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Unformatted text preview: ( ’CXOL-i.) LL 10/21/2010 Printable View of: Lecture Notes Blackboard Learning System Print Saveto File Vi Mdim 7 File: Lecture 29 /\E> , . N‘ f l \ ‘5 Led“ 29 Exam 141600,ch | l \ ‘lq a \ :5 BCMB 4010/6010 Lectures ‘\< 3 Fall, 2009 3 H lingfisianme-DL .....a) Garrett and Gisham, Cha ter 10 Nucleotides and Nucleic A s .....b) fie gfiapter 2, pages 54-58 fix, a . ' n (KL 2) Bases, Nucleosldes, and Nucleotides .a) Bases (also known as nucleobases) .1. so name ecause they are W: pKa = 2 to 5) .2. purine and pyrimidine (Figure 10%) ...a. nunbering scheme merino lo (:1 .3. com-non pyrimidines (Figure 10.3) .4. corrman purines (Figure 10.4) QIQMC, W00", Thymmc Nucl os ase +5 er) .a. fi—D-ribofuranose and p-D-2«deoxynbofuranose "th number C/S. nurrberlng schen‘e - . yrlm'dlne and purine N—qucosldes (Figure 10.10) 53-N 0046090413 U" K619 C condensation reaction will glycosidlc linkage in pyrin'idine nucleosides . 0499'erde linkage In purine nucleosldes . ......a. note hypoxanthlne/Inosine sugar .1. nucleoslde rnonophosphates .a. condensation reaction .0. phosphoester linkage to sugar .2. common nucleaside monophosphates (Figure 10.11) ...a. phosphoryl at 5' position .3. uncom-non nucleoslde monophosphates (Figures 10.11 and 10.12) .a. ohosphoryl at 2' or 3' position rather than 5' .b. phosphoryl at more than one position (e.g., 5' and 3') .c. cyclic phosphod‘iester .4. nucleoslde dl- and trlphosphates (Figure 10.13) condensation reaction anhydride linkage . . group transfer reactions (Figure 10.14) phosphoryl transfer (NDP released) pyrophosphoryl transfer (NMP released) nucleotidyl (NMP) transfer (PH released) adding pow . .. + iskJ/mal ...uga.edu/.../cobaliMainFramedowebct 1/7 .5. other purines (Figure 10.5) Adenine ,muanmv; ”VP" *0“ Mme (“m’fif’gfigigb . D—ribose and D-Z-deoxyrlbose (Figure 10.9) prefers (P mom *1 butfi‘nzgmc W565 Ribonucicomer Whose lihlceoi To numoflmmm nurrbenng schene: prime added to sugar nurrberingC) f3”Mci'UwWC Linkage .3 common noonucleosldes (Figure 10.10) AMPWanS phosphate group 600 S C or . .c) Nucleot figs (base 4» sugar + one or more phosphogl groups) "Ni/LCiCOS‘iCV. MMOPhDSFhmth 10/21/2010 Blackboard Learning System > deo t'dine deo c '0 late WWW .-..-..- ..-_’iy°y'_.-- NIT-351L- KNA U uracil urldine urldylate 1' [deoxyuridine] [deoxyuridylate] R’quidmc DNA 1' thymine [rlbothymidlne] [rlhothymldylate] thymidlne thyrn'nylate 7 #7 17—1-1 A-A. _ A adenine adenosine adenylate i deoxyadenosine deoxyadenylate pooh“); l G guanine guanosine guanylate deoxyguanosine deoxyguanyiate l I. H]! hypoxanthineinoslne inosinate S nntn Consequences 1. 'l! cloud Z. (1% ...uga.edu/.../cobaItMainFrame.dowebct ...1. rlbose is undeistood (so rlbocytldine, etc. is unnecessary) ..a. exception: thymldine is assumed to be deoxythymidlne, etc. 2. nucleotide = nucleoolde rriono-, dl-, or triphosphate a. edenylate = adenosine mono-, di—, or triphosphate 1. three letter (for nucleotides) a. prefix r = rlbo, d = deoxyribo (may be Implied) b. prefix 2'-, 3'-, 5'- = phasphoryi location (may be implied) c. first letter a nucleoside ( C, U, T, A, G, 1, etc.; N = any base) ..d. second letter = n'iono-, dl‘, trl- (M, D, T) ..e. third letter = phosphate (P) f. examples: ATP; dNTP; ..ATP = adenoslne Idahosphate, etc. nDQSC sugar ..dNDP = deoxynbonucleoslde dlnhosphate one letter (for nuclosldes and nucleotides) a. capital letter = nucleoside (C, U, T, A, G, 1, etc.; N = any base) ( ..|magine 5‘ OH at lower left, 3' OH at lower right ..|n'egine 2' OH (or 2' H) at upper right 0. phosphoryl groups indicated by lower case p ..c. examples: pppA = ATP (or dATP); Ap = 3‘—AMP (or 3’-dAMP) 3) Chemistry of Bases, Nucleosldes Jag )1 Kiggfg "I .a orrpe e eectronc structure of the bases (Handout Kyte tructures 3-2 to 3-5} 1. amnetic: 4N + 2 = 6 (pyrimidines) or 10 (purines) 6a!“ are mosfly fat 2. all non— hydrogen aton's sp2 hybridized (except We on T) ..a. Includes -NH2 because of resonance (Handout Resonance/Tauton'erism) 3. trigonal, planar sp2 hybrid orbitals, perpendicular p orbital . so or my a. hydrophobic surfaces W .; 12303117. 3.0.34 am van der Weaisaoontect) "vs tat‘ranedrai geometry a. H—bond donors, acceptors: in plane, 120° ..b. hindered rotation of - 3. UV absorbence (Figure 10.8) rTMP; 3'-AMP; 3',5'—cyciicAMP (Taxi not him inch/{dbl arm iapmchw Qééunccci in amrnalia a mumaric NH; due to p overlap (resonance) 1 giaotrrbi'i‘ai abo Vécmd inflow ' (XFOW'IODIC on 2/7 gal rFau/p'ngic on fily ~I-lbo tars 0' in 90266,! flOi‘IQOHS p6 ...
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