BMSC 200 Lecture Notes - Lecture 5: Hydrogen Bond, Amine, Acid Dissociation Constant
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Q: Which biomolecules are polymers?
Peptides, proteins and nucleic acids are all polymers. The building blocks (monomers) are
amino acids (peptides and proteins) and nucleotides (DNA and RNA).
Q: Does the strength of the hydrogen bonds vary, and does it depend on the positions of the
participating atoms relative to each other?
Both the donor-hydrogen-acceptor angle and the distance between the donor and the acceptor
atoms can vary quite a bit, and with that the strength of the bond itself. Remember that the
hydrogen bond is an electrostatic interaction, and like any electrostatic interaction, its strength
depends on the distance between the interacting charges.
Q: How is the ionic product of water related to pH and concentrations of H+ and OH- ions ?
Ionic product of water, KW= [H+][OH-]= 10-14 , no matter what pH. Therefore if you know pH,
you can always calculate [OH-], and, conversely, if you know [OH-] you can always calculate
[H+] and pH. Example: if pH=4.0, then [H+]=10-4 M, and [OH-]=10-14/[H+]=10-10M.
Q: How to calculate the net charge of a triprotic amino acid, when pH equals pKa of one of
the ionizable groups? As an example, what is the net charge of aspartate at pH=1.9?
From the table given at the exam, the pKa values of aspartate are:
Asp 1.9 (Cα-carboxyl) 9.6 (Cα-amino) 3.6 (sidechain)
From the definition of pKa, at pH 1.9, Cα-carboxyl is 50% dissociated, so half of the aspartate
molecules at any given time have the Cα- carboxyl in the uncharged form (COOH), and half
have it in the negatively charged form (COO-), or, averaged over all the aspartate molecules in
solution, a charge of -1/2. The sidechain carboxyl is almost fully protonated (COOH), and has a
charge of 0, the amino group is fully protonated (NH3+) and has a charge of +1, Therefore the
net charge of the aspartate at pH 1.9 will be -1/2+0+1=1/2.
Q: How to calculate the isoelectric point of histidine?
The isoelectric point of a triprotic amino acid is calculated as the mean of the pKas of the two
ionizable groups on either side of the isoelectric point, i.e. the point where the molecule changes
the sign of its net electrostatic charge. From the table given at the exam, the pKas of histidine
His 1.8(Cα-carboxyl) 9.3(Cα-amino) 6.0 (sidechain)
We have two pH ranges to consider: 1.8<pH<6.0 and 6.0<pH<9.3. In which of these two
ranges will histidine change the sign of its net charge? Let’s calculate the electrostatic charge of
histidine at pH 1.8, 6.0 and 9.3. As explained for aspartate above, let’s add the charges of the
Cα-carboxyl, the sidechain, and the Cα-amino groups, in this order, at each pH. At pH 1.8, the