Question

7. Amino acids are molecules with the general structure shown below, where R can be H or various groups of bonded atoms. The 20 different R groups reflect the 20 naturally occurring amino acids. Although amino acids overall are polar, their relative polarity and relative degree of interaction with other substances is governed by the R group. R 0. Amino acids bond together (like "chains") to form proteins, which exhibit complex 3-dimensional structures resulting from various folds, H twists, and turns of the amino acid "chains". These specific structures OH occur to provide very specific functions of the protein in an organism. HŇ I-0070 Ferritin is a protein that stores iron in its core as Fe+3 and releases the Fe as Fe+2 for use in reactions elsewhere in an organism. The iron as Fe+2 (technically in a more complicated form, but we'll treat it as a simple ion) travels to and from the protein core via two major channels, a 3-fold and a 4-fold channel, illustrated below J ? RA S 3-fold channel 4-fold channel . (substances enter through the central hole) The 3-fold channel is lined primarily with the amino acids aspartic acid and glutamic acid, illustrated below. The 4-fold channel is lined primarily with the amino acid leucine, also illustrated below. HIC CH: CH CH, CH2) 0 HN-C-C H2N-C- H OH Aspartic acid (Asp) Glutamic acid (Glu) Leucine (Leu) Lines 3-fold channel Lines 3-fold channel Lines 4-fold channel (Note: all of the O atoms in the above structures have 2 nonbonding electron pairs on them, and all of the N atoms have one nonbonding electron pair)

(a) Into which channel is Fe2+ most likely to travel? Briefly explain your answer by including the dominant interparticle force between it and the amino acid R groups that line the channel.

(b) Into which channel is O2 most likely to travel? Briefly explain your answer by including the dominant interparticle force between it and the amino acid R groups that line the channel.

(c) Suppose there is a region in a protein where a significant amount of H bonding occurs between R groups of amino acids. Which of the amino acids on the previous page do you expect to be present in such a region? Illustrate one possible H bonding interaction between R groups of the amino acid(s) you chose.

Answer 1

Answer 7a. Fe2+ most likely to travel into 3-fold channel. Now we explain here briefly our answer by including the dominant interparticle force between it and the amino acid R groups that line the channel as follwos:

The presence of polar amino acid like Aspartic acid and glutamic acid in 3-fold channel and the polarity of these hydrophilic moieties allows for favourable electrostatic interaction between Fe2+ ion and H2O as well as negatively charged, polar amino acid such as Asp-127 and Glu-130 present at the ferritin site where Fe2+ ion binds due to electrostatic force of attraction and attraction of opposite charges which favour Fe2+ ion binding whereas since 4-fold channel are lined with hydrophobic amino acid like leucine; there are no such force of attraction acting on Fe2+ ion thus it does not bind in 4 fold channel.

Answer 7b. O2 most likely to travel into 3-fold channel irrespective of 4-fold channel. Now we explain here briefly our answer by including the dominant interparticle force between it and the amino acid R groups that line the channel as follwos:

The presence of hydrophilic, polar amino acid like Aspartic acid and Glutamic acid in 3 -fold channel favours Fe2+ binding in 3-fold channel (and explanation is given above). As we know that Fe2+ is the site at which O2 binds so O2 binds more likely at 3-fold channel since 3-fold channel binds more Fe2+ and it will provide more oxygen binding site for its binding.

Answer 7c. As we suppose there is a region in a protein where a significant amount of H bonding occurs between R groups of amino acids. Those amino acids are glutamic acid - 130 and Aspartic acid -127 which we expect to be present in such a region. We have illustrated one possible H bonding interaction between R groups of the amino acid(s) I have chosen as follows in the form of pictorial representation.