Atoms
The periodic table lists all known types of atoms beginning with hydrogen at number 1 (one proton) and continuing to unstable synthesized atoms (with over 100 protons). The more important molecules involved in life processes are carbon (6 protons), hydrogen (1 proton), oxygen (8 protons), nitrogen (7 protons), phosphorous (15 protons), and sulfur (16 protons).
Atoms and their Interactions
Atoms are the fundamental particles that make up all matter. They combine (via several kinds of chemical bonding) to form compounds. A compound is a substance with two or more elements, combined in a specific ratio. Water is an example; it has two hydrogen atoms and one oxygen atom.
The chemical activity of atoms is determined by how full the outer electron shell of the atom is. As well as listing the atomic numbers (the number of protons), the periodic table organizes atoms by the available spots they have in their outer electron shells for more electrons. In order to fill these openings, atoms will receive, donate or share electrons.
Oxygen, carbon, hydrogen and nitrogen compose over 96% of the human body's weight. Insulin has the chemical formula C257 H383 N65 O77 S6. The numbers in subscript indicate how many each of the named atoms goes into this molecule.
Covalent and hydrogen bonding
In covalent bonding, two atoms share outer electron shell electrons. Molecules are atoms that are held together by covalent bonds. The shape and charges on the outside of molecules is very important to their biological activity.
Water is a molecule with important chemical properties for living things. The two hydrogen atoms are held tightly to the oxygen atom by covalent bonds. It is a polar molecule, which means the electrical charges are not distributed equally around the molecule. The oxygen end of the molecule is slightly more negative, and the region of the molecule around the two hydrogen atoms is slightly more positive. This feature of water makes it very useful for this molecule to dissolve solutes. The differing charges at the ends allow the water molecule to surround and isolate the solute particles. In fact, water is called the "universal solvent".
Oxygen, carbon, hydrogen and nitrogen and sulfur make proteins.
Hydrogen bonds are very weak bonds that result from the interactions between the slightly positive end of the hydrogen atom and a slightly negative end of a molecule. Water atoms hydrogen bond with each other. This feature allows water molecules to adhere to each other, a feature called water cohesion.
We will also see the importance of hydrogen bonding when we look at the DNA molecule in our transcription and translation sections. It is hydrogen bonding which holds the double stranded molecule of DNA together.
Protein chemistry
Atoms combine to make small molecules such as glucose or amino acids. Some small molecules are monomers that combine via covalent bonds with other monomers to make larger molecules called polymers. In living systems, there are four main groups of polymers: lipids, carbohydrates, proteins and nucleic acids. We will consider the latter two in detail.
There are billions of different kinds of proteins in the natural world. They are all built from among the twenty amino acids, and it is the sequence of these amino acids, their primary structure, which is the first step in the protein's individuality. There are eight essential amino acids which humans must obtain from our food, as we cannot assemble them ourselves. These are tryptophan, lysine, methionine, phenylalanine, threonine, valine, leucine, and isoleucine.
Amino acids are molecules that are composed of an amino group (a molecule composed of nitrogen and hydrogen), a central carbon, and a carboxyl group (a molecule of carbon, oxygens and hydrogen). Located off the central carbon atom is an R group. The R group is a molecule that makes each amino acid different from the next, and what is responsible for the specific chemical activity of each amino acid.
These amino acids are linked together to form protein polymers by means of dehydration (condensation) reactions. As the name of the reaction suggests, a water molecule is released when the carboxyl end of one amino acid is linked to the amino group of the next amino acid. This creates a peptide bond that is a strong chemical bond between amino acids. This is why protein molecules are also called polypeptides.
When the amino acids bonds are broken by digestion or other chemical process, a hydrolysis reaction must happen, which involves adding a water molecule to the end of each amino acid.
Proteins have a secondary structure that is dictated by the arrangement of hydrogen bonds between the ends of the amino acids. Depending on the arrangement of these hydrogen bonds, the protein may fold into a sheet or helical formation.
The tertiary level of structure is very important to the overall function of the protein. The overall three-dimensional folding, generally a result of interactions among the R groups of the individual amino acids, results in a molecule that has a shape to meet its functional needs. Insulin, for example, facilitates transport of glucose into the cell by docking to receptors on the surface of the cell and causes a change in the cell membrane, which permits glucose to enter.
Insulin is composed of two chains, an A and B chain. The A chain has 21 amino acids, the B chain has 30 amino acids. Two disulphide bonds link this polypeptide, another disulphide bond is formed in A chain. The disulphide bonds occur between cystine amino acids on each chain, and there is a third disulphide bond which links part of the A chain back on itself.
There are many good images of this molecule on the internet, such as those on these pages.
http://www.expasy.org/spotlight/back_issues/sptlt009.shtml
http://www.pharmaceutical-technology.com/projects/eli_lilly/eli_lilly1.html