Questions and answers on aminoacid and proteins set 5

Questions and answers on aminoacid and proteins set 5

Why does the α -helix form more readily than many other possible conformations?

  • It makes optimal use of internal hydrogen bonds.
  • The structure is stabilized by a hydrogen bond between the hydrogen atom attached to the electronegative nitrogen atom of a peptide linkage and the electronegative carbonyl oxygen atom of the fourth amino acid on the amino-terminal side of that peptide bond.
  • Within the α -helix, every peptide bond (except those close to each end of the helix) participates in such hydrogen bonding. Each successive turn of the α -helix is held to adjacent turns by three to four hydrogen bonds.
  • All the hydrogen bonds combined give the entire helical structure considerable stability.

Why Glycine occurs infrequently in α-helices?

Glycine has more conformational flexibility than the other amino acid residues. Polymers of glycine tend to take up coiled structures quite different from an α-helix.

Why negatively charged amino acids are often found near the amino terminus of the helical segment?

  • A small electric dipole exists in each peptide bond.
  • These dipoles are connected through the hydrogen bonds of the helix, resulting in a net dipole extending along the helix that increases with helix length.
  • The four amino acid residues at each end of the helix do not participate fully in the helix hydrogen bonds.
  • The partial positive and negative charges of the helix dipole actually reside on the peptide amino and carbonyl groups near the amino-terminal and carboxyl-terminal ends of the helix, respectively.
  • For this reason, negatively charged amino acids are often found near the amino terminus of the helical segment, where they have a stabilizing interaction with the positive charge of the helix dipole; a positively charged amino acid at the amino – terminal end is destabilizing.
  • The opposite is true at the
    carboxyl – terminal end of the helical segment.

Does protein function depend on the linear sequence of amino acids?

  • The function of a protein is directly dependent on its three dimensional structure.
  • But the  sequence of amino acids in the protein polymer determines the three-dimensional structures of a protein.
  • Change in aminoacid sequence in the primary structure in turn affects the folding and 3D structure and hence the proteins function too.

 

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