3. Amino Acid Sequence and Protein Structure Our growingunderstanding of how proteins fold allows researchers to makepredictions about protein structure based on primary amino acidsequence data. Consider the following amino acid sequence.135678 910Ile - Ala - His - Thr - Tyr - Gly - Pro - Phe-Glu – Ala--11121314151720Ala - Mat - Cys- Lys - Trp - Glu-Ala-Gln-Pro - Asp-1618 192122232425262728Gly - Met-Glu - Cys - Ala - Phe - His - Arg(a) Where might bends or ß turns occur?(b) Where might intrachain disulfide cross-linkages be formed?(c) Assuming that this sequence is part of a larger globular protein,indicate the probable location (external surface or interior of the protein)of the following amino acid residues: Asp, lle, Thr, Ala, Gln, Lys. Explainyour reasoning.

Proteins are made up of amino acids that are linked together by peptide bonds. The simple linear…

Answered: (a) Where might bends or 3 turns occur?…

Biochemistry

9th Edition

ISBN:9781319114671

Author:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Publisher:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Chapter1: Biochemistry: An Evolving Science

Section: Chapter Questions

Problem 1P

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B) An aqueous solution (pH ~7) containing mixture of three amino acids; glycine (G), arginine (R) and glutamic acid (E), was dropped onto center of a solid matrix (e.g chromatographic paper) which is incorporated in an electrical circuit (a). After applying electrostatic potential, the aminoacids are separated as shown in b. Determine amino acids that are labeled as 1, 2 and 3. a) DC Power Supply (OFF) b) DC Power Supply (ON) Solid matrix Solid matrix Cathode Anode Cathode Anode buffer buffer buffer buffer Sample containing amino acids G, R, E
What does this statement mean: "Upon folding of a protein many main chain amides replace their hydrogen bonds to water for those with other amide bonds" Is this true for alpha helix in proline racemase? and is there a pattern?
4) For various amino acid pairs (for example: F to A, E to R, D to N, V to L, S to W), ask yourself: a) Based on what you know about the chemical properties of the side chains, what effect would you expect on the stability of the protein if you mutated one residue of the pair into the other in the interior of the protein? What forces might have an impact on this change (ie: what types of interactions would you expect that amino acid to be involved in?) How would your answer change if the amino acid were located on the surface of the protein? b) c)
Draw a structural formula for a nucleoside composed of the following. Q.) a-d-Ribose and adenine
A tetrameric protein dissociates into dimers when the detergent sodium dodecyl sulfate (SDS) is added to a solution of the protein. But the dimers are termed SDS-resistant because they do not further dissociate into monomers in the presence of the detergent. What intermolecular forces might be acting at the dimer-dimer interface? Are the intermolecular forces acting at the monomer-monomer interface different? Explain.
Valine is an amino acid with a nonpolar side chain and serine is one with a polar side chain. Draw the two amino acids.(a) Why is the side chain for valine nonpolar, whereas the side chain for serineis polar?(b) Which amino acid has a hydrophilic side chain and which has a hydrophobic sidechain?
Consider the peptide in the image and answer the following questions.
What are the functions of thesurprisingly large amount of unfoldedpolypeptide chain found in proteins?
Which of the following statements are False? (i) Parallel b-sheets characteristically distribute hydrophobic side chains on both sides of the sheet, and antiparallel B-sheets are usually arranged with all their hydrophobic residues on one side of the sheet. (ii) Planarity of the peptide bond means that no rotation occurs about the N-Ca bond while rotation is allowed about the C(O)-N and Ca-C(O) bonds. (iii) Silk fibers consist of fibroin proteins consisting of alternating A and G or S residues. (iv) If an aspartic acid residue were present in the interior of a globular protein, it would most likely be deprotonated and thus negatively charged.
Identify and encircle the peptide bonds in this polypeptide (Ala-Leu-Glu-Ala-Asn-Asp-Arg-Ala)?
How do the following noncovalent interactions help to stabilize the tertiary and quaternary structure of a protein? Give an example of a pair of amino acids that could giverise to each interaction.(a) Hydrophobic interactions(b) Salt bridges (ionic interactions)
Glutamine is an amino acid that has -CH₂-CH2-CO-NH₂ as its R group. The R group of the amino acid isoleucine is -CH2-CH-(CH3)2. If these amino acids were in a globular protein in aqueous solution, where would they most likely be? O Both glutamine and isoleucine would be in the interior and on the exterior of the globular protein. O Glutamine would be in the interior, and isoleucine would be on the exterior of the globular protein. O There isn't enough information O Both glutamine and isoleucine would be on the exterior of the globular protein. O Isoleucine would be in the interior, and glutamine would be on the exterior of the globular protein.

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