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2. Draw a dipeptide with a trans linkage and a net charge of -1 at pH 7 a. Indicate which six atoms are part of the planar structure of the peptide bond. b. Is the Cis or Trans linkage of a peptide preferred? Why?

2. Draw a dipeptide with a trans linkage and a net charge of -1 at pH 7 a. Indicate which six atoms are part of the planar structure of the peptide bond. b. Is the Cis or Trans linkage of a peptide preferred? Why?

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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10:16 AM Fri Sep 2 < то 1. A simplified structure of the peptide Lys-Glu-Ser with just the ionizable groups in the charged state is shown with the pKa of each group. Calculate the pl for this peptide. Show your work. pka = 8.5 H3N+ NH3* pKa 10.0 2. Draw a dipeptide with a trans linkage and a net charge of -1 at pH 7 a. Indicate which six atoms are part of the planar structure of the peptide bond. b. Is the Cis or Trans linkage of a peptide preferred? Why? COO- OH pka=4.2 3. A mutation that changes an alanine residue in the interior of a protein to a valine is found to lead to a loss of activity. The activity is regained when a second residue is mutated from an isoleucine to a glycine. Why would this mutation restore activity? 5. Tetrahydrofuran, THF, a water-soluble ether, has a lower dielectric constant (less polar) than water. When THF is added to an aqueous solution of a protein, would you expect the a-helix content of the protein to increase or decrease. Why? 6. Given the following three amino acid sequences: 7. What is SDS and what is its purpose in gel electrophoresis? +: 4. The proteases chymotrypsin and trypsin cleave on the C terminal side of Phe and Arg respectively. During purification, one must be more careful with trypsin since it is known to cleave itself much more readily than chymotrypsin. Why? Peptide # 1: Val-Phe-Val-lle-Val-Pro-Gly-Tyr-Val-Phe-Leu-Val-Pro-Gly-Val Peptide # 2: Met-Ala-Glu-Ala-Glu-Ala-Ala-Met-Lys-Lys-Ala-Ala-Met-Lys Peptide # 3: Pro-Gly-Ala-Pro-Gly-Ala-Pro-Gly-Gly-Pro-Gly-Pro-Ala-Gly-Pro a. Which peptide is most likely to form an a-helix? Explain pka = 3.5 COO- @83% b. Which peptide is most likely to form a ß-sheet? Circle the most likely residues involved in the turns of the ß-sheet on the peptide your chose above. c. What is the net charge of Peptide #2 at pH 14? (113 +
Transcribed Image Text:10:16 AM Fri Sep 2 < то 1. A simplified structure of the peptide Lys-Glu-Ser with just the ionizable groups in the charged state is shown with the pKa of each group. Calculate the pl for this peptide. Show your work. pka = 8.5 H3N+ NH3* pKa 10.0 2. Draw a dipeptide with a trans linkage and a net charge of -1 at pH 7 a. Indicate which six atoms are part of the planar structure of the peptide bond. b. Is the Cis or Trans linkage of a peptide preferred? Why? COO- OH pka=4.2 3. A mutation that changes an alanine residue in the interior of a protein to a valine is found to lead to a loss of activity. The activity is regained when a second residue is mutated from an isoleucine to a glycine. Why would this mutation restore activity? 5. Tetrahydrofuran, THF, a water-soluble ether, has a lower dielectric constant (less polar) than water. When THF is added to an aqueous solution of a protein, would you expect the a-helix content of the protein to increase or decrease. Why? 6. Given the following three amino acid sequences: 7. What is SDS and what is its purpose in gel electrophoresis? +: 4. The proteases chymotrypsin and trypsin cleave on the C terminal side of Phe and Arg respectively. During purification, one must be more careful with trypsin since it is known to cleave itself much more readily than chymotrypsin. Why? Peptide # 1: Val-Phe-Val-lle-Val-Pro-Gly-Tyr-Val-Phe-Leu-Val-Pro-Gly-Val Peptide # 2: Met-Ala-Glu-Ala-Glu-Ala-Ala-Met-Lys-Lys-Ala-Ala-Met-Lys Peptide # 3: Pro-Gly-Ala-Pro-Gly-Ala-Pro-Gly-Gly-Pro-Gly-Pro-Ala-Gly-Pro a. Which peptide is most likely to form an a-helix? Explain pka = 3.5 COO- @83% b. Which peptide is most likely to form a ß-sheet? Circle the most likely residues involved in the turns of the ß-sheet on the peptide your chose above. c. What is the net charge of Peptide #2 at pH 14? (113 +
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