Oligosaccharide nomenclature

Last updated

Oligosaccharides and polysaccharides are an important class of polymeric carbohydrates found in virtually all living entities. [1] Their structural features make their nomenclature challenging and their roles in living systems make their nomenclature important.

Contents

Oligosaccharides

Oligosaccharides are carbohydrates that are composed of several monosaccharide residues joined through glycosidic linkage, which can be hydrolyzed by enzymes or acid to give the constituent monosaccharide units. [2] While a strict definition of an oligosaccharide is not established, it is generally agreed that a carbohydrate consisting of two to ten monosaccharide residues with a defined structure is an oligosaccharide. [2]

Some oligosaccharides, for example maltose, sucrose, and lactose, were trivially named before their chemical constitution was determined, and these names are still used today. [2]

Trivial names, however, are not useful for most other oligosaccharides and, as such, systematic rules for the nomenclature of carbohydrates have been developed. To fully understand oligosaccharide and polysaccharide nomenclature, one must understand how monosaccharides are named.

An oligosaccharide has both a reducing and a non-reducing end. The reducing end of an oligosaccharide is the monosaccharide residue with hemiacetal functionality, thereby capable of reducing the Tollens’ reagent, while the non-reducing end is the monosaccharide residue in acetal form, thus incapable of reducing the Tollens’ reagent. [2] The reducing and non-reducing ends of an oligosaccharide are conventionally drawn with the reducing-end monosaccharide residue furthest to the right and the non-reducing (or terminal) end furthest to the left. [2]

Naming of oligosaccharides proceeds from left to right (from the non-reducing end to the reducing end) as glycosyl [glycosyl]n glycoses or glycosyl [glycosyl]n glycosides, depending on whether or not the reducing end is a free hemiacetal group. [3] In parentheses, between the names of the monosaccharide residues, the number of the anomeric carbon atom, an arrow symbol, and the number of the carbon atom bearing the connecting oxygen of the next monosaccharide unit are listed. [3] Appropriate symbols are used to indicate the stereochemistry of the glycosidic bonds (α or β), the configuration of the monosaccharide residue (D orL), and the substitutions at oxygen atoms (O). [2] Maltose and a derivative of sucrose illustrate these concepts:

Maltose Maltose struct.svg
Maltose
Maltose: α-D-Glucopyranosyl-(1→4)-β-D-glucopyranose
Methyl 2,3,4-tri-O-benzyl-6-deoxy-6-fluoro-a-D-galactopyranosyl-(1-4)-2,3,6-tri-O-acetyl-b-D-glucopyranoside Sucrose derivative struct.svg
Methyl 2,3,4-tri-O-benzyl-6-deoxy-6-fluoro-α-D-galactopyranosyl-(1→4)-2,3,6-tri-O-acetyl-β-D-glucopyranoside
Methyl 2,3,4-tri-O-benzyl-6-deoxy-6-fluoro-α-D-galactopyranosyl-(1→4)-2,3,6-tri-O-acetyl-β-D-glucopyranoside

In the case of branched oligosaccharides, meaning that the structure contains at least one monosaccharide residue linked to more than two other monosaccharide residues, terms designating the branches should be listed in square brackets, with the longest linear chain (the parent chain) written without square brackets. [3] The following example will help illustrate this concept:

Allyl a-L-fucopyranosyl-(1-3)-[a-D-galactopyranosyl-(1-4)]-a-D-glucopyranosyl-(1-3)-a-D-galactopyranoside Branched oligosaccharide struct.svg
Allyl α-L-fucopyranosyl-(1→3)-[α-D-galactopyranosyl-(1→4)]-α-D-glucopyranosyl-(1→3)-α-D-galactopyranoside
Allyl α-L-fucopyranosyl-(1→3)-[α-D-galactopyranosyl-(1→4)]-α-D-glucopyranosyl-(1→3)-α-D-galactopyranoside

These systematic names are quite useful in that they provide information about the structure of the oligosaccharide. They do require a lot of space, however, so abbreviated forms are used when possible. [4] In these abbreviated forms, the names of the monosaccharide units are shortened to their corresponding three-letter abbreviations, followed by p for pyranose or f for furanose ring structures, with the abbreviated aglyconic alcohol placed at the end of the name. [2] Using this system, the previous example would have the abbreviated name α-L-Fucp-(1→3)-[α-D-Galp-(1→4)]-α-D-Glcp-(1→3)-α-D-GalpOAll.General Formula_Cn+1(H2o)n.. Structure Formula..C12'H22'O11.

Polysaccharides

Polysaccharides are considered to be polymers of monosaccharides containing ten or more monosaccharide residues. [2] Polysaccharides have been given trivial names that reflect their origin. [2] Two common examples are cellulose, a main component of the cell wall in plants, and starch, a name derived from the Anglo-Saxon stercan, meaning to stiffen. [2]

To name a polysaccharide composed of a single type of monosaccharide, that is a homopolysaccharide, the ending “-ose” of the monosaccharide is replaced with “-an”. [3] For example, a glucose polymer is named glucan, a mannose polymer is named mannan, and a galactose polymer is named galactan. When the glycosidic linkages and configurations of the monosaccharides are known, they may be included as a prefix to the name, with the notation for glycosidic linkages preceding the symbols designating the configuration. [3] The following example will help illustrate this concept:

(1-4)-b-D-Glucan Homopolysaccharide struct.svg
(1→4)-β-D-Glucan
(1→4)-β-D-Glucan

A heteropolysaccharide is a polymer containing more than one kind of monosaccharide residue. [3] The parent chain contains only one type of monosaccharide and should be listed last with the ending “-an”, and the other types of monosaccharides listed in alphabetical order as “glyco-” prefixes. [3] When there is no parent chain, all different monosaccharide residues are to be listed alphabetically as “glyco-” prefixes and the name should end with “-glycan”. [3] The following example will help illustrate this concept:

((1-2)-a-D-galacto)-(1-4)-b-D-Glucan Heteropolysaccharide struct.svg
((1→2)-α-D-galacto)-(1→4)-β-D-Glucan
((1→2)-α-D-galacto)-(1→4)-β-D-Glucan

See also

Related Research Articles

Carbohydrate Organic compound that consists only of carbon, hydrogen, and oxygen

A carbohydrate is a biomolecule consisting of carbon (C), hydrogen (H) and oxygen (O) atoms, usually with a hydrogen–oxygen atom ratio of 2:1 (as in water) and thus with the empirical formula Cm(H2O)n (where m may or may not be different from n). However, not all carbohydrates conform to this precise stoichiometric definition (e.g., uronic acids, deoxy-sugars such as fucose), nor are all chemicals that do conform to this definition automatically classified as carbohydrates (e.g. formaldehyde and acetic acid).

Disaccharide Complex sugar

A disaccharide is the sugar formed when two monosaccharides are joined by glycosidic linkage. Like monosaccharides, disaccharides are simple sugars soluble in water. Three common examples are sucrose, lactose, and maltose.

Hemicellulose Class of plant cell wall polysaccharides

A hemicellulose is one of a number of heteropolymers, such as arabinoxylans, present along with cellulose in almost all terrestrial plant cell walls. While cellulose is crystalline, strong, and resistant to hydrolysis, hemicelluloses have random, amorphous structure with little strength. They are easily hydrolyzed by dilute acid or base as well as a myriad of hemicellulase enzymes.

Polysaccharide Long carbohydrate polymers comprising starch, glycogen, cellulose, and chitin

Polysaccharides, or polycarbohydrates, are the most abundant carbohydrates found in food. They are long chain polymeric carbohydrates composed of monosaccharide units bound together by glycosidic linkages. This carbohydrate can react with water (hydrolysis) using amylase enzymes as catalyst, which produces constituent sugars. They range in structure from linear to highly branched. Examples include storage polysaccharides such as starch, glycogen and galactogen and structural polysaccharides such as cellulose and chitin.

A glycosidic bond or glycosidic linkage is a type of covalent bond that joins a carbohydrate (sugar) molecule to another group, which may or may not be another carbohydrate.

Maltose Chemical compound

Maltose, also known as maltobiose or malt sugar, is a disaccharide formed from two units of glucose joined with an α(1→4) bond. In the isomer isomaltose, the two glucose molecules are joined with an α(1→6) bond. Maltose is the two-unit member of the amylose homologous series, the key structural motif of starch. When alpha-amylase breaks down starch, it removes two glucose units at a time, producing maltose. An example of this reaction is found in germinating seeds, which is why it was named after malt. Unlike sucrose, it is a reducing sugar.

Reducing sugar Sugars that contain free OH group at the anomeric carbon atom

A reducing sugar is any sugar that is capable of acting as a reducing agent. In an alkaline solution, a reducing sugar forms some aldehyde or ketone, which allows it to act as a reducing agent, for example in Benedict's reagent. In such a reaction, the sugar becomes a carboxylic acid.

An Endoglycosidase is an enzyme that releases oligosaccharides from glycoproteins or glycolipids. It may also cleave polysaccharide chains between residues that are not the terminal residue, although releasing oligosaccharides from conjugated protein and lipid molecules is more common.

Carbohydrase is the name of a set of enzymes that catalyze 5 types of reactions, turning carbohydrates into simple sugars, from the large family of glycosidases.

A glucan is a polysaccharide derived from D-glucose, linked by glycosidic bonds. Many beta-glucans are medically important. They represent a drug target for antifungal medications of the echinocandin class.

Beta-amylase Enzyme that hydrolyses alpha-1,4-D-glucosidic bonds in polysaccharides

Beta-amylase is an enzyme with the systematic name 4-alpha-D-glucan maltohydrolase. This enzyme catalyses the following chemical reaction:

Carbohydrate chemistry is a subdiscipline of chemistry primarily concerned with the detection, synthesis, structure, and function of carbohydrates. Due to the general structure of carbohydrates, their synthesis is often preoccupied with the selective formation of glycosidic linkages and the selective reaction of hydroxyl groups; as a result, it relies heavily on the use of protecting groups.

Cyclomaltodextrin glucanotransferase

In enzymology, a cyclomaltodextrin glucanotransferase is an enzyme that catalyzes the chemical reaction of cyclizing part of a 1,4-alpha-D-glucan molecule through the formation of a 1,4-alpha-D-glucosidic bond. They are bacterial enzymes belonging to the same family of the α-amylase specifically known as glycosyl-hydrolase family 13. This peculiar enzyme is capable of catalyzing more than one reaction with the most important being the synthesis of non-reducing cyclic dextrins known as cyclodextrins starting from starch, amylose, and other polysaccharides.

Carbohydrate conformation refers to the overall three-dimensional structure adopted by a carbohydrate (saccharide) molecule as a result of the through-bond and through-space physical forces it experiences arising from its molecular structure. The physical forces that dictate the three-dimensional shapes of all molecules—here, of all monosaccharide, oligosaccharide, and polysaccharide molecules—are sometimes summarily captured by such terms as "steric interactions" and "stereoelectronic effects".

Monosaccharide nomenclature is the naming system of the building blocks of carbohydrates, the monosaccharides, which may be monomers or part of a larger polymer. Monosaccharides are subunits that cannot be further hydrolysed in to simpler units. Depending on the number of carbon atom they are further classified into trioses, tetroses, pentoses, hexoses etc., which is further classified in to aldoses and ketoses depending on the type of functional group present in them.

Carbohydrate NMR Spectroscopy is the application of nuclear magnetic resonance (NMR) spectroscopy to structural and conformational analysis of carbohydrates. This method allows the scientists to elucidate structure of monosaccharides, oligosaccharides, polysaccharides, glycoconjugates and other carbohydrate derivatives from synthetic and natural sources. Among structural properties that could be determined by NMR are primary structure, saccharide conformation, stoichiometry of substituents, and ratio of individual saccharides in a mixture. Modern high field NMR instruments used for carbohydrate samples, typically 500 MHz or higher, are able to run a suite of 1D, 2D, and 3D experiments to determine a structure of carbohydrate compounds.

Carbohydrate synthesis is a sub-field of organic chemistry concerned specifically with the generation of natural and unnatural carbohydrate structures. This can include the synthesis of monosaccharide residues or structures containing more than one monosaccharide, known as oligosaccharides.

Glucansucrase

Glucansucrase is an enzyme in the glycoside hydrolase family GH70 used by lactic acid bacteria to split sucrose and use resulting glucose molecules to build long, sticky biofilm chains. These extracellular homopolysaccharides are called α-glucan polymers.

Glucanase

Glucanases are enzymes that break down large polysaccharides via hydrolysis. The product of the hydrolysis reaction is called a glucan, a linear polysaccharide made of up to 1200 glucose monomers, held together with glycosidic bonds. Glucans are abundant in the endosperm cell walls of cereals such as barley, rye, sorghum, rice, and wheat. Glucanases are also referred to as lichenases, hydrolases, glycosidases, glycosyl hydrolases, and/or laminarinases. Many types of glucanases share similar amino acid sequences but vastly different substrates. Of the known endo-glucanases, 1,3-1,4-β-glucanase is considered the most active.

Isomaltooligosaccharide (IMO) is a mixture of short-chain carbohydrates which has a digestion-resistant property. IMO is found naturally in some foods, as well as being manufactured commercially. The raw material used for manufacturing IMO is starch, which is enzymatically converted into a mixture of isomaltooligosaccharides.

References

  1. (a) R. W. Bailey, Oligosaccharides, MacMillan (Pergamon), New York, 1965; (b) S. Tsuiki, Y. Hashimoto, and W. Pigman, in Comprehensive Biochemistry, M. Florkin and E. H. Stotz, Eds., Vol,. 5, Elsevier, Amsterdam, 1963, pp. 153; (c) J. Stanek, M. Cerny, and J. Pacak, The Oligosaccharides, Academic Press, New York, 1965.
  2. 1 2 3 4 5 6 7 8 9 10 J. H. Pazur, The Carbohydrates: Chemistry and Biochemistry, 2nd Edition, Academic Press, New York, 1970.
  3. 1 2 3 4 5 6 7 8 D.C. Baker; J. Defaye; D. Horton; E. F. Hounsell; J. P. Kamerling; A.S. Serianni (1997). "Nomenclature of Carbohydrates". Carbohydrate Research . 297 (1): 1–92. doi:10.1016/S0008-6215(97)83449-0. PMID   9042704.
  4. "IUPAC-IUB Combined Commission on Biochemical Nomenclature. Abbreviations and Symbols for Chemical Names of Special Interest in Biological Chemistry. Revised Tentative Rules (1965)". Biochemistry . 5 (5): 1445–53. 1966. doi:10.1021/bi00869a001. PMID   5961269.