tion 1Predicting Secondary Structure Which of the following peptides is more likely to take up an -helical structure, and why? (a) LKAENDEAARAMSEA (b) CRAGGFPWDQPGTSN
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Question 1Predicting Secondary Structure Which of the following peptides is more likely to take up an -helical structure, and why?
(a) LKAENDEAARAMSEA
(b) CRAGGFPWDQPGTSN
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- TERTIARY STRUCTURE (A) (B) (C) Fg Eet Galand Sen 20e Figure 6. Examples of the arrangement of a-helices and B-sheets in folded protein domains. Copyright 2013 from Essential Cell Biology, 4th Edition by Alberts et al. Reproduced by permission of Garland Science/ Taylor & Francis LLC. Figure 6 shows three examples of how secondary structure elements can be arranged in relation to one another in the functional, folded form of a complete protein or one compact portion of a protein. The overall three-dimensional shape (or conformation) of a protein is its tertiary structure. • What do you think holds together the various secondary structural elements in a particular three-dimensional pattern? (Hint: Look back at Figure 5 - what is sticking out from the sides of the a-helices and B-strands?)Question What is the net charge for the following peptide at pH = 1? Ser-Trp-Arg-Gln-Glu-His-Lys-AspTABLE 3-1 Properties and Conventions Associated with the Amino Acids pk, values Amino acid Phenylalanine Tyrosine Tryptophan 5.66 5.48 9.59 5.89 Abbreviation/ symbol 6.14 Phe F Tyr Y Trp W pk, M, (-COOH) 165 181 204 . 1.83 2.20 2.38 Using the table 3-1, calculate the pl of Tyrosine. Hint: Consider the structure and overall charge of the molecule between each pka. pK₂2 (-NH) 9.13 9.11 9.39 PKR (R group) 10.07
- Question What is the net charge for the following peptide at pH = 7 (neutral pH)? Ser-Trp-Arg-Gln-Glu-His-Lys-AspWhich of the following peptides is more likely to take up an α-helical structure, and why?(a) LKAENDEAARAMSEA(b) CRAGGFPWDQPGTSNHis-Met-Asp-Tyr-Phe-Ser Calculate an approximate pI (isoelectric point) for this peptide. Please use the pKa's listed within Table 3-1 of Lehninger. Show and/or explain all your work; you must be very clear about WHY you use particular pKa's in your calculation.
- Question 13 About the protein structure: |A The primary structure of a protein corre- sponds to its sequence and is always writ- ten from its C-terminus to its N-terminus. B The secondary structures of a protein are formed by hydrophobic bonds between the different atoms of the main chain. C The quaternary structure of a protein in- volves only covalent bonds established be- tween the different peptide chains. D The tertiary structure of a protein in- volves, among other things, hydrogen and ionic bonds between the side chains of the different amino acid residues. E None of the above statements is right.Question: 1. Identify the amino acids in this peptide 2. Which amino acid sidechains are protonated at physiological pH 3. What is the overall charge of this peptide H₂N O NH₂ IZ ZI O OH IZ OH OHOne round of Edman degradation of the peptide: H2N- Gly-Arg-Lys- Phe-Asp- COOH which of the following structures would result when add cyanogen bromide ? A) H2N-Gly-Arg-COOH + H2N–Lys-Phe- Asp-COOH B) H2N-Arg-Lys-Phe-Asp-C0OH+ Gly C) H2N- Gly-Arg-Lys-Phe-Asp- COOH D) H2N-Gly-Arg-Lys-Phe-COOH + Asp E) H2N-Gly-Arg-Lys-COOH + H2N-Phe-Asp-COOH
- Protein-4YU4 is given, choose a part of it (containing at least 30 amino acid residues), find the amino acid sequence (sequence in it), identify what functional groups the amino acid substitutes contain (carboxyl group and 2-position the Nitro group will form amide bonds, forming the covalent basic structure of the protein). What different interactions can occur between these functional groups? How will it relate to the spatial structure of the protein?Need help The β chains of HbA and HbS were treated with trypsin, and the sequence of the N-terminal tryptic peptides are as given below. Do these peptides separate from each other in an electric field if the pH is 7.0? Explain in detail the reasoning behind your answer and include your calculations for the charge of each peptide in your answer. HbA: Val-His-Leu-Thr-Pro-Glu-Glu-Lys HbS: Val-His-Leu-ThrGlycine is a highly conserved amino acidresidue in proteins (i.e., it is found in the same position in theprimary structure of related proteins). Suggest a reason why thismight occur.