Survey
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
History of polymer science and the determination of DNA structure • Books on reserve: “Inventing Polymer Science” by Yasu Furukawa “The Path to the Double Helix” by Robert Olby Biopolymers: The ultimate “block” copolymers • Three main biopolymers ¬ Peptides/proteins: monomer units: α-amino acids, linked by amide bonds (20 or more units) ¬ Nucleic acids: monomer units: nucleotides, linked by phosphate esters of sugar-phosphate backbone (4 units) ¬ Polysaccharides: sugars linked by acetal linkages between anomeric center of sugar and alcohols of next sugar: can be branched and stereochemistry of linkage matters • Nucleic acids and peptides are made naturally with a particular order of “mers” which determines in part both 3-D structure and function. Peptides • Inherently chiral R L-amino acids make • Two distinct ends: amino (N) OH up proteins and terminus and carboxyl (C) H2N peptides from terminus mammalian sources O • Primary structure: sequence of the “blocks” Rn-1 O Rn+1 H N OH • Secondary structure: folding H2N N H of short segments into O Rn O helices, turns, and sheets R group (side-chain) can be • Tertiary structure: overall aromatic,polar, acidic, basic, folding of 2° structural aliphatic,cyclic elements into larger domains “φ/ψ Space” of Peptides and Proteins O H C O N φ C C ω ψ C N C H H(C) C α-Helix φ = -57°, ψ = -47° 3.6 residues/turn 1.5 Å rise/res. 310-Helix β-Sheet/extended φ = -49°, ψ = -26° φ = -135 – 180° 3 residues/turn ψ = 113 – 180° 2.0 Å rise/res. 2 residues/repeat 3.4 Å rise/res. α-Helical Secondary Structure β-Sheet secondary structure Transmission electron micrograph (TEM) of amyloid β protein (10-35 fragment). Fibrils are 50-100 nm wide and several microns long. This is a selfassembly mediated by predominantly βsheet interactions. Tertiary structure Carboxypeptidase HIV protease symmetrical dimer First high-resolution X-ray structure of HIV protease was done using a fully synthetic protein (made by chemical synthesis; Stephen Kent) and synthetic inhibitor (Dan Rich). NUCLEIC ACIDS: Polymers of nucleotides O "bases" pyrimidines and purines R NH sugar: D-ribose or 2-deoxy-ribose furanoside O O O X O P O O Ribonucleic Acid X = OH, R = H N O NH2 N N O N N NH2 N O X O P O O O N O O NH N Deoxyribonucleic Acid X = H, R = CH3 O X O P O O phosphodiester linked via 3',5' of sugar N O O X N NH2 β-linked bases Pyrimidines, Purines, Nucleosides and Nucleotides 6 8 2 N 1 C NH2 N N H O N N H HO N HO O O HO HO 1-(2'-deoxy-D-ribofuranosyl)thymine = (deoxy) thymidine N O HO OH uridine-5'-(mono)phosphate or uridylic acid or 5'-UMP O O P O O O P O O N O HO HO OH X pyranose Why not pyranosyl DNA or RNA?? N HO O O N N HO 9-(D-ribofuranosyl)guanine 9-(2'-deoxy-D-ribofuranosyl)adenine = deoxyadenosine = guanosine O N O b N NH2 N N NH2 NH path NH2 HO OH 1-(2'-deoxy-D-ribofuranosyl)cytosine = deoxycytidine O CH3 O N HO X NH N OH furanose O N O b X = OH, D-ribose X = H, 2-deoxy-D-ribose NH2 N O a path H X OH a O H CH2OH NH2 guanine adenine NH O N N H HO O O P O O NH N O CH3 H H H O N O cytosine R = CH3, thymine R = H, uracil O purine NH2 NH N H HO 2 N 4 N 9 H 3 pyrimidine O R N 1 O O deoxycytidine-3',5'-bisphosphate O O P O O O P O O NH2 NH N N N O HO OH guanosine-5'-diphosphate or (5')GDP NH2 O O O P O P O O O O P O N N O O N N HO deoxy-adenosine-5'-triphosphate or (5')dATP Nucleotides 7 N 5 N 3 + purine or pyrimidine "bases" 6 Nucleosides 4 5 natural nucleoside Sugars Heteroaromatic "bases" DNA Double Helix: Factors that control formation and stability • Hydrogen bonding of the bases • Ionic nature of backbone (repulsion) • Base stacking of purine and pyrimidine bases in the duplex: main contributor to stability How can DNA/RNA be a repetitive double helix with different units? D A H A N H D C D H N N A N R O D O A C-G N D H N H N H N G A H A C N R N H N H N N G A N(Pu) θ1 55.7° 57.4° θ2 54.4° 56.2° X 10.72 Å 10.44 Å N(Py) θ2 θ1 C1' X C1' N H D O A T-A A N R ove r gro mino D O T R H D A A R N N O D A O N R major groove major groove D A D A H H N A N A R N A N A O T N R A H H N N H N N N N A R N O R A A A ove r gro mino Ability to form repetitive hydrogen bonding structures in DNA and RNA is due to the isostructural (isomorphic) nature of the C-G and A-T(U) basepairs. That is, the fact that a C-G, G-C, A-T, and T-A basepairs have same geometries provides the template to make a polymeric duplex structure with different bases. The only caveat is that the bases must occur pairwise(A w/ T(U), G w/ C) to get the repetitive structure. Polysaccharides made from Sugars Sugars form diastereomeric cyclic forms: furanoses and pyranoses Sugars form diastereomeric cyclic forms: pyranoses α and β anomers Polysaccharides of even on sugar type “homopolymer” can vary in structure • Units linked via acetal bond at the anomeric carbon: α or β • For hexopyranoses can have 4 possible links to hydroxyl group • Branching can occur as in amylopectin Polysaccharides of even on sugar type “homopolymer” can vary in structure • Cellulose is a structural polymer • Insoluble in water Amylose (Starch) α-linked gives a helical structure Polymers for Biopolymers • Polyacrylamide gel electrophoresis for analysis of size of DNA, RNA, and protein • Agarose gels for double-stranded DNA and RNA size analysis • Solid-phase or polymer-supported synthesis: Peptide Synthesis Because amino acids have two functional groups, a problem arises when one attempts to make a particular peptide Strategy for Making a Specific Peptide Bond Amino acids can be added to the growing C-terminal end by repeating these two steps When the desired number of amino acids has been added to the chain, the protecting group can be removed An Improved Peptide Synthesis Strategy