7. What do you think holds together the various secondary structural elements in aparticular three-dimensional pattern? (Hint: Look back at Figure 4 - what issticking out from the sides of the a-helices and B-strands?)glutamic acidH.-N-C-C-ČH2CH2H.CH3CHa-HCH3CHCHH-NvalineCH2CH2HvalineCH2alanineCH2онlysineFigure 4-4 Essential Cell Biology 3/e (© Garland Science 2010)Figure 6. Three examples of bonding interactions that stabilize the tertiarystructures of proteins (indicated by arrows A, B,and C). cCopyright 2013 from EssentialCell Biology, 4th Edition by Alberts et al. Reproduced by permission Garland Science/ Taylor &Francis LLC.CH2CH2SHSHCH2CH2OXIDATIONCH2SHCH2REDUCTIONSHCH2CH2Figure 4-26 Essential Cell Biology 3/e (O Garland Science 2010)Figure 7. Disulfide bonds within proteins can form (left-pointing arrow) or bebroken (right- pointing arrow), depending on their chemical surroundings(oxidative or reducing). Copyright 2013 from Essential Cell Biology,4th Edition by Albertset al. Reproduced by permission of Garland Science/ Taylor & Francis LLC. 4. Do the "Bond X" bonds in Figure 4 involve atoms in the amino acid R groups or inthe 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 primarysequence of the polypeptide, while the different arrows may be formed from aminoacids that are removed from each other in the primary sequence. Each arrow isreferred to as a B-strand, and the structure formed through interaction of the B-strandsis the B-sheet. In a complete protein, other segments of the protein would connect thedifferent B-strands.6. Do the "Bond X" bonds in the B-sheet connect atoms from the same B-strand orneighboring strands?TERTIARY STRUCTURE(A)(B)(C)Figure 4-17 Essential Cell Biology 3/e (o Garland Science 2010)Figure 5. Examples of the arrangement of a-helices and B-sheets in foldedprotein domains. Copyright 2013 from Essential Cell Biology, 4th Edition by Alberts et al.Reproduced by permission of Garland Science/ Taylor & Francis LLC.Figure 5 shows three examples of how secondary structure elements can be arrangedin relation to one another in the functional, folded form of a complete protein or onecompact portion of a protein. The overall three-dimensional shape (or conformation)of a protein is its tertiary structure.

Answered: What do you think holds together the…

What do you think holds together the various secondary structural elements in a particular three-dimensional pattern? (Hint: Look back at Figure 4 - what is

Human Anatomy & Physiology (11th Edition)

11th Edition

ISBN:9780134580999

Author:Elaine N. Marieb, Katja N. Hoehn

Publisher:Elaine N. Marieb, Katja N. Hoehn

Chapter1: The Human Body: An Orientation

Section: Chapter Questions

Problem 1RQ: The correct sequence of levels forming the structural hierarchy is A. (a) organ, organ system,...

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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
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 F
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 PH35? Provide 3 reasons to justify your answer.
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 RAIMEILKVDAQFN
4. 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…
4. 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-ETATKAELLAKYEATHK-CONH2 (а) 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
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-
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.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
3b) Both a-helical 2° structure and b-pleated sheet 2° structure result from the same type of interaction; briefly explain in your own words why you might observe an a-helix in one region of a protein and a b-pleated sheet in another region of the same protein.
1. Which of the following structures could the following polypeptide form? And why? The non- polar amino acids are italicized. Gly-Leu-Asp-Glu-lle-Ala-Lys-Ser-Val-Arg-His-Phe-Cys-His-Ala- lle A. A hydrophobic alpha helix B. An amphipathic a- helix C. A hydrophilic a helix D. A hydrophobic B sheet E. An amphipathic B sheet Where would you expect to find the N-term and C-term amino acids in the polypeptide?
5. Indicate whether the following amino acid residues would be more likely to be found on the surface or in the interior of a folded protein: Leu, Arg, Phe, Asn, and Glu. Give your reasoning for each case (diagrams not required).