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4:47 PM Wed Mar 27 ... lyceum.bates.edu 5 of 8 primer 3'-end WAT1 2.12 H₂O dCTP 2.25 (2.86) 2.11 (N/A) - 2.25 (2.44) MgA 2.35 (2.45) (2.26) 2.01 (2.31) 3.79 MgB 1.87' 1.86 (3.87) 1.98 (2.50) (2.41) (2.39) 1.86 1.97 1.87 (2.24) (2.45) (2.34) WAT2 D654 A476 D475 4. RNA hydrolysis As discussed in class, we can predict how much of RNA we expect to be in a reactive form using general chemistry calculations(Henderson Hasselbach). a) Calculate the percent of RNA at pH=8 that will have the 3'OH in its reactive alkoxide form (O-). The pKa of the 3'OH is approximately 13. b) Now redo the calculation to get the percent O-/OH at pH=6, and pH=10. c) What conditions favor more reactive RNA? How could we use a catalyst to enable more RNA to be in its reactive form? ດ 92% 4:47 PM Wed Mar 27 4 of 8 lyceum.bates.edu b. What are the implications on the RNA world from the fact we cannot currently get RNA purine nucleotides with this synthetic system? c. What kind of geochemical scenario does this synthesis favor/require? Can it be adapted to other systems? d. What are some energy inputs of this system? e. Pick a branch of the synthesis (say, the making of Proline, or the synthesis of lipids) from the Patel et al paper and describe what is happening chemically with words. What molecules/functional groups are getting added to what? Is there energy input? What pH, temperature, etc are necessary. 3. Enzymatic catalysis. Below is an image from the active site of RNA polymerase. This enzyme catalyzes RNA polymerization in cells (primer extension with NTPs). What intermolecular interactions are occurring in the image? What is the nucleophile/electrophile for primer extension? How does Mg(A) aid in catalysis? Mg(B)? H₂O 92%

4:47 PM Wed Mar 27 ... lyceum.bates.edu 5 of 8 primer 3'-end WAT1 2.12 H₂O dCTP 2.25 (2.86) 2.11 (N/A) - 2.25 (2.44) MgA 2.35 (2.45) (2.26) 2.01 (2.31) 3.79 MgB 1.87' 1.86 (3.87) 1.98 (2.50) (2.41) (2.39) 1.86 1.97 1.87 (2.24) (2.45) (2.34) WAT2 D654 A476 D475 4. RNA hydrolysis As discussed in class, we can predict how much of RNA we expect to be in a reactive form using general chemistry calculations(Henderson Hasselbach). a) Calculate the percent of RNA at pH=8 that will have the 3'OH in its reactive alkoxide form (O-). The pKa of the 3'OH is approximately 13. b) Now redo the calculation to get the percent O-/OH at pH=6, and pH=10. c) What conditions favor more reactive RNA? How could we use a catalyst to enable more RNA to be in its reactive form? ດ 92% 4:47 PM Wed Mar 27 4 of 8 lyceum.bates.edu b. What are the implications on the RNA world from the fact we cannot currently get RNA purine nucleotides with this synthetic system? c. What kind of geochemical scenario does this synthesis favor/require? Can it be adapted to other systems? d. What are some energy inputs of this system? e. Pick a branch of the synthesis (say, the making of Proline, or the synthesis of lipids) from the Patel et al paper and describe what is happening chemically with words. What molecules/functional groups are getting added to what? Is there energy input? What pH, temperature, etc are necessary. 3. Enzymatic catalysis. Below is an image from the active site of RNA polymerase. This enzyme catalyzes RNA polymerization in cells (primer extension with NTPs). What intermolecular interactions are occurring in the image? What is the nucleophile/electrophile for primer extension? How does Mg(A) aid in catalysis? Mg(B)? H₂O 92%

Biochemistry
Biochemistry
9th Edition
ISBN:9781319114671
Author:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.
Publisher:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.
Chapter1: Biochemistry: An Evolving Science
Section: Chapter Questions
Problem 1P
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Can you help with q3 please, thank you. 

4:47 PM Wed Mar 27 ... lyceum.bates.edu 5 of 8 primer 3'-end WAT1 2.12 H₂O dCTP 2.25 (2.86) 2.11 (N/A) - 2.25 (2.44) MgA 2.35 (2.45) (2.26) 2.01 (2.31) 3.79 MgB 1.87' 1.86 (3.87) 1.98 (2.50) (2.41) (2.39) 1.86 1.97 1.87 (2.24) (2.45) (2.34) WAT2 D654 A476 D475 4. RNA hydrolysis As discussed in class, we can predict how much of RNA we expect to be in a reactive form using general chemistry calculations(Henderson Hasselbach). a) Calculate the percent of RNA at pH=8 that will have the 3'OH in its reactive alkoxide form (O-). The pKa of the 3'OH is approximately 13. b) Now redo the calculation to get the percent O-/OH at pH=6, and pH=10. c) What conditions favor more reactive RNA? How could we use a catalyst to enable more RNA to be in its reactive form? ດ 92%
Transcribed Image Text:4:47 PM Wed Mar 27 ... lyceum.bates.edu 5 of 8 primer 3'-end WAT1 2.12 H₂O dCTP 2.25 (2.86) 2.11 (N/A) - 2.25 (2.44) MgA 2.35 (2.45) (2.26) 2.01 (2.31) 3.79 MgB 1.87' 1.86 (3.87) 1.98 (2.50) (2.41) (2.39) 1.86 1.97 1.87 (2.24) (2.45) (2.34) WAT2 D654 A476 D475 4. RNA hydrolysis As discussed in class, we can predict how much of RNA we expect to be in a reactive form using general chemistry calculations(Henderson Hasselbach). a) Calculate the percent of RNA at pH=8 that will have the 3'OH in its reactive alkoxide form (O-). The pKa of the 3'OH is approximately 13. b) Now redo the calculation to get the percent O-/OH at pH=6, and pH=10. c) What conditions favor more reactive RNA? How could we use a catalyst to enable more RNA to be in its reactive form? ດ 92%
4:47 PM Wed Mar 27 4 of 8 lyceum.bates.edu b. What are the implications on the RNA world from the fact we cannot currently get RNA purine nucleotides with this synthetic system? c. What kind of geochemical scenario does this synthesis favor/require? Can it be adapted to other systems? d. What are some energy inputs of this system? e. Pick a branch of the synthesis (say, the making of Proline, or the synthesis of lipids) from the Patel et al paper and describe what is happening chemically with words. What molecules/functional groups are getting added to what? Is there energy input? What pH, temperature, etc are necessary. 3. Enzymatic catalysis. Below is an image from the active site of RNA polymerase. This enzyme catalyzes RNA polymerization in cells (primer extension with NTPs). What intermolecular interactions are occurring in the image? What is the nucleophile/electrophile for primer extension? How does Mg(A) aid in catalysis? Mg(B)? H₂O 92%
Transcribed Image Text:4:47 PM Wed Mar 27 4 of 8 lyceum.bates.edu b. What are the implications on the RNA world from the fact we cannot currently get RNA purine nucleotides with this synthetic system? c. What kind of geochemical scenario does this synthesis favor/require? Can it be adapted to other systems? d. What are some energy inputs of this system? e. Pick a branch of the synthesis (say, the making of Proline, or the synthesis of lipids) from the Patel et al paper and describe what is happening chemically with words. What molecules/functional groups are getting added to what? Is there energy input? What pH, temperature, etc are necessary. 3. Enzymatic catalysis. Below is an image from the active site of RNA polymerase. This enzyme catalyzes RNA polymerization in cells (primer extension with NTPs). What intermolecular interactions are occurring in the image? What is the nucleophile/electrophile for primer extension? How does Mg(A) aid in catalysis? Mg(B)? H₂O 92%
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