Please be reasonable. Limit your responses to a reasonable length, while showing
ID: 525722 • Letter: P
Question
Please be reasonable. Limit your responses to a reasonable length, while showing your work and giving references where necessary. Use your own words in answering these questions. If you google something and use that answer without specifying it as a reference (which is OK, as long as you do this) you will receive a zero for that answer due to plagiarism (1) If you change the structure of a small molecule, and the Delta G degree of protonation of the molecule changes by -2.94 kcal/mol, what happens to the pK_A? (2) In a study of the nonredundant subset of the PDB, Lovell et al. found that of the 1480 leucine residues present on elements of secondary structure, 836 were on alpha helices and 644 were on beta sheets. (a) Use this data to predict the energy difference between a leucine on a helix and a leucine on a beta sheet. (b) Given a peptide containing 5 consecutive leucine residues, what will the relative populations of all-helical vs all-beta strand conformation be? (For the purposes of this question, ignore any possible interaction between adjacent residues.)Explanation / Answer
The given molecule is assumed to be an acid.
Change in delta G = -2.94 kcal/mol
Mathematical expression between pka and ka.
Pka = - log ka …(I)
Ka is the equilibrium constant of the dissociation or protonation of acid.
More is the value of ka, more stronger acid.
From the pka and ka relation, we can say that when ka is large, pka is small and therefore we can say that stronger acid has lower pka value.
When we reduce the size of the molecule, it’s delta G is decreased. Now we need to get relation between pka and delta G.
We know,
Delta G = -RTlnka ….(II)
Here R is the gas constant , T is the temperature in K, ka is the acid dissociation constant.
When delta G decreased ( -2.94 kcal/mol), ka value should increase. ( from equation II)
When value of ka increases, pka should decrease ( from equation I)
So the effect of decrease in delta G, decreased the pka value.
And the pka of this smaller molecule will be lower than the larger (original)