2.1: Introduction

In this chapter, we start with a review basic chemistry from atomic structure to molecular bonds to the structure and properties of water, followed by a review of key principles of organic chemistry - the chemistry of carbon-based molecules. You may find it useful to have your old general chemistry textbook handy, or check out the excellent introduction to general chemistry by Linus Pauling (1988, General Chemistry New York, Springer-Verlag). We’ll see how the polar covalent bonds define the structure and explain virtually all of properties of water. These range from the energy required to melt a gram of ice to vaporize a gram of water to its surface tension to its ability to hold heat…, not to mention its ability to dissolve a wide variety of solutes from salts to proteins and other macromolecules. We will distinguish water’s hydrophilic interactions with solutes from its hydrophobic interactions with fatty molecules. Then, we review some basic biochemistry. Well-known biological molecules include monomers (sugars, amino acids, nucleotides, lipids…) and polymers (polysaccharides, proteins, nucleic acids, fats…).

Biochemical reactions that link glucose monomers into polymers on the one hand, and break the polymers down on the other are essential reactions for life on earth. Photosynthetic organisms link glucose monomers into starch, a polysaccharide. Amylose is a simple starch, a large homopolymer of repeating glucose monomers. Likewise, polypeptides are heteropolymers of 20 different amino acids. DNA and RNA nucleic acids are also heteropolymers, made using only four different nucleotides.

When you eat, digestive enzymes in your gut catalyze the hydrolysis of the plant or animal polymers we ate back down to monomers. Hydrolysis adds a water molecule across the bonds linking the monomers in the polymer. Our cells then take up the monomers. Once in our cells, condensation (dehydration synthesis) reactions remove water molecules from participating monomers to grow new polymers that are more useful to us. While they are not, strictly speaking, macromolecules, triglycerides (fats) and phospholipids are also broken down by hydrolysis and synthesized in condensation reactions. Triglycerides are energy-rich molecules, while phospholipids (chemical relatives of triglycerides) are the basis of cellular membrane structure.

Relatively weak interactions between macromolecules, for example, hydrogen bonds (H-bonds), electrostatic interactions, Van der Waals forces, etc., hold many cellular structures and molecules together. Individually, these bonds are weak. But millions of them hold can the two complementary DNA strands tightly in a stable double helix. We will see this theme of strength in numbers repeated in other molecular and cellular structures. Monomers also serve other purposes related to energy metabolism, cell signaling etc. Depending on your chemistry background, you may find “Googling” these subjects interesting and useful. The short VOPs in this chapter might help as a guide to understanding the basic chemistry and biochemistry presented here.

Learning Objectives

When you have mastered the information in this chapter, you should be able to:

1. compare and contrast the definitions of atom, element and molecule.

2. List differences between atoms, elements and molecules and between energy and

position-based atomic models.

3. describe sub-atomic particle behavior when they absorb and release energy.

4. state the difference between atomic shells and orbitals.

5. state how kinetic and potential energy applies to atoms and molecules.

6. explain the behavior of atoms or molecules that fluoresce when excited by high- energy radiation…, and those that do not.

7. distinguish polar and non-polar covalent bonds and their physical-chemical properties.

8. predict the behavior of electrons in compounds held together by ionic interactions.

9. explain how the properties of water account for the solubility of salts and macromolecules and the role of H-bonds in support those properties.

10. consider why some salts are not soluble in water in terms of water’s properties.

11. describe how molecular linkages form during polymer metabolism and place hydrolytic and dehydration synthetic reactions in a metabolic context.

12. distinguish between chemical “bonds” and “linkages” in polymers.

13. categorize different chemical bonds based on their strengths.