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Biochemistry Amino Acids and Protein Structure

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Biochemistry 2280A
Bonnie Deroo

Amino Acids and Protein Structure September-11-13 3:04 PM Amino acids in solution are surrounded by H20 and hydrogen molecules that interact with them Topic 2-3 Page 2 Glycine can carry a negative charge on the amino terminus There is no charge on a carboxylic acid Topic 2-3 Page 3 Molecule possessing a highly polar covalent bond between a hydrogen and another atom dissolves in water The hydrogen atom has given up its electron almost entirely to the companion atom, and so exists as an almost naked positively-charged hydrogen nucleus (a proton) When the polar molecule is surrounded by water, the proton will be attracted to the partial negative charge on the O atom of an adjacent water molecule. This proton can dissociate from its original partner and associate instead with the oxygen atom of the water molecule, generating a hydronium ion. The reverse can also occur, so one has to imagine an equilibrium state in which billions of protons are constantly flitting to and fro between one molecule and another. pKa describes the tendency to attract a proton Substances that release protons when dissolved in water, thus forming hydronium ions, are termed acids. The higher the concentration of hydronium ion, the more acidic the solution. The hydronium ion is also present in pure water, at a concentration of 10-7M. By tradition, the hydronium ion concentration is usually referred to as the H+ concentration, even though most protons are present as the H3O+. To avoid the use of unwieldy numbers, the concentration of H3O+ is expressed using
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