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- 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. 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.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
- 4. Do the "Bond X" bonds in Figure 4 involve atoms in the amino acid R groups or in the polypeptide "backbone"/ "main chain" atoms? 5. Given Your Answer To “b," are each of the following statements True or False? Be able to explain your reasoning. o Only very specific primary sequences can form a-helices and B-sheets. o Many different primary sequences can form a-helices and B-sheets. Each arrow depicted in Figure 4D represents consecutive amino acids in the primary sequence of the polypeptide, while the different arrows may be formed from amino acids that are removed from each other in the primary sequence. Each arrow is referred to as a B-strand, and the structure formed through interaction of the B-strands is the B-sheet. In a complete protein, other segments of the protein would connect the different B-strands. 6. Do the "Bond X" bonds in the B-sheet connect atoms from the same B-strand or neighboring strands? TERTIARY STRUCTURE (A) (B) (C) Figure 4-17 Essential Cell Biology 3/e (o…5. Bread contains mixture of polypeptides known as gluten. This polypeptide has two types which are gliadins and glutenins. If both polypeptides have presence of short a-helix sections because of high proline content, what level of protein structure is being depicted? 5a. If intermolecular bonds form between glutenin and gliadin, what level of protein structure is being depicted? 5b. During analysis, hydrophobic amino acids (i.e., glutamine and proline) were not found on gluten protein surfaces. In this case, what level of protein structure is being shown?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. A. Briefly discuss the four levels of structure in proteins. Knowing that the 3-dimensional shape of a protein is important to its function, discuss on a qualitative basis whether the changes below will likely alter the function of a protein, justifying your answer with why or why not. B. What would happen to a protein's functionality if a serine residue were replaced with threonine? C. What would happen if serine were replaced with leucine? D. What would happen if serine were replaced with cysteine? E. What would happen if aspartic acid were replaced with tryptophan in the part of the protein (an enzyme) that serves as an active site to catalyze a reaction? F. What would happen if aspartic acid were replaced with tryptophan in a non-active site?4. What is the net charge (approximately) on the polypeptide shown below at pH 12.5? Lys - Arg - Val-Cys - Glub. What is the difference between the 3' and the 5' ends of a nucleotide chain? C. Do the chains run the same way? d. How are the chains connected? e. Which bases bond to each other? f. What kinds of bonds hold the chain together? 3. What are the main differences between RNA and DNA? 4. Distinguish between the structure of pyrimidines and purines. Explain why adenine bonds only to thymine. 5. Name the five nitrogenous bases in the table below, and put an X in the correct column for each base. Then indicate if the base if found in DNA (D), RNA (R), or both (B) hp
- 16) Which of the following occurs when proteins fold? O The protein adopts Its lowest energy state form O Most of the non-polar and hydrophoblc residues are found burled in the proteln O The charged residues are found on the outside of the protelin O Secondary structural elements form O All of the above 17) Which of the following is NOT true about an a-helix? O The side chains extend radially outward from the helix axis DRis held together primarly by hydrogen bonds Ot usually involves multiple polypeptide chains O The peptide backbone is on the inside of the helix1. 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…