Question

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3) Protein structure and amino acid side chains a) Give examples of the types if attractive forces found between the side chains of the following amino acid residue pairs at pH 7.4 00 Leu and Phe (ii) Two Cys (ii) Asp and Thr (iv) Asp and Arg b) Of the 4 levels of protein structure, which ones are stabilized by interactions between amino acid side chains? c) Identify the two regular types of secondary structures and describe the key difference between the amino acid side chain position in these structures.

Answer 1

3.a) [i] The type of interaction occurring between Leucine and Phenylalanine at pH 7.4 is primarily hydrophobic interactions between the alkyl side chain of leucine and the bulky benzyl group of phenylalanine

[ii] Two cysteine molecules will interact to form a di-sulphide linkage and the resultant will be a cystine molecule.

[iii] Electrostatic interactions can occur between aspartate (which will have a negative charge at pH 7.4) and threonine's hydroxyl group.

[iv] Electrostatic interactions can occur between Aspartate and arginine at pH 7.4

b) Secondary and tertiary structures of amino acids are stabilised by interactions between amino acid side chains.

c) Two types of secondary structures are alpha helix and beta sheets.

In alpha helix, the side chains are placed out of the helix in a plane similar to that of the helix for the formation of stabilising bonds whereas in beta sheets the side chains are placed out of the structure but in a plane perpendicular to that of the beta-sheet plane.