VL 14 (Jörg Fettke) Flashcards

1
Q

Carbohydrates

A

Carbohydrates are present in all kingdoms of life and fulfill various functions apart from building cell walls or in energy metabolism

  • Formula (CH2O)n, n => 3
  • Oligosaccharides: linked monosaccharides (building blocks)
  • Polysaccharides (cellulose, glycogen, starch)
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2
Q

Important definitions

A
  • Glycan: term for sugars in glycoproteins/-lipids
  • Glucan: only glucose
  • Glycoconjugate: protein/lipid + sugar
  • Glycoprotein: protein containing covalently linked sugar molecules (added as co-/post-translational modifications)
  • Glycome: total complement of glycans in cell/tissue/organism
  • Glycosyltransferase: E; sugar transfer from donor→acceptor→form: glycosidic link
  • Glycosidase: E; hydrolyzes glycosidic linkage
  • Lectin: glycan binding protein; E with sugar S, sugar-binding Ab are usually not classified as lectins; classified in different families based on CRD-sequence similarities
  • Carbohydrate-recognition domain (CRD): part of glycan-binding protein (lectin) that contains sugar-binding site
  • O-linked oligosaccharide/glycan: linked through O-atom, attached to Ser/Thr
  • N-linked oligosaccharide/glycan: linked through N-atom (Asp)
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3
Q

Stereochemistry of Carbohydrates

A
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4
Q

D-Aldoses

A
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4
Q

D-Ketoses

A
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5
Q

Confirmations of hexoses

A
  • H-atom at C1/4→destabilize boat conformation→stabilize chair conformation
  • 4C1-chair conformation preferred: all OH-groups equatorial
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6
Q

Form of Pyranose and Furanose

A
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7
Q

Common Monosaccharide Building Blocks

A
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8
Q

Disaccherides and Polysaccherides

A

Disaccherides:
* Two monosaccharide
* O-glycosidic bond
* Reducing sugars: aldehyde/keto group conserved on one end (i.e. lactose, maltose)
* Non-reducing sugars: OH-group at C1 of one of both partners has condensed
→acetal (no keto/aldehyde function present in molecule (i.e. saccharose))

Monosaccherides:
* Cellulose: insoluble zick-zack layers of carbohydrates
* Starch: helic, double-helix structure

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9
Q

Function of glycans

A

Intrinsic glycan functions
* providing structural components
–> cell walls
–> ECM
* modifying protein properties
–> solubility
–> stability

Extrinsic functions resulting from glycan-lectin interactions
* directing trafficking of glycoconjugates; mediating, modulating signaling
–> Intra-/extracellular
* Mediating, modulating cell adhesion
–> Cell-cell/matrix interactions

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10
Q

Steps in encoding and decoding information in glycan structures

A
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11
Q

Comparison of glycans and proteins

A
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12
Q

Glycosyltransferase

A
  • activation: nucleotide coupling
  • need activated sugars
  • Glycosyltransferases need
    activated sugars
  • Activation via nucleotide
    coupling
  • Highly specific enzymes! („One
    linkage, one enzyme“)
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13
Q

N-linked Glycans

A
  • generated trough pathway in ER; Asn-linked (motive: Asn-X(no Pro)-Ser(Thr), X = aa)
  • differential action of glycosidases, glycosyltransferases (GTs) generates high Man, complex, hybrid typ e
  • particular structures on proteins depend on GTs + their expression level
  • spec. terminal elaborations added to core structures mediate spec. functions
  • key objective: how GT expression, activity, regulation influences glycosylation
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14
Q

O-linked glycosylation:

A
  • lack common biosynthetic pathway
  • attached: Ser, Thr, Hydroxylysine
  • O-GlcNAc in cytoplasm, nucleus
  • O-GalNAc in mucins that hold H2O
  • IgA: O-glycosylated in hinge region
  • Proteoglycans: O-glycosylated proteins → strengthen ECM
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15
Q

O-GlcNAc:

A
  • Not elongated or modified, only GlcNAc
  • Cycling rapidly at different rates
  • Similar to phosphorylation in signaling
  • Essential for viability at the single-cell level in mammalian cells
16
Q

Glycobiology Toolboxes

A

Glycosidase:
* Sequential protocol
–> Glycan release (PNGase F)
–> Reducing end labelling
–> Sequential degradation with spec. glycosidases (“restriction E”) o Monitoring by chromatography of digestion products

Mass Spectrometry
MS is an indispensable glycomics tool
* Resolve components of glycan mixture (glycan profiling)
→structure information (masses + glycosylation sites + fragmentation experiments (tandem MS))
* Combine with sequential degradation with E
* Detect modifications (phosphorylations, sulfatations)

NMR
Ultimate source of definitive information on glycan structures!
* Used to determine structures of a large number of typical oligosaccharides
* Substantial amount of material required (~mg), not well adapted for mixtures
* Unique patterns for equatorial and axial protons
* Anomeric protons well resolved and deshielded
* Information obtained about stereochemistry of sugars (monosaccharide and linkage configurations) Taylor/Drickamer, Inroduction to Glycobiology 2nd ed.

glycan arrays:
Studies on glycan arrays are leading to better understanding of biological roles of glycans
* determine parts of glycans that form epitopes recognized by receptors
* screening of glycan-binding proteins DB for

Databases for glycobiology:
* examples: CFG, SweetDB, KEGG, CAZy, Animal lectin resource

17
Q

Starch

A

Starch: a special type of storage carbohydrate
* world need more energy (e.g. Bioethanol, Biodiesel)
* food-Fuel-Environment Trilemma
–> problem: Competition for
Land-use
–> reduction: food production/area + ecosystems
–> problems associated with monocultures
–> breeding goals divergent (resources)
* development of oil/sugar prices: sugar decreased; oil increased
* production: bio-fuels, food, bio-materials, paper & cardboard production
* storage carbohydrate
* subcellular distribution
–> three eukaryotic chloroplast containing lines
–> glacuophytes (freshwater algae harbouring cyanelles containing peptidoglycans): cytosolic starch
–> rhodophytes (red algae): cytosolic starch
–> chlorophytes (green algae, land plants) plastidial starch

  • biochemistry
    –> plastidial starch metabolism is more complex than that of glycogen
    –> starch-related E either derived from prokaryotic chloroplast precursor of from host o evolutionary origin of starch-phosphorylating E = unknown
  • organization of A-, B-type allomorphs
    –> a-type: storage starch (produced once); less H2O; more stable
    –> b-type: tubule structure; transitory starch (synthesized: day, degradation: night)
  • structural models, localisation of amylose