1. JDE 2002 Essentials of Glycobiology April 4, 2000 Jeff Esko Lecture 1 Course Overview & General Introduction

2. JDE 2002 Lecture 1 - Key Points What is Glycobiology? Central Dogma Basic definitions Monosaccharides - the structural units of glycans Oligoaccharides consist of monosaccharides linked together Nomenclature and symbolic representations Major classes of glycoconjugates and oligosaccharides Clustered oligosaccharides Proteins can bind at either the ends of glycans or within the chains

3. JDE 2002 What is Glycobiology?  In its simplest form, glycobiology is the study of the structure, chemistry, biosynthesis, and biological functions of glycans and their derivatives.  Glycobiology is an integrative science, crossing all subfields of chemistry, biology and medicine.  Chemical analysis and biochemistry dominated the field in the early part of the century.  In the 1960’s, glycans in the extracellular matrix, on the cell surface, and in the interior of cells were found to have biological properties independent of the underlying protein or lipid.  The term “glycobiology” was coined in 1988 by Rademacher, Parekh, and Dwek: Annu Rev Biochem. 57:785-838.

4. JDE 2002 Macromolecules DNA æ RNA æ Protein æ Cell æ Organism

5. JDE 2002 Revised Paradigm DNARNAProteinEnzymes Carbohydrates Lipids Organisms Cells Glycoconjugates

6. JDE 2002 Glycocalyx All cells are covered by a glycocalyx, a meshwork of complex carbohydrates EM of endothelial cells from a blood capillary showing the lumenal plasmalemma decorated with particles of cationized ferritin (courtesy of George E. Palade, UCSD).

7. JDE 2002 Glycoproteins Proteoglycans Glycolipids Cytoplasmic Glycosylation

8. JDE 2002 Central Dogma  Glycans occur in patterns that are characteristic of the cell, tissue and organism  Patterning is not template driven  Glycan composition and pattern depends on enzyme expression (transferases), substrate specificity, and the availability of precursors

9. JDE 2002 Lecture 1 - Key Points What is Glycobiology? Central Dogma Basic definitions Monosaccharides - the structural units of glycans Oligoaccharides consist of monosaccharides linked together Nomenclature and symbolic representations Major classes of glycoconjugates and oligosaccharides Clustered oligosaccharides Proteins can bind at either the ends of glycans or within the chains

10. JDE 2002 Basic Definitions Carbohydrate, glycan, saccharide, sugar: Generic terms used interchangeably. Includes monosaccharides, oligosaccharides, polysaccharides, and derivatives of these compounds. Carbohydrates consist of “hydrated carbon”, [CH 2 O] n Monosaccharide: A carbohydrate that cannot be hydrolyzed into a simpler carbohydrate. The building block of oligosaccharides and polysaccharides. Oligosaccharide: Linear or branched chain of monosaccharides attached to one another via glycosidic linkages. The number of monosaccharide units can vary. Polysaccharide: Glycan composed of repeating monosaccharides, generally greater than ten monosaccharide units in length.

11. JDE 2002 Monosaccharides 5-carbon and 6- carbon sugars predominate Chirality - optical active centers

12. JDE 2002 Common Monosaccharides Neutral Sugars Amino Sugars Acidic Sugars

13. JDE 2002 Monosaccharides - the basic structural unit  Carbonyl group at the end of the carbon chain (aldoses) or at an inner carbon (ketoses) has potential reducing power - the reducing terminus  The ring form of a monosaccharide generates a chiral (anomeric) center (at C-1 for aldo sugars or at C-2 for keto sugars).

14. JDE 2002 Oligosaccharides and Polysaccharides  -linkage  -linkage Glycosidic linkage can be  or  The convention is to draw the reducing end to the right. The terms “upstream” and “downstream” are sometimes used.

15. JDE 2002 Lecture 1 - Key Points What is Glycobiology? Central Dogma Basic definitions Monosaccharides - the structural units of glycans Oligoaccharides consist of monosaccharides linked together Nomenclature and symbolic representations Major classes of glycoconjugates and oligosaccharides Clustered oligosaccharides Proteins can bind at either the ends of glycans or within the chains

16. JDE 2002 Symbolic Representation of Common Monosaccharides  To simplify the structural complexity of glycans, we will generally use a standard set of symbols to represent sugars.

17. JDE 2002 Saccharide Modifications increase the diversity and functionality of glycans Ac = O-acetyl P = Phosphate S = O-Sulfate NS = N-Sulfate NH 2 = free amino group NSNSNSNSNSNSNS2S2S2S2S 6S6S6S6S6S6S 3S

18. JDE 2002 Lecture 1 - Key Points What is Glycobiology? Central Dogma Basic definitions Monosaccharides - the structural units of glycans Oligoaccharides consist of monosaccharides linked together Nomenclature and symbolic representations Major classes of glycoconjugates and oligosaccharides Clustered oligosaccharides Proteins can bind at either the ends of glycans or within the chains

19. JDE 2002 Glycoconjugates Glycoconjugate: A compound in which one or more glycans (the glycone) are covalently linked to a non-carbohydrate moiety (the aglycone). Glycoproteins: A protein with one or more covalently bound glycans. Glycolipids: A molecule containing a saccharide linked to a lipid. Proteoglycans: Any glycoprotein with one or more covalently attached glycosaminoglycan chains. Schematic representation of the Thy-1 glycoprotein

20. JDE 2002 Major Classes of Animal Glyconconjugates

21. JDE 2002 Symbolic Representation of Oligosaccharides Symbolic Representation Simplified Traditional Full Traditional

22. JDE 2002 Clustered O-linked Oligosaccharides  Electron micrograph of a cartilage proteoglycan shows the classical “bottle-brush” appearance  Many mucins contain clustered O-GalNAc linked oligosaccharides  These highly hydrated conjugates fill space, provide lubrication, and create clustered glycan ligands for binding receptors

23. JDE 2002 Lecture 1 - Key Points What is Glycobiology? Central Dogma Basic definitions Monosaccharides - the structural units of glycans Oligoaccharides consist of monosaccharides linked together Nomenclature and symbolic representations Major classes of glycoconjugates and oligosaccharides Clustered oligosaccharides Proteins can bind at either the ends of glycans or within the chains

24. JDE 2002 Several Glycans Contain Terminal Sialic Acids O Ser/Thr N Asn N-LINKED CHAIN O-LINKED CHAIN GLYCOSPHINGOLIPID OUTSIDE INSIDE S = Sialic acid CELL MEMBRANE

25. JDE 2002 Glycosaminoglycan Chains Contain Multiple Protein Binding Sites � Proteins can bind at the ends of N-linked and O-linked chains, and typically have binding pockets � Other proteins bind to internal sugar sequences, and have binding clefts � Valency is a major factor in determining overall affinity AntithrombinFGF-1