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Biochemistry I: Problem Set #2 Please show all calculations, when applicable. Highlight final answers. A table with the three-letter and one-letter shorthand codes for amino acids is on the inside of the back cover of your textbook. These shorthand codes are also found Table 3-1, pg 77 (attached at the end of the problem set) 1. A peptide has the following sequence: NH 2 -Ser-Arg-Phe-Ala-Leu-His-Asp-Gly-COOH a. Approximately what net charges would you expect on the peptide at pH values of 1, 5, 7 and 11, respectively? To solve, fill out the chart below. At each pH, please show the charges on each relevant group in the peptide. pK a values for common amino acids are found in Table 3-1, pg 77, in your text (and at end of PS). (6 pts) b. At what pH would you expect this peptide to be the least soluble? Why? (2pts) NH 2 Ser Arg Phe Ala Leu His Asp Gly COOH Net charge ↓ pKa → pH =1 pH = 5 pH = 7 pH =11 2. A typical transmembrane protein will have a bundle of alpha helices running across the width of the membrane. This requires each α-helix to be about 30 angstroms long. (3pts) a. How many residues would you expect this helix to have? b. How many turns does this helix have? c. The typical residue in an α-helix is involved in two H-bonds. How many H-bonds are present in this helix?
3. You are performing site-directed mutagenesis to test predictions about which residues are essential for a protein’s function. For each pair of amino acid substitutions listed below, which substitution would you expect to disrupt protein structure the most? Explain. (3 pts) a. Val replaced by Ala or Phe b. Lys replaced by Asp or Arg c. Gln replaced by Glu or Asn d. (1 bonus) Pro replaced by His or Gly Answer:u 10/2020
4. For each peptide listed below, explain why it would or would not form an α helix. (3pts) a. QEASVKMAVDNSG b. SEDNFGAPKSILW c. CKRGNRKIVLETY 5. Hair grows at a rate of 15 to 20cm/year. All this growth is concentrated at the base of the hair fiber, where α-keratin filaments are synthesized inside living epidermals cells and assembled into rope-like structures. The fundamental structural element of α-keratin is the α-helix. Based on the dimension of a helix (residues per turn, and the length of the rise), calculate the following: Assuming that the biosynthesis of α-helical keratin chains is the rate-liming factor in the growth of hair, calculate the rate at which peptide bonds of α-keratin are synthesis (peptide bonds per second) to account for the observed yearly growth of hair. YOU MUST SHOW YOUR WORK. a. Report the following dimensions for and α-helix (1pt) i. _____ residues per turn. ii. Rise = ______ nm per turn b. Calculate the rate of kertain synthesis (peptide bonds/sec). SHOW YOUR WORK. (2pt) 10/2020
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6. Solving the sequence of an oligopeptide from sequence analysis: consult Table 3-6 and the charts provided at the end of PS. (6 pts) An octapeptide consisting of 1 Asp, 1 Lys, 2 Met, 1 Phe, 1 Pro, 1 Ser, and 1 Tyr residue was subjected to sequence studies. The following was found. Note: when fragment sizes are given, they are listed in order of decreasing size and this does not necessarily indicate the order the fragments are found in the intact peptide. a. Edman sequencing of the intact octapeptide yielded b. A second round of Edman sequencing yielded , c. Upon treatment with carboxypeptidases A, B, and Y, only carboxypeptidase Y had any effect. d. Staphylococcal protease yielded a pentapeptide and a tripeptide e. Trypsin treatment gave two tetrapeptides f. Cyanogen bromide treatment gave two tripeptides and a dipeptide. What is the amino acid sequence of this octapeptide? For full points, list each hint above (a-f) and tell me how that informs your octapeptide sequence. For instance, include as much info as you know about position, and amino acid identity, based on the enzyme mentioned. 10/2020
10/2020
10/2020
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Bonus (1 pt). What fragments would be generated by a chymotrypsin digest of the octopeptide? 10/2020
10/2020
For Problem 6. Source: Garrett & Grisham, Biochemistry , 7 th ed, 2016 Carboxypeptidases: enzymes which cleave amino acid residues from the C-termini of polypeptides in a successive manner. They have varying specificity, some only cleaving C- terminal peptide bonds for particular C-terminal residues. Carboxypeptidase A: hydrolyzes C-terminal peptide bond for any C-terminal residue except Pro, Asp, Glu, Arg, and Lys. Carboxypeptidase B : only effective when Arg or Lys are C-terminal residues Carboxypeptidase Y: broad specificity; cleaves off any C-terminal residue. 10/2020
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