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- 8. Explain the role of post-translational modifications of protein molecules: the formation of disulfide bridges, hydrolysis of peptide bonds under the action of specific proteases, glycosylation, phosphorylation / dephosphorylation, hydroxylation, acylation of the terminal amino transformation of the terminal carboxyl group into an amide one group and10. (a) Provide the scheme of Merrifield peptide synthesis with suitable example. (b) Describe the mechanism of action of the enzyme lysozyme.18. Chaperones are frequently associated with polypeptides as they are being synthesized from the amnio to carboxy terminus. Provide TWO reasons why it would be advantageous for chaperones to associate with a protein while it is being made?
- 4. The molecular structure of the last 12 amino acid residues (dodecapeptide) that comprise the C- terminal segment of semaglutide is shown below. NH₂ H₂N NH HO NH NH CH 3 NH CH3 CH 3 NH NH ΝΗ CH3 CH3 O NH H3C NH CH3 a) Determine the sequence of the dodecapeptide in one-letter code: b) Convert your sequence in (a) into three-letter code: H₂N. NH NH NH NH H₂N NH NH NH Im c) How many of the a-carbons in this peptide sequence are chiral? d) How many peptide bonds are in this peptide? e) Predict the overall charge of this peptide at physiological pH. f) A biochemist synthesized the C-terminal dodecapeptide version of semaglutide but found that there were other contaminating peptides. Based on your answer in (4.e), which ion exchange chromatography technique would you use to effectively purify the dodecapeptide from the mixture? (encircle one) anion exchange cation exchange g) Briefly explain your answer in (4.f).3. Which best describes the contribution of tertiary (3’) structure of to the native conformation of polypeptides and proteins: a) Structure that results from intrachain interactions of amino acid side chains b) Structure that results from interchain interactions of amino acid side chains c) Structure that results from base pairing d) Structure that results from the linear sequence of amino acids from beginning to end of molecule4. Which best describes the contribution of quaternary (4’) structure of polypeptides to the native conformation of proteins: a) Structure that results from intrachain interactions of amino B) Structure that results from interchain interactions of amino acid side chains c) Structure that results from base pairing d) Structure that results from the linear sequence acid side chains of amino acids from beginning to end of molecule
- 2. | Calculate the overall charge (pH 7) on the following three polypeptides and answer the questions below. Assume the following pKa values: N-terminal -NH3®, 7.0; all -COOH groups, 4.0; Arg, 12.5; Cys, 8.4; His, 6.0; Lys, 10.0; Tyr, 10.0. (A) Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly-Lys-Pro-Val-Gly-Lys-Lys-Arg-Arg-Pro-Val-Lys-Val-Tyr-Pro-Asp-Ala -Gly- Glu-Asp-Gln- Ser-Ala-Glu-Ala-Phe-Pro-Leu-Arg-Glu-Phe (B) Ser-Tyr-Ser-Met-Glu–His-Phe-Arg–Trp–Gly-Ala-Pro-Val-Gly-Glu-Glu-Cys-Asp-Pro-Val-Glu–Val-Tyr-Pro-Asp- Ala-Gly-Glu-Asp-Gln-Ser-Ala-Glu-Ala-Phe-Pro-Leu-Glu-Phe-Cys-Ser-Tyr-Ser-Met-Glu-His-Phe-Asp-Trp-Gly- Asp-Pro-Val-Gly-Pro-Asp-Ala-Gly-Asp-Gln-Pro-Val-Gly-Glu-Glu-Cys-Asp-Pro-Val-Glu-Val-Tyr-Pro-Asp-Ala | (C) Gly-Ser-Val-Arg-Asp-Pro-Val-Lys-Glu–Val-Tyr-Pro-Asp- Lys-Ala-Gly-Arg-Glu-Ser-Arg-Ala (a) Which of the three peptides would elute first from a gel filtration column? (b) Which of the three peptides would migrate the fastest on SDS-PAGE (c) Which of the three peptides could be…2. | Calculate the overall charge (pH 7) on the following three polypeptides and answer the questions below. Assume the following pKa values: N-terminal -NH3®, 7.0; all -COOH groups, 4.0; Arg, 12.5; Cys, 8.4; His, 6.0; Lys, 10.0; Tyr, 10.0. (A) Ser-Tyr-Ser-Met-Glu–His–Phe–Arg–Trp-Gly-Lys-Pro–Val-Gly-Lys-Lys-Arg-Arg-Pro–Val-Lys-Val-Tyr-Pro-Asp-Ala -Gly- Glu--Asp-Gln- Ser-Ala-Glu-Ala-Phe-Pro-Leu-Arg-Glu-Phe (B) Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly-Ala-Pro-Val-Gly-Glu-Glu-Cys-Asp-Pro-Val-Glu-Val-Tyr-Pro-Asp- Ala-Gly-Glu-Asp-Gln-Ser-Ala-Glu-Ala-Phe-Pro-Leu-Glu-Phe-Cys-Ser-Tyr-Ser-Met-Glu-His-Phe-Asp-Trp-Gly- | Asp-Pro-Val-Gly-Pro-Asp-Ala-Gly-Asp-Gln-Pro-Val-Gly-Glu-Glu-Cys-Asp-Pro-Val-Glu-Val-Tyr-Pro-Asp-Ala (C) Gly-Ser-Val-Arg-Asp-Pro-Val-Lys-Glu–Val-Tyr-Pro-Asp- Lys-Ala-Gly-Arg-Glu-Ser-Arg-Ala 11. - - I C'IL- - 1! (e) Which of the above peptides would elute last from a gel filtration column? (f) Which of the three peptides would migrate the slowest on SDS-PAGE (g) Which of the three…1. What are the effects of a) amino acid composition and sequence and b) intramolecular and intermolecular forces of attraction to protein folding? 2. What molecular property of amino acids can be used to justity the concept that the "molecular part of the protein can exhibit the same property as the molecular 'whole' (protein molecule?). Provide a comprehensive discussion using one molecular property. 3. Discuss two metabolic disorders which are caused by protein misfolding. Explain the metabolic consequence of the disorder. 4. If a non-science person asks you what protein folding is and how the concept is related to metabolic disorders, how are you going to explain the concept? (please summarize the concepts used, thank you!)
- 13. One or more of the compounds shown below will satisfy each of the following statements. Not all compounds may be used; some may be used twice. Put the letter(s) in the blank. (a) Found in chitin. (b) An L-saccharide. (c) The first residue attached to asparagine in N-linked glycans. (d) A uronic acid. (e) A ketose. CH,OH COO CO- H OH H OH ОН Н но OH OH H H но OH Но - CH3 óso, NHC- OH (a) (b) (c) CH,OH CH,OH CH,OH c=0 CHOH C=0 H-C-OH CH,OH но-с—н ČH,OH CH,OH (d) (e) (f) 우4. You're working on a structure of a protein and its folding. You think that the interaction between Asp123 and Arg29 is important in determining the structure of the protein. a) What type of amino acid is Asp (acidic, basic, hydrophobic, or polar)? b) What type of amino acid is Arg (acidic, basic, hydrophobic, or polar)? c) What is the strongest interaction that can form between Asp123 and Arg29? You create a mutant Arg29> Lys d) What type of amino acid is Lys (acidic, basic, hydrophobic, or polar)? e) Would you expect this substitution mutation to cause major folding problems? Why or why not? You create mutant Arg29> Glu you discover that this mutant is unable to fold properly, so the protein is nonfunctional. f What type of amino acid is Glu (acidic, basic, hydrophobic, or polar)? g) How does this amino acid substitution cause the protein to fold incorrectly? You find another mutant that also as the same Arg29> Glu mutation. However, this mutant protein įs able to fold normally.…13. What value do N-linked saccharides serve for membrane surface proteins? Which amino acid residue(s) do we find involved in N-linked bonds?