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Chapter 5 : Organic Functional Group Diversity: the Unity of Biochemistry Is Dwarfed by Its Diversity

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Abstract:

The compounds to be considered in the context of biodegradation and biocatalysis are the known organic molecules, an ever-expanding set of over 10 million compounds. This chapter presents evidence from the natural-product literature to support the idea that many functional groups typically referred to as xenobiotic are in fact found in the natural biological world, exclusive of organic synthesis. A common practice in correlating the types of organic molecule with their ease of biodegradation is to define them as (i) natural products or (ii) industrial chemicals. Many organic functional groups are acted upon by the individual enzymes of biodegradation. A given enzyme typically transforms one organic functional group in isolation, for example, oxidizing an alcohol to an aldehyde or hydrolyzing an amide to a carboxylic acid and an amine. The chapter highlights the impressive diversity of biologically relevant chemical structures and provides a framework for categorizing their microbial metabolism. The diversity of organic compounds is effectively infinite, and over 10 million compounds are currently described in the chemical literature. Understanding the microbial metabolism of such a broad range of compounds necessitates an efficient categorization of microbial reactions.

Citation: Wackett L, Hershberger C. 2001. Organic Functional Group Diversity: the Unity of Biochemistry Is Dwarfed by Its Diversity, p 71-93. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch5

Key Concept Ranking

Organic Chemicals
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Polycyclic Aromatic Hydrocarbons
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Figures

Image of Figure 5.1
Figure 5.1

Schematic depiction of the carbon cycle, in which CO is incorporated into organic compounds by plants and microbial autotrophs and complex organic compounds are oxidized back to CO, largely by prokaryotes.

Citation: Wackett L, Hershberger C. 2001. Organic Functional Group Diversity: the Unity of Biochemistry Is Dwarfed by Its Diversity, p 71-93. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch5
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Image of Figure 5.2
Figure 5.2

Major biological cycling of the elements of carbon, hydrogen, nitrogen, oxygen, and sulfur is catalyzed largely by microorganisms. Some representative microorganisms catalyzing certain transformations are shown.

Citation: Wackett L, Hershberger C. 2001. Organic Functional Group Diversity: the Unity of Biochemistry Is Dwarfed by Its Diversity, p 71-93. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch5
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Image of Figure 5.3
Figure 5.3

Thousands of aromatic hydrocarbons are made naturally; several representative structures are shown.

Citation: Wackett L, Hershberger C. 2001. Organic Functional Group Diversity: the Unity of Biochemistry Is Dwarfed by Its Diversity, p 71-93. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch5
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Image of Figure 5.4
Figure 5.4

Cliloromethane is made principally by microorganisms; 0.5% of the world output is made industrially.

Citation: Wackett L, Hershberger C. 2001. Organic Functional Group Diversity: the Unity of Biochemistry Is Dwarfed by Its Diversity, p 71-93. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch5
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Image of Figure 5.5
Figure 5.5

Some representative nitrogen heterocycles found in natural products.

Citation: Wackett L, Hershberger C. 2001. Organic Functional Group Diversity: the Unity of Biochemistry Is Dwarfed by Its Diversity, p 71-93. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch5
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Image of Figure 5.6
Figure 5.6

Some representative oxygen heterocycles found in natural products.

Citation: Wackett L, Hershberger C. 2001. Organic Functional Group Diversity: the Unity of Biochemistry Is Dwarfed by Its Diversity, p 71-93. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch5
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Image of Figure 5.7
Figure 5.7

Sulfur and mixed heterocycles found in natural products.

Citation: Wackett L, Hershberger C. 2001. Organic Functional Group Diversity: the Unity of Biochemistry Is Dwarfed by Its Diversity, p 71-93. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch5
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Image of Figure 5.8
Figure 5.8

Organic functional groups known to undergo transformation by microbes and represented in the UM-BBD.

Citation: Wackett L, Hershberger C. 2001. Organic Functional Group Diversity: the Unity of Biochemistry Is Dwarfed by Its Diversity, p 71-93. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch5
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Tables

Generic image for table
Table 5.1

Major classes of secondary plant compounds

Citation: Wackett L, Hershberger C. 2001. Organic Functional Group Diversity: the Unity of Biochemistry Is Dwarfed by Its Diversity, p 71-93. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch5
Generic image for table
Table 5.2

Organic functional groups found in natural products

Citation: Wackett L, Hershberger C. 2001. Organic Functional Group Diversity: the Unity of Biochemistry Is Dwarfed by Its Diversity, p 71-93. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch5
Generic image for table
Table 5.3

Naturally produced cycloalkane ring compounds

Citation: Wackett L, Hershberger C. 2001. Organic Functional Group Diversity: the Unity of Biochemistry Is Dwarfed by Its Diversity, p 71-93. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch5

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