Basic Chemistry

The universe is composed of essentially three things: matter, energy, and empty space. Chemistry is the study of how matter interacts and we need to understand some of the basic rules and ideas about matter to understand how living things work.

An element is the most basic form of matter. It is a substance that cannot be separated into simpler substances by chemical means. A compound is a combination of two or more elements.

A typical living thing is mainly composed (99.9% by weight) of just six elements: carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulphur. Seventeen other elements occur in minute quantities or as just traces.

Elements are composed of identical particles are called atoms. We can define atoms as the smallest particle into which an element can be divided and still have the properties of that element. A molecule is two or more atoms joined together by something called molecular bonds.

Atomic Organization

Atoms are made up of smaller (or subatomic) particles and the three most important are called protons, neutrons, and electrons.

A Proton - is a positively charged particle with a

weight of one atomic mass unit.

A Neutron - has no charge and a weight of one atomic

mass unit (weighs the same as a proton).

An electron - is a negatively charged particle with a

weight 1/2000th of a proton (we will consider it to have no weight)

It is important to remember that particles with the same charge will repel each other and particles with opposite charges (like protons and electrons) will attract each other. Protons and the electrically neutral neutrons make up the center or nucleus of an atom and the electrons occur in orbits moving around the nucleus; they are held there by the attraction of oppositely charged particles.

The Atomic Number of an element is the number of protons in the nucleus of its atoms. Since hydrogen, the simplest atom, has only a single proton in its nucleus (and no neutrons - see text figure of the first 20 elements), its atomic number is 1. Oxygen is 8 and carbon is 6. Note: in a "normal" atom the number of electrons equals the number of protons; therefore "normal" atoms have no net charge - the positive cancels the negative.

The Atomic Mass of an element is the sum of the number of protons and the number of neutrons, since each has a weight of 1 atomic mass unit (amu).

Atomic Variants

1. Isotopes - isotopes of an element differ in the number of neutrons in the nucleus. For example, uranium normally exists as U238 with 92 protons and 146 neutrons. An important isotope of U238 is U235 with three fewer neutons. This isotope is radioactive; its nucleus is unstable and emits energy (which humans have used for power plants and bombs).

2. Ions - ions are atomic variants with either a net negative or a net positive charge because the number of electrons differs from the number of protons. Sodium (Na) normally has 11 protons and 11 electrons. One biologically important ion is symbolzed as Na+; it has lost an electron and so has a net positive charge.

Electrons in Orbit

What gives each atom its unique chemical behavior? Why is hydrogen an odorless gas and carbon a black powdery substance? The answer lies in the number and position of electrons in the energy levels (or shells), especially in the outer energy level, the one in closest contact with the rest of the universe.

Electrons swirl around an atom's nucleus in specific paths called orbitals (orbitals are where the electron spends most of its time). The innermost energy level can only hold two electrons in one orbital, the next energy level can hold eight in 4 different orbitals, the third can hold eight, and so on. When these energy levels contain their maximum number of electrons, they are said to be filled. If the outermost energy level of any particular atom is filled, that element is said to be inert meaning it is very stable and generally can only interact with other atoms with a great deal of added energy. Hydrogen has only one electron, so its outermost energy level is not filled; it can hold one more. Consequently, hydrogen can react with other atoms to form molecules. Helium has two electrons in its one energy level, therefore it is filled; helium is inert. Other inert elements are neon and argon, sometimes called the Noble gases because they do not react with other elements easily; they are "nobility". Carbon has two electrons in its innermost level and four in its outermost level for a total of six. Therefore, its outermost level needs four more electrons to be filled; carbon can combine (share electrons) with up to four more atoms; it can form a huge number of different compounds. Sodium has only one electron in its outer level (can hold eight); it is very unstable. Chlorine has 7 electrons in its outer energy level; it needs only one to fill it. As you might guess, sodium and chlorine react very easily with each other. Most atoms with unfilled energy levels tend to react (we will discuss chemical reactions later) in such a way as to completely fill the outer energy level when the reaction is over.

We will discuss energy later, but for now understand that the further an electron is from the nucleus, the more potential energy it possess. To understand this concept, it may be useful to make an analogy to a boulder that is pushed up to a hill top. When it arrives there, the boulder has a certain amount of potential energy. If it is allowed to roll down the hill, the potential energy is converted to kinetic energy (i.e can do work, like smash things at the bottom of the hill). Just like the rock that will tend to move to the bottom of the hill, electrons tend to seek their lowest unfilled energy level, the one closest to the nucleus. It takes energy to move them to higher energy levels; unlike the rock, an electron cannot go partway up a hill; it must go to a discrete energy level. This discrete amount of energy needed to move an electron from one level to the next highest is called a quantum. Later, we will see how the energy in sunlight can be used by green plants to raise electrons to higher energy levels - this is the source of almost all chemical energy available to living things.

Molecular Bonds

Molecules are formed when two or more atoms are bonded together. These bonds are energy links between the atoms, not physical couplings (like glue). There are three main types of chemical bonds.

1. Covalent Bonds - the most common type of bond. They occur when a pair of electrons is shared by two or more atoms. A single bond, occurrs when one electron is shared between, for example, a hydrogen and the carbon atom. Double bonds occur when two electrons are shared between a pair of atoms.

If the sharing is equal between the atoms, we say the bond (and the molecule) is nonpolar. The electrical charge (the electron) is equally shared with both ends (the poles)of the molecule. If the shared electrons spend more time orbiting one atom in the molecule over another, the bond (and the molecule) is said to be polar. For example, the electrons shared between oxygen and hydrogen in a water molecule spend more time with the oxygen atom than the hydrogen atom; the oxygen pole of the molecule has a slight negative charge (because the electron has a negative charge) while the hydrogen pole has a slight positive charge (because at times it has no electron, just a positively-charged proton).

2. The polarity mentioned above leads to another kind of bond called a hydrogen bond. This is a bond between the negative pole of a polar molecule and the slight positive charge on a hydrogen atom that is participating in another polar molecule. For example, the oxygen in a water molecule (which is polar) will form a hydrogen bond with a hydrogen atom of another water molecule. These bonds are weak and easily broken. In any given quantity of liquid water, countless hydrogen bonds are forming and breaking all the time. These bonds give water many unusual properties.

3. Ionic bonds are the third type of chemical bond important for our understanding of chemistry. Here there is a complete transfer of electrons from one molecule to another. It is most common when one molecule needs just one or two to complete its outermost shell and the other has only one or two in its outermost shell, like the situation in chlorine and sodium described earlier. When sodium come in contact with chlorine, the sodium loses one electron and the chlorine gains one. Now the two atoms are oppositely-charged ions so they will remain in contact (like magnets) to form the compound sodium chloride (NaCl or table salt). Ionic bonds are not as strong as covalent bonds in many situations, for example they will dissociate (fall apart) when dissolved in water.

Before we begin a discussion of organic compounds (compounds containing carbon) that constitute living things, we need to briefly discuss one of the most important compounds for life: water.

Water Chemistry : Life began in water and organisms are composed of anywhere from 50 to 90% water. Today, so many kinds of living things live in water. What is so special about it and why is it so special chemically? The answer lies in the hydrogen bonding between water molecules and other water molecules as well as with other substances; recall water is a polar compound, it has positive and negative ends.

Properties of Water

1. Water is slow to heat up and slow to release heat compared to other liquids. More heat is needed to raise the temperature of a quantity of water than other liquids. Most of the heat energy applied to water is used to break the hydrogen bonds before the temperature can be raised. Water is said to have among the highest specific heat of compounds that normally exist as a liquid. This ability of water is important to organisms because it keeps the environment in and around them more constant. Rapid temperature fluctuations impede many life processes; few organisms can cope with the physiological stresses associated with them.

2. Water has a high heat of vaporization. This means that when water evaporates, a great deal of heat is required; this heat is drawn from the surrounding environment. Organisms can use this property to cool themselves (sweating) by allowing water to evaporate from their bodies.

3. Water molecules exhibit a high degree of cohesion (tendency of water molecules to cling to each other) and adhesion (tendency of unlike molecules to cling to each other). These properties account for capillarity, where water moves upward against the pull of gravity in narrow spaces. Plants use this property of water to move materials up their stems from the roots to the leaves.

4. Water exhibits a high surface tension - the tendency of molecules at the surface of a liquid to cohere to each other and not to the air above. Some organisms can utilize this property and literally walk on water!

5. Ice floats! Ice is less dense than liquid water and hence floats in it. If it didn't, lakes would freeze solid each winter, resulting in grave consequences for organisms that live in lakes.

6. Water is sometimes referred to as the universal solvent because so many substances (both ionic molecules and many polar covalent molecules) can dissolve in it. A solvent is a substance capable of dissolving other substances while the solute is the substance that is dissolved. Together they make a solution. Hydrophilic ("water-loving") substances readily dissolve in water while hydrophobic ("water-fearing") substances do not dissolve in water.

7. Water dissociation - water has a slight tendency to fall apart (dissociate) into hydrogen ions (H+) and hydroxide ions (OH-). Other substances can also dissociate in water. An acid is a substance that gives off hydrogen ions when dissolved in water while a base is a substances that accepts hydrogen ions (thereby increasing the hydroxide ions). The concentration of hydrogen ions is very important to living cells; many processes will only occur at the proper rate under very specific hydrogen ion concentrations. We measure this hydrogen ion concentration by the pH scale. Pure water has a certain hydrogen ion concentration its pH is 7 (neutral). The pH scale goes from 0 (the most acidic; highest hydrogen ion concentration) to 14 (the most basic; least hydrogen ion concentration). The pH of most cells is between 6.5 and 7.5; it is at these concentrations that life processes occur at optimal speed

Carbon - carbon is the element that life on earth is based upon; its bonding versatility is its key characteristic, allowing it to accept 4 other atoms.

Most organic compounds possess a similar "backbone" of carbon atoms bonded together in chains or rings. The specific properties of the compounds are associated with functional groups that hang on the backbone.

Classes of Organic Molecules

1. Carbohydrates - the most abundant organic compounds. They function as energy sources for cells and as structural components of cells. The simplest carbohydrate is glucose - C6H12O6

Monosaccharides are monomers or simple sugars. Examples are glucose, fructose, and galactose. All three have the chemical formula C6H12O6, but they differ in their arrangement of the individual atoms and have different properties

Disaccharides - are two simple sugars bonded together. Many plants typically store carbohydrates as disaccharides. Other examples are lactose or milk sugar and maltose, the sugar in barley used to make beer.

Polysaccharides - may consist of thousands of monomers of glucose or other simple sugars. Examples include starch (carbohydrate storage in plants), cellulose (a structural polysaccharide in plants and fungi), and fructans (storage products in leaves and stems). All of these are composed of repeated monomers of glucose.

2. Lipids - include fats, oils, waxes, steroids, and phospholipids. They function as an energy storage, as waterproof coatings, and as chemical messengers.

A. Triglycerides - fats and oils

a). Saturated fats are those in which all the carbon atoms of the fatty acids are

bonded to at least two hydrogen atoms. They form straight chain polymers in

which the fatty acids are packed very closely and include fats such as bacon fat and lard.

b). Unsaturated fats are those two adjacent carbon atoms on the fatty acids share a double bond and therefore have fewer hydrogens. They cannot pack

as tightly as saturated fats. At normal temperatures they are liquids (These are

the oils). Polyunsaturated fats have even more of these double bonds.

B. Waxes - insoluble in water, useful as waterproof coatings for organisms, as a structural component of cell walls.

C. Phospholipids - consist of only two fatty acids attached to a glycerol molecule and a

phosphate group in place of the third fatty acid. The phosphate group is water

soluble while the rest of the molecule is insoluble in water. The cell membranes surrounding every cell is made of a bilayer of phospholipids.

3. Proteins - The specialized shapes and functions of different cell types (something we will explore later in the course) depend upon the bewildering variety of proteins. Proteins have many roles in cells (and between cells). They include, but are not limited to:

1. Structural proteins - form cell parts

2. Regulatory proteins - control cell processes

3. Enzymes - facilitate (help) many chemical reactions; they do this by

lowering the amount of energy needed to start the reaction; the

enzyme is not permanently altered in the process.

4. Hormones - chemical messengers

5. Transport proteins - carry other substances around cells or from cell to cell.

Proteins consist of long chains of amino acids, the building blocks of proteinsroteins are made of one or more polypeptides. There are usually 100 to 10,000 amino acids in a typical protein molecule. Many millions of combinations of amino acids are possible.

Protein Structure - proteins have four levels of organization (see Figures in Text)

1. Primary structure - simply the order of amino acids in a polypeptide strand.

2. Secondary structure - regions of localized bending resulting in a) an alpha helix

and/or b) pleating (like an accordion) called beta sheets give proteins their

secondary structure. Weak hydrogen bonds cause this structure.

3. Tertiary structure - the three-dimensional folding of the entire polypeptide chain.

4. Quaternary structure - the fitting together of two or more polypeptide chains,

thus forming a functional protein.

4. Nucleic Acids

Large organic molecules whose chief function is to carry the genetic information in the form of a code. There are two main types: Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Nucleic acids are made up of polymers of nucleotides, their building blocks. DNA exists as a double helix while RNA is a single helix. See Structure of a single nucleotide in text:

In DNA the four different nitrogen bases are adenine, thymine, guanine, and cytosine. RNA substitute uracil for thymine, otherwise it is the same,

Another, very important molecule that is composed of nucleotides is adenosine triphosphate (ATP); it is technically not a nucleic acid like DNA and RNA. It is known as the energy molecule; it provides immediate energy for the activities of every living cell. We will discuss this vital molecule in further detail when we discuss Cell Respiration.