C attracted to the positive (Na+) or negative Polar substances such as urea HO (Cl_) charge of each ion. dissolve because their molecules HH HH form hydrogen bonds with the OO HH surrounding water molecules.
Many substances, such as household sugar, dissolve in water. That is, their molecules separate from each other, each becoming surrounded by water molecules.
When a substance dissolves in a liquid, the mixture is termed a solution. The dissolved substance (in this case sugar dissolves sugar) is the solute, and the liquid that does the dissolving (in this case water) is the solvent. Water is an excellent solvent for many substances because of its polar bonds.
Many of the acids important in the cell are only partially dissociated, and they are therefore weak acids—for example, the carboxyl group (–COOH), which dissociates to give a hydrogen ion in solution.
(weak acid) Note that this is a reversible reaction.
The acidity of a solution is defned by the concentration of H+ ions it possesses. For convenience we use the pH scale, where
H+ conc. moles/liter
Positively charged hydrogen ions (H+) can spontaneously move from one water molecule to another, thereby creating two ionic species.
hydronium ion (water acting as a weak base) often written as: H2O hydroxyl ion (water acting as a weak acid)
Since the process is rapidly reversible, hydrogen ions are continually shuttling between water molecules. Pure water contains a steady-state concentration of hydrogen ions and hydroxyl ions (both 10–7 M).
Substances that reduce the number of hydrogen ions in solution are called bases. Some bases, such as ammonia, combine directly with hydrogen ions.
Other bases, such as sodium hydroxide, reduce the number of H+ ions indirectly, by making OH– ions that then combine directly with H+ ions to make H2O.
Many bases found in cells are partially associated with H+ ions and are termed weak bases. This is true of compounds that contain an amino group (–NH2), which has a weak tendency to reversibly accept an H+ ion from water, increasing the quantity of free OH– ions.
PaNel 2–3: The Principal Types of Weak Noncovalent bonds that Hold Macromolecules Together
Organic molecules can interact with other molecules through three types of short-range attractive forces known as noncovalent bonds: van der Waals attractions, electrostatic attractions, and hydrogen bonds. The repulsion of hydrophobic groups from water is also important for the folding of biological macromolecules.
Weak noncovalent chemical bonds have less than 1/20 the strength of a strong covalent bond. They are strong enough to provide tight binding only when many of them are formed simultaneously.
As already described for water (see Panel 2–2), hydrogen bondsform when a hydrogen atom is (usually oxygen or nitrogen).
Hydrogen bonds are strongest when the three atoms are in a straight line:
Examples in macromolecules: together. These stabilize the structure of folded proteins.
Two bases, G and C, are hydrogen-bonded in a
DNA double helix.
If two atoms are too close together they repel each other very strongly. For this reason, an atom can often be treated as a sphere with a fxed radius. The characteristic “size” for each atom is specifed by a unique van der Waals radius. The contact distance between any two noncovalently bonded atoms is the sum of their van der Waals radii.
0.12 nm 0.2 nm 0.15 nm 0.14 nm radius radius radius radius
At very short distances any two atoms show a weak bonding interaction due to their fuctuating electrical charges. The two atoms will be attracted to each other in this way until the distance between their nuclei is approximately equal to the sum of their van der Waals radii. Although they are individually very weak, van der Waals attractions can become important when two macromolecular surfaces ft very close together, because many atoms are involved.