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Lecture1Notes - Physical Chemistry of Biomacromolecules...

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Unformatted text preview: Physical Chemistry of Biomacromolecules Lecture 1 September 23, 2010 BE/BME 104/204 1 Monday, September 20, 2010 1 What you will learn in this course: • • • Application of classic polymer physical chemistry/physics to biological macromolecules Definition, description and characterization of macromolecules Static and dynamic bulk and solution behavior We will talk about the physical chemistry of polymers, and apply the concepts of polymer physical chemistry to biological macromolecules. 2 Monday, September 20, 2010 2 Class Business • At the end of class, students waiting to enroll please leave your name and student number so I may issue PTE numbers • Syllabus • Homework 3 Monday, September 20, 2010 3 Books • • • • • • • • Essentials of Polymer Science and Engineering, Paul C. Painter and Michael M. Coleman Fundamentals of Polymer Science, 2nd Ed, Paul C. Painter and Michael M. Coleman The Physics of Polymers, Gert Stobl, 3rd Ed. (online access) Introduction to Physical Polymer Science, 4th Ed. L.H. Sperling Polymer Physics, Rubinstein and Colby Principles of Polymer Chemistry, P. Flory Physical Chemistry of Macromolecules, S.F. Sun Principles of Polymerization 4th Ed., G. Odian I have requested these books to be on reserve in the library; I will also post electronic reference material. 4 Monday, September 20, 2010 4 “I am inclined to think that the development of polymerization is perhaps the biggest thing chemistry has done, where it has had the biggest impact on everyday life” (Lord Todd, President of the Royal Society, 1957 Nobel Laureate in Chemistry) “The colloid chemistry of proteins provides then an approach to the obscure region which scientists contemplate today only with a silent longing for the promised land - the physical chemistry of living matter.” (W. Pauli, Kolloid Z. 1908, 3,2) 5 Monday, September 20, 2010 5 Mr. McGuire: Benjamin: Mr.. McGuire: Benjamin: Mr.. McGuire: Benjamin: “I want to say one word to you. Just one word.” “Yes, sir.” “Are you listening?” “Yes I am” “Plastics.” “Just how do you mean that sir?” The Graduate, 1967 6 Monday, September 20, 2010 6 • Engineering genius Scott Heyward posing as Tom Wilson (played by Elvis Presley) goes to the lab to invent a revolutionary polymer-based boat varnish to beat a competitor in speed boat racing and win the girl of his dreams, Dianne. Clambake, 1967 7 Monday, September 20, 2010 7 Polymer Science meets pop culture Polymer science major Polymer science major 8 Monday, September 20, 2010 8 Nobel Prizes in Polymer Science • • • • • • • 1953 (Chemistry) Hermann Staudinger, “for his discoveries in the field of macromolecular chemistry” 1963 (Chemistry) Giulio Natta and Karl Ziegler "for their discoveries in the field of the chemistry and technology of high polymers” 1974 (Chemistry) Paul J. Flory “for his fundamental achievements, both theoretical and experimental, in the physical chemistry of the macromolecules” 1984 (Chemistry) Bruce Merrifield “for his development of methodology for chemical synthesis on a solid matrix” 1991 (Physics) Pierre-Gilles de Gennes “for discovering that methods developed for studying order phenomena in simple systems can be generalized to more complex forms of matter, in particular to liquid crystals and polymers” 2000 (Chemistry) Alan G. MacDiarmid, Alan J. Heeger and Hideki Shirawa “for the discovery and development of conductive polymers” 2005 (Chemistry) Yves Chauvin, Robert H. Grubbs, and Richard R. Schrock, “for the development of the metathesis method in organic synthesis” 9 Monday, September 20, 2010 9 Course Overview 1A 10-10 1 nm -9 10 10-8 10-7 1m -6 10 10-5 10-4 1 mm -3 10 1 cm 10-2 10-1 organ collagen tropohelix red blood cell small blood vessel atoms, e. coli capillaries critical size bone defect bond lengths DNA, virus eyeball tooth 1m 0 10 person How do we connect the molecular attributes of a polymeric material (natural or synthetic) to the macroscopic behavior we utilize in our applications? 10 Monday, September 20, 2010 10 Course Overview 1A 1 nm -9 10-10 10-7 10-8 10 1m -6 10 10-5 10-4 1 mm -3 10 1 cm 10-2 10-1 organ collagen tropohelix red blood cell small blood vessel atoms, e. coli capillaries critical size bone defect bond lengths DNA, virus eyeball tooth Lectures 1 and 2: Polymer chains at the 1m 0 10 person molecular scale, looking at repeat unit chemistry and orientation O HO O HO O H N O H peptides drugs N H O HO H N NH2 O OH HN H 2N NH 11 Monday, September 20, 2010 11 Course Overview 1A 10-10 1 nm -9 10-7 10-8 10 1m -6 10 10-5 10-4 1 mm -3 10 1 cm 10-2 10-1 organ collagen tropohelix red blood cell small blood vessel atoms, e. coli capillaries critical size bone defect bond lengths DNA, virus eyeball tooth 1m 0 10 person Lectures 3 and 4: enthalpic and entropic effects on chain conformation based on interactions of repeat units (not atoms) O HO O H N O N H O HO H N O OH HN H 2N NH Monday, September 20, 2010 NH2 = = 12 12 Course Overview 1A 10-10 1 nm -9 10 10-8 10-7 1m -6 10 10-5 10-4 1 mm -3 10 1 cm 10-2 10-1 organ collagen tropohelix red blood cell small blood vessel atoms, e. coli capillaries critical size bone defect bond lengths DNA, virus eyeball tooth 1m 0 10 person Lectures 5 and 6: Polymers mixing with other polymers, and polymers mixing with solvent 13 Monday, September 20, 2010 13 Course Overview 1A 10-10 1 nm -9 10 10-8 10-7 1m -6 10 10-5 10-4 1 mm -3 10 1 cm 10-2 10-1 organ collagen tropohelix red blood cell small blood vessel atoms, e. coli capillaries critical size bone defect bond lengths DNA, virus eyeball tooth 1m 0 10 person Lectures 7 and 8: Characterizing polymers in solution 14 Monday, September 20, 2010 14 Course Overview 1A 10-10 1 nm -9 10 10-8 10-7 1m -6 10 10-5 10-4 1 mm -3 10 1 cm 10-2 10-1 organ collagen tropohelix red blood cell small blood vessel atoms, e. coli capillaries critical size bone defect bond lengths DNA, virus eyeball tooth 1m 0 10 person Lectures 9 - 11: Polymers in the solid state; matching bulk behavior with microscopic observations? 15 Monday, September 20, 2010 15 Course Overview 1A 10-10 1 nm -9 10 10-8 10-7 1m -6 10-5 10 10-4 1 mm -3 1 cm 10 10-2 10-1 organ collagen tropohelix red blood cell small blood vessel atoms, e. coli capillaries critical size bone defect bond lengths DNA, virus eyeball tooth 1m 0 10 person X X X X Lectures 12 and 13: Polymer networks – linking multiple chains together 16 Monday, September 20, 2010 16 Course Overview 1A 10-10 1 nm -9 10 1m -6 10-7 10-8 10 10-5 10-4 1 mm -3 10 1 cm 10-2 10-1 organ collagen tropohelix red blood cell small blood vessel atoms, e. coli capillaries critical size bone defect bond lengths DNA, virus eyeball tooth 1m 0 10 person X X X X Lecture 14: Viscoelasticity – unique polymer behavior that comes from chains interacting 17 Monday, September 20, 2010 17 Course Overview 1A 10-10 1 nm -9 10 10-8 10-7 1m -6 10 10-5 10-4 1 mm -3 10 1 cm 10-2 10-1 organ collagen tropohelix red blood cell small blood vessel atoms, e. coli capillaries critical size bone defect bond lengths DNA, virus eyeball tooth 1m 0 10 person Bovine Chondrocytes. Live/ Dead Cell Stain.! Lecture 15: Hydrogels - biomedically relevant and biologically relevant polymer networks Lectures 16-18: Special topics, TBD. 18 Monday, September 20, 2010 18 Things you will learn today: • • • • • Polymers are important biomaterials Polymers are made up of monomers There are polymers found in nature, and man-made polymers; some man-made polymers mimic those found in nature Polymers are defined by their monomer chemistry, their length, and the uniformity of their length within a collection Polymers may have different architectures 19 Monday, September 20, 2010 19 What is a polymer? • • “polymeric” coined in 1832 by J.J. Berzelius, a German chemist Polymers as macromolecules (versus colloids) proposed by Staudinger in 1919 paper - controversial! “Drop the idea of large molecules. Organic molecules with a molecular weight higher than 5000 do no exist.” (Advice given to Staudinger) • • COLLOID: A dispersion of one substance within another; not a homogenous solution, as the dispersed substance is in a different phase than the other (solvent). Aggregation of (small??) molecules due to weak attractive forces. Example: Micelle POLYMER: A long chain molecule. Unlike a colloid, where only weak associations hold the “units” together, monomers in a polymer are covalently bound together. Polymers can FORM colloids (polymer micelle) but are not inherently colloids. 20 Monday, September 20, 2010 20 Polymers are nature’s structural materials • • • • • • • • • Wool Silk Leather Cellulose Proteins DNA Natural Rubber Marine Adhesives Others??? http://allergyadvisor.com/Educational/ images/Latex%20tree.jpg http://www.naturalwanders.com/GOLDEN%20SILK %20SPIDER%20UNDER1.jpg http://www.joe-ks.com/archives_jul2006/ WoolCap.jpg http://vivaldi.zool.gu.se/PersonalPages/LenaMartensson/LenaMa1.jpg 21 Monday, September 20, 2010 21 Polymers are used in different forms Use Natural Synthetic Fibers Wool, silk, cellulose Nylon, PET, lycra Elastomers Natural rubber, elastin SBR, silicones, polybutadiene Plastics Gutta percha, DNA, proteins Polyethylene, polypropylene, polystyrene Composites Wood, bone, teeth Polyester/glass, epoxy/ carbon fiber, formica Adhesives Barnacles (marine adhesives) Elmer’s glue, super glue Paints shellac acrylics 22 Monday, September 20, 2010 22 Function of Materials in Medicine 1) Structural Replacement (implants) 2) Disease Treatment (drug delivery) 3) Remodel and/or Regenerate Tissue (scaffolds) 4) Devices/Diagnostics (detect diseases, microfluidics) 23 Monday, September 20, 2010 23 Structural Replacement: Arterial Graft O O O Poly(ethylene terephthalate) O FF n F F Synthetic vascular grafts from W.L.Gore! Intraoperative view of a replaced ascending aorta with a gelatine coated Dacron prosthesis (A). Anastomoses are usually augmented with Teflon felt strips (B) http://www.health.gov.mt/impaedcard/issue/ issue19/fleckt/fig05.jPG Monday, September 20, 2010 24 24 Structural: Soft Tissue Reconstruction R R Si O R Si R O O R Si R O Si R R R Si R O R R Si O Si R R R O Si O R Silicone 25 Monday, September 20, 2010 25 Structural Repair: Bone cement • • • Basic formulation – PMMA powder [~70 wt%] – PMMA monomer [~18 wt%] – BaSO4 [~10 wt%] n O O – benzoyl peroxide [<2 wt%] addition of particles – HAp, glass, glass-ceramic, ABS rubber addition of fibers – stainless steel, titanium, Kevlar, UHMWPE, carbon, HAp 26 Monday, September 20, 2010 26 Drug delivery: Norplant Crosslinked silicone rubber tubes used to delivery estrogen/progesterone over 5 YEARS R R Si O R O Si R R Si O R O Si R R R Si R O R R Si O Si R R R O Si O R 27 Monday, September 20, 2010 27 Drug Delivery for Glioblastoma Multiforme Uniformly Fatal Untreated - 4 wks Surgery - 16 wks Surgery + Radiation - 40 wks Surgery + Radiation + Chemo - 50 weeks ! ! ! 1 year survival! 2 year survival With Gliadel Delivery:! 63%! 31% Traditional Treatment:! 19%! 6% O O O O O O O (CH2)8 O Cl NO N H N Cl O 28 Monday, September 20, 2010 28 Polymeric Scaffolds: Neural Tissue Three-dimensional growth and function of neural tissue in degradable polyethylene glycol hydrogels M.J. Mahoney and K.S. Anseth Biomaterials 2006, 27, 2265-2274 O n Neural cells in degradable hydrogels were fluorescently labeled with calcein-AM (green, live) or ethidium bromide (red, dead). on day 10 (a) and day 12 (b) of culture. day 14 (c) and day 16 (d) of culture. 29 Monday, September 20, 2010 29 Polymeric Scaffold: Injured Knees • • • TM Carticel (Genzyme) Autologous cartilage cells, no scaffold) Other approaches in the literature include hyaluronic acid scaffolds, PEG scaffolds, others TE Scaffold: Collagen (ReGen Biologics, under clinical trials) Type I collagen resorbable mesh to generate new meniscus-like tissue http://www.arthroscopy.com/sp08001.htm Monday, September 20, 2010 30 30 Polymers are used to fabricate (diagnostic) devices R R R Si R O R R Si O Si R R High-Efficiency Single-Cell Entrapment and FISH Analysis Using a PDMS Microfluidic Device Integrated with a Black Poly(ethylene terephthalate) Micromesh Anal. Chem. 2008, 80, 5139–5145 T. Matsunaga,* M. Hosokawa, A. Arakaki, T. Taguchi, T. Mori, T.i Tanaka, and H. Takeyama R O Si O R Edd JF, Di Carlo D, Humphry KJ, Koester S, Irimia D, Weitz DA, Toner M. Controlled Encapsulation of SingleCells into Monodisperse Picolitre Drops. Lab on a Chip 2008; 8:1262-4 O O O O 31 Monday, September 20, 2010 31 Nature Materials 7, 52 - 56 (2008) Polymerization for detection Using polymeric materials to generate an amplified response to molecular recognition events H. D. Sikes, R. R. Hansen, L. M. Johnson, R. Jenison, J. W. Birks, K. L. Rowlen & C. N. Bowman n O O OH 32 Monday, September 20, 2010 32 How it all started … function dictates function? 33 Monday, September 20, 2010 33 Off the Shelf Material Initial Use Medical Use Polyether Urethane girdles Artificial heart Cellulose acetate Sausage casing Dialysis tubing Dacron clothing Vascular graft silicone lubricant Breast implants polyurethane Mattress stuffing Breast implants 34 Monday, September 20, 2010 34 Off the Shelf Material Initial Use Medical Use Polyether Urethane girdles Artificial heart Cellulose acetate Sausage casing Dialysis tubing Dacron clothing Vascular graft silicone lubricant Breast implants polyurethane Mattress stuffing Breast implants What makes each of these polymers good for their medical use? How do we know which polymer to choose? 34 Monday, September 20, 2010 34 What are polymers defined by? • • • • Monomer chemistry and connectivity Molecular weight Molecular weight distribution Molecular architecture 35 Monday, September 20, 2010 35 Polymers What is a polymer? Poly many mer repeat unit repeat unit repeat unit HHHHHH CCCCCC HHHHHH HHHHHH CCCCCC H Cl H Cl H Cl Polyethylene (PE) Polyvinyl chloride (PVC) Examples of Natural Polymers – Wood – Rubber – Cotton – Wool repeat unit H C H HH CC CH3 H HH CC CH3 H H C CH3 Polypropylene (PP) Adapted from Fig. 14.2, Callister 7e. – Leather – Silk – DNA – Proteins Examples of Common Synthetic Polymers – Poly(styrene) – Poly(ethylene terephthalate) – Poly(ethylene) – Poly(ethylene glycol) – Kevlar 36 Monday, September 20, 2010 36 Polymers are Synthesized from Monomers FF F F F F n FF Cl n n O O n O Cl n n n O O H N H Cl O O N n n Cl Cl Cl O n H3C n CH3 O O O n R N H n O O n O O R R H N NH2 HO Nn N n O O OH HO O O O O O O O O O HN O O O R O n O O O O O N H O O n O n O O O NH O Cl O O OH + HO HO O OH O O OH + H N 2 HO O Monday, September 20, 2010 H N NH2 O + HO R' O OH O O R' n + (n-1)HCl n O O + (n-1)H2O O Cl N Hn + (n-1)H2O 37 37 basic O H2N CHC OH H2N CH2 CH2 CH2 CH2 NH2 lysine K O O CHC OH H2N CHC OH CH2 CH2 CH2 N CH2 NH NH C NH histadine H NH2 arginine R hydrophobic Amino Acids O H2N CHC OH CH2 OH serine S acidic O H2N CHC OH CH2 CO OH O H2N CHC OH CH2 CH2 CO OH O H2N CHC OH CH2 CO NH2 asparagine N aspartic acid D glutamic acid E O O O H2N CHC OH H2N CHC OH H2N CHC OH H2N CHCH3 CHCH3 CH3 CH3 CH2 alanine A CH3 valine V O CHC OH H2N CH2 CHCH3 CH3 isoleucine I leucine L O CHC O H CH2 CH2 S CH3 special cysteine C glycine G O H2N CHC OH CHOH CH3 threonine T O H2N CHC OH CH2 CH2 CO NH2 glutamine Q O O H2N CHC OH H2N CHC OH CH2 CH2 OH phenylalanine F tyrosine Y methionine M O O H2N CHC OH H2N CHC OH H CH2 SH Monday, September 20, 2010 polar O H2N CHC OH CH2 HN tryptophan W O C OH HN proline P 38 38 DNA is a polymer of 2’-deoxyribonucleotides • • • • 2’-deoxyribose sugar Phosphodiester linkages Direction chain (5’ to 3’) Four bases – – O N 5’ end Purines: adenine and guanine Pyrimidines: cytosine and thymine NH N HO H H O NH2 N NH2 H O H OP O- O N H H GCTA N H O OP O- O O O NH H H H N O H H O OP O- O O NH2 H H N H N O H H O N N H O H OPO O- H 3’ end 39 Monday, September 20, 2010 39 RNA is a polymer of ribonucleotides • • • • Ribose sugar Phosphodiester linkages Direction chain (5’ to 3’) Four bases – – Purines: adenine and guanine Pyrimidines: cytosine and uracil O 5’ end N NH N HO H O NH2 N GCUA NH2 H N H H O OH OP O- O N H H O OP O- O O O NH H H OH N O H H O OP O- O O NH2 H N H OH N O H O N N H H H O OH O P OO- 3’ end 40 Monday, September 20, 2010 40 Some structures HO HO O HO O OH OH ribose Pyrimidines OH HO 2’-deoxyribose NH2 Purines N C NH2 N A N H N N NH2 N N HO H O N N H O NH T NH N O O O G N H N H O NH U N H O NH2 N N H H O H O P OO- H 41 Monday, September 20, 2010 41 Interactions of the DNA Base Pairs O N H N NHN O HN NH N T-A N H N H N O O O N N NH H C-G N N H N H NH N NHN O N N U-A “It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material” -- J.D. Watson & F.H.C. Crick, Nature 171: 737 (1953) 42 Monday, September 20, 2010 42 Now, a fun example… 43 Monday, September 20, 2010 43 DNA Origami “Folding DNA to create nanoscale shapes and patterns” P.W.K. Rothemund Nature 2006, 440, 297-302 44 Monday, September 20, 2010 44 DNA Origami “Folding DNA to create nanoscale shapes and patterns” P.W.K. Rothemund Nature 2006, 440, 297-302 45 Monday, September 20, 2010 45 Polysaccharides found in Mammals Glycosaminoglycans Glycosaminoglycan Repeat Disaccharide Hyaluronic Acid β-D-glucaronic acid + β-D-N-acetyl glucosamine β-D-glucaronic acid + β-D-N-acetyl galactosamine β-D-glucaronic acid or β-L-Iduronic acid + α-D-N-acetyl galactosamine β-D-glucaronic acid or β-L-Iduronic acid + α-D-N-acetyl glucosamine β-D-galactose + β-D-glucosamine Chondroitin sulfate Dermatan Sulfate Heparin, heparan sulfate Keratan Sulfate α-D-N-acetyl galactosamine β-D-Galactose HO CO2H O OH OH O OH OH HN OH O OH OOH H OH OH OH OH O β-D-N-acetyl Galactosamine Monday, September 20, 2010 OH OH OH OH β-L-Iduronic acid NHCCH3 O CH2OH O OH O OH OH HN OH OH OH -O2C O O OH O OH OH β-D-Glucaronic acid HO CH2OH O OH OH HO H2OH C β-D-N-acetyl Glucosamine OH NHCCH3 O α-D-N-acetyl glucosamine 46 46 Glycosaminoglycans Chondroitin-4-sulfate N-acetyl-D-galactosamine-4sulfate Chondroitin-6-sulfate N-acetyl-D-galactosamine-6sulfate Sulfate groups can be distributed in many ways ⇒ many types Monday, September 20, 2010 47 47 What are polymers defined by? • • • • Monomer chemistry and connectivity Molecular weight Molecular weight distribution Molecular architecture 48 Monday, September 20, 2010 48 Molecular Weight Molecule Molecular weight (g/mol) Atoms/molecule Ethanol 46.07 9 Ethylene 28.05 6 Ethylene glycol 62.07 10 Lysine 146.19 24 Water 18.02 3 Styrene 104.15 18 Poly(ethylene) n × 28.05 + CE n × 6 + CE Poly(ethylene glycol) (n × 44.05) + 18.02 n ×7 + 3 Poly(lysine) (n × 128.17) + 18.02 n × 21 + 3 Poly(styrene) n × 104.15 + CE n × 18 + CE 49 Monday, September 20, 2010 49 States of Matter: Small Molecules Gas Evaporation Volume (typically) temperature Condensation Liquid Crystallization Glass Transition Melting Crystalline Solid Glassy Solid 2 50 Monday, September 20, 2010 50 States of Matter: Polymers Volume (typically) temperature No Gaseous State Viscoelastic Liquid Crystallization Glass Transition Melting (Semi)-Crystalline Solid 51 Monday, September 20, 2010 51 Molecular weight affects bulk properties: A simple example H CH2 H n Compound n State MW Methane 1 gas 16 Ethane 2 gas 30 Propane 3 gas 44 Butane 4 gas 58 Octane 8 liquid 114 Low MW PE (oligomer) HMWPE 32 semi-solid 450 3002 solid 420030 52 Monday, September 20, 2010 52 Molecular Weight and Polydispersity Molecular weight (Mw, Mn) Mi = Mn Mw ∑N M = ∑N M i 2 i i ∑w M = ∑w i i i Mi = Mw i Mn ∑N M = ∑N i i i decreasing Mi Polydispersity (pdi) - uniformity of weight distribution; pdi=1 perfectly uniform, pdi = 1.5 - 2.0 very typical, can be much broader pdi = Mw Mn Degree of polymerization (DPn) = Mn/monomer weight; is the number of repeat units in a polymer chain 53 Monday, September 20, 2010 53 Molecular Weight; Example Calculations • • Darice is using a peptide derived from laminin in a hydrogel on which she is culturing neurite forming cells. The sequence is Cys - Ser - Arg Ala - Arg - Lys - Gln - Ala - Ala - Ser - Ile - Lys - Val - Ala - Val - Ser - Ala - Asp - Arg (C to N) What is the molecular weight of this oligopeptide? What is the degree of polymerization? What are the end groups? 54 Monday, September 20, 2010 54 Molecular Weight Calculations, cont. 55 Monday, September 20, 2010 55 Natural versus Synthetic Polymers intensity RNA sample Mn = 9,656 pdi = 1.00 m/z Poly(ethylene glycol) pdi = GUESS intensity Mn = 6,273 m/z Monday, September 20, 2010 56 56 Why do we care about Mw, Mn and pdi? If a mixture is non-uniform, not all components of the mixture contribute to the physical properties proportionally Extensive properties depend on the size of the sample (mass, volume) Intensive properties are characteristic of the sample being studied (density, concentration) Colligative properties depend on the number of particles (and not their individual size) in a solution Higher MW species have a greater impact on some physical properties, and therefore knowing the Mn and Mw (or pdi) can allow us to better predict how a sample will behave. 57 Monday, September 20, 2010 57 What are polymers defined by? • • • • Monomer chemistry and connectivity Molecular weight Molecular weight distribution Molecular architecture 58 Monday, September 20, 2010 58 How does polymer architecture vary? 59 Monday, September 20, 2010 59 Architecture Linear! ! Star! Branched! ! Hyperbranched! Comb or Graft Dendrimer 60 Monday, September 20, 2010 60 Proteoglycan A core protein molecules to which a large number of GAGs are attached. Example: a proteoglycan from cartilage matrix contains about 30 keratan sulfate and 100 chondroitin sulfate chains 61 Monday, September 20, 2010 61 Proteoglycan Complex In cartilage matrix, individual proteoglycans are linked to (a nonsulfated GAG) hyaluronic acid to form a giant complex with a mass of 3,000,000. 62 Monday, September 20, 2010 62 Proteoglycan Complex Electron micrograph Isolated from cartilage matrix 63 Monday, September 20, 2010 63 The Ultimate Macromolecule? 64 Monday, September 20, 2010 64 Crosslinked Networks • crosslinks – physical or chemical • crosslinking – increases molecular weight – swell in solvents • organogel • hydrogel 65 Monday, September 20, 2010 65 Basal Lamina Specialized areas of ECM for cell attachment (~100 nm thick) Perlecan Laminin Entactin Type IV collagen 66 Monday, September 20, 2010 66 Molecular Architecture affect Physical Properties secondary bonding Linear B ranched Cross-Linked Network Direction of increasing strength Adapted from Fig. 14.7, Callister 7e. 67 Monday, September 20, 2010 67 Copolymers 68 Monday, September 20, 2010 68 Copolymers Adapted from Fig. 14.9, Callister 7e. copolymers two or more monomers polymerized together • • • • random – A and B randomly vary in chain alternating – A and B alternate in polymer chain block – large blocks of A alternate with large blocks of B graft – chains of B grafted on to A backbone A– B– random alternating block graft 69 Monday, September 20, 2010 69 Structure of Nucleic Acids NH2 N N HO HO N N N O OPO O- N N N N N O OPO O- N NH2 N N N N N N O OPO O- N NH2 N O N N N N NH2 N O N N N O O OH OPO O- NH2 O N O OH OPO O- NH2 O N O OH OPO O- NH2 O NH2 O OH OPO O- NH2 N N N O O OH OPO O O- N N N N NH2 O N O OPO O- N N N O O O P OO- 70 Monday, September 20, 2010 70 Natural Vs. Synthetic 71 Monday, September 20, 2010 71 Polymers Synthetic versus Biological (Protein) • • • • Synthetic Polymer Mostly homopolymers or simple mer chemistries • • • • • Protein Primary structure exactly defined Copolymers Unique folding Fixed molecular weight Chains do not interpenetrate Random coil, many conformations Molecular weight distribution Chains interpenetrate 72 Monday, September 20, 2010 72 Nomenclature Synthetic polymers are usually easy: IUPAC Rules: poly(monomer), poly(monomer-co-other monomer) Trade names are frequently used. With proteins/DNA/RNA, sequence is not always well defined, but at least you know the monomers. GAGs are usually heterogenous and variable, but you know the monomers Some other terms: Oligomer (polymer science): a polymer with a low number of repeat units (often between 10-100). Physical behavior has not leveled. Oligomer (biochemistry): short, single stranded DNA fragments, OR a protein complex made of two or more subunits (homo versus hetero -oligomer) Telomer: a really short polymer, 2-5 repeat units. Small molecule Telomere: a region of highly repetitive DNA at the end of a linear chromosome that functions as a disposable buffer. Related to aging. Telechelic Polymer: A polymer with one or more active/functional end groups 73 Monday, September 20, 2010 73 Natural Polymeric Materials • Proteins - polymers of amino acids; natural and synthetic; includes peptides, oligopeptides; include collagens, elastins, lamnin, albumin, actin, tubilin… • Polysaccharides: polymers made up of monosaccharides joined by glycosidic bonds • DNA and RNA: a polymer consisting of a phosphaste(deoxy)ribose backbone and nucleotide side groups • Glycosaminoglycans (GAGs): long unbranched polysaccharides consisting of a repeating disaccharide unit, includes chondroitin sulfate, dermaten sulfate, heparin, heparan sulfate, keratan sulfate • Glycoproteins and Proteoglycans: proteins that contain an oligosacharride chain (glycans) covalently attached to a polypeptide (proteoglycans are heavily glycosylated); example: fibrinogen 74 Monday, September 20, 2010 74 Summary • • • • • • • • Polymers are essential to life Polymeric materials are used by nature in many different ways In order to emulate/replicate nature, we can emulate/replicate natural materials (polymers) Polymers are made of monomers connected in a chain Synthetic polymers have simple chemistries, typically only one or two monomers, or possibly a few Natural polymers are copolymers composed of different monomers, and include proteins, DNA, RNA, polysaccharides Polymers are long chain molecules with repeating monomer units, and are characterized by a molecular weight and molecular weight distribution, which will affect their bulk properties Polymers can be linear chains, or form different branched architectures (star, comb, dendrimer), or form crosslinked networks 75 Monday, September 20, 2010 75 Sources Book Chapter Essentials of Polymer Science and Engineering 1 Fundamentals of Polymer Science and Engineering 1 Principles of Polymerization 1 Polymer Physics 1 76 Monday, September 20, 2010 76 Next Lecture Book Chapter Essentials of Polymer Science and Engineering 1, 2 Fundamentals of Polymer Science and Engineering 1, 6 Principles of Polymerization 8 Polymer Physics 1 77 Monday, September 20, 2010 77 ...
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This note was uploaded on 11/29/2010 for the course BME 104 taught by Professor Kasko during the Fall '10 term at UCLA.

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