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Essentials of Glycobiology
March 30th, 2004
Ajit Varki
Lecture 1
Course Overview & General Introduction
Online at NCBI
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Books
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
DNA
RNA
PROTEIN
?
DNA
ORGANISM
CELL
?
ORGANISM
All Cells Are Coated with “Glycans”
Electron micrograph of a human lymphocyte (Ruthenium Red staining)
RNA
DNA
PROTEINS
ENZYMES
TRANSCRIPTION
FACTORS
SUGARS
SIGNALLING
MOLECULES
LIPIDS
GLYCOLIPIDS
MICROBES
PARASITES
PHYSICAL
ENVIRONMENT
CELL
GLYCOPROTEINS
PROTEOGLYCANS
MATRIX
TISSUES & ORGANS
DNA
ORGANISM
DNA
DIET
Macromolecules
Macromolecule
Building Block
Aproximate
Mass
Possible
Variations in a
Trimer
Protein
Amino acids
125  104-105
6
Nucleic Acid
Nucleotides
330  103-109
6
Lipid
Fatty acids
Carbohydrate
Monosaccharides
250 ’
200 ’
103
NA
102-106
1,056 to 27,648!
What is Glycobiology?
¶ Study of the structure, biosynthesis and biology of
saccharides (sugar chains or “glycans”) in nature.
¶ 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.
“Central Dogma”
 Glycans occur in patterns that are characteristic of
the cell-type, tissue and organism
 Glycan patterning is not template driven
 Instead, the glycan composition and pattern
depends on expression of biosynthetic enzyme
(transferases), substrate specificity, and the
availability of precursors (i.e., more like “assemblyline driven)
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
Basic Definitions
• 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.
• Carbohydrate, glycan, saccharide, sugar: Generic terms used
interchangeably. Includes monosaccharides, oligosaccharides,
polysaccharides, and derivatives of these compounds.
Carbohydrates consist of “hydrated carbon”, [CH2O]n
• Preferred generic term is “Glycan”
Monosaccharides - the basic structural unit
1
CHO
HO
HO
H
H
2
3
4
5
6
H
H
•
•
5
O
H
OH
4
OH
H
OH
3
OH
H
2
H
Hayworth
6
4
1
HO
OH O
5
HO
OH
OH
6
CH2OH
Fischer
H
H OH
CH2OH
H
3
2
1
H
H
H
OH
Stereochemical
Carbonyl group at the end of the carbon chain (aldoses) or at an inner
carbon (ketoses) has potential reducing power. This end is called the
reducing terminus, or reducing end
The ring form of a monosaccharide generates a chiral (anomeric) center
(at C-1 for aldo sugars or at C-2 for keto sugars). Notice that other
positions are chiral, which therefore imparts stereochemical information
Oligosaccharides and Polysaccharides
6
OH
6
CH2OH
5
O
H
OH
4
H
H
H
5
4
1
6
CH2OH
O
H
OH
3
H
2
OH
3
H
a-linkage
1
H
O 4
5
O
H
H
OH
OH
3
2
1
OH
H
O
H
H
CH2OH
2
H
OH
H
b-linkage
Glycosidic linkage can be a or b
The convention is to draw the reducing end to the right and the nonreducing end to the left.
Once in glycosidic linkage, ring can no longer open
Reducing end is still called the same even when it is covelantly bound to
another macromolecule (tying up its reducing power)
Common Monosaccharides
Neutral
Sugars
CH 2 OH
CH 2OH
O
O
HO
OH
OH
Amino
Sugars
HO
OH
OH
NAC
NAC
N-acetyl Glucosamine
(GlcNAc)
N-acetyl Galactosamine
(GalNAc)
COOH
O
O
COOH
OH
Acidic
Sugars
HO
HO OH
OH
OH
OH
OH
Glucuronic acid
(GlcA)
Iduronic acid
(IdoA)
AcN
O
CHOH
CHOH
COOH
CH 2OH
OH
OH
Sialic acids
(Sia)
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
Symbolic Representation of Common Monosaccharides
 To simplify the structural complexity of glycans, we will generally use a
standard set of symbols to represent sugars.
 Symbol set is being modified for second edition of “Essentials”,
in a consensus agreement with NCBI, Consortium for Functional
Glycomics, KEGG and other national and international bodies
Saccharide Modifications increase the diversity and
functionality of glycans
6S
6S
6S
NS 2S NS 2S NS 2S
= Xyl
Ac = O-acetyl
NS = N-Sulfate
NS
= Gal
6S
NS
NS 2S NS
3S
= GlcA
P = Phosphate S = O-Sulfate
NH2 = free amino group
6S
6S
= GlcNAc
= IdoA
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
Glycoconjugates




Schematic representation of the
Thy-1 glycoprotein
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.
Major Classes of Animal Glyconconjugates
*
*Several additional kinds of O-glycans have emerged recently
Major
Glycan
Classes in
Animal Cells
CHONDROITIN
SULFATE
HYALURONAN
P
GLYCOSAMINOGLYCANS
HEPARAN SULFATE
S
S
S
S
S
Ser-O-
S
S
NS
NS
-O-Ser
Proteoglycan
N-LINKED CHAINS
Ac
O-LINKED
CHAIN
GLYCOPHOSPHOLIPID
ANCHOR
P
S
O
Ser/Thr
GLYCOSPHINGOLIPID
N
Asn
N
Asn
NH 2
INOSITOL
Glycoprotein
Ac
OUTSIDE
Sialic Acids
O-LINKED GlcNAc
INSIDE
O
Ser
Etn
P
P
S
Symbolic Representation of Oligosaccharides
Fuc
pa1
3
Siapa2-3Galpb1-4GlcNAc pb1-2Manpa1
Fuc
pa1
6
6
Man
pb1-4GlcNAc pb1-4GlcNAc p
3
Full Traditional
9OAc-Sia pa2-6Galpb1-4GlcNAc pb1-2Manpa1
Fuca
3
Siaa3Galb4GlcNAc b2Mana
Simplified
Traditional
9Ac-Siaa6Galb4GlcNAc b2Mana
a3
Symbolic
Representation
9Ac
a6
b4
a3
b4
Fuca
6
6
Man
b4GlcNAc b4GlcNAc 
3
a3
b2
b2
a
6
3
a
b4
a3
a6
b4
9Ac
a3
b4
b4
b2
b2
a6
a3
b4
b4
a6
9Ac
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
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
Outer Chains Shared by Different Classes of
Glycans can be recognized by Specific Proteins
= Sialic acid
S
N-LINKED CHAIN
O
Ser/Thr
N
Asn
O-LINKED CHAIN
GLYCOSPHINGOLIPID
Secreted Protein
S
O
Ser/Thr
N
Asn
Membrane Protein
OUTSIDE
CELL
MEMBRANE
INSIDE
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 shallow binding pockets
�
Other proteins bind to internal sugar sequences, and have
binding clefts
�
Valency is a major factor in determining overall affinity
Essentials of Glycobiology
March 30th, 2004
Ajit Varki
Lecture 1
Course Overview & General Introduction