1. For a free amino acid with an ionizable side chain. such as cystein. there ar

Question

1. For a free amino acid with an ionizable side chain. such as cystein. there are four posibve solution. Draw the two predominant species at pH 7.4 and using the pK, values listed in there are four possible-species in your textbook, determine the ratio of the concentrations for the two predominant species at p arine mussels, such as the blue mussel, M. edulis, attach to a variety of surfaces in shown environment by using a natural adhesive that is incredibly strong and durable. Research has that one of the proteins in the adhesive, Mytilus edulis foot protein I (Mefp-I), bonds to g wood, acids lalanine, P represents trans-2,3-cis-3.4-dihydroxyproline, and p" represents trans-4-hydroxy-L-proline) occurs of the amino concrete, and Teflon®. The major decapeptide consensus repeat, consisting of ARPSYP P TYK (in which P represents proline, Y represents 3,4-dihydroxypheny times in Mefp-1. Draw this 10 amino-acid peptide repeat sequence in its predominant form at 1.4. (Please refer to Table 3-1 in your textbook for common amino acid pÅ, values& the table below for uncommon amino acid pK, values) pk. pka trans-23-cis-3,4-dihydroxyproline NA ans-4-hydroxy-L-proling 3. Explain the probable effect(s) of the following amino acid replacements on the properties of a peptide. Consider size, hydrophobicity, polarity, charge, ete. a. b. c. d. e. changing a Phe to a Tyr changing a Gin to a Glu changing an Ala to a Val changing a Gly to an Ala changing a Ser to a Cys You have been asked to design a four-turn a helix that is destined to assemble into a three-helix in aqueous solution. Draw out the helical wheel projection of your prototype a- helix and select an amino acid sequence that would not only form an alpha helix-but would also self assemble into a stable three-helix bundle. Be sure to consider all the factors that affect helix stability in addition to the placement of hydrophobic residues 5. Several human genetic defects in collagen structure including osteogenesis imperfecta and Ehlers- mu) Danlos syndrome stem from a single glycine substitution in the a chain of one of the more than 30 a structural variants of collagen. Explain the structural basis of how/why a single glycine substitution can disrupt collagen structure/function. Hair splits most easily along its fiber axis, whereas fingernails tend to split across the finger rather than along it. Given what you know about the structure of keratin, what are the directions of the keratin fibers in hair and in fingernails? Explain your reasoning. 6. 1 Using the RCSB Protein Data Bank (PDB) database and the following : (a)i RCP, (b) RLB, (c) 2ZTA and (d) 20R8 For each protein: 7. Provide the protein name .Classify the protein secondary structure elements as: all a, all ßof, or + Identify if any of the following tertiary structural features are present; 4-helix bundle, leucine-zipper, an aß barrel, a -barrel, motif, or a Rossman fold ().

Explanation / Answer

Question 2-

First we need to calculate the isoelectric point (PI) of the amino acid 3,4 dihydroxyphenylalanine (Y). We use the following formula.

PI = (pKa1+ pKa2)/2

PI= (9.6 +13.4)/2

PI= 11.5

Now for the sequence AKPSYP’P”TYK, calculate the whole PI.

Peptide PI = Total PI of all amino acids/Total Numbers of amino acids

Peptide PI = (6+9.74+6.3+5.68+11.5+0+0+5.87+11.5+9.74)/10

Peptide PI = 6.63

Here we took PIs of two amino acids as zero because of their not known PIs. However, we are getting significant lower PI of peptide chain than 7.4 pH.

Now find out the cumulative PI of the two amino acids.

For amino acids trans 2,3 cis 3,4 dihydroxyproline and trans-4-hydroxy-L-proline, each have x PI value.

Again using the above formula of Peptide PI = Total PI of all amino acids/Total Numbers of amino acids

Peptide PI =(6+9.74+6.3+5.68+11.5+x+x+5.87+11.5+9.74)/10

We know that the actual PI that we need is 7.4. therefore, we take Peptide PI as 7.4

7.4= (66.3 + 2x)/10

74 = 66.3 + 2x

2x= 74 - 66.3

2x =7.7

x = 3.85

It means one amino acid must have the above PI value, which cannot be consider because normal proline has 6.3 pI. Therefore, one amino acid must be change. We can take aspartic acid D as a new amino acid because it has PI of 2.77 which on addition with one of the two amino acids P’ and P” can give demanded PI.

Therefore, the net Peptide sequence is

AKPSYDP’/P”TYK

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