7. Why proteins prefer to have a-helices or ẞ-sheets in their interior core, instead of random coil loops?
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- 6) Proline is not commonly found in the middle of a-helices because its ring structure prevents it from adopting the proper value and because it disrupts the hydrogen-bonding pattern of the helix. Looking at the structure of proline in the amino acid sequence below, suggest how this residue would disrupt the hydrogen-bonding pattern of an a-helix. 'N H R N N H *** R11. A polypeptide is making a short a-helix. A typical residue in an a-helix is involved in two H-bonds. At a minimum, how many residues this helix could have?17. Protein folding results in a large decrease in entropy since a polypeptide is now constrained and more ordered. However, what counterbalances the loss of entropy associated with protein folding?
- 4. 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.…2. Of the two sequences, which is more likely to have helical structure. Explain. a) -Glu-Asp-Glu-Glu-Asp-Leu- b) -Glu-Leu-Asp-Arg-Val-Lys-3. β sheets are less likely to form than α helices during the earliest stages of protein folding. Explain why this is the case. (hint: think about the hydrogen bonding requirements).
- 1. Hydrogen bonds can form an alpha helix or beta sheet. The hydrogen atom has a partial positive because of the atom it is covalently bound to. Name the two most common atoms hydrogen bonds within biological systems that give hydrogen a partial positive charge. 2. Are the atoms named in the question above in the backbone of the protein or are they found in R groups? Which R groups? 3. Besides hydrogen, what other atom is involved in the hydrogen bonds in an alpha helix or beta sheet? In other words, hydrogen is interacting with what other atoms when it makes a hydrogen bond? 4. Write out, in order, the full names of the seven amino acids circled in the picture.4. What is the net charge (approximately) on the polypeptide shown below at pH 12.5? Lys - Arg - Val-Cys - Glu4. 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).
- 1. Which of the following structures could the following polypeptide form? And why? The non- polar amino acids are italicized. Gly-Leu-Asp-Glu-lle-Ala-Lys-Ser-Val-Arg-His-Phe-Cys-His-Ala- lle A. A hydrophobic alpha helix B. An amphipathic a- helix C. A hydrophilic a helix D. A hydrophobic B sheet E. An amphipathic B sheet Where would you expect to find the N-term and C-term amino acids in the polypeptide?1. What is the length in AA’s of the LilP protein? Assume fMet is NOT CLEAVED. 2. Write out the sequence of the polypeptide in AA: use the three letter notation, e.g. Met-Ser-Pro-1. The figure above shows some of the more common modifications, such as phosphorylation (1), acetylation or methylation (2), adding sugars or lipids (3,4), or adding another polypeptide (5). There are many other possibilities as well.Find and label each of these on the diagram. How might these modifications affect the protein?