The amino acid that is often used as a tag (in a run of 6-8 of this amino acid in a row) for protein purification, at pH 5.0. Discuss the significance of the Ramachandran plot. Contrast the conformational states of Gly and Pro in proteins to those of other amino acid residues.

At which pH would the peptide with the amino acid sequence 'KEYHR' be found in an IPG (Immobilized pH gradient) strip after successful isoelectric focusing. Show calculation. lonizable groups Alpha amine group of K Side chain group of K Side chain group of E Side chain group of Y Side chain group of H Side chain group of R Alpha carboxylic acid group of R pka 8.95 10.53 4.25 10.07 6 12.48 2.17

Suppose you have a solution of a protein, which contains a specific Tyr residue that has an actual (measured) pKa of 8.8. The protein binds a ligand by several noncovalent interactions, one of which is a hydrogen bond in which the Tyr phenolic hydroxyl group must serve as a hydrogen bond donor. Calculate the percentage of the protein molecules in which that tyrosyl residue's phenolic hydroxyl group could serve as a hydrogen bond donor at pH 8.5

Titration curve of an unknown amino acid The graph below shows a curve, which was obtained following titration of an unknown amino acid. Include a suitable descriptive title stating the identity of the unknown amino acid Use rectangles to precisely outline the regions in the graph where ionisable groups show buffering activity (base/acid ratio 1:10 to base/acid ratio 10:1); clearly associate the name of the ionisable group with the buffering regions; indicate within the graph all observable titration mid-points and all observable titration end-points and indicate estimates of the pKa of the three functional groups (do not provide pka values from the literature, you need to read the pka from the titration curve provided). Note that it is not possible to estimate the pka with more than one decimal precision due to limited resolution of the shown graph.

Explain the Rf value obtained on the basis of the structure of amino acids use. Explain in 1-3 sentence only.

Do not give handwriting solution.

How does a protein 'know' how to fold into its native conformation and in general why is folding fast (ie. faster than trial - and - error process - recall levinthals paradox)? Breiefly explain using proper terminology.