In this chapter, you will be introduced to some of the most fundamental principles of organic chemistry. With the concepts we learn about, we can begin to understand how carbon and a very small number of other elements in the periodic table can combine in predictable ways to produce a virtually limitless chemical repertoire. As you read through, you will recognize that the chapter contains a lot of review of topics you have probably learned already in an introductory chemistry course, but there will likely also be a few concepts that are new to you, as well as some topics which are already familiar to you but covered at a greater depth and with more of an emphasis on biologically relevant organic compounds.
- 1.1: Prelude to Atoms, Electron Configurations, and Lewis Structures
- We will begin with a reminder of how chemists depict bonding in organic molecules with the 'Lewis structure' drawing convention, focusing on the concept of 'formal charge'. We will review the common bonding patterns of the six elements necessary for all forms of life on earth - carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus - plus the halogens (fluorine, chlorine, bromine, and iodine).
- 1.2: Drawing Organic Structures
- Now that you have had a chance to go back to your introductory chemistry textbook to review some basic information about atoms, orbitals, bonds, and molecules, let's direct our attention a little more closely to the idea of charged species. You know that an ion is a molecule or atom that has an associated positive or negative charge.
- 1.3: Functional groups and organic nomenclature
- Functional groups are structural units within organic compounds that are defined by specific bonding arrangements between specific atoms. The structure of capsaicin, the compound discussed in the beginning of this chapter, incorporates several functional groups, labeled in the figure below and explained throughout this section.
- 1.4: Structures of some important biomolecules
- Because we are focusing in this textbook on biologically relevant organic chemistry, we will frequently be alluding to important classes of biological molecules such as lipids, carbohydrates, proteins, and nucleic acids (DNA and RNA). Now is a good time to go through a quick overview of what these molecules look like.