Provide one or two x Describe three of the important Seatures sennences for eash
ID: 213105 • Letter: P
Question
Provide one or two x Describe three of the important Seatures sennences for eash eaeure, G points) eatures of a B sheet polyperptide structure. ap g Which amino acids may alter the directions of polypeptide chains and interrupt What is this structure called and how many amino acids are associated with this secondary structure? structure? (3 points) ine peptides, Linus Pauling and Robert Corey found that the C-N bond in othe pepide link is intermediate in length (1.32 A) between a tbypical C-N single bond (1.49 A) and a i What does the length of the C-N bond in the peptide linkage indicate about its strength and its 1o. In x-ray studies of erystall C-N double bond (1.27 A) (3 points) bond onder (i.e, whether it is single, double, or triple)? b. What do the observations of Pauling and Corey tell us about the ease of rotation about the C-N peptide bond? Draw the resonance form of the peptide bond. Indicate the bonds that define the phi and psi torsion angles. c. ?t rl 11. Which type of non-covalent interaction is likely to be responsible for stabilizing amyloid fibril? What secondary structure is mainly associated with these interactions? (3 points) 12. Why is silk fibroin so strong, but at the same time so soft and flexible? (3 points)Explanation / Answer
ANS 8. Three features of beta sheet polypeptide structure:
ANS 9.
Polypeptide chains can change direction by making reverse turns and loops. Alpha helices and beta strands are connected by these turns and loops. Most proteins have compact, globular shape owing to reversals in the direction of their polypeptide chains, which allows the polypeptide to create folds back onto itself.
The alpha-helix is taken as the default structure, thus amino acids which destabilizes alpha-helices are often found in beta-pleated sheets or loops and turns. For instance, valine, threonine, and isoleucine destabilizes the helix because of branching of the beta carbon. These three amino acid residues are more often found in beta-pleated sheets, where their side chains will lie in a separate plane than the main chain. There are also amino acid residues like Proline has a restricted phi angle of ~60 degrees and no NH group, all due to the fact that it is cyclic. This will disrupt both alpha-helices and beta-pleated sheets, thus is found mostly in loops and turns. Glycine which, according to its small size, it tends to avoid alpha-helices and beta-sheets also. The folding relies on chemical interactions between the side chains so the surrounding amino group interactions also affect the tendency of folding. These tendencies are reflected in the frequencies of secondary structure for individual amino acids.
The relative tendencies of secondary structures for particular amino acids are listed below:
alpha-helix: Glu, Ala, Leu, Met, Lys, Arg, Gln, His
beta-sheet: Val, Ile, Tyr, Cys, Trp, Phe, Thr
turns and loops: Gly, Asn, Asp, Pro, Ser
example: Myoglobin -ribbon tracing the path of the polypeptide chain. The polypeptide forms eight helical segments as helix A through H. The presence of "breaker" amino acids at strategic locations interrupts the helix, allowing the polypeptide to change direction and to fold up into a more compact form. The breaker amino acids are Pro, Gly, Ser, Asn, Asp (plus Thr, an alpha breaker, but relatively common in beta sheets).
ANS 10
A] Bond order and bond length indicate the type and strength of covalent bonds between atoms. Bond order and length are inversely proportional to each other: when bond order is increased, bond length is decreased.
B] Pauling and Corey concluded that the peptide C-N bonds are unable to rotate freely because of their Partial double-bond character. But with the help of Ramachandran plot, ease of rotation can be done in C-N peptide bond. Rotation is permitted about the N-C and the C -C bonds. By convention the bond angles resulting from rotations at C are labeled (phi) for the N-C bond and (psi) for the C-C bond. Both and are defined as 1800 when the polypeptide are in its fully extended conformation and all peptide groups are in the same plane. and have any value between +180 and -1800, but many values are prohibited by steric interference between atoms in the polypeptide backbone and amino acid side chains. The conformation in which both and are 00 is prohibited for the reason; this conformation is used as a reference point for describing the angles of rotation. Allowed values for and are graphically revealed when is plotted versus in a Ramachandran plot.
ANS 11.
As proteins aggregate to form amyloid fibers, their secondary structure changes from its native form to cross-beta-sheet. As like-charged protein molecules aggregate, the total charge of the colloidal sphere increases until it repels additional monomers from coming close enough to bind, limiting the size of the colloidal particle. Energy analysis and X-ray diffraction data suggests that the aggregation of multiple protein monomers onto the growing colloid drives their misfolding into hairpin loops. These loops stack together to form a U-shaped trough which initially adopts a cross-alpha-sheet structure with a strong dipole moment and by charge-dipole interactions, the colloidal spheres aggregate into a linear chain. The peptide strands are oriented perpendicular to the direction of the dipole of each sphere and which states and evolves into the mature fiber. The cross alpha-sheet then evolves into the thermodynamically more stable cross beta-sheet.
ANS 12
Silk Fibroin is an insoluble protein present in silk created by spiders. Silk in its raw state consists of two main proteins, sericin and fibroin.
Fibroin protein consists of layers of antiparallel beta sheets. Its primary structure mainly consists of the recurrent amino acidsequence (Gly-Ser-Gly-Ala-Gly-Ala)n. The high glycine (and, to a lesser extent, alanine) content allows for tight packing of the sheets, which contributes to silk's rigid structure and tensile strength.
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