insect infestations. Finally, the book explores the absorption, metabolism and potential impact on health of dietary caffeine, theobromine and trigonelline
The book provides comprehensive information on nucleotide structures and metabolic pathways and is a unique resource on a diversity of topics and as such is essential reading for students, researchers, and lecturers in plant biochemistry, physiology, chemistry, agricultural sciences, nutrition and the associated applied fields of research.
We owe special thanks Professors Tatsuhito Fujimura, Claudio Stasolla and Takao Yokota for their help with some of the figures and advice on genes encoding key enzymes and chemical structures for the book.
Hiroshi Ashihara
Iziar A. Ludwig
Alan Crozier
1 Structures of Nucleotide-Related Compounds
1.1 Introduction
The chemistry of purine, pyrimidine, and pyridine nucleobases, nucleosides, and nucleotides constitute one of the oldest topics in biochemistry. In this chapter, the nomenclature and structures of nucleotides are briefly described.
1.2 Nomenclature and Abbreviations of Nucleotide-Related Compounds
The nucleotide nomenclature and abbreviations employed in the text are those used by Henderson and Paterson (1973) in their textbook ‘Nucleotide Metabolism – An Introduction’. The terms ‘nucleoside’ and ‘nucleotide’ in the strictest sense refer, respectively, to N-glycosides and phosphorylated N-glycosides derived from nucleic acids. However, they are now used in a wider context. N-Ribosides, such as nicotinamide mononucleotide (NMN), are called nucleotides only by extension and analogy, and nicotinamide adenine dinucleotide (NAD) and nicotinamide adenine dinucleotide phosphate (NADP) are referred to as dinucleotides. Flavin mononucleotide (FMN) is a step further removed, as it contains ribitol, a pentose alcohol formed by the reduction of ribose, instead of ribose, while flavin adenine dinucleotide (FAD) similarly extends the meaning of dinucleotide. N-Glycosides such as orotidine 5′-monophosphate (OMP) and adenylosuccinate (SAMP) are called nucleotides through their close relationship to the ‘true’ nucleotides. The terms ribonucleoside and ribonucleotide are used in preference to riboside and ribotides. The IUPAC-IUB Combined Commission on Biochemical Nomenclature has abbreviations and symbols for nucleotides and related compounds. However, as argued by Henderson and Paterson (1973), while they are appropriate for polynucleotides, the distinction between bases and nucleosides is not always immediately obvious, and this has limited their use. The abbreviations used here are more intuitive and better suited to the portrayal of reaction schemes in which the addition or removal of substituent groups occurs.
In Table 1.1, the abbreviations for the major nucleotides, ribo- and deoxyribonucleotides and nucleobases are presented. For readers convenience, the styles used both in this book (style #1) and those recommended by IUPAC (style #2) are shown.
Table 1.1 Nomenclature and abbreviations of purine and pyridine ribo- and deoxyribonucleotides and related compounds.
| Ribonucleotides | Ribonucleosides | #1 | #2 | Nucleobases | #1 | #2 | |
| Adenosine-5′-monophosphate | AMP | Adenosine | AR | Ado | Adenine | A | Ade |
| Guanosine-5′-monophosphate | GMP | Guanosine | GR | Guo | Guanine | G | Gua |
| Inosine-5′-monophosphate | IMP | Inosine | IR | Ino | Hypoxanthine | H | Hyp |
| Xanthosine-5′-monophosphate | XMP | Xanthosine | XR | Xao | Xanthine | X | Xan |
| Uridine-5′-monophosphate | UMP | Uridine | UR | Urd | Uracil | U | Ura |
| Cytidine-5′-monophosphate | CMP | Cytidine | CR | Cyd | Cytosine | C | Cyt |
| Orotidine-5′-monophosphate | OMP | Orotidine | OR | Ord | Orotic acid | O | Oro |
| Deoxyribonucleotides | Deoxyribonucleosides | #1 | #2 | Nucleobases | #1 | #2 | |
| Deoxyadenosine-5′-monophosphate | dAMP | Deoxyadenosine | AdR | dAdo | Adenine | A | Ade |
| Deoxyguanosine-5′-monophosphate | dGMP | Deoxyguanosine | GdR | dGuo | Guanine | G | Gua |
| Deoxyuridine-5′-monophosphate | dUMP | ||||||
