3. The primary amino acid sequence of a stretch of polypeptide is Asp-Glu-Pro- Lys-His-Arg. Would you expect this portion of the polypeptide to form an alpha helix at pH=5? Provide 3 reasons to justify your answer.
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- 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. Consider the following α helix from myoglobin at pH 7. Gln-Gly-Ala-Met-Asn-Lys-Ala-Leu-Glu-His-Phe-Arg-Lys-Asp-Ile-Ala-Ala-Lys-Tyr(a) Label amino acids in the polypeptide above as follows: p for polar and uncharged, np for non polar, – for negatively charged, and + for positively charged.(b) How many complete turns are there in this helix?(b) Which side chains are likely to be on the side of the helix that faces the aqueous solvent? Why?(c) Which side chains are likely to face the interior of the protein? Why?1.Draw these phosphorylated structures as they would be connected in a polinucleotide (e.g.RNA) in the order A-B. / Show how they combine to form the polynuleotide (i.e. only the end product). Show at any one of these structures where the glycosidic bond occurs 2.Sanger sequencing revealed the sequence of an oligonucleotide to be: d-AGATGCCTGACT. Draw a diagram of the gel banding pattern post capillary electrophoresis i.e. where on the gel would the fragments feature
- 2. The mature form of TEM-1 ß-lactamase, an enzyme of 290 amino acid residues that hydrolyzes penicillin antibiotics. The protein has the following polar amino acid side chains: 18 Arg; 11 Lys; 6 His; 4 Tyr; 16 Asp; 20 Glu; 8 Asn; 5 Gln. Approximate pKa values 1.5 Arginine 12.5 Lysine 10.0 Histidine 6.5 OD 280nm Tyrosine 10.0 Aspartate or Glutamate 4.0 Terminal NH3+ 8.0 Terminal COOH 4.0 0.0 A 0.01 0.10 KCI B Volume (mL) The chromatogram above shows a typical result in the purification of TEM-1 ß-lactamase overex- pressed in E. coli cells. The protein is eluted from an anion exchange column at pH 6.25 with an increasing gradient of KCI. Fraction A is shown to correspond to native enzyme. Since Fraction B has the same amino acid sequence for the first 10 residues, the conclusion is that this fraction represents enzyme in which side chains of glutamine or asparagine residues have been hydrolyzed (deamidated). (a) ( ) What is the isoelectric point of the native enzyme? (b) ( ) Compared to…2. The mature form of TEM-1 ß-lactamase, an enzyme of 290 amino acid residues that hydrolyzes penicillin antibiotics. The protein has the following polar amino acid side chains: 18 Arg; 11 Lys; 6 His; 4 Tyr; 16 Asp; 20 Glu; 8 Asn; 5 Gln. Approximate pKa values 1.5 Arginine 12.5 Lysine 10.0 Histidine 6.5 OD 280nm Tyrosine 10.0 Aspartate or Glutamate 4.0 Terminal NH3+ 8.0 Terminal COOH 4.0 0.0 Α - 0.01 0.10 KCI B Volume (mL) The chromatogram above shows a typical result in the purification of TEM-1 ß-lactamase overex- pressed in E. coli cells. The protein is eluted from an anion exchange column at pH 6.25 with an increasing gradient of KCI. Fraction A is shown to correspond to native enzyme. Since Fraction B has the same amino acid sequence for the first 10 residues, the conclusion is that this fraction represents enzyme in which side chains of glutamine or asparagine residues have been hydrolyzed (deamidated). (a)( ) What is the isoelectric point of the native enzyme? (b)( ) Compared to…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 *** R
- 2. Using the standard 3.6 amino acids per turn (360°) and the helical wheel below, plot each sequence on a helical wheel. Circle the hydrophobic residues and draw a square around the hydrophilic residues. Clearly indicate which of the 4 sequences creates an amphipathic helix where one side is buried on the inside of the protein and the other is exposed to water. Explain why the peptide you chose is the correct one and why the other 3 are incorrect. CRAAPNRKIVLETY SIEPDANFRACISLW EKATVEMAVRNSA RAIMEILKVDAQFN3) You are working on a protein with the following sequence in an area of interest. -Asp-Leu-Leu-Gln-Glu-Glu-Asp-Glu-Ser-Arg a. The current structure, solved at pH 7.4, of this segment has an alpha helix that is disrupted a er the Gln. Why might the alpha helix stop at this residue? b. This protein is involved in Lysosomes in vivo. The secondary structure of this region is expected to change into a complete alpha helix. Why might this change into a complete helix? ( Hint: Lysosomes are acidic!)1. Explain why the primary structure sequence -Lys-Leu-Trp-Asp- may promote a-helix formation while the sequence -Lys-Leu-Trp-Arg- may inhibit it.
- 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).1. If you were to write the amino acid sequence of the polypeptide segment using one-letter abbreviations, the first two letters in the sequence would be ___. Note: For the tripeptide valylglycyltryptophan, its sequence in one-letter abbreviations will be written as VGW.Choices: EA DA AG AH GA 2. If this segment were to form an ?α-helix, the oxygen atom inside the red box will hydrogen bond with which of the indicated atoms? Write the letter pointing to the atom. [hbond_partner]Choices: A B C D E F4. A polypeptide comprised of 17 amino acid res- idues with the sequence on the right is ob-served by spectroscopic methods to undergo transitions from an a-helix conformation to a B-sheet as a function of pH and concentration. The acetyl and carboxamide groups are attached covalently to deri- vatize the N- and C-terminal residues, respectively, to avoid charge effects of the end groups. CH3CO-ΤAΤΚΑE LLAKYEATΗK-CONH2 (a) ( amino acid residues. Write the sequence of this polypeptide with corresponding 3-letter abbreviations for the (b) At pH < 4 the polypeptide forms an a-helix. (i) ( the helix? and (ii) (: · with respect to the positive and negative ends of the macrodipole? ) What is the direction of the macrodipole of | Are the charges on the N- and C-terminal residues stabilizing or de-stabilizing (c) (* stabilize the helical conformation. What are the most likely protonation states of the side-chains that provide a-helix stabilizing interactions? Use the helical wheel (at the back…