99. Carbohydrate Chemistry & Biochemistry

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99. Carbohydrate Chemistry & Biochemistry

 

 

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Syllabus

Chapter 1 Structures of the Open-chain Forms of Reducing Sugars, and

their Carbonyl Group Reactions
1.1 Definitions and Structures 1
1.1.1 R,S Stereochemical Designations in
Carbohydrate Chemistry – Prochirality 7

1.2 Nucleophilic Additions to Carbonyl Groups of
Sugars 11
1.2.1 Additions of Water, and OH Groups of the
Same Sugar 11
1.2.1.1 Equilibria 11
1.2.1.2 Kinetics of Mutarotation 16
1.2.1.3 General Acid and Base Catalysis of
Mutarotation 18
1.2.1.4 Kinetic Isotope Effects on
Mutarotation 23
1.2.1.4.1 Origin of kinetic isotope
effects 23
1.2.1.4.2 Hydrogen tunnelling 24
1.2.1.4.3 Solvent isotope effects 25
1.2.1.5 Mutarotation of 5-thioglucose 27
1.2.1.6 Synchronous Catalysis of
Mutarotation? 28
1.2.1.7 Mutarotases 29
1.2.2 Reaction with Low Molecular Weight
Alcohols – the Fischer Glycoside Synthesis 32
1.2.3 Formation, Anomerisation, and Hydrolysis of
Glycosylamines 34
1.3 Cyclitols 36
References 38

Chapter 2 Conformations of Monosaccharides

2.1 Differences Between Conformational Analysis of
Carbohydrates and Other Organic Molecules 41
2.2 The Gauche Effect 41
2.3 Conformations of Acyclic Sugars 42
2.4 Description of the Conformations of Sugar Rings 42
2.5 Analysis of Carbohydrate Conformation and
Configuration by NMR – the Key Role of The
Karplus Equation 48
2.6 The Anomeric Effect 51
2.7 Conformational Free Energies in Pyranoses 59
2.8 Rationalisation of the Composition of Aqueous
Solutions of Reducing Sugars 60
2.9 Conformations of Hydroxymethyl Groups 62
2.10 Conformations of Septanosides 63
References 64

Chapter 3 Nucleophilic Substitution at the Anomeric Centre

3.1 Stereochemistry of Oxocarbenium Ions 67
3.2 Lifetimes of Intermediates 67
3.2.1 The Jencks Clock 69
3.3 The Methoxymethyl System 70
3.3.1 a-Hydrogen Isotope Effects in the
Methoxymethyl System 72
3.4 Geminal Effects and Development of Conjugation 73
3.4.1 Geminal Effects 73
3.4.2 Development and Loss of Conjugation 73
3.5 Spontaneous Hydrolysis of Glycosyl Derivatives 75
3.5.1 Departure of Anionic Oxygen Leaving Groups
from Sugars 75
3.5.2 Departure of Pyridines 79
3.6 Lifetimes of Glycosyl Cations in Water and
Bimolecular Displacements at the Anomeric Centre 82
3.7 Acid-Catalysed Hydrolysis of Glycosides 83
3.7.1 Specific Acid Catalysis 83
3.7.2 Site of Productive Protonation 84
3.7.3 Differences in Structure – Reactivity Patterns in
Acid-catalysed and Spontaneous Hydrolyses –
Effect of the Pre-equilibrium Protonation 88
3.7.4 Acid-catalysed Hydrolysis of Nucleosides 88
3.7.5 Intermolecular General Acid Catalysis of
Glycoside Hydrolysis 92
3.7.6 Intramolecular General Acid Catalysis of
Glycoside Hydrolysis 94

3.8 Electrophilic Catalysis of Glycoside
Hydrolysis 97
3.9 Hydrolysis of Thioglycosides and Thioacetals 99
3.10 Heavy Atom and Remote Hydrogen Kinetic Isotope
Effects in Glycosyl Transfer 100
3.10.1 Measurement of Small Isotope Effects 100
3.10.2 Inductive and Steric Effects of Isotopes of
Hydrogen 103
3.10.3 b-Hydrogen Kinetic Isotope Effects 104
3.10.4 Heavy Atom Kinetic Isotope Effects 105
3.10.5 Transition State Structure Determination
from Multiple Kinetic Isotope Effects 106
3.11 Hydrolyses of Ketosides 109
3.11.1 Hydrolysis of Sialic Acid (Neuraminic Acid)
Derivatives 109
3.12 Neighbouring Group Participation in Glycoside
Hydrolyses 112
3.12.1 Participation by Acetamido 112
3.12.2 Participation by Carboxylate and Phosphate.
Electrostatic Catalysis? 114
3.12.3 Participation by Ionised Sugar Hydroxyls –
Base-catalysed Hydrolysis of Glycosides 115
3.13 Reactions in Organic Media 119
3.13.1 Solvolyses 119
3.13.2 Synthesis of Glycosides 125
3.13.2.1 Reaction of Phenoxides with
Glycosyl Halides in Organic and
Aqueous-Organic Solutions 125
3.13.2.2 Leaving Groups 126
3.13.2.3 Effect of Protecting Groups 131
3.13.2.4 Effect of Solvent 132
References 133

Chapter 4 Primary Structure and Conformation of Oligosaccharides

and Polysaccharides
4.1 Introduction – Depiction and Isolation of
Polysaccharides 140
4.2 Determination of Structure and Conformation of
Oligo- and Polysaccharides 143
4.2.1 Determination of Constituent Sugars and
Substitution Pattern 143
4.2.2 Mass Spectrometry 146
4.2.3 Diffraction by Single Crystals, Crystal Powders
and Fibres 148
4.2.4 The Role of Fourier Transforms 156

4.2.5 Use of NMR Pulse Sequences in the Determi-
nation of Sequence – an Example 162

4.2.6 High-resolution Solid-state 13C NMR –
CP-MAS 168
4.2.7 Atomic Force Microscopy 170
4.3 Description of Oligosaccharide and Polysaccharide
Conformation 172
4.4 The Exo-Anomeric Effect 176
4.5 Polysaccharides in Solution 178
4.5.1 Separation on the Basis of Molecular Size 181
4.5.2 Rheological Properties of Polysaccharides 182
4.5.3 Laser Light Scattering and Related Techniques 187
4.5.4 Chiroptical Methods 189
4.6 Some Important Polysaccharides 192
4.6.1 1-4-Linked Diequatorial Pyranosides 192
4.6.1.1 Undecorated, Fibrous,
1-4-Diequatorial Polysaccharides 194
4.6.1.1.1 Cellulose 194
4.6.1.1.2 Chitin 206
4.6.1.1.3 Chitosan 207
4.6.1.2 Decorated 1-4-Diequatorially Linked
Polysaccharides – the Plant
Hemicelluloses 208
4.6.1.3 Conformationally Mobile, Originally

1-4 Diequatorially Linked Polysac-
charides 211

4.6.2 1-4-Linked Equatorial–Axial Pyranosides 213
4.6.2.1 Starch 213
4.6.2.1.1 Amylose 213

4.6.2.1.2 Derivatisation of cyclo-
amyloses and catalysis 219

4.6.2.1.3 Amylopectin 219
4.6.2.1.4 Biosynthesis of starch 223
4.6.2.1.5 Interaction of starch
and water – cooking and
retrogradation 226
4.6.3 1-4-Diaxially Linked Pyranosides 228
4.6.3.1 Marine Galactans 228
4.6.3.2 Pectin 228
4.6.3.2.1 Homogalacturonan 229
4.6.3.2.2 Rhamnogalacturonan I 230
4.6.3.2.3 Rhamnogalacturonan II 233
4.6.3.2.4 Biosynthesis and
biodegradation of pectin 233
4.6.4 1,3-Diequatorially Linked Pyranosides 238
4.6.4.1 b-(1-3)-Glucans 239
4.6.4.2 b-(1-3)-Galactans 240
4.6.5 (1-3)-Linked Axial–Equatorial
Pyranosides 241
4.6.6 (1-2) Pyranosidic Homopolymers 242
4.6.7 Pyranosidic Homopolymers Without Direct
Linkages to the Ring 243
4.6.8 Furanosidic Homopolymers 248
4.6.8.1 Inulin 248
4.6.8.2 Phleins, Levans and Fructans 250
4.6.9 Polysaccharides from One Sugar but with
more than One Linkage in the Main Chain 250
4.6.10 Heteropolysaccharides with Several Sugars in
the Main Chain 252
4.6.10.1 Glycosaminoglycans 252
4.6.10.1.1 Initial polymer chains
and their biosynthesis 252
4.6.10.1.2 Hyaluronan 254

4.6.10.1.3 Sulfation and epimeri-
sation 255

4.6.10.1.4 Chondroitin, derma-
tan and their sulfates 256

4.6.10.1.5 Heparan sulfate and
heparin 259
4.6.10.2 Marine Galactans 268
4.6.10.3 Industrially and Commercially

Important Bacterial exo-Polysac-
charides 274

4.6.10.3.1 Xanthan family 274
4.6.10.3.2 Gellan family 276
4.6.10.4 Bacterial Cell Wall Peptidoglycans
and Related Material 281
References 281

Chapter 5 Enzyme-catalysed Glycosyl Transfer

5.1 Types of Enzyme-Catalysed Glycosyl Transfer 299
5.2 Stereochemistry and Steady-state Kinetics of Enzymic
Glycosyl Transfer 304
5.3 Reversible Inhibition 312
5.3.1 Competitive Inhibition 312
5.3.2 Transition State Analogues and Adventitious
Tight-binding Inhibitors 314
5.3.3 Anticompetitive Inhibition 324
5.4 Determination of the Mechanism of Enzymic
Glycosyl Transfer – Modification of Tools from
Small-molecule Physical Organic Chemistry and
New Tools from Protein Chemistry 326
5.4.1 Temperature Dependence of Rates and
Equilibria 326
5.4.2 Effect of Change of pH 327
5.4.3 Determination of Stereochemistry 330
5.4.4 Kinetic Isotope Effects 332
5.4.5 Structure–Reactivity Correlations 335
5.4.5.1 Variation of Substrate Structure 335
5.4.5.2 Variation of Enzyme Structure –
Site-directed Mutagenesis 339
5.4.5.3 Large Kinetic Consequences of
Remote Changes in Enzyme or
Substrate Structure: Intrinsic
Binding Energy and the Circe
Effect 340
5.4.6 The Use and Misuse of X-Ray Crystallographic
Data in the Determination of Enzyme
Mechanism 341

5.5 Enzymes with Multiple Subsites such as
Polysaccharidases 343
5.6 General Features of O-Glycohydrolases 347
5.6.1 Reactions with Enol Ethers 350
5.7 Inverting O-Glycosidases 352
5.7.1 Evidence from Action on the ‘‘Wrong’’
Fluorides 353
5.7.2 Mutation of Catalytic Groups 356
5.7.3 Some Inverting Glycosidase Families 357
5.7.3.1 GH 6 357
5.7.3.2 GH 8 358
5.7.3.3 GH 9 358
5.7.3.4 GH 14 358
5.7.3.5 GH 15 Glucoamylase 358
5.7.3.6 GH 28 360
5.7.3.7 GH 47 360
5.7.3.8 GH 48 360
5.7.3.9 GH 67 361
5.8 Reaction of N-Glycosides with Inversion 361
5.9 Retaining O-Glycosidases and Transglycosylases 372
5.9.1 Inactivation of Glycosidases – Exo and
Paracatalytic Activation 372
5.9.2 Direct Observation of Glycosyl-enzyme
Intermediates 380
5.9.3 Effect of Mutation of the Nucleophilic
Carboxylate 385
5.9.4 The Acid–Base Catalytic Machinery 387
5.9.5 Effects of Mutation of the Catalytic Acid–Base 387
5.9.6 Retaining Glycosidase Families 388
5.9.6.1 GH 1 388
5.9.6.2 GH 2 388
5.9.6.3 GH 7 391
5.9.6.4 Non-chair Pyranosyl-Enzyme
Intermediates – GH 11, 26, 29, 31
and 38 392
5.9.6.5 GH 13 394
5.9.6.6 The Many Activities of GH 16 395
5.9.6.7 Nucleophilic Assistance by
Vicinal trans-Acetamido Group of
Substrate – Mechanisms of GH 18,
GH 20, GH 56, GH 84, GH 102,
GH 103, GH 104 and Sometimes
GH 23 395
5.9.6.8 GH 22 – Lysozyme 400
5.9.6.9 GH 31 401
5.9.6.10 Sialidases (Neuraminidases) 403
5.9.6.11 GH 32 and 68: Fructofuranosidases
and Transfructofuranosylases 406
5.10 Carbohydrate Binding Modules and the Attack of
Glycosidases on Insoluble Substrates 408
5.10.1 Occurrence of CBMs 408
5.10.2 Methods of Study of CBMs 409
5.10.3 Types of CBM 410
5.10.4 Type CBM A Function 413
5.10.5 Type B CBM Function 414
5.10.6 Type C CBMs 416
5.11 Retaining N-Glycosylases and Transglycosylases 416
5.11.1 Retaining NAD+-Glycohydrolases and
Cyclases 416
5.11.2 tRNA Transglycosylases 417
5.11.3 20
-Deoxyribosyl Transferases 420
5.12 Glycosyl Transferases 420
5.12.1 Inverting Glycosyl Transferases 423
5.12.1.1 GT 63 423
5.12.1.2 GT 1 423

5.12.1.3 GT 2 425
5.12.1.4 GT 7 425
5.12.1.5 GT 9 and GT 13 428
5.12.1.6 GT 28 428
5.12.1.7 GT 42 – Sialyl Transferases 428
5.12.1.8 GT 43 – Glucuronyltransferases 430
5.12.1.9 GT 66 – Oligosaccharyl Transferase 431
5.12.2 Retaining Glycosyltransferases 435
5.12.2.1 GT 5 438
5.12.2.2 GT 6 438
5.12.2.3 GT 8 439
5.12.2.4 GT 15 442
5.12.2.5 GT 20 442
5.12.2.6 GT 27 443
5.12.2.7 GT 35 – Glycogen Phosphorylase 443
5.12.2.8 GT 44 449
5.12.2.9 GT 64 449
5.12.2.10 GT 72 450
5.12.3 UDPGlcNAc Epimerase 450
5.12.4 UDP Galactopyranose Mutase 452
References 455

Chapter 6 Heterolytic Chemistry Other than Nucleophilic Attack

at the Anomeric or Carbonyl Centre
6.1 Rearrangements of Reducing Sugars 478
6.1.1 Types of Rearrangements 478
6.1.2 Isomerisation by Enolisation – the Classic
Lobry de Bruyn–Alberda van Ekenstein
Reaction 481
6.1.2.1 Non-enzymic Enolisation 481
6.1.2.2 Enzymic Enolisation – the Classic
Aldose–Ketose Phosphate Isomerase
Mechanism 484
6.1.3 Isomerisation of Reducing Sugars by Hydride
Shift 488
6.1.4 The Bı ́lik and Related Reactions 489
6.1.5 Beyond the Lobry de Bruyn–Alberda van
Ekenstein Rearrangement – Deep-seated
Reactions of Sugars in Base 492
6.2 Further Reactions of Glycosylamines 497
6.2.1 The Amadori and Heyns Rearrangements 497
6.2.2 Osazone Formation 500
6.2.3 The Maillard Reaction 502

6.3 Aromatisation 511
6.4 Acidic and Basic Groups in Carbohydrates 511
6.5 Nucleophilic Reactions of OH Groups 515
6.5.1 Alkylation 516
6.5.2 Silylation 519
6.5.3 Acylation and Deacylation 522

6.5.3.1 Non-enzymic Acylation, Deacyla-
tion and Migration 522

6.5.3.2 Enzymic Acylation, Deacylation
and Transesterification 525
6.5.3.2.1 Serine carbohydrate
esterases and transacylases 525
6.5.3.2.2 Zn2+-dependent
carbohydrate esterases 528
6.5.3.2.3 Aspartic carbohydrate
esterases 529
6.5.3.2.4 Twin Group VIII metal
esterases (urease type) 531
6.5.4 Carbohydrate Esters of Carbonic Anhydride
and Their Nitrogen and Sulfur Analogues 534
6.5.5 Acetals of Carbohydrates 536
6.5.6 Borates and Boronates 546
6.5.7 Nitrites and Nitrates 550
6.5.8 Phosphorus Derivatives 559
6.5.8.1 General Considerations 559
6.5.8.2 Phosphonium Intermediates in the
Activation of OH to Nucleophilic
Substitution 561
6.5.8.3 Phosphite Esters 561
6.5.8.4 Phosphates 563
6.5.8.4.1 Mechanistic features of
phosphoryl transfer and
methods of investigation 563
6.5.8.4.2 Mechanisms of biological
phosphate transfer to and
from carbohydrates 567
6.5.9 Sulfites, Sulfates and Sulfonates 576
6.5.10 Stannylene Derivatives 580
6.6 Oxidations 581
6.6.1 Oxidations of Individual OH Groups 581
6.6.1.1 By Valence Change of an Oxyacid
Ester or Related Species 581
6.6.1.2 By Hydride Transfer 587
6.6.1.2.1 Non-enzymic hydride

abstraction from carbo-
hydrates 587

6.6.1.2.2 NAD(P)-linked enzymic
oxidations 588
6.6.2 Oxidations of Diols 597
6.7 Eliminations and Additions 599
6.7.1 General Considerations 599
6.7.2 Electrophilic Additions to Glycals 603
6.7.3 SN0 Reactions at the Anomeric Centre –
the Ferrier Rearrangement 605
6.7.4 Epimerisations a and Eliminations a,b to the
Carboxylates of Uronic Acids 608
6.7.4.1 Non-enzymic Epimerisation and
Elimination 608
6.7.4.2 Polysaccharide Lyases 611
6.7.4.2.1 Polysaccharide lyase
Family 8 (PL 8) 612
6.7.4.2.2 Pectin and pectate lyases 613
6.7.4.2.3 Alginate lyase 616
6.7.4.2.4 PL9 – Both chondroitin
and alginate lyase 617
6.7.4.2.5 PL18 – Hyaluronan lyase 617
6.7.5 C5 Uronyl Residue Epimerases 618
6.8 Biological Oxidation–Elimination–Addition and
Related Sequences 619
6.8.1 S-Adenosylhomocysteine Hydrolase 619
6.8.2 Biosynthesis of Nucleotide Diphospho
6-Deoxy Sugars 622
6.8.3 GH Family 4 625
6.8.4 L-Myoinositol 1-Phosphate Synthetase 626
References 629

Chapter 7 One-electron Chemistry of Carbohydrates

7.1 Classes of Radical Reactions of Carbohydrates 648
7.2 Methods of Investigation of Radicals in Carbohydrate
Chemistry and Biochemistry 650
7.2.1 Electron Spin Resonance – Aspects of
Importance to Carbohydrates 652
7.2.2 Conformations of Carbohydrate Radicals as
Determined by ESR 655
7.2.3 Kinetics of Radical Elementary Steps 661
7.3 Generation of Radicals 666
7.3.1 Direct Transfer of Electrons 666
7.3.1.1 Reducing Sugar Assays 666
7.3.1.2 Ascorbic Acid, the Natural
Antioxidant 667

7.3.1.3 Glucose Oxidase and Related
Enzymes 669
7.3.1.4 Pyrroloquinoline Quinone (PQQ)-
dependent Glucose Dehydrogenase 671
7.3.2 Hydrogen Abstraction 674
7.3.2.1 By Hydroxyl and Alkoxyl and
Related Species and Reactive Oxygen

Species. The Autoxidation of Carbo-
hydrates 674

7.3.2.2 Hydrogen Abstraction by Halogens 681
7.3.2.3 Selective Oxidation of Hydroxymethyl
Groups 681
7.3.2.3.1 Galactose oxidase 684
7.3.3 Fission of Weak Bonds 685
7.3.3.1 Radical Deoxygenation 685
7.3.3.2 Radicals from Carboxylic Acids 689
7.4 Reactions of Radicals 692
7.4.1 Stereochemistry of Atom Transfer to
Oxygenated Radicals 692
7.4.2 Heterolysis of Carbohydrate Radicals 694
7.4.2.1 Ribonucleotide Reductase 704
7.4.3 Acyloxy and Related Rearrangements 709
7.5 Carbohydrate Carbenes 714
References 721

Appendix Elements of Protein Structure 727
Subject Index 731

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