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Appendix E Glossary1 Amino sugar: A monosaccharide in which an alcoholic hydroxyl group is replaced by an amino group. Anomeric carbon: The carbon atom of a monosaccharide that bears the hemiacetal functionality (C-1 for most sugars; C-2 for sialic acids). Anomers: Stereoisomers of a monosaccharide that differ only in configu- ration at the anomeric carbon of the ring structure. Carbohydrate: Generic term used interchangeably in this report with sugar, saccharide, or glycan. This term includes monosaccharides, oligosaccharides, and polysaccharides as well as derivatives of these compounds. Carbohydrate recognition domain: The domain of a polypeptide that is specifically involved in binding to a carbohydrate. In lectins it is often a highly evolutionarily conserved region of the polypeptide. Cellulose: A repeating homopolymer of 14-linked glucose residues. Chemoenzymatic synthesis: Glycan synthesis that uses both chemical and enzymatic transformations to obtain the desired product. Chitin: A repeating homopolymer of 14-linked N-acetyl-glucosamine residues. It is the main component of the cell walls of fungi and the exoskeletons of arthopods, among other functions. 1Adapted from Essentials of Glycobiology, 2nd ed., A. Varki et al., eds., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2009; used with permission. 187

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188 APPENDIX D Complex glycan: A glycan containing more than one type of monosaccharide. Deoxy sugar: A monosaccharide in which a hydroxyl group is replaced by a hydrogen atom. Epimers: Two isomeric monosaccharides differing only in the configura- tion of a single chiral carbon. For example, mannose is the C-2 epimer of glucose. Furanose: Five-membered (four carbons and one oxygen; i.e., an oxygen heterocycle) ring form of a monosaccharide named after the structural similarity to the compound furan. Galectins: S-type (sulfhydryl-dependent) -galactoside-binding lectins, usually occurring in a soluble form, expressed by a wide variety of animal cell types and distinguishable by the amino acid sequence of their carbohydrate recognition domains. Genome: The complete genetic sequence of one set of chromosomes. Glycan: Generic term for any sugar or assembly of sugars, in free form or attached to another molecule, used interchangeably in this report with saccharide or carbohydrate. Glycan array: A collection of glycans attached to a surface in a spatially addressed manner. Glycan-binding proteins: Proteins that recognize and bind to specific gly- cans and mediate their biological function. Glycobiology: Study of the structure, chemistry, biosynthesis, and biologi- cal functions of glycans and their derivatives. Glycocalyx: The cell coat consisting of glycans and glycoconjugates sur- rounding animal cells that is seen as an electron-dense layer by elec- tron microscopy. Glycoconjugate: A molecule in which one or more glycan units are cova- lently linked to a noncarbohydrate entity. Glycoforms: Different molecular forms of a glycoprotein, resulting from variable glycan structure and/or glycan attachment site occupancy. Glycogen: A polysaccharide comprising 14- and 16-linked glucose residues that functions in short-term energy storage in animals; some- times referred to as animal starch. Glycolipid: General term denoting a molecule containing a glycan linked to a lipid aglycone. In higher organisms most glycolipids are glyco- sphingolipids, but glycoglycerolipids and other types exist.

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APPENDIX D 189 Glycome: The total collection of glycans synthesized by a cell, a tis- sue, or an organism under specified conditions of time, space, and environment. Glycomics: Systematic analysis of the glycome. Glycomimetics: Noncarbohydrate compounds that mimic the properties of glycans. Glycopeptide: A peptide having one or more covalently attached glycans. Glycoprotein: A protein with one or more covalently bound glycans. Glycoproteomics: The systems-level analysis of glycoproteins, including their protein identities, sites of glycosylation, and glycan structures. Glycosaminoglycans: Polysaccharide side chains of proteoglycans or free complex polysaccharides composed of linear disaccharide repeating units, each composed of a hexosamine and a hexose or a hexuronic acid. Glycosidase: An enzyme that catalyzes the hydrolysis of glycosidic bonds in a glycan. Glycoside: A glycan containing at least one glycosidic linkage to another glycan or an aglycone. Glycosidic linkage: Linkage of a monosaccharide to another residue via the anomeric hydroxyl group. The linkage generally results from the reaction of a hemiacetal with an alcohol (e.g., a hydroxyl group on another monosaccharide or amino acid) to form an acetal. Glycosidic linkages between two monosaccharides have defined regiochemistry and stereochemistry. Glycosyl acceptor: The nucleophile in a glycosylation reaction, usually containing a free hydroxyl group. Glycosylation: The enzyme-catalyzed covalent attachment of a carbohy- drate to a polypeptide, lipid, polynucleotide, carbohydrate, or other organic compound, generally catalyzed by glycosyltransferases, uti- lizing specific sugar nucleotide donor substrates. Glycosyl donor: The electrophile in a glycosylation reaction; the nucleo- tide sugar in an enzymatic glycosylation reaction. Glycosyltransferase: The enzyme that catalyzes transfer of a sugar from a sugar nucleotide donor to a substrate. Heparan sulfate: A glycosaminoglycan defined by the disaccharide unit (GlcNAc14GlcA14/IdoA14), containing N- and O-sulfate esters at various positions, and typically found covalently linked to a proteoglycan core protein. Heparin: A type of heparan sulfate made by mast cells that has the highest amount of iduronic acid and N- and O-sulfate residues. Pharmaceuti- cal heparin binds and activates antithrombin.

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190 APPENDIX D Heteropolysaccharide: A polysaccharide containing more than one type of monosaccharide. Hexosamine: Hexose with an amino group in place of the hydroxyl group at the C-2 position. Common examples found in vertebrate glycans are the N-acetylated sugars, N-acetylglucosamine, and N-acetylgalactosamine. Hexose: A six-carbon monosaccharide typically with an aldehyde (or potential aldehyde) at the C-1 position (aldo-hexose) and hydroxyl groups at all other positions. Common examples in vertebrate glycans are mannose, glucose, and galactose. Homopolysaccharide: A polysaccharide composed of only one type of monosaccharide. Lectin: A protein (other than a glycan-specific antibody) that specifically recognizes and binds to glycans without catalyzing a modification of the glycan. Ligand: A molecule that is recognized by a specific receptor. In the case of lectins the ligands are partly or completely glycan based and are sometimes called counterreceptors. Methylation analysis: A method for carbohydrate structure analysis based on the acid stability of methyl ethers and the acid lability of glycosidic linkages; used to determine the linkage positions of monosaccharide residues in an oligosaccharide chain. Microheterogeneity: Structural variations in a glycan at any given glyco- sylation site on a protein (one source of glycoforms). Monosaccharide: A carbohydrate that cannot be hydrolyzed into a simpler carbohydrate. It is the building block of oligosaccharides and poly- saccharides. Simple monosaccharides are polyhydroxyaldehydes or polyhydroxyketones with three or more carbon atoms. N-Glycan: A glycan covalently linked to an asparagine residue of a polypeptide chain in the consensus sequence: -Asn-X-Ser/ Thr. Unless otherwise stated, the term N-glycan is used generi- cally in this report to denote the most common linkage region, Man14GlcNAc14GlcNAc1-N-Asn. Nucleotide sugars: Activated forms of monosaccharides, such as UDP- Gal, GDP-Fuc, and CMP-Sia, typically used as donor substrates by glycosyltransferases.

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APPENDIX D 191 O-Glycan: A glycan glycosidically linked to the hydroxyl group of the amino acids serine, threonine, tyrosine, or hydroxylysine. Unless oth- erwise stated, the term O-glycan is used in this report to denote the common linkage GalNAc1-O-Ser/Thr. Oligosaccharide: A linear or branched chain of monosaccharides attached to one another via glycosidic linkages. The number of monosaccha- ride units can vary; the term polysaccharide is usually reserved for large glycans with repeating units. Polysaccharide: A glycan composed of repeating monosaccharides, gener- ally greater than 10 monosaccharide units in length. Protecting group: A chemical moiety commonly used in glycan synthesis that masks hydroxyl groups in order to prevent them from reacting with other chemical reagents. Proteome: The total collection of proteins in a cell, tissue, or organism, under specific conditions of time, space, and environment. Pyranose: Six-membered (five carbons and one oxygen; i.e., an oxygen heterocycle) ring form of a monosaccharide; the most common form found for hexoses and pentoses. The name is based on the structural similarity to the compound "pyran." Saccharide: Generic term for any carbohydrate or assembly of carbo- hydrates, in free form or attached to another molecule, used inter- changeably in this report with carbohydrate and glycan. Sialic acids: Family of acidic sugars with a nine-carbon backbone, of which the most common is N-acetylneuraminic acid, in vertebrates. Siglecs: Sialic acidbinding proteins that are members of the I-type lectin family and have an amino-terminal V-set domain with typical con- served residues. Sugar: Generic term often used to refer to any carbohydrate but most frequently to low molecular weight carbohydrates that are sweet in taste. Table sugar, sucrose, is a nonreducing disaccharide (Fru 2- 1Glc). Oligosaccharides are sometimes called "sugar chains," and individual monosaccharides in a sugar chain are sometimes referred to as "sugar residues." Transcriptome: The total collection of RNA transcripts in a cell, a tis- sue, or an organism, under specific conditions of time, space, and environment.

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