Question

2. Silk contains the repeating sequence (Gly-Ser-Gly-Ala-Gly-Ala)n. This sequence is present in beta strands that interact with each other. Considering just a single strand within a sheet, the Ser and Ala side chains will be
(on both sides of the sheet in a single repeat) (in first repeat, on one side; in the next repeat on the other side) (the answer depends on whether the strands are parallel or antiparallel) (on the same side of the sheet).

Tyr-51 His-113 N. NH 1 Trp-23 H -Н -- H4 ОН NH, 9- OI OI ен Asn-309 OI HHS -...Н НО НО Asp-50 Н Gly$46

4. The figure above shows the details of an enzyme substrate interaction. The substrate is shown interacting with enzyme on the left and on its own on the right. Only the R groups of residues that interact with substrate are shown; the polypeptide backbone of the enzyme is not shown.

4A. The red numbers indicate atoms in the substrate. Circle all that are correct.
i. Which atom or atoms have a + charge? (1) (2) (3) (4) (none of these)
ii. Which atom or atoms have a - charge? (1) (2) (3) (4) (none of these)
iii. Which atom or atoms have no partial charge? (1) (2) (3) (4) (none of these) iv. Which atom or atoms have a full + or – charge? (1) (2) (3) (4) (none of these)

4B. How many carbons does the substrate have? (3) (4) (5) (6) (7)

4C. The amino acids of the enzyme that interact with the substrate are shown. Five interactions are indicated by ovals. For each amino acid listed below, what is the strongest interaction with the substrate:

Asp-50: (hydrogen bond) (ion-dipole bond) (ionic bond) (hydrophobic interaction) (none of these). Gly-46: (hydrogen bond) (ion-dipole bond) (ionic bond) (hydrophobic interaction) (none of these). Asn-309: (hydrogen bond) (ion-dipole bond) (ionic bond) (hydrophobic interaction) (none of these). Tyr-51: (hydrogen bond) (ion-dipole bond) (ionic bond) (hydrophobic interaction) (none of these).

Answer 1

2. Silk fibre has antiparallel beta-strands of the sequence (Gly-Ser-Gly-Ala-Gly-Ala)n present in it.

In this the R-groups (-OH of Ser and -CH₃ of alanine), alternate up and down the strand and across the strands.

So, they are either both up in the first repeat or both down across the strands in the next repeat and so on.

Reference:Thierry Lefèvre, Marie-Eve Rousseau, Miche lPézolet, Protein Secondary Structure and Orientation in Silk as Revealed by Raman Spectromicroscopy, Biophy. journal.,Volume 92, Issue 8, 15 April 2007, Pages 2885-2895.

4. Enzyme-substrate interactions:

4A. i) None of these have positive charge.

ii) 1, 2 and 3 oxygen atoms have negative charge.

iii) 4 (H) doesn't have a partial charge.

iv) 2 and 3 have full negative charge.

4B. Substrate has 5 carbon atoms in total.

4C. Strongest interaction with each amino acid:

Asp-50: Ion-dipole interactions

Gly-46: none of these

Asn-309: H-bonding

Tyr-51: Hydrophobic interaction