Background Chemistry

Atoms of elements have various numbers of protons (+), neutrons (neutral) and electrons (-). Protons and neutrons are situated in the nucleus of the atom. Electrons are found in orbit around the outside of the nucleus in orbitals or shells. In general atoms are more stable if they have their outermost shell full of electrons and will gain, lose or share electrons to have full outer shells.

Atoms of elements join together (react) to make molecules of compounds in an effort to achieve full outer shells with two types of chemical bonds: ionic bonds and covalent bonds.

Ionic Bonds: When a metallic element completely gives up electron(s) to a non-metal element leaving the metallic element positively charged and the non-metal negatively charged. The oppositely charged ions are then attracted to each other. The compounds formed from this type of reaction are generally called salts.

Covalent Bonds: When two or more non-metal elements share electrons so that at least part of the time each atom can be counted as having a full outer shell of electrons. A single covalent bond is when the atoms involved each share one of their electrons. The pair of shared electrons represents a single covalent bond, often represented by a short line joining the two atoms. In some cases, the atoms may share two pairs of electrons in which case a double covalent bond is made (two lines). Similarly, a triple covalent bond is also possible(three lines).

Water: The liquid of life.

Water is a compound made of hydrogen and oxygen in which oxygen is bonded to two hydrogen atoms. Each hydrogen atom is bonded with a single covalent bond. The molecule takes the shape of a boomerang because the oxygen distributes it’s four pairs of electrons towards the four points of a tetrahedron. Two pairs are unshared. The other two pairs are shared, one pair for each hydrogen.

Oxygen is a larger atom than hydrogen, the shared pair of electrons end up spending more time around the oxygen atom than the hydrogen. Oxygen therefore has a slight negative charge, and the hydrogens have a slight positive charge. A water molecule is a polar molecule.

When two water molecules are near each other, they arrange themselves such that the negative end of molecule #1 is adjacent to the positive end of molecule #2. This is referred to as a HYDROGEN BOND. Often represented by a dotted line.

In other larger molecules where oxygen is bonded to a hydrogen like in proteins and DNA, these polar regions exist, and therefore hydrogen bonding happens. In DNA, it is hydrogen bonding that holds the two sides of the twisted ladder together in it’s helical shape. Proteins are folded chains of amino acids, and hydrogen bonds are responsible for maintaining certain folds of proteins. Without a very specific fold, a protein (enzyme) may become inactive.

These hydrogen bonds give water the following properties that benefit life.

1. Water is a liquid for much of the temperature range on earth because of the hydrogen bonds. This allows water to be the universal solvent for polar (charged) molecules and thereby facilitates chemical reactions both outside and within our bodies. Many of the reactions that occur in our bodies would not occur if they were not in a solution. Furthermore, ions would not form like Na⁺ or Cl^- ions.

2. Water molecules are cohesive, and therefore liquids fill vessels, such as blood vessels. Water is an excellent transport medium. Water’s cohesiveness also makes it a suitable component of lubricants for epithelial tissues (gut lining) as well as inbetween joints.

3. The temperature of liquid water rises and falls slowly. It has a very high specific heat capacity (1 calorie heats 1 gram 1˚C), and therefore prevents drastic temperature changes. Drastic temperature changes would alter many enzymes and metabolic reactions would not occur at sufficient rates.

4. Water has a high heat of vaporization due to the energy needed to break all of the hydrogen bonds. When one sweats (sweat is mostly water) a large amount of body heat is required to evaporate that sweat. Heat loss = keeping cool.

Acids, Bases & Buffers

Water is a solvent for polar molecules. For example NaCl is highly polar and it dissociates in water to Na⁺ and Cl^- ions because of water’s polar regions. Water itself even dissociates to H⁺ and OH^- ions in very small quantities. For each litre of water there are 1.0x10^-7 moles of H⁺ ions and 1.0x10^-7 moles of OH^- ions (ie. equal amounts of each).

A ‘mole’ is 6.023 x 10²³ of something just like a ‘dozen’ is 12 of something or a ‘couple’ is 2 of something.

If you dissolve a compound that disturbs the number of H+ and OH- ions in water, it is said to be acidic or basic.

An acid is a compound that will increase the number of H⁺ ions when put into solution. For example if you put HCl (hydrochloric acid) into water it dissociates into H⁺ and Cl^-. Now there’s more than 1x10^-7 moles/l of H⁺ ions. The solution is acidic. In general acids are:

· sharp/sour taste

· turn litmus paper red

· ↑[H⁺] or ↓[OH^-]

· ex. lemon juice, vinegar, tomato juice, coffee

A base is a compound that will decrease the number of H+ ions when put into solution OR increase the number of OH- ions. For example if you put NaOH into water it dissociates into Na+ and OH- ions. The extra OH- ions react with the H+ ions from dissociated water and there will be less than 1x10-7 moles per litre of H+ ions. The solution is acidic. In general bases are:

· bitter

· slippery

· turn litmus paper blue

· ↓[H⁺] or ↑[OH^-]

The pH scale is an easy way of indicating the acidity or basicity (alklalinity) of a solution. It ranges from 0 to 14. A pH of 0 to 7 is acidic. A pH of 7 to 14 is basic. A pH of 7 is neutral. The number corresponds to the exponent on the concentration of H⁺ ions in the solution or body fluid.

[H⁺] = 1x10^-6, pH=6 Acidic

[H⁺] = 1x10^-7, pH=7 This is the [H+] in pure water. Neutral.

[H⁺] = 1x10^-8, pH=8 Basic

There are varying optimum pH levels in different parts of the body and these pH levels must be held constant or the H⁺ or OH^- ions will react easily with many other compounds and will disturb hydrogen bonding in important proteins and DNA molecules. Acids and bases are therefore kept at different but constant levels in various parts of the body by compounds or combinations of compounds called buffers. These compounds can take up excess H⁺ or OH^- ions.

For example, optimum pH in the blood is about 7.4 (slightly basic). If the blood accumulates excess H+ ions as it does during exercise then there is potential for those ions to react or disturb hydrogen bonding. The blood has carbonic acid H₂CO₃ and bicarbonate ions HCO₃^- in it which can adjust the [H+] through the following reactions.

If excess H⁺ ions then:

H⁺ + HCO₃^- → H₂CO₃

If excess OH^- ions then:

OH^- + H₂CO₃ → HCO₃^- + H₂O

There are varying optimum pH levels in different parts of the body.

1. Stomach Acid (HCl) has a pH of about 2. This pH must be maintained in the stomach to:

· kill potentially harmful bacteria

· help breakdown the connective tissue in meat

· activate digestive enzymes (pepsin)

2. In the small intestine, proper functioning of digestive enzymes requires a slightly basic solution, so pancreatic juice contains NaHCO₃ which neutralizes the HCl in chyme (the thick soupy liquid leaving stomach). HCl itself in the small intestine triggers release of pancreatic juice.

3. Sperm are more viable in a slightly basic solution, and seminal fluid is found to have a pH of 7.5.

4. Our kidneys help keep blood pH at approximately 7.4 on a long term basis by excreting H⁺ ions and reabsorbing HCO₃^- ions as needed. Urine usually has a pH of 6 or lower because our diet has many acidic foods.

5. On the short term the blood pH is held constant through buffering and special chemoreceptors in brain. When pH lowers (ie. high [H⁺] ions), the receptors stimulate breathing. This gets rid of excess CO₂ and the following reaction occurs in the blood:

H₂CO₃ → H₂O + CO₂

This occurs since there is now low [CO₂] due to exhalation. The decrease in H₂CO₃ affects the buffering reactions above such that the first buffering reaction above is driven towards the products side thereby using up the excess H+ in the blood.

H⁺ + HCO₃^- → H₂CO₃

Overall, the buffering reactions considering [H⁺]can be summarized as:

H⁺ + HCO₃^- ⇄ H₂CO₃ ⇄ H₂O + CO₂

6. Blood in turn keeps the pH of tissues at normal levels through it’s buffering capabilities