09/18/08biochemistry: carbo2/lipid1 carbohydrates ii; lipids i andy howard introductory biochemistry...

09/18/08Biochemistry: Carbo2/Lipid1

Carbohydrates II; Lipids I

Andy HowardIntroductory Biochemistry

18 September 2008

09/18/08 Biochemistry: Carbo2/Lipid1 p. 2 of 35

What we’ll discuss

Carbohydrates (concluded): Structural

polysaccharides Glycoconjugates

Proteoglycans Peptidoglycans Glycoproteins

Lipids Characteristics Fatty acids Phospholipids


Structural polysaccharides I Insoluble compounds designed to

provide strength and rigidity Cellulose: glucose -14 linkages

Rigid, flat structure: each glucose is upside down relative to its nearest neighbors (fig.7.27)

300-15000 glucose units Found in plant cell walls Resistant to most glucosidases Cellulases found in termites,

ruminant gut bacteria Chitin: GlcNAc -14 linkages:

exoskeletons, cell walls (fig. 7.29)


Structural polysaccharides II Alginates: poly(-D-mannuronate),

poly(-L-guluronate), linked 14 Cellulose-like structure when free Complexed to metal ions:

3-fold helix (“egg-carton”) Agarose: alternating D-gal, 3,6-anhydro-L-gal,

with 6-methyl-D-gal side chains Forms gels that hold huge amounts of H2O Can be processed to use in the lab for gel exclusion

chromatography Glycosaminoglycans: see next section


iClicker question 1 Suppose you isolate a polysaccharide

with 5000 glucose units, and 3% of the linkages are 1,6 crosslinks. This is:

(a) amylose (b) amylopectin (c) glycogen (d) chitin (e) none of the above.


iClicker question 2 Suppose you isolate an enzyme that

breaks down -1,4-glycosidic linkages between GlcNAc units. This would act upon:

(a) glycogen (b) cellulose (c) chitin (d) all of the above (e) none of the above.


Glycoconjugates Poly or oligosaccharides

covalently linkedto proteins or peptides

Generally heteroglycans Categories:

Proteoglycans (protein+glycosaminoglycans)

Peptidoglycans (peptide+polysaccharide) Glycoproteins (protein+oligosaccharide)

Image courtesy Benzon Symposia


Proteoglycans: Glycosaminoglycans Unbranched heteroglycans of repeating

disaccharides One component is

GalN, GlcN, GalNAc, or GlcNAc Other component: an alduronic acid —OH or —NH2 often sulfated Found in cartilage, joint fluid


Proteoglycans in cartilage Highly hydrated,

voluminous Mesh structure

(fig.7.47 or this fig. from Mathews & Van Holde)

Aggrecan is major proteoglycan

Typical of proteoglycans in that it’s extracellular


Peptidoglycans

Polysaccharides linked to small proteins Featured in bacterial cell walls:

alternating GlcNAc + MurNAclinked with -(14) linkages

Lysozyme hydrolyzes these polysaccharides Peptide is species-specific: often contains D-

amino acids


Peptidoglycans in bacteria

Gram-negative: thin peptidoglycan layer separates two phospholipid bilayer membranes

Gram-positive: only one bilayer, with thicker peptidoglycan cell wall outside it

Gram stain binds to thick wall, not thin layer Fig. 7.36 shows multidimensionality of these

walls


Peptide component (fig. 7.34) Sugars are crosslinked with entities

containing(L-ala)-(isoglutamate)-(L-Lys)-(D-ala)

Gram-neg: L-Lys crosslinks via D-ala Gram-pos: L-lys crosslinks via

pentaglycine followed by D-ala


Gram-negative bacteria:the periplasmic space (fig. 7.37)

Periplasmic space: space inside cell membrane but inside just-described peptidoglycan layer (note error in fig. legend!)

Peptidoglycan is attached to outer membrane via 57-residue hydrophobic proteins

Outer membrane has a set of lipopolysaccharides attached to it; these sway outward from the membrane


Gram-negative membranes and periplasmic space

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.

Figure courtesy Kenyon College microbiology Wiki


Glycoproteins 1-30 carbohydrate moieties per protein Proteins can be enzymes, hormones,

structural proteins, transport proteins Microheterogeneity:

same protein, different sugar combinations

Eight sugars common in eukaryotes PTM glycosylation much more common

in eukaryotes than prokaryotes


Diversity in glycoproteins Variety of sugar monomers or glycosidic linkages Linkages always at C-1 on one sugar but can

be C-2,3,4,6 on the other one Up to 4 branches But:

not all the specific glycosyltransferases you would need to get all this diversity exist in any one organism


O-linked and N-linked oligosaccharides

Characteristic sugar moieties and attachment chemistries


O-linked oligosaccharides(fig. 8.34)

GalNAc to Ser or Thr;often with gal or sialic acid on GalNAc

5-hydroxylysines on collagen are joined to D-Gal

Some proteoglycans joined viaGal-Gal-Xyl-Ser

Single GlcNac on ser or thr


N-linked oligosaccharides

Generally linked to Asn Types:

High-mannose Complex

(Sialic acid, …) Hybrid

(Gal, GalNAc, Man)

Diagram courtesy Oregon State U.


Lipids Hydrophobic biomolecules;

most have at least one hydrophilic moiety as well

Attend to “periodic table of lipids”(next slide)

Functions Membrane components Energy-storage molecules Structural roles Hormonal and signaling roles


Periodic table of lipids


Fatty acids Unbranched hydrocarbons with carboxylate

moieties at one end Usually (but not always) even # of C’s Zero or more unsaturations: generally cis Unsaturations rarely conjugated (why?) Resting concentrations low because they could

disrupt membranes

saturated

unsaturated


Trans fatty acids Not completely absent in biology But enzymatic mechanisms for

breakdown of cis fatty acids are much more fully developed

Trans fatty acids in foods derived from (cis-trans) isomerization that occurs during hydrogenation, which is performed to solidify plant-based triglycerides


Fatty acids:melting points and structures

Longer chain higher MPbecause longer ones align readily

More unsaturations lower MP Saturated fatty acids are entirely flexible;

tend to be extended around other lipids Unsaturations introduce inflexibilities and

kinks


Sources for fatty acids Bacterial lipids

• Mostly C12-C18

• 1 unsaturation Plant lipids

High concentration of unsaturated f.a.s

Includes longer chains

Animal lipds Somewhat higher

concentrations of saturated f.a.’s

Unsaturations four carbons from methyl group (omega f.a.) common in fish oils


Triglyceride composition by source

Courtesy Charles Ophardt, Elmhurst College

Beef

Linoleic

Other

Oleic

Stearic

Palmitic

Soybean

Palmitic

Stearic

Oleic

Linoleic

Other


Nomenclature for fatty acids IUPAC names: hexadecanoic acid, etc. Trivial names from sources (Table 8.1)

Laurate (dodecanoate) Myristate (tetradecanoate) Palmitate (hexadecanoate) Palmitoleate (cis-9-hexadecenoate) Oleate (cis-9-octadecenoate) Linoleate (cis,cis-9,12-octadecadienoate) Arachidonate

(all cis-5,8,11,14-eicosatetraeneoate)


Saturated Fatty AcidsMelting points for saturated FAs

40

45

50

55

60

65

70

75

80

85

90

8 12 16 20 24 28

# of Carbons

Melting point, Deg C

Contrast withmelting points ofUnsaturated C18 FAs:16ºC, -5ºC -11ºC;C20, 4 double bonds: -50ºC


How fatty acids really appear Almost always esterified or otherwise

derivatized Most common esterification is to

glycerol Note that glycerol is achiral but its

derivatives are often chiral Triacylglycerols; all three OHs on

glycerol are esterified to fatty acids Phospholipids: 3-OH esterified to

phosphate or a phosphate derivative

glycerol


Triacylglycerols Neutral lipids R1,2,3 all aliphatic Mixture of saturated &

unsaturated; unsaturatedmore than half

Energy-storage molecules Yield >2x energy/gram as

proteins or carbohydrates, independent of the water-storage issue …

Lipids are stored anhydrously; carbohydrates & proteins aren’t


Catabolism of triacylglycerol Lipases break these molecules

down by hydrolyzing the 3-O esters and 1-O esters

Occurs in presence of bile salts(amphipathic derivatives of cholesterol)

These are stored in fat droplets within cells, including specialized cells called adipocytes


Glycerophospholipids Also called phosphoglycerides Primary lipid constituents of

membranes in most organisms Simplest: phosphatides

(3’phosphoesters) Of greater significance: compounds in

which phosphate is esterified both to glycerol and to something else with an —OH group on it


Categories of glycerophospholipids Generally categorized first

by the polar “head” group; secondarily by fatty acyl chains

Usually C-1 fatty acid is saturated

C-2 fatty acid is unsaturated Think about structural

consequences!


Varieties of head groups

Variation on other phosphoester position

Ethanolamine (R1-4 = H) (—O—(CH2)2—NH3

+) Serine (R4 = COO-)

(—O—CH2-CH-(COO-)—NH3+)

Methyl, dimethylethanolamine(—O—(CH2)2—NHm

+(CH3)2-m) Choline (R4=H, R1-3=CH3) (—O—

(CH2)2—N(CH3)3+)

Glucose, glycerol . . .


Chirality in common lipids Fatty acyl chains themselves are

generally achiral Glycerol C2 is often chiral (unless C1 and

C3 fatty acyl chains are identical) Phospholipid polar groups are achiral

except for phosphatidylserine and a few others

09/18/08biochemistry: carbo2/lipid1 carbohydrates ii; lipids i andy howard introductory biochemistry...

Documents

carbo2lipid1 carbohydrates

extracellular slide

peptidoglycans polysaccharides

poly d

joint fluid slide

alternating dgal

polysaccharides peptide

glcnac units