Question

a. Identify hydrogen bond donors and acceptors in each Watson-Crick base pair. Why won't adenine base hydrogen bond with cytosine or guanine hydrogen bond with thymine?

b. Name an important structure stabilized by Van der Waals interactions. Explain how the Van der Waals interactions work in this instance

c. Explain how the ionization state of any amino acid (or its side chain in a protein) at any

pH can be predicted, based on its pKa value.

Answer 1

a. Watson and Crick base pairs follow a specific rule of hydrgen bonding. In a nucleotide, oxygen (O) and nitrogen (N) atoms are potential hydrogen bond acceptors while hydrogen atoms attached to O and N atoms are potential hydrogen bond donors. Adenine joins to thymine by two hydrogen bons and guanine with cytosine by three hydrogen bonds. Adenine and Thymine have favourable configuration for their bonds. They both have two -Oh/ -NH groups which can form hydrogen bridges. In pairing of Adenine and Cytosine, various groups are in each others way and thus the bonding between them two would be chemically unfavourable.

b. Protein structures are stabilized by Van der Waals interactions. Van der Waals interactions are caused by temporary attractions between electron-rich regions of one molecule and electron-poor regions of another. They play an important role in protein structure and also in protein-protein recognition.

c. The structure of an amino acid allows it to act as both an acid and a base. An amino acid has this ability because at a certain pH value, nearly all amino acid molecules exist as zwitter ions. The isoelectric point or pI of an amino acid is the pH at which an amino acid has a net charge of zero. The pKa value given for the amino group on any amino acid specifically refers to the equilibrium between the protonated positive nitrogen and deprotonated neutral nitrogen.