1. Covalent and ionic bonds.

• Na and Cl form an ionic bond because Na has only one electron in its outer shell (2:8:1) and Cl has one "hole" in its outer shell (2:8:7). Donation of an electron from Na to Cl leaves Na with a + charge and Cl with a - charge. Look at (look here) to inspect the arrangement of electrons in Na, Cl and other common atoms.
• Carbon has a half filled outer shell (2:4:0) so it can accept or donate electrons with almost the same energy. So, carbon is ideal for sharing electrons - forming covalent bonds.
• There is a continuous range between pure ionic bonds and pure covalent bonds. ("Comparison of Bonds")
• In vacuum and in water, a covalent bond is strong - 90 kcal or so. In Vacuum, ionic bonds are strong - 80 kcal/mole - but in water only 1-3 kcal/mole. )

2. Water is THE solvent in which biological molecules are dissolved. The polar character of water permits other polar molecules to dissolve in it and excludes nonpolar (oily) molecules. The polar and nonpolar interactions are major determinants of the structure of biologically important molecules and of cells themselves.

• Water is a polar molecule. The hydrogen atoms take on a slight positive charge and the oxygen atom takes on a slight negative charge due to unequal sharing of electrons. Hydrogen bonds are the result of the weak bonding between the + charge on one water molecule and the - charge on a part of an adjacent water molecule. (fig. 2-5, Lodish)
• Water forms hydrogen bonds between adjacent molecules, giving some stability to liquid water. ("Water Structure")
• Solid water (ice) is very stable and has the unusual property of being less dense than liquid.
• Water also forms transient Hydrogen bonds to polar, hydrophilic, groups on proteins, lipids, and carbohydrates and to ions in solution. (look here) The transient nature of hydrogen bonds is very important to biological structure - Since the bonds break and reform very rapidly, molecules and cellular components can move. If hydrogen bonds were strong, long-lasting bonds like covalent bonds, then molecules and cellular components would be rigidly connected and would require the help of enzymes to break the covalent bonds and permit movement.
• Ionic bonds, such as those between Na and Cl, would be quite strong, like covalent bonds, IF they existed in a vacuum. But, water, clustering around these ions shields the ion to ion bonds, weakens the ion to ion interaction to about the strength of a hydrogen bond. (look here) Since ionic bonds in water are weak, they too, like hydrogen bonds, can easily be broken. As a result, ions can move quite easily through water.
• Hydrogen bonds can form NOT ONLY between water molecules and from water molecules to polar (hydrophylic, "water-loving") groups on biologically important molecules (fig. 2-8, Lodish) BUT ALSO between polar groups on biomolecules. As we shall see, the interactions between polar groups on biomolecules such as proteins and nucleic acids and between these polar groups and water, PLAY A VERY IMPORTANT ROLE IN DETERMINING AND STABILIZING THE THREE-DIMENSIONAL STRUCTURE of biomolecules and subcellular structures.
• Non-polar groups form hydrophobic bonds between each other. Hydrophobic bonds aren't actually bonds - They are formed because water molecules hydrogen bond to each other and not to the nonpolar groups. Thus the nonpolar groups are excluded from the water and adhere together.
• Ammonia (NH₃) is similar to water but boils at -33.5 deg. C, freezes at -77.7 deg C, and the solid is MORE DENSE than the liquid. We'll discuss why Ammonia would not be a good choice for a biological solvent.

3. Biological molecules are based upon a carbon skeleton and polar and non-polar side chain groups.

• The carbon skeleton is very stable because of the strong covalent bonds formed by the equal sharing of electrons between carbon atoms.

• It takes almost 100 kcal/mole to form a C-C bond and about the same amount of energy is released when the bond is broken. So, it takes energy to make large molecules from small ones and energy is released when the bonds are broken. That's what metabolism does .. bonds are broken and energy is released to be used for building new molecules or powering contractile activity. But !!!!!! - Whenever bonds are broken, new bonds must be reformed. So, it turns out that energy is released when molecules are broken down into smaller pieces but the energy is the difference between the energy release when breaking the bonds and the energy required to form the new ones. Typically, 10 or fewer kcal/mole net energy is released when a covalent bond is broken in an organic molecule.

The carbon skeleton forms covalent bonds equally well with many different types of atoms. This allows tremendous molecular diversity in organic (carbon-based) molecules.

The carbon-based molecules can form relatively stable interactions between each other through the combined use of the weak hydrogen bonds, ionic bonds, hydrophobic and van der Waals interactions. (fig. 2-12, Lodish)

Here are some details of how polar groups interact with each other.

All text and images, not attributed to others, including course examinations and sample questions, are Copyright, 2007, Thomas J. Herbert and may not be used for any commercial purpose without the express written permission of Thomas J. Herbert.