WATER & HYDROGEN BONDING

Drinking Duck

I. Waterπs interesting properties relative to life.

A. Water is a highly unusual substance. It has an important biological role because it is the matrix of many living reactions as well as being a highly reactive compound itself. Some of its unusual properties are:

1. Liquid at room temperature

a) high boiling point

b) high freezing point

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2. high heat of vaporization (evaporation)

3. high surface tension

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4. solid is less dense than the liquid (that is ice floats, freezing water expands)

5. excellent solvent

B. Polar Covalent Bond

1. The covalent bond between the oxygen atom and the hydrogen atom is not an equal sharing of electrons. The 'shared' electrons spend more time around the electronegative oxygen atom than they do the electropositive hydrogen atom. The result is a small localized negative charge around the oxygen and a small localized positive charge around the hydrogen (about 1/20 the amount of a full charge)(the partial charge is often represented by a delta: d+.) Since there is a separation of charge, this type of covalent bond is called a polar bond. In water the partial negative on the oxygen is twice the strength of a hydrogen since it 'shares' electrons with two hydrogens.

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C. Hydrogen bond - the magic of water

1. Water has a strong affinity for itself. Through partial charges of hydrogen bonding, each water molecule can bind up to four other water molecules. These can be arranged into a variety of ways to create various forms of lattice work (e.g., as seen in various types of ice).

2. Liquid water has almost about as much hydrogen bonding as does ice!!; but in liquid water bonds are forming and breaking faster with a half life of 10-11 sec (yet the water molecules still have a high affinity for themselves). Thus, the liquid quality actually depends more on the half life of hydrogen bonds rather than the actual number of hydrogen bonds. It turns out that liquid water is not all that different from that of ice.

3. Hydrogen bonds associated with other biological compounds.

(If hydrogen is not involved, then more generalized term for the phenomenon is dipole-dipole interaction.)

a) Other groups commonly found in carbohydrates, proteins, and nucleic acids forming hydrogen bonds: See following page

(note: H tends to be electropositive while O and N tend to be electronegative. C tends to electro-neutral.)

b) Coopertivity. Once one hydrogen bond forms the probability of a second forming may be increased, leading to an increased probability of a third forming, etc. This can lead to a very strong and stable structure even though it is made up of individually weak hydrogen bonds. This phenomenon is very common and important in the structure and function of both proteins and nucleic acids.

c) Hydrogen bonds can form and break rapidly. This has little energy consequences to a cell but has important implications in rapid functional changes related to conformational changes of molecules.

4. Water as a solvent.

a) Ions are quite soluble in liquid water being attracted to the partial charges on the water.

Sodium chloride for example:

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(1) One must be impressed with the ability of water to break strong ionic bonds (e.g., dissolving solid NaCl in water)

(2) Dissolved ions alter the structure, and therefore the properties of water.

(3) Dissolved ions will have several water molecules associated with it ,thus affecting the properties of the ion. The smaller the ion, the stronger its charge density. This means more water molecules will be attracted to it and thus the smaller the ion the larger the hydrated radius (and the slower the mobility it has and the more difficult time it has in getting through the membrane).

b) Polar compounds are quite soluble in water (carbohydrates, proteins, and nucleic acids are generally soluble). However, dissolved polar compounds will alter the structure of water (gelatin being a good case in point).

c) There are several polar groups in biology which have partial charges that can associate with water. Most fall into the following categories (hydroxyl, carboxyl, amino):

d) Of course any organic groups with full charges would associate with water too. These are usually weak acids or bases that tend to fall into three broad categories (carboxylic acid, phospho- acid, amine):

(To reduce clutter, the partial charges that would exist as well in these acids and bases are not shown)

e) Then what does not associate with water?! The most common and significant one is the methyl group. It does not associate well with water because it has no full or partial charges. The methyl group is found in all biological organic molecules, but when it makes up a high proportion of the molecule then it tends to reduce the water solubility of the molecule and increase its lipid solubility (methyl).:

D. Covalent bonds - sharing of electrons between atoms

1. Very strong and hard to break. Allow for a great deal of structure.

2. When broken or formed, covalent bonds involve a great deal of energy.

3. Water as a reactant. Water is probably the one molecule that is involved in more chemical reactions in the cell than any other. Some important examples:

a) C6H12O6 + 6 O2 --->--->---> 6 H2O + 6 CO2 + energy

b) ATP + H2O ----> ADP + H3PO4 + energy

c) The formation of polymers seems to always involve a condensation (or the term dehydration synthesis can also be used) reaction of the form:

H-unit-OH + H-unit-OH <====> H-unit-unit-OH + H2O.

And the breakdown of polymers would be the opposite reaction (often referred to as hydrolysis or decondensation), which would require the addition of water!

E. Acid-base chemistry is centered on water:

1. H2O <====> H+ + OH-

2. pH = -log10(Hydrogen ion concentration)

3. Weak acids and weak bases can 'absorb' OH- or H+, and thus act as buffers (prevent large changes in pH)