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Consider the following peptide. Gly-Lys-Ala-Val-Asp-Gly-lle-Val-Lys-Ala-Gly-His-Glu-Ala a) What would be net charge (positive or negative) on the peptide at pH 7.0? b) The peptide known to have some therapeutic value only if it has no overall charge at pH 7.0. Assuming that the single amino acid replacement does not alter the therapeutic potential of the peptide, which amino acid replacement do you suggest so peptide has no charge at pH 7.0? Explain your answer. Write three most important characteristics of a peptide bond.

Consider the following peptide. Gly-Lys-Ala-Val-Asp-Gly-lle-Val-Lys-Ala-Gly-His-Glu-Ala a) What would be net charge (positive or negative) on the peptide at pH 7.0? b) The peptide known to have some therapeutic value only if it has no overall charge at pH 7.0. Assuming that the single amino acid replacement does not alter the therapeutic potential of the peptide, which amino acid replacement do you suggest so peptide has no charge at pH 7.0? Explain your answer. Write three most important characteristics of a peptide bond.

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
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1. Consider the following peptide. Gly-Lys-Ala-Val-Asp-Gly-lle-Val-Lys-Ala-Gly-His-Glu-Ala a) What would be net charge (positive or negative) on the peptide at pH 7.0? b) The peptide known to have some therapeutic value only if it has no overall charge at pH 7.0. Assuming that the single amino acid replacement does not alter the therapeutic potential of the peptide, which amino acid replacement do you suggest so peptide has no charge at pH 7.0? Explain your answer. 2 Write three most important characteristics of a peptide bond. 3 Explain change in Entropy and Enthalpy during process of protein folding. 4 Write short note on the following. (a) Ramachandran Plot (c) Zwitterion of amino acid (b) a-helix of protein (d) Levinthal Paradox of protein folding List four major differences of protein folding invitro versus folding in the cell. What are molecular Chaperones? What do you mean by Kinetic partitioning? Explain the conditions under which chaperones act as Holdase, foldase, and Unfoldase? What are the characteristics of amyloid fibrils (formed as a result of Inter-molecular Interaction). Do you think such a structural feature can be capitalized for development of drugs that can be used to treat two diseases involving aggregation of two different proteins? 8 6 It is known that native proteins are only marginally stable (-0.4KJ/amino acid). Explain its significance How does glycosylation affect the physico-chemical properties of proteins? Suppose that a protein contains six potential N-linked glycosylation sites. How many possible proteins can be generated, depending on which of these sites is actually glycosylated? Do not include the effects of diversity within the carbohydrate added. 10 11 The figure shown below depicts the glycan shield models of several viruses, many of which have huge potential to cause an epidemic, if not a pandemic. The glycans and proteins are shown in blue and grey, respectively. What difficulties (at least 3) does such a dense sugar (glycan) coating on viral protein surfaces present from the drug development perspective? Are there any opportunities one can harness from such structural features of viral proteins for development of perhaps more effective (Potent) therapeutics? Lassa GPC Nipah F protein Ebola GP Influenza НА HIV-1 Env Coronavirus S protein Write a short note on 12 a) protein acetylation b) Protein phosphorylation 13 Assume that the Editor of a journal sends an review article on Protein folding to you for proof reading before it is sent out for final publication. There are one or more scientifically incorrect statements in the manuscript. With your understanding of underlying concept of protein folding, you are expected to identify them and make the necessary corrections with appropraite justification. Discuss the roles of ell surface glycans in determining human blood group types 14
Transcribed Image Text:1. Consider the following peptide. Gly-Lys-Ala-Val-Asp-Gly-lle-Val-Lys-Ala-Gly-His-Glu-Ala a) What would be net charge (positive or negative) on the peptide at pH 7.0? b) The peptide known to have some therapeutic value only if it has no overall charge at pH 7.0. Assuming that the single amino acid replacement does not alter the therapeutic potential of the peptide, which amino acid replacement do you suggest so peptide has no charge at pH 7.0? Explain your answer. 2 Write three most important characteristics of a peptide bond. 3 Explain change in Entropy and Enthalpy during process of protein folding. 4 Write short note on the following. (a) Ramachandran Plot (c) Zwitterion of amino acid (b) a-helix of protein (d) Levinthal Paradox of protein folding List four major differences of protein folding invitro versus folding in the cell. What are molecular Chaperones? What do you mean by Kinetic partitioning? Explain the conditions under which chaperones act as Holdase, foldase, and Unfoldase? What are the characteristics of amyloid fibrils (formed as a result of Inter-molecular Interaction). Do you think such a structural feature can be capitalized for development of drugs that can be used to treat two diseases involving aggregation of two different proteins? 8 6 It is known that native proteins are only marginally stable (-0.4KJ/amino acid). Explain its significance How does glycosylation affect the physico-chemical properties of proteins? Suppose that a protein contains six potential N-linked glycosylation sites. How many possible proteins can be generated, depending on which of these sites is actually glycosylated? Do not include the effects of diversity within the carbohydrate added. 10 11 The figure shown below depicts the glycan shield models of several viruses, many of which have huge potential to cause an epidemic, if not a pandemic. The glycans and proteins are shown in blue and grey, respectively. What difficulties (at least 3) does such a dense sugar (glycan) coating on viral protein surfaces present from the drug development perspective? Are there any opportunities one can harness from such structural features of viral proteins for development of perhaps more effective (Potent) therapeutics? Lassa GPC Nipah F protein Ebola GP Influenza НА HIV-1 Env Coronavirus S protein Write a short note on 12 a) protein acetylation b) Protein phosphorylation 13 Assume that the Editor of a journal sends an review article on Protein folding to you for proof reading before it is sent out for final publication. There are one or more scientifically incorrect statements in the manuscript. With your understanding of underlying concept of protein folding, you are expected to identify them and make the necessary corrections with appropraite justification. Discuss the roles of ell surface glycans in determining human blood group types 14
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