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As you begin a course in organic chemistry, you probably have many questions. Here are my attempts to answer a few of the questions that you are most likely to be wondering about.

What is organic chemistry, and why do I need to study it?

As you probably already know, organic chemistry is defined as the study of molecules that contain the element carbon. If you are interested in the science of living things, then you are also interested in organic chemistry - organic molecules and the reactions they undergo form the basic currency of life on earth. You cannot understand how a human cell breaks down carbohydrate or fat for energy without gaining a solid understanding of the basic processes of organic chemistry that underlie these metabolic events. You cannot appreciate how drugs work, on a molecular level, until you have first learned about the three dimensional structure of organic molecules and how different organic 'functional groups' interact with one another. And if you don't know your organic chemistry, you will have difficulty understanding and explaining the molecular underpinnings of diseases such as depression, cancer, or diabetes.

The relevance of organic chemistry is not restricted to the study of living systems, however. You need a firm grasp of the subject to understand many ongoing developments in renewable energy, nanomaterials, environmental clean-up, and drug development and regulation, just to name a few examples. Society always has - and probably always will - need people who know how to synthesize, analyze, and break down organic molecules in useful ways, and this need translates to rewarding careers with good salaries and working conditions.

How is organic chemistry going to be different from general chemistry?

Depending on your experience with general chemistry, you may be pleased (or dismayed) to learn that most students find organic chemistry to be an entirely new breed of beast. It is common to see students, who felt very much at home with general chemistry, struggle with organic – and vice versa. To begin with, an introductory course in organic chemistry tends to focus much more on the qualitative than it is does on the quantitative (translation – there much less math!) But don't get too comfortable just yet – despite its scarcity of math, you undoubtedly are aware that very few people find organic to be an easy course. In fact, many science and pre-health majors report that it was for them the single most challenging part of their undergraduate career. You are going to be asked to take in and digest a lot of new concepts, many of which involve visualization in three dimensions, and some of which are, at first pass at least, quite abstract. But that is just a start – the really hard part comes when you are asked to connect several of the ideas that you have learned, in a process of deductive reasoning. It is not enough, in other words, to understand A, B, and C as isolated concepts– you must also be able to solve chemical problems for which you need to find and follow the connections from A to B to C in order to arrive at a valid solution. It is this aspect of organic chemistry that students find the most challenging, yet also the most rewarding. Another major difference between general chemistry and organic chemistry has to do with the way you will be thinking about chemical reactivity. In general chemistry, you mainly saw reactions depicted by chemical equations of the type:

In this type of treatment, you focused mainly on changes in molecular formulas, and on basic ideas of thermodymanics (energy changes) and kinetics (rates of reactions). For the most part, you disregarded the structure of the molecules involved and the details of how the reaction proceeded. In organic chemistry, we will be very concerned with the structures of the reacting molecules, and we will also think very carefully about how the reaction takes place – which bonds break, which bonds form, and in what order this happens.

This is known as the mechanism of a reaction. We will also think carefully about why reactions take place as they do: we'll be thinking, in other words, about the connections between structure and reactivity, and also about how chemical structure relates to the thermodynamics and kinetics of an equation. Why, for example, does one specific carbon-carbon bond break in the reaction sequence above, and not others? What is the importance of the carbon-oxygen double bonds? How is the reaction accelerated by an enzyme catalyst? By necessity, an understanding of structure must come before we tackle reactivity. We will spend the first several chapters learning about how molecules are put together (their structure), and then turn, for the remainder of the book, to discussion about how our knowledge of molecular structure can help us to understand the many different ways in C6H3O7 CO2(g) + C5H4O5 which organic molecules react with each other. By the end of the course, your understanding of chemical reactions will have taken on entirely new dimensions. How is this textbook different from other organic chemistry textbooks? In this text, we focus our attention primarily on biological organic chemistry - the organic reactions that take place in living things - simply because this is, for most people, the most interesting and relevant context in which to learn the principles of the subject. This is not, however, the traditional way to approach the subject – if you take a look at most other organic chemistry textbooks, you will see a much stronger emphasis on examples that come not from biology but from the chemical synthesis laboratory, where chemists work to create new synthetic molecules for medicinal or industrial use. In this text we will study some of the most important reactions of laboratory synthesis with which professional chemists need to be familiar - these are usually in sections entitled 'synthetic parallel' in order to highlight the conceptual similarities between laboratory and biological chemistry. You will notice, however, that the biological chemistry almost always comes first, and always forms the heart of the discussion – this is by design.

What are the differences between laboratory and biological chemistry?

Although the fundamental principles of organic chemistry are the same regardless of whether we are looking at a biological or laboratory example, there are a few key differences that we will need to keep in mind as we study the subject from both angles. The most important difference between a biological organic reaction and a reaction that takes place in the laboratory is that biological reactions are, almost exclusively, catalyzed by enzymes. The role of an enzyme is both to speed up a reaction and also to guide it, making sure that a specific product results. Laboratory reactions generally take place free in solution (or perhaps on the surface of a metal) without guidance by an enzyme. This means that often more than one possible reaction can take place, and more than one product can form. When we study laboratory reactions, we often have to consider several possible reaction outcomes, learn to predict which one will predominate, and sometimes suggest how a chemist might be able to control reaction conditions so as to maximize the formation of the desired product. When we study enzyme-catalyzed biological reactions, in contrast, one of the central things that we try to understand is how the enzyme is able to guide the reaction so that only the desired product is formed. Another point to keep in mind is that biological reactions take place exclusively in aqueous (water-based) solution, and at physiological pH and temperature, which for most organisms is pH 7 and about 37o C. In the laboratory, a chemist can run a reaction in many different kinds of solvent, use strong bases or acids, and raise or lower the reaction temperature. One of the most fascinating aspects of studying enzyme-catalyzed organic chemistry is that we can apply our knowledge of the central principles of the subject in order to understand how an enzyme is able to overcome the natural limitations on reaction conditions.

How will this class, with its focus on biological organic chemistry, be different from a class in biochemistry? You should not make the mistake of thinking that a course built around biological examples is going to be more biochemistry than organic chemistry. Although there will inevitably be some overlap with the biochemistry course you may take later in your career (just as there is overlap between courses in general chemistry and organic chemistry, between physical chemistry and physics, etc.), this is very much an organic chemistry text – it follows essentially the same outline and covers essentially the same topics as most other organic chemistry texts, and is fundamentally distinct from most biochemistry texts. In organic chemistry, we think about individual chemical reactions at the atomic level – concentrating on the 'how and why' details of what is happening with the organic molecule(s) in question. In a biochemistry course, you will see many of the same compounds and reactions that you saw in this text. In biochemistry, however, you will see them mainly from the perspective of complete biochemical pathways: you will spend much of your time studying how these pathways are interconnected and regulated. Biochemistry, then, is a 'bigger picture' course where we study the forest, while in organic chemistry we study the trees.