Glycan structure and complexity

'an' stands for polysaccharide (sugar), its nomenclature

Does genome size correlate with complexity of an organism?Organism Est size

(bp)Est gene #

Mean gene density Chromosome #

human 3.2 x 109 ~ 25 K 1 gene

per 100 K bases

46

mouse 2.6 x 109 ~ 25 K 1 gene

per 100 K bases

40

Fruit fly 137 x 106 13 K 1 gene

per 9 K bases

8

Round

worm

97 x 106 19 K 1 gene

per 5 K bases

12

yeast 12 x 106 6 K 1 gene

per 2 K bases

32

http://www.ornl.gov/sci/

Genome size does not correlate with complexity of the organism. The number of genes is not proportionate with genome size.

Genomics Genes, deoxyribonucleic acid (DNA) sequence at the organismal level

Intra-organismal cell-specific variations

Proteomics Proteins and peptides, at levels of the organism, the tissue, or the cell

Post-translational modifications

Glycomics Glycans, at levels of the organism, the tissue, or the cell

It is dynamicState 1 State 2

Embryonic stem cell Differentiated cellNormal cell Cancer cellHealthy cell Injured cell

study of genes

Starch and glycogen not too complex, they're all made of glucose

Cellulose made from N-acetyl galactosamine

different monosaccharide increase complexity

embryonic stem cell have different structure from differentiated

Where in the cell are glycans and glycoconjugates localized ?

What are their functions at these localities?

What properties are required for these functions?

What molecular features support these properties?

cell surface recognition mechanisms need glycogen present on cell surface (peri or extra cellular signal)

Glycolipids

Glycoproteins

Glycans are exposed to the extracellular environment

extra, intra and transmembrane domain

hexagon to represent glucose (hexose)----can be attached to phospholipids

Lectin-saccharideinteractions

Kd = 10-6 - 10-7 mol/L,weaker than Ag-Ab interactions

Lectins are proteins that recognize saccharides, their interaction help mediate cell-cell interaction, making a cell cluster. Virus, bacteria and small organisms use this mechanism to recognize and invade cells.

Weak interactions, much weaker than antigen-antibody, as shown by low dissociation constant. Thats why its taken long to understand carbohydrates

Glycoproteins &Glycolipids

Cell-cell adhesion

Cell-cell interaction

fertilization immunity infection cancer

QC, trafficking, sorting

Carbohydrates in quality control, ensuring if proteins are properly folded.

If not properly folded, not secreted and caught in trafficking, they are stored in endoplasmic reticulum and modified. At times its carried to proteosomes and broken down

Different blood types due to presence of different types of glycans

In type A, N-acetyl galactosamine linked to galactose

In type B, galactose linked to galactose

different ppl have different blood types as genes code for different types of enzymes

More complex!

Cell surface proteoglycans

Another class of molecules with lots of carbohydrates. So, carbohydrates seem to be the parent structure

The name has all to do with history. Now many proteoglycans have been found with less carbohydrate parts

Syndecan refers to protein part of molecule, i.e. protein part is binded to cell membrane

Proteoglycans in the extracellular matrix

Extracellular proteoglycans serve as lubricants in synovial joints

ones sticking out in red are glycan structures

Aggrecan and Versican are attached to a molecule of large molecular weight (hyaluronan) and used in ECM

Glycosminoglycans DRUs tetrasaccharide - serine

Glycans Bonds between

saccharide units

Form

Cellulose -1,4 glycosidic bond linking Glc residues

Linear

Chitin -1,4 glycosidic bond

linking GlcNAc res

Linear

Glycosaminoglycans

hyaluronan Disaccharide repeats of GlcUA and GlcNAc, linked via alternating -1,4 and -1,3 glycosidic bonds

Linear

Structural polysaccharides

complexity comes about by linkages

Glucans Bonds between glc residues

Form Repeating glc units

Starch

amylose -1,4 glycosidic bond linear

1000

4000

amylopectin-1,4 glycosidic bond

-1,6 glycosidic bond

Linear

branched

20 25 per segment

Glycogen -1,4 glycosidic bond

-1,6 glycosidic bond

Linear

branched

12 18 per segment

Storage polysaccharides energy store

A segment of amylose

A segment of amylopectin

What strategies are used to release glucose units from

dietary vs stored glycogen?

Extracellular digestion ()

Intracellular digestion (, , )

Enzymatic cleavage

starch can be used as storage molecule as it has many enzyme cleavage site. It has many reducing ends which can be attacked to release glucose..... helps break up food

Alpha amylase is for extra cellular digestion

Enzymes that attack non-reducing ends are controlled by hormones.

Intra cellular digestion is highly regulated, attacks non-reducing end only

Debranching enzymes are inside the cell

Fates of digestion products Glucose from amylase action in gut lumen

Intestinal absorption, delivery via hepatic portal vein

Transport into hepatocytes

In hepatocytes, glycolysis .ATP

or glycogenesis ..storage in cells

Glucose 1-phosphate, from glycogen phosphorylase action in liver cells or myocytes

Isomerization to Glc 6-phosphate, then glycolysis

ATP

Back to Basics

aldehyde group gives reducing property

4 carbon structure built by adding carbon, sp2 hybrid, adding carbon from top or bottom, gives 2 isomers

Glucose and Mannose differ at carbon-2 only. They are said to be epimeric at carbon number 2 and are epimers of one another

Glucose and Galactose epimeric at C-4

Monosaccharides

Glucose, galactose, mannose Aldohexoses aldehyde group at C-1

Glc and man epimeric at C-2

Glc and gal epimeric at C-4

Fructose Ketohexose ketone group at C-2

Glc and fru are structural isomers.

Ribose Aldopentose aldehyde group at C-1

..linking by glycosidic bonds

alpha and beta structures also due to ablove and below attack, alpha above

sucrose is a non-reducing sugar as anomeric carbon is not free. The others have a reducing end, anomeric carbon is free

Towards new therapeutics

Infection by influenza virus

Drugs that inhibit neuraminidase prevent propagation of the virus

Inflammatory diseases

Drugs to perturb selectin-sugar ligand interactions interfere with recruitment of leukocytes

not covered in lecture

Influenza virus and therapeutic targets (1)

Hemagglutinin (HA)

HA binds to sialic acid residues on

surface glycoproteins of host cells and

triggers internalization of virus

Neuraminadase (NA)

NA cleaves sialic acid residues off

surface glycoproteins of host cells and

faciliatates viral propagation

M2 Ion Channel

Proton-selective ion channel lowers

the pH inside of the virus resulting in

dissociation of the RNPs from the

matrix protein (M1)

Ribonucleoprotein (RNP)

An independent transcription active

unit (containing a polymerase complex)

packaged in nucleoprotein

www.cdc.gov/h1n1flu/yearinreview/yir1.htm

not covered in lecture

Mukhopadhyay et al. Nature Reviews Microbiology 3, 13-22 (2005)

Haemaglutinin binds sialic acid residues on host cell

surface glycoproteins

Neuraminidase cleaves sialicacid residues off host cell surface glycoproteins

not covered in lecture

Influenza virus targets of therapeutic intervention

von

Itz

ste

in N

atu

re R

evie

ws D

rug

Dis

covery

6,

96

7-9

74 (

2007)

Amantadine

Amantadine

Ribavarin

Zanamivir,

oseltamivir

not covered in lecture

O-linked glycans

not covered in lecture

(1)

(2)

not covered in lecture

not covered in lecture