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Chemistry LibreTexts

6: Organic and Biological Chemistry

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  • Carbon is unique among the elements in its ability to catenate, to form a wide variety of compounds that contain long chains and/or rings of carbon atoms. Some of the most complex chemical structures known are those of the organic molecules found in living organisms. In spite of their size and complexity, these biological molecules obey the same chemical principles as simpler organic molecules. Thus we can use Lewis electron structures to understand the preferred mode of reactivity of a variety of organic compounds, relative electronegativities and bond polarities to predict how certain groups of atoms will react, and molecular orbital theory to explain why certain organic species that contain multiple bonds are especially stable or undergo particular reactions when they interact with light.

    In this chapter, we continue our description of organic compounds by focusing on their molecular structures and reactivity; we will also introduce some of the fundamental types of reactions and reaction mechanisms you will encounter in organic and biological chemistry. We discuss why butter is a solid and oils are liquids despite the apparent similarities in their structures, why the widely used anti-inflammatory drug ibuprofen takes longer than half an hour to relieve pain, and the identity of the major carcinogen in grilled meats and cigarette smoke. The chapter concludes with a brief introduction to the molecules of life, which will explain how the consumption of lactose can result in mental retardation and cirrhosis of the liver in some individuals, how hibernating animals survive during the winter, and how certain groups of antibiotics kill bacteria that are harmful to humans.

    • 6.0: General Characteristics of Organic Molecules
      Organic chemistry is the study of carbon compounds, nearly all of which also contain hydrogen atoms.
    • 6.1: Introduction to Hydrocarbons
      Hydrocarbons are organic compounds that contain only carbon and hydrogen. The four general classes of hydrocarbons are: alkanes, alkenes, alkynes and arenes. Aromatic compounds derive their names from the fact that many of these compounds in the early days of discovery were grouped because they were oils with fragrant odors.
    • 6.2: Alkanes
      Simple alkanes exist as a homologous series, in which adjacent members differ by a CH2 unit.
    • 6.3: Unsaturated Hydrocarbons
      As noted before, alkenes are hydrocarbons with carbon-to-carbon double bonds (R2C=CR2) and alkynes are hydrocarbons with carbon-to-carbon triple bonds (R–C≡C–R). Collectively, they are called unsaturated hydrocarbons because they have fewer hydrogen atoms than does an alkane with the same number of carbon atoms, as is indicated in the following general formulas:
    • 6.4: Functional Groups
      Functional groups are atoms or small groups of atoms (two to four) that exhibit a characteristic reactivity. A particular functional group will almost always display its characteristic chemical behavior when it is present in a compound. Because of their importance in understanding organic chemistry, functional groups have characteristic names that often carry over in the naming of individual compounds incorporating specific groups
    • 6.5: Compounds with a Carbonyl Group
      Aldehydes and ketones are characterized by the presence of a carbonyl group (C=O), and their reactivity can generally be understood by recognizing that the carbonyl carbon contains a partial positive charge ( δ+ ) and the carbonyl oxygen contains a partial negative charge ( δ− ). Aldehydes are typically more reactive than ketones.
    • 6.6: Chirality in Organic Chemistry
      Stereoisomers are isomers that differ in spatial arrangement of atoms, rather than order of atomic connectivity. One of their most interesting type of isomer is the mirror-image stereoisomers, a non-superimposable set of two molecules that are mirror image of one another. The existence of these molecules are determined by concept known as chirality.
    • 6.7: Introduction to Biochemistry
      Biochemistry is the study of chemical processes in living organisms, including, but not limited to, living matter. Biochemistry governs all living organisms and living processes. By controlling information flow through biochemical signaling and the flow of chemical energy through metabolism, biochemical processes give rise to the incredible complexity of life.
    • 6.8: Proteins
      The proteins in all living species are constructed from the same set of 20 amino acids, so called because each contains an amino group attached to a carboxylic acid. The amino acids in proteins are α-amino acids, which means the amino group is attached to the α-carbon of the carboxylic acid. Humans can synthesize only about half of the needed amino acids; the remainder must be obtained from the diet and are known as essential amino acids.
    • 6.9: Carbohydrates
      All carbohydrates consist of carbon, hydrogen, and oxygen atoms and are polyhydroxy aldehydes or ketones or are compounds that can be broken down to form such compounds. Examples of carbohydrates include starch, fiber, the sweet-tasting compounds called sugars, and structural materials such as cellulose. The term carbohydrate had its origin in a misinterpretation of the molecular formulas of many of these substances.
    • 6.10: Nucleic Acids
      Nucleotides are composed of phosphoric acid, a pentose sugar (ribose or deoxyribose), and a nitrogen-containing base (adenine, cytosine, guanine, thymine, or uracil). Ribonucleotides contain ribose, while deoxyribonucleotides contain deoxyribose.
    • 6.E: Organic and Biological Chemistry (Exercises)
      These are homework exercises to accompany the Textmap created for "Chemistry: The Central Science" by Brown et al.
    • 6.S: Organic and Biological Chemistry (Summary)

    Thumbnail: DNA Double Helix. Image used with permission (Public Domain; National Human Genome Research Institute)