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Remaining Time: 1 hour, 26 minutes, 57 seconds

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Remaining Time: 1 hour, 26 minutes, 57 seconds. Question Completion Status: Wey TW LUST Yes O No QUESTION 2 7 points A student is trying to measure the absorbance of an RNA stock solution. First, the student placed 1,061 uL of water in a cuvette and measured the absorbance at 260 nm, at 85°C. Then the student added 9 uL of the RNA stock to the cuvette and measured the absorbance again. The results obtained are summarized below. Absorbance (260 nm, 85 °C) Water (1,061 PL) 0.047 Water + 9 uL of sample 0.7792 Calculate the absorbance of the stock solution. Please enter only numbers in your answer and include at least 2 decimal places in your answer. QUESTION 3 10 points Suppose you are trying to figure out the absorbance of an RNA stock and the percentage of error associated with these measuments. The table below shows the absorbance (at 260 nm, 85 °C) of 1000 ML of water and the absorbances after adding 3 aliquotes of RNA (first 4 PL are added, then additional 3 ul are added and then 2 additional ul are added). Calculate the absorbance of the RNA stock based on each aliquot (write your answers in the table). Please include at least 2 decimal places in your answers: (The difference between absorbance values is already calculated and listed in the table.) Sample Absorbance (260 nm, 85 °C) Difference Absorbance of RNA Stock 1000 l water 0.0346 + 4 PL of RNA stock 0.1266 0.0920 Click Save and Submit to save and submit. Click Save All Answers to save all answers. Save All Answers Close Window Save an CO 62 FS F7 QUESTION 3 10 points Suppose you are trying to figure out the absorbance of an RNA stock and the percentage of error associated with these measuments. The table below shows the absorbance (at 260 nm, 85 °C) of 1000 ML of water and the absorbances after adding 3 aliquotes of RNA (first 4 uL are added, then additional 3 PL are added and then 2 additional uL are added). Calculate the absorbance of the RNA stock based on each aliquot (write your answers in the table). Please include at least 2 decimal places in your answers: (The difference between absorbance values is already calculated and listed in the table.) Sample Absorbance (260 nm, 85 °C) Difference Absorbance of RNA Stock 1000 L water 0.0346 + 4 PL of RNA stock 0.1266 0.0920 + 3 additional PL of RNA stock 0.1908 0.0642 + 2 additional uL of RNA stock 0.2391 0.0483 Calculate also the average absorbance of the RNA stock and write it here. Please enter at least 2 decimal palces in your answer Average Absorbance of RNA stock: Calculate the percentage of error associated with these measurements. Calculate this error in the same we we calculated it in the lab. Please include at least 2 decimal places in your answer. Percentage of error: 7 points Say QUESTION 4 Suppose you conducted a CD titration where an RNA molecule was titrated with a ligand. You have the RNA solution in a cuvette and the initial volume of the RNA solution is 2100 ML. Then you added various Save All Answers Close Window Save an Click Save and Submit to save and submit. Click Save All Answers to save all answers. ESS 20 . F3 F5 FG F7 Fa F2 % A & 2 3 5 6 7 8 . 9 Remaining Time: 1 hour, 26 minutes, 26 seconds. Question Completion Status: the RNA is in a smaller volume that it was after the electroelution the RNA is in a different buffer than it was after the electroelution the RNA is ready to be used in experiments to measure the absorbance of the RNA stock QUESTION 8 Match the experiment with a brief description of the experiment Electroelution CD sample preparation Absorbance of RNA stock CD titration ? Curve Expert A. Processed data from a binding experiment is fitted to a binding equation to obtain the binding affinity (K) B. a measured amount (some uL) of a concentrated solution of ligand is mixed with some PL of a NaCl solution, some uL of a MgCl2 solution and some uL of buffer. C. A large scale transcription reaction is loaded into a gel and the gel is run for several hours. Subsequently, a piece of gel containing the RNA of interest is sliced out of the gel D. a measured amont of RNA stock (some uL) is mixed with some uL of buffer, NaCl solution, MgCl2 solution to produce a final solution with an absorbance of 1 at 260 nm E. Aliquots of an RNA stock are added to a cuvette containing water and the absorbance after each . addition is measured. This experiment is done at 85°C F. Gel pieces are placed in an apparatus and subjected to electrical current G. Aliquots of a ligand are added to a cuvette containing the RNA of interest QUESTIONS Suppose you are preparing a sample for your CD experiment. You have an RNA stock with an absorbance of 76 and you also have a NaCl stock solution with a concentration of 2850 mM and a MgCl2 stock solution with a concentration of 475 mM. Here is a summary of the materials you have: RNA Stock Absorbance = 76 NaCl stock = 2850 MM MgCl2 stock = 475 MM Calculate the PL of RNA, NaCl, MgCl2 and buffer that should be mixed to prepare 1900 ML of a solution with an RNA absorbance of 1, a concentration of NaCl of 51 mM and a concentration of MgCl2 of 1.5 mM. Here is a summary of the conditions you want: 1900 uL of total solution Desired RNA Absorbance = 1 Desired NaCl = 51 mm Desired MgCl2 = 1.5 mm Fill out this table to indicate the ul that need to be mixed to obtain 1900 ul of the desired solution for a CD experiment: Click Save and Submit to save and submit. Click Save All Answers to save all answers. Save All Answers QUESTION 4 7 points Save Answer Suppose you conducted a CD titration where an RNA molecule was titrated with a ligand. You have the RNA solution in a cuvette and the initial volume of the RNA solution is 2100 ML. Then you added various aliquots of a ligand stock and measured the CD signal at 245 nm. The concentration of the ligand stock that you used was 199. After finishing the experiment, you constructed the following table. Additions (UL) Total Volume Added (ul) CD at 245 nm Concentration of Ligand (UM) Corrected CD at 245 nm lo 0 -2.3790 2 2 -2.6664 2 4 -2.9497 3 7 -3.3653 3 10 -3.7673 5 15 -4.3954 5 20 -4.9457 7 27 -5.5203 7 34 -5.8487 9 43 -6.0434 9 52 -6.1251 14 66 -6.1686 20 86 -6.1679 30 116 -6.1226 50 166 -6.0149 100 266 -5.7805 Calculate the concentration of ligand in the cuvette (i.e. the value for the 4th column) for the following data point: Total volume added: 10 CD signal at 245 nm: -3.7673 In other words, what is the concentration of ligand in the cuvette after the addition of 10 uL of the ligand stock (ligand stock concentration is 199 PM) into the cuvette containing the RNA? (the initial volume of the cuvette was 2100 ML) Please enter your answer in PM but don't write the units in your answer. Enter only numbers and include at least 4 decimal places in your answer. QUESTION 5 7 points Save Answer Suppose you conducted a CD titration where an RNA molecule was titrated with a ligand. You have the RNA solution in a cuvette and the initial volume of the RNA solution is 2100 UL. Then you added various aliquots of a ligand stock and measured the CD signal at 245 nm. After finishing the experiment, you constructed the following table. Additions (L) Total Volume Added (UL) CD at 245 nm Concentration of Ligand (UM) Corrected CD at 245 nm 0 0 -2.3790 2 2 -2.6664 2 4 -2.9497 3 7 -3.3653 3 10 -3.7673 5 15 -4.3954 5 20 -4.9457 7 27 -5.5203 17 34 -5.8487 9 43 -6.0434 9 52 -6.1251 14 66 -6.1686 20 86 -6.1679 30 116 -6.1226 50 166 -6.0149 100 266 -5.7805 Calculate the corrected CD signal (i.e. the value for the 5th column) for the following data point: Total volume added: 266 CD signal at 245 nm: -5.7805 In other words, what is the value of the corrected CD signal after the addition of 266 uL of the ligand stock into the cuvette containing the RNA? (the initial volume of the cuvette was 2100 ML) Please enter only numbers in your answer and include at least 4 decimal places in your answer. Don't forget to include the sign. QUESTION 6 7 points Save Answer What is the purpose of electroelution? to concentrate the RNA to make the RNA come out from the gel pieces to separate the desired RNA from other RNAs (side products) to fold the RNA QUESTION 7 8 points Save Answer After the experiment with amicon filters is complete: (choose all that apply; this means that you may choose one or more options) the RNA is more concentrated that before the amicon experiment started the RNA is in a smaller volume that it was after the electroelution the RNA is in a different buffer than it was after the electroelution the RNA is ready to be used in experiments to measure the absorbance of the RNA stock QUESTION 8 8 points Save Answer Match the experiment with a brief description of the experiment Electroelution 4 CD sample preparation Absorbance of RNA stock 4 CD titration 4 Curve Expert A. Processed data from a binding experiment is fitted to a binding equation to obtain the binding affinity (K) B. a measured amount (some PL) of a concentrated solution of ligand is mixed with some uL of a NaCl solution, some PL of a MgCl2 solution and some uL of buffer. C. A large scale transcription reaction is loaded into a gel and the gel is run for several hours. Subsequently, a piece of gel containing the RNA of interest is sliced out of the gel D.a measured amont of RNA stock (some uL) is mixed with some uL of buffer, NaCl solution, MgCl2 solution to produce a final solution with an absorbance of 1 at 260 nm E. Aliquots of an RNA stock are added to a cuvette containing water and the absorbance after each addition is measured. This experiment is done at 85°C F. Gel pieces are placed in an apparatus and subjected to electrical current G. Aliquots of a ligand are added to a cuvette containing the RNA of interest QUESTIONS 10 points Save Answer Suppose you are preparing a sample for your CD experiment. You have an RNA stock with an absorbance of 76 and you also have a NaCl stock solution with a concentration of 2850 mM and a MgCl2 stock solution with a concentration of 475 mM. Here is a summary of the materials you have: RNA Stock Absorbance = 76 NaCl stock = 2850 MM MgCl2 stock = 475 mm Calculate the ul of RNA NaCl Mocha and buffer that should be mixed to prepare 1900 ul of a solution with an RNA absorbance of 1 a concentration of NaCl of 51 mM and a concentration of Mo 12 of 15 mM Here is a summary of the conditions vou. pieces are pla di appan G. Aliquots of a ligand are added to a cuvette containing the RNA of interest QUESTION 9 10 points Save Answer Suppose you are preparing a sample for your CD experiment. You have an RNA stock with an absorbance of 76 and you also have a NaCl stock solution with a concentration of 2850 mM and a MgCl2 stock solution with a concentration of 475 mM. Here is a summary of the materials you have: RNA Stock Absorbance = 76 NaCl stock = 2850 mm MgCl2 stock = 475 mm Calculate the uL of RNA, NaCl, MgCl2 and buffer that should be mixed to prepare 1900 uL of a solution with an RNA absorbance of 1, a concentration of NaCl of 51 mM and a concentration of MgCl2 of 1.5 mM. Here is a summary of the conditions you want: 1900 uL of total solution Desired RNA Absorbance = 1 Desired NaCl = 51 mm Desired MgCl2 = 1.5 mm Fill out this table to indicate the ul that need to be mixed to obtain 1900 ML of the desired solution for a CD experiment: Component JuL needed RNA stock (Abs = 76) NaCl stock (2850 mm) MgCl2 stock (475 mm) Buffer QUESTION 10 7 points Save Answer The final part of the CD titration analysis included the use of Curve Expert. Suppose a student completed a titration and fitted the data and obtained a graph like this: Top Results 5.0 Data Binding 4.5 4.0 3.5 Corrected CD at 223 nm 3.0 Ottp://www.curveexpert.net/ordt 2.5 O?NREGISTERED) otë 30 day..trial Help-Activate MgCl2 stock (475 mm) Buffer QUESTION 10 7 points Save Answer The final part of the CD titration analysis included the use of Curve Expert. Suppose a student completed a titration and fitted the data and obtained a graph like this: Top Results 5.0 Data Binding 4.5 4.0 3.5 cted CD at 223 nm Corrected 3.0 2.5 2.0 UNREGISTERED) Activate 30 day. trial. 'Help-ŠActivate urchase: https://www.curveexpert.net/order 1.5 0 2 4 5 6 [Ligand) UM Looking at fitting parameters, the student noticed the following parameters: Equation :((((x+0.8+1/a)-(sqrt(((x+0.8+(1/a))**2)-(4*0.8*x))))/(2*0.8))*(b-c))+c a = 5.000000001408931E+00 b = 4.799999999639722E+00 C= 1.600000000340843E+00 And the student figured that the parameter needed is "a". Thus, the student obtained a value of 5 um-1 for parameter "a" What is the value of parameter "a" in M-1 units? (If entering a number using the scientific notation, please use the format accepted by Blackboard. For example 5.43 x 10-12 would be entered as 5.43E-12) What does parameter "a" represents? In other words, what is the name of this parameter? QUESTION 11 7 points Save Answer Supposed you have determined that your RNA stock solution has an absorbance of 142.4. Now you want to determine the concentration of your RNA solution. The RNA you have has 85 nucleotides and you know that the extinction coefficient for RNA is 9.6 mm-'cm per nucleotide. Also, when you measured the absorbance, you used a cuvette that had 1 cm pathlenght. -1 What is the concentration of your RNA stock solution in mMunits2 Write the answer in mM units but do not write the units Write only numbers in your answer and include at least 4 decimal nlaces in your answer QUESTION 11 7 points Save Answer Supposed you have determined that your RNA stock solution has an absorbance of 142.4. Now you want to determine the concentration of your RNA solution. The RNA you have has 85 nucleotides and you know that the extinction coefficient for RNA is 9.6 mM-cm-2 per nucleotide. Also, when you measured the absorbance, you used a cuvette that had 1 cm pathlenght. What is the concentration of your RNA stock solution in mM units? Write the answer in mM units but do not write the units. Write only numbers in your answer and include at least 4 decimal places in your answer. QUESTION 12 7 points Save Answer Order the experiments as they should occur for performing a CD titration • Prepare ligand solution with some chosen concentrations of NaCl and MgCl2 • Prepare cuvette containing RNA solution with some chosen concentrations of NaCl and MgCl2 4 Measure CD spectra of RNA after each addition of a small aliquot of ligand Amicon Filters 4 Electroelution 4 Measure Absorbance of RNA stock QUESTION 13 6 points Save Answer A student is performs a CD titration, collects data and obtains a nice curve and a high binding affinity. However, upon reviewing the experiment, the student notices a mistake in the CD sample preparation. The student had calculated the RNA volume incorrectly. The student added 78 PL of RNA but the correct value should have been 98 uL of RNA. Thus, the CD titration was performed with less RNA than it was planned. Which of the following statements about this experiment is correct? Select all that apply (this means you may select one or more options) The experiment is still valid because the student was able to obtain a binding curve. The value of K that the student obtained is still valid. This experiment has to be repeated and the results are not valid. There is no way to obtain the correct binding affinity if the incorrect amount of RNA was added. The experiment does not need to be repeated but the results need to be re-analyzed. The concentration of RNA can be recalculated and the recalculated concentration can be used in the analysis to obtain the binding affinity. The experiment has to be repeated and there is no way to use the results. If the experiment was performed with less RNA than expected, there is no way to calculate the correct concentration of ligand in the cuvette. In the analysis of the results, the corrected CD signal and the concentration of ligand in the cuvette would still be correct because those calculations don't need to use the concentration of RNA QUESTION 14 7 points Save Answer The ligand solution for the CD experiment is prepared such that: (select all that apply; this means that you may choose one or more options) it contains a relatively high concentration of ligand it does not contain any NaCl or MgCl2. The NaCl and the MgCl2 are added only to the cuvette containing RNA it contains a very low concentration of ligand. It contains the same concentration of NaCl and MgCl2 that are present in the cuvette containing the RNA solution QUESTION 4 7 points Save Answer Suppose you conducted a CD titration where an RNA molecule was titrated with a ligand. You have the RNA solution in a cuvette and the initial volume of the RNA solution is 2100 ML. Then you added various aliquots of a ligand stock and measured the CD signal at 245 nm. The concentration of the ligand stock that you used was 199. After finishing the experiment, you constructed the following table. Additions (UL) Total Volume Added (ul) CD at 245 nm Concentration of Ligand (UM) Corrected CD at 245 nm O 10 -2.3790 2 2 -2.6664 2 4 -2.9497 3 7 -3.3653 3 10 -3.7673 15 15 -4.3954 5 20 -4.9457 7 27 -5.5203 17 34 -5.8487 9 43 -6.0434 9 52 -6.1251 14 66 -6.1686 20 86 -6.1679 30 116 -6.1226 50 166 -6.0149 100 266 -5.7805 Calculate the concentration of ligand in the cuvette (i.e. the value for the 4th column) for the following data point: Total volume added: 10 CD signal at 245 nm: -3.7673 In other words, what is the concentration of ligand in the cuvette after the addition of 10 uL of the ligand stock (ligand stock concentration is 199 PM) into the cuvette containing the RNA? (the initial volume of the cuvette was 2100 ML) Please enter your answer in PM but don't write the units in your answer. Enter only numbers and include at least 4 decimal places in your answer. QUESTION 5 7 points Save Answer Suppose you conducted a CD titration where an RNA molecule was titrated with a ligand. You have the RNA solution in a cuvette and the initial volume of the RNA solution is 2100 ML. Then you added various aliquots of a ligand stock and measured the CD signal at 245 nm. After finishing the experiment, you constructed the following table. Additions (L) Total Volume Added (ul) CD at 245 nm Concentration of Ligand (UM) Corrected CD at 245 nm 0 0 -2.3790 2 2 -2.6664 2 4 -2.9497 3 7 -3.3653 3 10 -3.7673 5 15 -4.3954 5 20 -4.9457 17 27 -5.5203 17 34 -5.8487 9 43 -6.0434 19 52 -6.1251 14 66 -6.1686 20 86 -6.1679 30 116 -6.1226 50 166 -6.0149 100 266 -5.7805 Calculate the corrected CD signal (i.e. the value for the 5th column) for the following data point: Total volume added: 266 CD signal at 245 nm: -5.7805 In other words, what is the value of the corrected CD signal after the addition of 266 uL of the ligand stock into the cuvette containing the RNA? (the initial volume of the cuvette was 2100 PL) Please enter only numbers in your answer and include at least 4 decimal places in your answer. Don't forget to include the sign. E. Aliquots of an RNA stock are added to a cuvette containing water and the absorbance after each addition is measured. This experiment is done at 85°C F. Gel pieces are placed in an apparatus and subjected to electrical current G.Aliquots of a ligand are added to a cuvette containing the RNA of interest QUESTION 9 10 points Save Answer Suppose you are preparing a sample for your CD experiment. You have an RNA stock with an absorbance of 76 and you also have a NaCl stock solution with a concentration of 2850 mM and a MgCl2 stock solution with a concentration of 475 mM. Here is a summary of the materials you have: RNA Stock Absorbance = 76 NaCl stock = 2850 mm MgCl2 stock = 475 mm Calculate the ul of RNA, NaCl, MgCl2 and buffer that should be mixed to prepare 1900 uL of a solution with an RNA absorbance of 1, a concentration of NaCl of 51 mM and a concentration of MgCl2 of 1.5 mM. Here is a summary of the conditions you want: 1900 uL of total solution Desired RNA Absorbance = 1 Desired NaCl = 51 mm Desired MgCl2 = 1.5 mm Fill out this table to indicate the ul that need to be mixed to obtain 1900 ML of the desired solution for a CD experiment: Component uL needed RNA stock (Abs = 76) NaCl stock (2850 mm) MgCl2 stock (475 mm) Buffer QUESTION 10 7 points Save Answer The final part of the CD titration analysis included the use of Curve Expert. Suppose a student completed a titration and fitted the data and obtained a graph like this: Top Results 5.0 Data Binding 4.5 4.0 CD at 223 nm trial Help->Activate curveexpert.net/ord 3.5 CGISTERED