users know some information about the structure of the modeled proteins, the information can be conveniently uploaded to the I-TASSER server. The information can significantly improve the quality of structural and function predictions. The I-TASSER server currently accepts two types of user-specified restraints: 1 inter-residue contact and distance restraints; 2 template structures and template-target alignment; 3 secondary structure assignment.
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• Carbohydrates, Lipids, Proteins - Biology LibreTexts
  Specify template without alignment: You can actually use any 3D structure as the template, which does not necessary exist in the PDB library. In this case, you can use this option to upload the 3D structure. This structure file must be in the standard PDB format. You do not need to input the target-template alignments. Specify template with alignment: This option allows you usually the advanced users to specify both template structure and the target-template alignment.
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• Chem2OB3 - Experiment 5
  The homology is defined based on the sequence identity cutoff, i. Exclude specific template proteins: This option allows users to upload a list of template structures that will be excluded from the I-TASSER template library. Users can also specify a different sequence identity cutoff, e.
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• Qualitative Analysis Of Proteins (Procedure) : Class 12 : Chemistry : Amrita Online Lab
  Unknown Post-Lab Questions Record your hypothesis about what will happen when Biuret solution is mixed with the solutions from test tubes 1, 2, 3, and 4 here. Be sure to use scientific reasoning to support your hypothesis. Write a statement to explain the molecular composition of the unknown solution based on the results obtained during testing with the Biuret solution and each sample solution.
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• Carbohydrates, Lipids, Proteins - Biology LibreTexts
  Diet and nutrition are closely linked to the study of biomolecules. How should you monitor your food intake to ensure the cells in your body have the materials necessary to function? There are other types of reagents used to determine what type of biomolecule a substance is. Originally blue in color, these copper ions are reduced by the sugar, and produce an orange-red colored precipitate. Alternatively, iodine-potassium iodide IKI may also be used when working with starch. IKI contains special tri-iodine ions which interact with the coiled structure of a starch polymer. Prior to a reaction, the IKI displays a yellow-brown color; however, after reacting with starch, a dark purple or black color is presented. Based on the structure shown below and these chemical results, what kind of biomolecule is this?
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