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Chapter 2: Properties of Water Essential for Life

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The Chemical Basis of Life

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Chemical Bonds

The basics of bonding

Atoms are made of charged particles that follow the rules of all electrically-charged objects. Electrons are negatively charged, and repel other electrons because they have the same charge type. Protons are positively-charged, and also repel each other, except in the extremely close confines of a nucleus, where the positive repulsion is mitigated by the strong nuclear force (discussion of this phenomenon is beyond the scope of this text). But oppositely-charged particles attract one another, so electrons in the atom are attracted to the positively-charged nucleus and follow odd but close paths around it.

The same positive charge exists in other nuclei, so the nucleus of one atom can attract the electrons of another atom.

Atoms 1

Covalent bonds form when atoms with equally strong nuclear forces attract electrons in each others' shells. The entire electron population shifts around to a new stable balance of forces, and at least two electrons wind up between the bonded atoms, attracted equally to two different nuclei. Pushing the atoms into position for the bond to form takes work, so we say that the energy we put into creating the bond is stored in the bond. If breaking the bond releases more energy than the work required to break it, we can use the extra energy to fuel other chemical reactions, breaking and forming new bonds. Many metabolic processes depend on the ability to form or break covalent bonds.

atoms 2

Ionic bonds form when one atom loses an electron to an atom with a stronger attractive force. An outer-rim electron is torn off and moves into an orbital around the atom with the strong electronegative force. The resulting atoms are both ions, since both now have a net charge. Remember that the proton count in the nucleus doesn't change, so in the neutral atom that loses an electron, there is now one more proton than electron, and the net charge on that atom (or cation> is positive. The neutral atom that gains an electron is now an anion with a net negative charge, since it has one more electron than it has protons. The net charges are opposite, so the atoms are attracted to each other.

Electron moves

Electron is attracted to nucleus of atom with stronger pull

Electron changes atoms

Electron moves to new atomic home

Net electrical force

Ions now attracted by net electrical charge

Ionic bonds are often not as strong as covalent bonds. Because the whole atom is involved and not just specific electrons, ions tend to form lattice structures, where the difference in electrical charge can attract other charged atoms in all directions.

Often one atom can hold the electron from another closely, but not detach it entirely from its parent atom. These bonds are polar covalent bonds, like water (see below). In a polar molecule, like water, the overall atom is usually neutral, but there will be local pockets of net charge, which can create weak bonds with other similarly "polar" atoms.

There is no strict boundary between covalent and ionic bonds. Instead, we find a continuous range of increasingly polar bonds, where the more negative charge lies within one atom.

Polarity Types

The Special Properties of Water

Water is probably the single most important compound on the planet for life forms. Some forms of bacteria get along just fine without oxygen, but nothing gets along without water.

There are several properties that make water unique among simple molecules. Atoms combine to form various kinds of structures, including molecules, crystals, and metal solids. In all of these, the electrons of one atom are attracted to the nucleus of another atom, and repelled by its electrons. In water, the electrons of the hydrogen atom are strongly attracted to the oxygen atom's nucleus, because it has 8 protons, and each hydrogen atom has only one proton. The hydrogen doesn't quite give up its electron to the oxygen, but its electron spends more time closer to the nucleus of the oxygen than to the nucleus of the hydrogen.

oxygen in water

This concentration of electrons makes the area near the oxygen atom negatively charged, so much so that all the electrons shift a bit to maximize their attraction to the positive nuclei and minimize their mutual repulsion. The hydrogen protons, which have become islands of positive charge as a result of the partial desertion of their electrons, shift too, and wind up together on one side of the oxygen atom. This leaves the water molecule with a dipole: the oxygen side is negative, and the hydrogen side is positive. If you put two water molecules together, one of the positive hydrogens of one water molecule with form a bond to the negative oxygen on the other molecule. This hydrogen bond holds the molecules together, and it takes energy to pull them apart.

We call this water-to-water stickiness cohesion. Cohesion is what causes surface tension in water. It ties the molecules together strongly enough to support the weight of small insects, as though it were a stretchy rubber sheet. Water molecules will also stick to other polar molecules with adhesion -- the same process, just a different term to show that we have two different kinds of molecules involved. Adhesion is what allows for capillary action: the "drawing up" of water in narrow tubes. Adhesion is a fundamental requirement for the tranport of water in plants.

Acids, bases, and neutrality


Chemists and biologists use a unit called a mole to count atoms and molecules, the same way we use a dozen to count 12 doughnuts or people at a meeting. The main difference is that a mole has a lot of objects in it: 6.022 * 1023, more or less. In a mole of water, there would be 6.022 * 1023 water molecules if no other factors were involved. But because of the polarity of the water molecule and the hydrogen bonds between water molecules, putting stress on the molecules, at any given moment, some water molecules will dissociate (come apart). Pure water is not made up of just water molecules (H2O), but also includes hydroxide ions (OH-) and hydronium (H3O+), where the H+ dissociated from its watermolecule has attached itself to the "back" side of another water molecule. In neutral water, there are equal numbers of H3O+ and OH- ions. In water at room temperature, this will be about 10-7 moles of each or 6.023 * 1016 H3O+ ions and 6.023 * 1016 OH- ions per liter of water.

Acids are proton-donating compounds (they have hydrogen) and dissolve into an H+ ion and an anion (negatively-charged molecule). Common acids include vinegar and lemon juice, and the solutions in batteries. Biological acids include molecules called amino acids, which are major components of proteins, and nucleic acids, which form DNA and RNA.

Bases are proton-receiving compounds (they have hydroxide ions that want to combine with hydrogen ions) and dissolve into an OH- ion and a cation (positively charged molecule). Common bases are sodium bicarbonate (weak) and lye (strong). Biological bases are often part of buffering systems which keep the acidity of a solution such as blood relatively constant.

Acid solutions have a surplus of H+ ions, so the number of hydrogen ions ranges from 100 (1) to 10-7 moles per liter solution. Base solutions have a surplus of OH- ions; the number of H+ ions ranges from 10-7 to 10-14 moles per liter solution.

A little math side trip: Exponents and logs

Scientists like to compare things easily, so here what they really want to compare are the exponents for the powers of ten involved. To get an exponent from an expression like y = xa, we take the logarithm of the expression. The operation logx y = a means that in order to get y, we have to raise x to the power a. The x is called the base, the number we "raise" to a given power. The log of 10-7 in base 10 is the exponent -7.

Another simplification the scientist likes to use involves inverting numbers to get rid of the fractional representation. (As long as we are doing comparisons and perform the same operation on all the pieces, we can perform just about any operation). x is the reciprocal of 1/x.

Now, the exponent 10-7 really means 1/107. So the reciprocal of 10-7 is 107, and the log of the reciprocal for 10-7 is 7. It is a lot easier for the biologist or chemist to compare 7 to 9 than to compare 10-7 to 10-9.

Chemists use this method to measure concentrations of H+ according the pH scale. Acidity or alkalinity (how basic the solution is) is expressed as the log of the reciprocal of the amount of H+ in a solution. If the solution has 10-5 H+ ions per liter, the reciprocal is 105, and the log10 is just the exponent by itself: 5. A pH less than 7 indicates that there is an excess of H+: the solution is acidic; a pH greater than 7 indicates an excess of OH-: the solution is basic.

The pH scale goes from 0 (pure acid, since 100 = 1) to 7 (neutral) to 14. There is no practical reason for extending the scale to 23 (pure base), since neither pure acids or pure bases are observed.

Why do you have to know all this? Because biologists explain all those metabolic processes (eating, growing, getting rid of wastes) in terms of the chemical changes going on at the cellular level. Most of these involve acid-base reactions and the exchange of electrons or an H+ particle, so we need to know what acids and bases are to talk about chemical reactions in cells.