Transcript Lectures 1 and 2

Essentials of Glycobiology
April 4, 2000
Jeff Esko
Lecture 1
Course Overview & General Introduction
JDE 2002
Lecture 1 - Key Points
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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
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Clustered oligosaccharides
Proteins can bind at either the ends of glycans or
within the chains
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.
JDE 2002
Macromolecules
DNA RNA Protein Cell Organism
JDE 2002
Revised Paradigm
DNA
RNA
Protein
Enzymes
Carbohydrates
Cells
Organisms
Glycoconjugates
Lipids
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).
JDE 2002
Proteoglycans
Glycolipids
Glycoproteins
Cytoplasmic
Glycosylation
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
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
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”, [CH2O]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.
JDE 2002
Monosaccharides
5-carbon and 6carbon sugars
predominate
Chirality - optical
active centers
JDE 2002
Common Monosaccharides
Neutral
Sugars
Amino
Sugars
Acidic
Sugars
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).
JDE 2002
Oligosaccharides and Polysaccharides
a-linkage
b-linkage
Glycosidic linkage can be a or b
The convention is to draw the reducing end to the right.
The terms “upstream” and “downstream” are
sometimes used.
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
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.
JDE 2002
Saccharide Modifications increase the diversity and
functionality of glycans
6S
6S
6S
NS 2S NS 2S NS 2S
Ac = O-acetyl
NS = N-Sulfate
NS
6S
6S
6S
NS
NS 2S NS
3S
P = Phosphate S = O-Sulfate
NH2 = free amino group
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
JDE 2002
Glycoconjugates
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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
JDE 2002
Major Classes of Animal Glyconconjugates
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Symbolic Representation of Oligosaccharides
Full Traditional
Simplified
Traditional
Symbolic
Representation
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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
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
JDE 2002
Several Glycans Contain Terminal Sialic Acids
= Sialic acid
N-LINKED CHAIN
O-LINKED CHAIN
GLYCOSPHINGOLIPID
S
O
Ser/Thr
N
Asn
OUTSIDE
CELL
MEMBRANE
INSIDE
JDE 2002
Glycosaminoglycan Chains Contain Multiple Protein
Binding Sites
6S
6S
NS 2S NS 2S NS 2S
FGF-1
6S
NS
6S
6S
6S
NS
NS 2S NS
3S
Antithrombin
�
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
JDE 2002