Hello I'm Hydrogen - Hello I'm Oxygen

Posted on 12/31/2008
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Meet the atoms: Their critical properties                               


Bondage in Molecular Biology
There are three kinds of interactions that are of primary importance to understanding Molecular Biology:

  • Covalent bonds, in which two atoms 'share' a pair of electrons
  • Hydrogen Bonds, in which a proton (=Hydrogen nucleus) interacts with a free (non-bonded) electron pair of another atom (usually Oxygen or Nitrogen)
  • Hydrophobic interactions, in which water-fearing (=hydro-phobic) groups protect one another from water

Covelent bonds: sharing electrons
In general, all atoms are 'happiest' when they have a full complement of electrons that they either 'own' or 'share'. Electrons are housed in 'orbitals' which are mathematically defined shapes around the nucleus. The so-called 's' orbital holds1 pair of electrons, while the 'p' orbital accommodates 3 pairs; thus 8 constitutes a filled s and p set. For hydrogen, a full house constitutes only two electrons, while for most other atoms important in biology, the 'magic number' is 8. Different atoms supply different numbers of electrons in their outer shells, one per proton in the nucleus. Thus as we progress through the periodic table, Hydrogen has one proton and one electron, Helium two of each, etc. Each atom's 'desires' in life correspond to the the number of electrons it needs to acquire to fill its outer shell. These desires can be met by sharing (forming a covalent bond constituting a pair of electrons shared between two atoms) or stealing (such as occurs when Chlorine rips an electron off Sodium such that Chlorine now has a full outer shell and a negative charge, and Sodium loses the loner electron in its outermost shell, revealing a full inner shell at the next level and a resulting charge of +1).

Hydrogen: has one outer electron, but a 'full house' for it is only one pair--so it seeks only one partner. Or it can go the other way, give up its only electron and become a wandering proton. That's acidity for you...

Carbon: has 4 outer electrons, so needs to 'share' 4 to make a full house (4 pairs). Thus it makes 4 bonds (i.e. engages in sharing with 4 'foreign' electrons from other atoms).

Nitrogen has 5 outer electrons, so it has one pair and seeks 3 to complete its 'hand'. The 'lone pair' of its own represents a region of negative charge that is happiest if offset by a proton--this pair would like to participate in hydrogen bonding.

Oxygen has 6 outer electrons--it forms 2 pair on its own and seeks only two other partners.

In order to reach the 'magic number' of 8, then, various combinations can be satisfying. At left is a 'happy' molecule of water, with oxygen sharing an electron pair with each of 2 hydrogens. At right, is a variation on this theme--an oxygen shares TWO pairs (a double bond) with another oxygen.

When atoms don't play nice: unequal sharing
As in life, not all partnerships are the result of equal sharing. Some nuclei are greedier than others. The lust for electrons is given the technical term 'electronegativity'.

To make a long story short, the order of electron-sucking for the atoms of interest is:
O > N > (C = H)

If two partners in bondage have similar electronegativities, then shared electrons are truly shared, with neither partner monopolizing the pair. Contrariwise, unequal sharing has several interesting consequences. The partner dominating the tug-of-war for electrons becomes partially negatively charged as a consequence, while the one losing out on the exchange is left with a partial positive charge. The resulting partially charged atoms seek extramarital charged atom pairs up with a partially positively charged hydrogen atom, the resulting pairing is called a hydrogen bond.

Hydrogen and Carbon thus form the following relationships:

  • MONOGAMOUS w/ each other: Electrons are equally shared, so neither is partially charged and neither is interested in other partners
  • OPEN RELATIONSHIP with Oxygen: Oxygen largely "controls" the shared electrons, so has partial negative charge and is seeking positively charged partners. The proton of the H or nucleus of the C is partially (+) in charge because of the absence of electrons. Thus the H and C will be attractive to (and 'interested in') (-) charged species, such as other oxygens, nitrogens, etc
  • OPEN RELATIONSHIP with Nitrogen, which is similar to Oxygen, though somewhat less greedy.

One of the implications of this is that water is the mother of all H-bonders. Consisting solely of H and O, every atom is either partially negatively charged or partially positively charged, and the whole morass forms a network of covalent and non-covalent interactions. The effects of this web of interaction are myriad, and account for most or all of the bizarre properties of water (liquid at room temperature, unlike other small molecules like CO2, CH4..., the solid is lighter than the liquid [ice floats], surface tension [you can siphon it and it hurts to belly flop into...]). While we think of these properties as normal because they match our everyday experience, their pretty weird as far as other elements tend.

Fleeing from water: hydrophobic interactions
The final important type of bondage is the so-called 'hydrophobic interaction'. In truth, this 'interaction' is an avoidance of a bad thing, rather than the seeking out of a good one as is observed with hydrogen bonding. It all comes down to water in the end. Water molecules are free spirits, rapidly moving about making and breaking hydrogen bonds with one another. This type randomness is referred to as 'entropy'. In general, things tend towards maximum randomness (= disorder) if left to themselves. Witness the state of your hair when you get out of bed in the morning or your room at the end of a busy week. Entropy is thus a Force of Nature, and nothing to be trifled with.

Hydrophobic molecules, however, want nothing to do with water. This arises from the fact that since shared electrons are shared equally, no partially charges are available for Hydrogen bonding. Thus when hydrophobic molecules areplaced in water, the water molecules surrounding them are limited in their movements and their hydrogen bonding opportunities--there's a 'dead zone' represented by the bonding-inert newcomers. In short, the Right to Randomness of many water molecules is infringed. The amount of infringement is proportional to the surface area of the offending molecules. What to do? The simplest thing is simply to minimize the exposed hydrophobic surface area thus decreasing the number of 'penalty points' lost for organizing water. This can be achieved by stacking all the hydrophobic molecules together. By doing so, the number of static, unhappy water molecules is minimized, and the universe is made happy. This phenomenon is referred to as the hydrophobic interaction or hydrophobic bonding, even though its actual cause is minimizing water non-interaction. It is the basis of the observation that oil and water do not mix--hydrophobic oil molecules cluster together, not because of innate affinities, but rather because they are excluded from water.

Who's afraid of water?
What molecules engage in hydrophobic interactions? Any that do not offer favorable interactions with water. In biology, the great majority of such groups consist of carbons bonded to other carbons or to hydrogens. Since these pairings share electrons evenly, no partial charges result, and there is nothing for water to interact favorably with. Thus, whenever you see carbon and hydrogen atoms in the absence of oxygens or nitrogens, remember that these hydrophobic groups are best sequestered away from water.

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