Tag Archives: Water

Osmosis and buffering

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Diffusion and osmosis

Collective or intensive properties like pressure or boiling and melting points, which are independent of the amount of a substance, are called colligative properties. The concentration of a solute is such a property. A solution wants to have the same concentration everywhere, as this represents the state of highest entropy (randomness). So in case of non-equilibrium, a solute will migrate from any region of higher concentration to regions of lower concentration — just like heat energy flows from hotter to cooler, and for similar reasons. When both regions are mixed and at the same concentration, the result is less ordered and so of higher entropy. This is diffusion.

Another very important colligative property is osmotic pressure. This is only a bit tricky to understand.

Normally, one expects a solute to diffuse from a region of higher concentration to one of lower concentration in order to bring about equal concentrations of the solute. But if the two regions are separated by a membrane which the solute cannot cross but the water can, then the opposite happens. Water flows from the region of lower concentration, i.e., where there is less solute, to the region of higher concentration, which has the effect of diluting the latter and lowering its concentration. At the same time, the solute concentration on the other (source) side goes up. This process is osmosis.  The force or pressure driving the water across the membrane is called osmotic pressure.

So, in diffusion, the solute migrates; in osmosis, the solute cannot cross the membrane, so water migrates.

The concentration of solute depends not on its mass but only on the number of atoms or ions.

If the membrane is a cell membrane, then water flows into or out of the cell, depending on the solute concentration inside and outside. Cells usually have a higher solute concentration of biomolecules inside than out, which drives water into the cells. If unchecked, the inflow of water could cause the cell to expand until it exploded, but nature has come up with mechanisms to prevent this catastrophe, including reinforcement of cell walls and pumps to remove water from the cell.

In plants, osmotic pressure stiffens cells with reinforced cell walls, giving the plant rigidity to support it standing up. The opposite thing happens when a salad leaf wilts.

Buffering — acids and bases

Water is naturally somewhat ionized.

Water ionization

Auto-ionization of water, by Cdang via Wikipedia

There are no free protons in water (even though we often will write them as such), hence the hydronium ion, H3O+, with an extra proton. An acid is defined as a proton donor (furnishes H+) and a base as a proton acceptor (consumes H+), so it can be seen that water is weakly both: H3O+ is a donor and OH– is an acceptor. The degree of acidity is frequently indicated by the pH value, where

pH = log(1/[H+]) = -log([H+])

where [H+] is the concentration of H+ in moles per liter.1A mole is the mass of a substance contianing the same number of fundamental units (atoms, molecules, etc.) as there are atoms in 12.000 g of 12C. This number is 6.023×1023, which is called Avogadro’s number, designated by NA. Water at 25°C has a pH of 7; ph < 7 means more H+ and therefore more acidic; pH > 7 means basic. Like all such chemical transformations, there is an equilibrium point for the above reactions. This is also true for any other weak acid dissolved in water. Consider acetic acid,

CH3COOH <-> CH3OOO– + H+

which occurs in an equilibrium state of acetic acid itself (an acid, therefore a proton donor) and CH3OOO– (a base, or proton acceptor). These two substances constitute a conjugate acid-base pair. When this weak acid is dissolved in water, two equilibria must be established at the same time, for water and for acetic acid, here represented simply as HAc.

H2O <-> H+ + OH–

HAc <-> H+ + Ac–

Now if we add a small quantity of a base, say NaOH, to this solution, the base will decompose into Na+ and OH-, the latter a proton acceptor or base. This will change the pH of the solution. But the equilibrium of HAc will adjust so as to decrease the pH and the basicity. The resulting overall increase in basicity will be, in the best of cases, less than expected just considering the addition of a small quantity of strong base. Seen from the point of view of radicals, the OH- from the strong base will combine with some of the protons from the water and acetic acid. But then the acetic acid will be out of equilibrium, so it will produce more free protons to re-establish its equilibrium, thereby attenuating the effects of the added NaOH. A similar but opposite mechanism acts to maintain pH if a small quantity of strong acid is added.

This ability to reduce induced acidity is called buffering. A buffer is an aqueous system which resists changes in acidity from a small amount of added base or acid. It is composed of a weak acid and its conjugate base. It is important as the mechanism by which living beings adjust the acidity of cells. If body acidity is not within rather strict limits, enzymes will not function and so neither will we. The body uses a buffer system based on the conjugate pair carbonic acid and bicarbonate:

H2CO3 <-> H+ + HCO3–

If blood acidity starts to become too high, bicarbonate leaps in and absorbs protons. If it becomes too low, carbonic acid supplies them.2It’s really a tad more complex because of another equilibrium: H2C03 ↔ CO2 + H2O. See Lehninger, 63. This is one of many regulative mechanisms the body has for maintaining the proper equilibrium of certain solutions and processes needed by the body in order to stay alive. We will see more.

The global water cycle

Let us briefly leave the microscopic considerations of chemistry and look at water on the scale of the Earth. Water circulates through the ground, streams, oceans and lakes and the atmosphere in what is called the water cycle.

The water cycle, from USGS

This is just one of a number of transformational processes which assure the distribution of an essential component of life on Earth. The diagram is pretty much self-explanatory.

That’s it for the introductory material. Now let’s look at the history of it all. That starts in the past. Way back in the past, about 13.7 billion years ago (Gya).

Notes

Notes
↑1 A mole is the mass of a substance contianing the same number of fundamental units (atoms, molecules, etc.) as there are atoms in 12.000 g of 12C. This number is 6.023×1023, which is called Avogadro’s number, designated by NA.
↑2 It’s really a tad more complex because of another equilibrium: H2C03 ↔ CO2 + H2O. See Lehninger, 63.

Water

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Water is tremendously important to us if only because around 70% of the surface of the globe is covered with it. Each of us is 55-75% water (by weight) and life most likely arose in water. Two properties of water are of fundamental importance for biochemistry and, therefore, for life.

  • the attractive force between water molecules and
  • the tendency of water to ionize slightly.

Polarization and hydrogen bonds

As we saw, the electron configuration of oxygen’s eight electrons is:

16O: 1s22s22p4

So it needs two more electrons in order to fill its valence shell. As everybody knows, it bonds with two atoms of hydrogen to make H2O. Each hydrogen atom shares its electron with the oxygen, making two covalent bonds. The oxygen atom now has the desired eight electrons in its valence shell. The resulting arrangement is triangular.

Oxygen is more electronegative1Electronegativity depends on the number of electrons and on the distance of the valence electrons from the nucleus. than hydrogen, meaning it has a stronger attraction for electrons, so the electrons spend more time in the vicinity of the oxygen, making that end of the molecule slightly more negative. The molecule is said to be polarized.

"Polarization

Since one end of the molecule is more negative than the other, the negative end of one molecule is electrostatically attracted to the positive end of another and this forms a weak bond called a hydrogen bond. In this image, one sees the proposed tetrahedral form of the molecule as well as the hyrdrogen bonds between molecules.

Model of hydrogen bonds between water molecules, from Wikimedia Commons

Hydrogen bonds are strongest when the electrostatic interaction of the participant atoms is maximized, as shown in the above figure. This directionality is responsible for the geometric structure of hydrogen-bonded molecules into crystals.

Hydrogen bonds do not only occur in water. They also form between an electronegative atom and a hydrogen atom covalently bonded to another electronegative atom, be it the same or different.

 

“Base pair GC” by Yikrazuul – Own work. Licensed under Public Domain via Wikimedia Commons.

Hydrogen bonds are much weaker than covalent bonds, typically on the order of a twentieth. But when there are many of them, their combined strength can be great indeed. A striking example is DNA, in which the opposing strands are held together by hydrogen bonds between the bases, as in the preceding figure. But more on that later.

If the molecules are rushing about (as in water), they are relatively independent and the substance is a liquid. Hydrogen bonds are constantly formed and broken, forming so-called “flickering clusters”. Heat them some more and they separate entirely and the water becomes a gas — water vapor. The hydrogen bonds between molecules hold them together pretty well, though, and this accounts for the rather high boiling temperature of water. Chill them down to a temperature where they do not move much any more and the hydrogen bonds assemble the molecules into a solid lattice or crystal — ice.

“Hex ice” by NIMSoffice (talk). via Wikipedia Commons

Ionization, hydrophobic and hydrophilic molecules

Because of its polarization, water can pull apart polar molecules, such as table salt, NaCl, where the positive sodium Na+ is attracted by the negative end of the water molecule and the negative chlorine Cl– by the positive end. This is what makes water a good solvent. One can see the advantage of this from another angle. Remember entropy? Nature wants higher entropy, meaning more disorder. But NaCl forms a highly ordered crystal structure. When the molecules are pulled apart in water, a more disordered state is achieved and entropy increases. Voilà!

On the other hand, non-polar molecules are not soluble. They are called hydrophobic, because they do not “like” water. NaCl likes it and so is called hydrophilic. This has some amazing and important consequences.

The behavior of solvents in aqueous solutions is a very important subject in biochemistry — and a fairly vast one. Let us look at one interesting and essential type of compound: Ampiphatic compounds have some regions that are polar or charged, therefore hydrophilic, and others that are not polar or charged and so are hydrophobic. In the figure below, we consider molecules illustrated as having a green hydrophilic head and long, yellow hydrophobic tails. When they are dissolved in water, the hydrophobic parts flee the water and tend to group together (like people grouped together facing outwards in the midst of a pack of threatening wolves), leaving the hydrophilic parts on the outside turned towards the water. The result is a spherical blob called a micelle.

“Micelle scheme-en” by SuperManu – Own work. Licensed under CC BY-SA 3.0 via Wikimedia Commons.

One can understand this from thermodynamics, too. The water molecules are highly ordered around the hydrophobic parts of the ampiphatic molecule. Hiding these on the interior of the micelle reduces the ordering and therefore represents a state of higher entropy.2Lehninger, 49.

And there is another possibility. Think of the micelle opened up, like an orange, and flattened out and another one put alongside it, so that the hydrophobic ends are against each other and isolated from the water by the hydrophilic ends on the outside, as in part 1 of this diagram.

Lipid bilayer and micelle by Stephen Gilbert via Wikipedia Commons

This ampiphatic substance could be a lipid (organic fat), in which case this is a lipid bilayer, which is what forms cell membranes. So we are ready to start looking at cells in the physiology chapter. And all that is due to electrostatics, QM and thermodynamics — it’s all simple physics.

There are a couple more, slightly more complex, attributes of water we should know about. They are the important ideas of osmosis and buffering.

Notes

Notes
↑1 Electronegativity depends on the number of electrons and on the distance of the valence electrons from the nucleus.
↑2 Lehninger, 49.