Miscellaneous Nomenclature

The full text of of the following documents are included under this heading:

IUPAC-IUB Abbreviations and symbols for the description of the conformation of polypeptide chains (1969)

IUPAC-IUB Symbols for specifying the conformation of polysaccharide chains. Recommendations 1981

IUPAC-IUB Abbreviations and symbols for the description of conformations of polynucleotide chains. Recommendations 1982

IUPAC-IUB Abbreviations and Symbols for Nucleic Acids, Polynucleotides and their Constituents. Recommendations 1970

IUPAC-IUB Nomenclature of glycoproteins, glycopeptides and peptidoglycans. Recommendations 1985

IUPAC-IUBMB Nomenclature of Glycolipids. (Recommendations 1997)

IUPAC-IUB Nomenclature of Tocopherols and Related Compounds. (Recommendations 1981)

IUPAC-IUB Nomenclature of Retinoids (Recommendations 1981)

IUPAC-IUB Nomenclature for Vitamins B-6 and Related Compounds. (Recommendations 1973)

IUPAC-IUB The Nomenclature of Corrinoids. (Recommendations 1975)

IUPAC-IUB Nomenclature and symbols for folic acid and related compounds. (Recommendations 1986)

IUPAC-IUB Prenol nomenclature. (Recommendations 1986)

IUPAC Extension of rules A-1.1 and A-2.5 concerning numerical terms used in organic chemical nomenclature. (Recommendations 1986)

Contents

• Preamble

• 1. General Principles of Notation
  • 1.1 Designation of atoms
  • 1.2 Amino acid residue numbering
  • 1.3 Peptide units
  • 1.4 Bond lengths
  • 1.5 Bond angles
  • 1.6 Torsion angles
  • 1.7 Conformational regions

• 2. The Sequence Rule, and Choice of Torsion Angle
  • 2.1. The sequence rule
  • 2.2. Choice of torsion angle and numbering of branches (tetrahedral configurations)
  • 2.3. Choice of torsion angle and numbering of branches (planar trigonal configurations)

• 3. The Main Chain (or Polypeptide Backbone)
  • 3.1. Designation of bonds
  • 3.2. Torsion angles
  • 3.3. Chain terminations

• 4. Side Chains
  • 4.1. Atoms
  • 4.2. Designation of atoms other than hydrogen
  • 4.3. Designation of branches
  • 4.4. Designation of hydrogen atoms
  • 4.5. Designation of bonds and torsion angles

• 5. Hydrogen Bonds
  • 5.l. Polarity of hydrogen bonds
  • 5.2. Dimensions of hydrogen bonds

• 6. Helical Segments
  • 6.1. Symbols
  • 6.2. Definition in terms of and
  • 6.3. Definition in terms of symmetry and hydrogen-bond arrangement

• Appendix
  • A. Conformation and Configuration
  • B. Definitions of Primary, Secondary, Tertiary, and Quaternary Structure
    • B.l. Primary Structure
    • B.2. Secondary Structure
    • B.3. Tertiary Structure
    • B.4. Quaternary Structure

• References

Contents

• 1. General principles of notation
  • 1.1. Direction of numbering
  • 1.2. Monomeric unit
  • 1.3. Atom numbering
  • 1.4. Interatomic distances
  • 1.5. Bond angles
  • 1.6. Ring shape
    • 1.6.1 Endocyclic torsion angles
    • 1.6.2 General notation of residue conformation
  • 1.7. Conformation of side groups

• 2. Orientation of the glycosidic linkage
  • 2.1. Designation of bonds
  • 2.2. Torsion angles

• 3. Helix characteristics

• References

Contents

• Introduction

• l. General principles of notation
  • 1.1 Chain direction
  • 1.2 Definition of the nucleotide unit
  • 1.3 Atom numbering
  • 1.4 Bonds, bond lengths and interatomic distances
  • l.5 Bond angles
  • 1.6 Torsion angles
  • 1.7 Conformational regions

• 2. The nucleotide unit
  • 2.1 Sugar-phosphate backbone chain
  • 2.2 Sugar ring
    • 2.2.1 Endocyclic torsion angles
    • 2.2.2 Puckered forms
    • 2.2.3 Pseudorotational analysis
  • 2.3 N-Glycosidic bond
  • 2.4 Orientations of side groups

• 3. Hydrogen bonds
  • 3.1 Polarity of hydrogen bonds
  • 3.2 Geometry of hydrogen bonds

• 4. Helical segments
  • 4.1 Base pairs
  • 4.2 Helix characteristics

• Addenda. Atom numbering in polynucleotides

• References

Contents

• Introduction
• N-1. Abbreviations
  • N-1.1. Simple Nucleotides
  • N-1.2. Nucleotide Coenzymes and Related Substances
  • N-1.3. Nucleic Acids
    • N-1.3.1. DNA and RNA
    • N-1.3.2. RNA Fractions
    • N-1.3.3. Transfer RNA's
• Symbols
• General Concepts and Conventions
• N-2. Three-Letter Symbols
  • N-2.1. Phosphoric Acid Radical
  • N-2.2. Purines and Pyrimidines
  • N-2.3. Nucleosides
    • N-2.3.1. The ribonucleosides
    • N-2.3.2. The 2'-deoxribonucleosides
  • N-2.4. Nucleotides
    • N-2.4.1. Mononucleotides
    • N-2.4.2. Cyclic phosphodiesters
    • N-2.4.3. Nucleoside diphosphate sugars
    • N-2.4.4. Points of attachment
• N-3. One-Letter Symbols
  • N-3.1. Phosphoric Acid Residues
  • N-3.2. Nucleosides
    • N-3.2.1. Ribonucleosides
    • N-3.2.2. Deoxyribonucleosides
    • N-3.2.3. Unusual Sugar Residues
  • N-3.3. Oligo- and Polynucleotides
    • N-3.3.1. Points of Attachment
    • N-3.3.2. Direction of the Phosphodiester Link
  • N-3.4. Polymerized Nucleotides
    • N-3.4.1. Single Chains
    • N-3.4.2. Association between Chains
• N-4. Modified Bases, Sugars, or Phosphates in Polynucleotides
  • N-4.1. Designation of Substituents on Bases
  • N-4.2. Designation of Substituents on Sugars
    • N-4.2.1. Internal Modifications
    • N-4.2.2. Terminal Radicals
  • N-4.3. Phosphoric Acid Protecting Goups
  • N-4.4. Locants and Multipliers
• References
• Addendum Hyphens in nucleic-acid sequences

Contents

• 1. Introduction

• 2. Applications of a standard nomenclature
  • 2.1. Recognition sequences in DNA for restriction enzymes
  • 2.2. Recognition sequences in DNA for other enzymes
  • 2.3. Recognition sequences in RNA for enzymes involved in translation
  • 2.4. Codon degeneracy
  • 2. 5. Construction of ancestral sequences by parsimony procedures
  • 2.6. Other uses

• 3. Allocation of symbols
  • 3.1. Guanine. adenine, thymine, cytosine: G,A,T,C
  • 3.2. Purine (adenine or guanine): R
  • 3.3. Pyrimidine (thymine or cytosine): Y
  • 3.4. Adenine or thymine: W
  • 3.5. Guanine or cytosine: S
  • 3.6. Adenine or cytosine: M
  • 3.7. Guanine or thymine: K
  • 3.8. Adenine or thymine or cytosine: H
  • 3.9. Guanine or cytosine or thymine: B
  • 3.10. Guanine or adenine or cytosine: V
  • 3.11. Guanine or adenine or thymine: D
  • 3.12. Guanine or adenine or thymine or cytosine: N

• 4. Other accessory symbols

• 5. Discussion
  • 5.1. Interpretation of primary sequencing data
  • 5.2. Modified nucleotides

• References

Contents

• l. Introduction

• 2. Nomenclature
  • 2.1. Glycoproteins, proteoglycans and glycosaminoglycans
  • 2.2. Glycopeptides, glyco-amino-acids and glycosyl-amino-acids
  • 2.3. Peptidoglycans

• 3. Comments
  • 3.1. Form of carbohydrate in glycoproteins
  • 3.2. Proteoglycans
  • 3.3. Microheterogeneity
  • 3.4. Glycopeptides, etc.
  • 3.5. N,O-Glycoproteins
  • 3.6. Asialoglycoproteins and asialo-agalactoglyco-proteins
  • 3.7. Condensed representation of sugar chains
  • 3.8. Representation of N-linked oligosaccharides
  • 3.9. Peptidoglycans

• 4. References

• 5. Appendix: Implied configurations and ring sizes

Contents

• GL-1. General considerations

• GL-2. Generic terms
  • GL-2.1. Glycolipid
  • GL-2.2. Glycoglycerolipid
  • GL-2.3. Glycosphingolipid
  • GL-2.4. Glycophosphatidylinositol
  • GL-2.5. Psychosine
  • GL-2.6. Other names

• GL-3. Principles of nomenclature
  • GL-3.1. Number of monosaccharide residues
  • GL-3.2. Naming of monosaccharide residues
  • GL-3.3. Use of symbols for defining oligosaccharide structures
  • GL-3.4. Ring size and conformation

• GL-4. Classification of glycolipids based on their lipid moieties
  • GL-4.1. Glycoglycerolipids
  • GL-4.2. Glycophosphatidylinositols
  • GL-4.3. Glycosphingolipids

• GL-5. Neutral glycosphingolipids
  • GL-5.1. Monoglycosylceramides
  • GL-5.2. Diosylceramides
  • GL-5.3. Neutral glycosphingolipids with oligosaccharide chains

• GL-6. Acidic glycosphingolipids
  • GL-6.1. Gangliosides
  • GL-6.2. Glycuronoglycosphingolipids
  • GL-6.3. Sulfatoglycosphingolipids
  • GL-6.4. Phosphoglycosphingolipids
  • GL-6.5. Phosphonoglycosphingolipids

• GL-7. Short abbreviations
  • GL-7.1. Recommended abbreviations
  • GL-7.2. The Svennerholm abbreviations for brain gangliosides

• GL-8. References

This document [Copyright IUBMB and IUPAC] was published in the following journals, Arch. Biochem. Biophys., 1982, 218, 347-348; Eur. J. Biochem., 1982, 123, 473-475; Mol. Cell. Biochem., 1982, 49, 183-185; Pure Appl. Chem., 1982, 54, 1507-1510; and in Biochemical Nomenclature and Related Documents, 2nd edition, Portland Press, 1992, pages 239-241.

Contents

• Preamble
• Ret-1. Class of Compounds
  • Ret-1.1. Vitamin A
• Ret-2. Stereoparents
  • Ret-2.1. Retinol
  • Ret-2.2. Retinal
  • Ret-2.3. Retinoic Acid
• Ret-3. Numbering
• Ret-4. Modification of Stereoparent
  • Ret-4.1. Basic Hydrocarbon
  • Ret-4.2. Change of the Functional Group
    • Ret-4.2.1. Derivatives of the basic hydrocarbon
    • Ret-4.2.2. Derivatives of retinal
    • Ret-4.2.3. Derivatives of retinoic acid
  • Ret-4.3. Changes in the Hydrogenation Level
  • Ret-4.4. Substituted Retinoids
  • Ret-4.5. Seco Retinoids
  • Ret-4.6. Nor Retinoids
  • Ret-4.7. Retro Retinoids
  • Ret-4.8. Other Modifications
• Ret-5. Stereochemistry
  • Ret-5.1. Chiral Groups
  • Ret-5.2. Double Bonds
• References
• Appendix Some Related Terpenoids Containing less than Twenty Carbon Atoms

Contents

Introduction
Rules
Vitamin B-6 Phosphates
Derivatives and Analogues
Abbreviated Designations
Use of Symbols in the Designation of Derivatives and Analogues
Isotopic Replacement
References

This document [Copyright IUBMB and IUPAC] was published in the following journals, Arch. Biochem. Biophys., 1974, 162, 1-5; Biochem. J., 1974, 137, 417-421; Biochemistry, 1974, 13, 1056-1058; Biochim. Biophys. Acta, 1974, 354, 155-159; Eur. J. Biochem., 1973, 40, 325-327; Pure Appl. Chem., 1973, 33, 445-452; and in Biochemical Nomenclature and Related Documents, 2nd edition, Portland Press, 1992, pages 269-271.

This document [Copyright IUBMB and IUPAC] was published in the following journals, Arch. Biochem. Biophys., 1974, 161(2), iii-xi (between pages 334-335); Biochem. J., 1975, 147, 1-10; Biochemistry, 1974, 13, 1555-1560; Eur. J. Biochem., 1974, 45, 7-12; Pure Appl. Chem., 1976, 48, 495-502; and in Biochemical Nomenclature and Related Documents, 2nd edition, Portland Press, 1992, pages 269-271.

Contents

Introduction
1. Class Name
2. Semisystematic names
3. Stereoparent Compounds
4. Numbering
5. Modification of the Triene System
6. Side Chain Modification
7. Dihydro Derivatives
8. Other Modifications
9. Combination of Prefixes
10. Additional Hydroxyl Groups
   a) designated by a suffix
   b) designated by a prefix
11. Other Substituents
   a) modification of the suffix
   b) designated by a prefix
References
Appendix. Trivial names of vitamin D compounds

This document [Copyright IUBMB and IUPAC] was published in the following journals, Arch. Biochem. Biophys., 1982, 218, 342-346; Endokrinol. Inform., 1982(2), 53-62; Eur. J. Biochem., 1982, 124, 223-227; Mol. Cell. Biochem., 1982, 49, 177-181; Pure Appl. Chem., 1982, 54, 1511-1516; and in Biochemical Nomenclature and Related Documents, 2nd edition, Portland Press, 1992, pages 242-246.

Contents

1. Introduction
2. Revised recommendations
2.1. Parent compound
2.2. Numbering
2.3. Glutamate conjugates
2.4. Folate and folic acid
2.5. Generic use of the term folates
2.6. Reduced compounds
2.7. Substituents
2.8. Symbols and abbreviations
3. References

This document [Copyright IUBMB and IUPAC] was published in the following journals, Eur. J. Biochem., 1987, 168, 251-253; J. Biol. Chem., 1987, 263, 605-607; Pure Appl. Chem., 1987, 59, 833-836; and in Biochemical Nomenclature and Related Documents, 2nd edition, Portland Press, 1992, pages 266-268.

Contents

• Introduction
• General terms
  • Pr-1. Prenol
  • Pr-2. Polyprenol
  • Pr-3. Esters and their derivatives
  • Pr-4. Number of residues
• Stereochemistry
  • Pr-5. Double bonds
  • Pr-6. Order of stereochemical prefixes
  • Pr-7. Multiplicative prefixes
• Specilic compounds
  • Pr-8. Trivial names
  • Pr-9. Isopentenyl diphosphate
  • Pr-10. Relationship between polyprenols and isoprenoids
  • Pr-11. Juvenile hormones
  • Pr-12. Dolichols
• References

Contents

Introduction
Discussion
Recommendations
NT-1 Numerical terms for simple features
NT-2 Numerical terms for complex features
References

This document [Copyright IUPAC] was published in the following journal, Pure Appl. Chem., 1986, 58, 1693-1696.