Carbohydrates II Lipids I Andy Howard Introductory Biochemistry
Carbohydrates II; Lipids I Andy Howard Introductory Biochemistry, Fall 2013 24 September 2013 Carbohydrates II; Lipids I 09/24/2013
Carbohydrates and Lipids n n Carbohydrates are the most abundant organic molecules on the planet, and they act as metabolites, components of complexes, and structural entities. Lipids are energy-storage molecules and membrane components, and are also used to make signaling molecules. 09/24/2013 Carbohydrates II; Lipids I p. 2 of 41
What we’ll discuss n Polysaccharides n n n Storage Structural Glycoconjugates n n n Proteoglycans Peptidoglycans Glycoproteins 09/24/2013 n Lipids n n n Periodic table Fatty acid properties Triacylglycerols Glycerophospholipids Sphingolipids Waxes, Eicosanoids Carbohydrates II; Lipids I p. 3 of 41
Amylopectin n n Mostly -1 4 linkages; 4% -1 6 Each sidechain has 15 -25 glucose moieties -1 6 linkages broken down by debranching enzymes 300 -6000 total glucose units per amylopectin molecule One reducing end, many nonreducing ends 09/24/2013 Carbohydrates II; Lipids I p. 4 of 41
Glycogen n n n Principal storage form of glucose in human liver; some in muscle Branched ( -1 4 + a few -1 6) More branches (~10%) Larger than starch: 50000 glucose One reducing end, many nonreducing ends Broken down to G-1 -P units Built up from G-6 -P G-1 -P UDP-Glucose units 09/24/2013 Carbohydrates II; Lipids I p. 5 of 41
Glycogen structure 09/24/2013 Carbohydrates II; Lipids I p. 6 of 41
Structural polysaccharides I n n Insoluble compounds designed to provide strength and rigidity Cellulose: glucose -1 4 linkages n n n 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: Glc. NAc -1 4 linkages: exoskeletons, cell walls (fig. 7. 26) 09/24/2013 Carbohydrates II; Lipids I p. 7 of 41
Structural polysaccharides II n Alginates: poly( -D-mannuronate), poly( -L-guluronate), linked 1 4 n n Cellulose-like structure when free Complexed to metal ions: 3 -fold helix (“egg-carton”) Sketch courtesy B. Nystrøm, U. Oslo 09/24/2013 Carbohydrates II; Lipids I p. 8 of 41
Structural polysaccharides III n Agarose: alternating D-gal, 3, 6 -anhydro-L-gal, with 6 -methyl-D-gal side chains n n Forms gels that hold huge amounts of H 2 O Can be processed to use in the lab for gel exclusion chromatography 09/24/2013 Carbohydrates II; Lipids I p. 9 of 41
Sugar Complexes and Lipids n n Sugars form complexes with proteins and lipids Lipids are critical as energy storage molecules and as components of membranes 09/24/2013 Carbohydrates II; Lipids I p. 10 of 41
Glycoconjugates n n n Poly or oligosaccharides covalently linked to proteins or peptides Generally heteroglycans Categories: n n n Image courtesy Benzon Symposia Proteoglycans (protein+glycosaminoglycans) Peptidoglycans (peptide+polysaccharide) Glycoproteins (protein+oligosaccharide) 09/24/2013 Carbohydrates II; Lipids I p. 11 of 41
Flowchart summary Glycoconjuguates (covalent sugar+peptide) Peptide or Protein? Protein Type of sugar unit Glycosaminoglycan Oligosaccharide Proteoglycan 10/03/2012 Glycoprotein Peptide Type of sugar unit Polysaccharide Peptidoglycan Biochem: Carbohydrates&Lipids p. 12 of 70
Proteoglycans: Glycosaminoglycans n n n Unbranched heteroglycans of repeating disaccharides One component is Gal. N, Glc. N, Gal. NAc, or Glc. NAc Other component: an alduronic acid —OH or —NH 2 often sulfated Found in cartilage, joint fluid 09/24/2013 Carbohydrates II; Lipids I p. 13 of 41
Proteoglycans in cartilage n n Highly hydrated, voluminous Mesh structure (fig. 7. 36 or this fig. from Mathews & Van Holde) Aggrecan is major proteoglycan Typical of proteoglycans in that it’s extracellular 09/24/2013 Carbohydrates II; Lipids I p. 14 of 41
Peptidoglycans (G&G fig. 7. 29) n n Polysaccharides linked to small proteins Featured in bacterial cell walls: alternating Glc. NAc + Mur. NAc linked with -(1 4) linkages Lysozyme hydrolyzes these polysaccharides Peptide is species-specific: often contains D-amino acids 09/24/2013 Carbohydrates II; Lipids I p. 15 of 41
Peptidoglycans in bacteria n n 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. 30 shows multidimensionality of these walls 09/24/2013 Carbohydrates II; Lipids I p. 16 of 41
Peptide component (G&G fig. 7. 29) n n n 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 09/24/2013 Carbohydrates II; Lipids I p. 17 of 41
Gram-negative bacteria: the periplasmic space (G&G fig. 7. 30 b, 7. 31) n n n 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 09/24/2013 Carbohydrates II; Lipids I p. 18 of 41
Gram-negative membranes and periplasmic space Figure courtesy Kenyon College microbiology Wiki 09/24/2013 Carbohydrates II; Lipids I p. 19 of 41
Glycoproteins n n n 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 09/24/2013 Carbohydrates II; Lipids I p. 20 of 41
Diversity in glycoproteins n n n 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 09/24/2013 Carbohydrates II; Lipids I p. 21 of 41
O-linked and Nlinked oligosaccharides n Characteristic sugar moieties and attachment chemistries 09/24/2013 Carbohydrates II; Lipids I p. 22 of 41
O-linked oligosaccharides (figs. 7. 32 a, 7. 33 in G&G) n n Gal. NAc to ser or thr; often with Gal or Sialic acid on Gal. NAc 5 -hydroxylysines on collagen are joined to D-Gal Some proteoglycans joined via Gal-Xyl-ser Single Glc. NAc on ser or thr 09/24/2013 Carbohydrates II; Lipids I p. 23 of 41
N-linked oligosaccharides (fig. 7. 32 b, c in G&G) n n Generally linked to Asn Types: n n n High-mannose Complex (Sialic acid, …) Hybrid (Gal, Gal. NAc, Man) 09/24/2013 Carbohydrates II; Lipids I Diagram courtesy Oregon State U. p. 24 of 41
i. Clicker question 1 n n n Suppose you isolate a polysaccharide with 5000 glucose units, and 4% of the linkages are 1, 6 crosslinks. This is: (a) amylose (b) amylopectin (c) glycogen (d) chitin (e) none of the above. 09/24/2013 Carbohydrates II; Lipids I p. 25 of 41
i. Clicker question 2 n Suppose you isolate an enzyme that breaks down -1, 4 -glycosidic linkages between Glc. NAc units. This would act upon: n (a) glycogen (b) cellulose (c) chitin (d) all of the above (e) none of the above. n n 09/24/2013 Carbohydrates II; Lipids I p. 26 of 41
Lipids n n n Hydrophobic biomolecules; most have at least one hydrophilic moiety as well Attend to “periodic table of lipids” (next slide) Functions n n Membrane components Energy-storage molecules Structural roles Hormonal and signaling roles 09/24/2013 Carbohydrates II; Lipids I p. 27 of 41
Periodic table of lipids 09/24/2013 Carbohydrates II; Lipids I p. 28 of 41
Fatty acids n n n 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 09/24/2013 Carbohydrates II; Lipids I p. 29 of 41
Trans fatty acids n n n 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 09/24/2013 Carbohydrates II; Lipids I p. 30 of 41
Fatty acids: melting points and structures n n Longer chain higher MP because 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 09/24/2013 Carbohydrates II; Lipids I p. 31 of 41
Sources for fatty acids n Bacterial lipids • • n Mostly C 12 -C 18 1 unsaturation Plant lipids n n n Animal lipids n n High concentration of unsaturated f. a. s Includes longer chains 09/24/2013 Carbohydrates II; Lipids I Somewhat higher concentrations of saturated f. a. ’s Unsaturations four carbons from methyl group (omega f. a. ) common in fish oils p. 32 of 41
Triglyceride composition by source n Courtesy Charles Ophardt, Elmhurst College 09/24/2013 Carbohydrates II; Lipids I p. 33 of 41
Nomenclature for fatty acids n n IUPAC names: hexadecanoic acid, etc. Trivial names from sources (Table 8. 1) n n n n Laurate (dodecanoate) Myristate (tetradecanoate) Palmitate (hexadecanoate) Palmitoleate (cis- 9 -hexadecenoate) Stearate (octadecanoate) Oleate (cis- 9 -octadecenoate) Linoleate (cis, cis- 9, 12 -octadecadienoate) Arachidonate (all cis- 5, 8, 11, 14 -eicosatetraeneoate) 09/24/2013 Carbohydrates II; Lipids I p. 34 of 41
Saturated Fatty Acids Contrast with melting points of Unsaturated C 18 FAs: 16ºC, -5ºC -11ºC; C 20, 4 double bonds: -50ºC 09/24/2013 Carbohydrates II; Lipids I p. 35 of 41
How fatty acids really appear n n n 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 09/24/2013 Carbohydrates II; Lipids I glycerol p. 36 of 41
Triacylglycerols n n n Neutral lipids R 1, 2, 3 all aliphatic Mixture of saturated & unsaturated; unsaturated more than half Energy-storage molecules Yield >2 x energy/gram as proteins or carbohydrates, independent of the water-storage issue … Lipids are stored anhydrously; carbohydrates & proteins aren’t 09/24/2013 Carbohydrates II; Lipids I p. 37 of 41
Catabolism of triacylglycerol n n n 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) Cartoon courtesy These are stored in fat droplets Adipocyte within cells, including specialized Proteome Database, Maxcells called adipocytes Planck Inst. 09/25/2012 Biochem: Carbo III, Lipids I p. 38 of 41
Glycerophospholipids (G&G § 8. 3) n n 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 09/25/2012 Biochem: Carbo III, Lipids I p. 39 of 41
Glycerophospholipid Types n n 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! 09/25/2012 Biochem: Carbo III, Lipids I Cartoon courtesy Nature Scitable p. 40 of 41
Varieties of head groups n n n Variation on other phosphoester position Ethanolamine (R 1 -4 = H) (—O—(CH 2)2—NH 3+) Serine (R 4 = COO-) (—O—CH 2 -CH-(COO-)—NH 3+) Methyl, dimethylethanolamine (—O—(CH 2)2—NHm+(CH 3)2 -m) Choline (R 4=H, R 1 -3=CH 3) (—O—(CH 2)2—N(CH 3)3+) Glucose, glycerol. . . 09/25/2012 Biochem: Carbo III, Lipids I p. 41 of 41
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