Class Note for CHEM 490 at UMass(11)
Class Note for CHEM 490 at UMass(11)
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This 24 page Class Notes was uploaded by an elite notetaker on Friday February 6, 2015. The Class Notes belongs to a course at University of Massachusetts taught by a professor in Fall. Since its upload, it has received 19 views.
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Date Created: 02/06/15
Nucleic acid structure and recognition Mon 41309 Nucleic acid structures Reminder classic double helix amp WatsonCrick H bonds Ch4 Alternate basepairing Range of structures double helix variations major amp minor grooves Ch 281 2 and 3 structure Palindromes structure amp recognition Protein DNA interactions DNAbinding domains Ch 311 Catalysis restriction enzymes Ch 93 35 e phosphodiester anage 35 phosphodiester linkage 35 phosphodiester nkage 339 end on Figure 191 Principles of Biochemistry 4e 2006 Pearson Prentice Hall ln What forces are important Hydrogen Bonding Electrostatics 39 Burial of Hydrophobic backbone polyanion 0 Surface amp Stacking 0 u o o Guanine ooVe g k m ICH H 0 H cC H I nixM C a N I Thymlne lN CC I o kM c Cytosine purine pyrimidine soswufo Hoogsteen face Purine major groove VA H 15 wafsonCrlck face c H A I C 539 339 I I Thymine c m m G H cNc139 In I 39 m Adenine 0 m A In T Ill 139 m A III c 5 Cytosine HI Em Guanine HI m T I A m c m G In HI A HI T purlne pyrlmldlne 339 539 L 4 N i HNlt 0 MI HNH N Nquot 0 39 A lt I A W v N N N I I l lt I A z N J WatsonCrick f J N O O 1 39 N HNH T1 WCHoogsteen face H N39 K lt A J 20 N N WatsonCrick faces i but AntiWatsonCrick orientation Bad Base Pairing Donors not matched to Acceptors QVO6 N T N I O HQH g N N G ltNgtNH o39NjfiNH l X H ltN I NANH x G l n H 0 N T HNX 0 terrible angles Wild but good Base Pairing H H wa wquot a O I I Gquartet Telomeres quot39 H39L amnminm Sixth Edikian Tmu ml Comparison pun 9 amy m Ham 1va I A a z shape aroadesl mermedlale Narrowest Rise perblsepair 13A 30A 2 Helix diamerer 255A 237A 134A screw 5 use Elamhanded mamharmed le handed Glym hnnd39 mm39 mm Bis pairs per mm nf helix n 104 Pilrh Pal mm of helix 253 A as A Tilkulbase pairslmm 19 1quot normal an helix axis Major glaave Narrow and vely deep e and quite deep flat Minorgrppve Very broad andshallow Narmwand quite deep Very narrowend deep Syrl Ind am My In me arknnllnn n39lhe Nglycnxldlz me name rrre ruse um enxyrlhnse In me an prlenrulemrne use uunds my rm rue peexyrl hasmlnlhexyn nrlen i onha par liibuva m deuxyllbuer yllml near a only In and prlerrrenprrrwnlle purlrremrr be null nrxyrl Y ahle zal Kiurhzml39stly Six m Edinun maon HFleellulldlld mullAlly hug um blLn S Majorg roove side Majorgroove side HNHmo CH quotVi4 W A quotNVaw N i Elms61K Hquot OGlymsidk Glym dic A OGchssidi H bow bu d a bnnd Minorgroove side Minorgroove side Adeninr lymine Gunnine Cylasine gmeu s mmmmmm mmWWMUWW Major groove Minor groove Figure 2H D Hivrncmv39 iy smh swimquot munw mnemmna Company Sequences read the same 5 to 3 on either strand Palindromic DNARNA can adopt alternate structures Stemhairpins Palindromes Hairpin RNA Secondary Structure Base stacking ll and pairing is maintained Hairpin double helix Hairpin tRNA transfer RNA nnnmngtmgtnngt o w Cnmncncn 2 structure 9 3 structure Ribosome protein rRNA ribosomal RNA 4 structure Palindromes gt Sequences read the same 5 to 3 on either strand 39 Aw Monomer Palindrome Easin recognized by Dier homodimeric protein DNAbinding motifs helixturnhelix CIA SH a helix inserted into DNA major groove wan e Dan39u h Wok DNAbinding motifs leucine zipper 7quot Leucine zipper Basic region eve B strands DNAbinding via beta strands DNAbinding motifs zinc ngers Restriction enzymes binding amp catalysis Che5 600 RA Added methyl group H cleaved Not cleaved N r r I K r N N 5 WGATATCWS s WGATAECWE A I gtH 3 W WW ITATAGWWM 539 TWCTATAGWS39 H N W ow N W squot deoxyribose signage V H d 3924 M reamsvd tc 7qu Mi acme mo qW Li Lio u A 539wwv GATATC wwn3 339WCTATAGNWV5 Symmetry axis sixm Edifiun 5334 Scissil bond Enzyme Enzyme nonspecific DNA cognate DNA 1 lt u lt V NV gt 9 E 5 E 5 684 w l u u E 3 E 3 we a a 9 wwm E u H 39 M Nonspecific Cognate Catalytically complex mplex competent A distortion rigm 942 5mmst Sixth Edition munW HFleemmlldud mnvuny
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