PS2-Key 2007 - BHB lflflh Problem Set#2 Name HE 1RasHol...

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Unformatted text preview: BHB lflflh Problem Set #2 Name HE? 1RasHol encercises, DNA structure, and more pflfpfl prohiams.] Hate: The class web site is http:ffhio-classes-ucsc.edufhmhluua! 1- Load RasHol into your computer using the links provided on Lht Elufifi Heb eite. Erihg up the structure or EPA, using the PDB file gpa.pdh which you can load from the web site, Practice rotating the molecule on the screenr using the mouse ihflld Lh: Inflet button dfiufi. dfid move the m¢H$¢ around]. Practice zooming in on details, by holding down the shift key and mouse button simultaneously. and moving the mouse. Tr? DUL Lhc dlflflerent may: to render the m¢1¢¢H1¢, under the 'display' menu. ”5: Lht lunctlfln$ cl HafiHfil to determine the Iollouing: a- Give the 1y: coordinates for the H9 atcm cf the guanine in Lht GER $LIUELUI¢ [it ”ill appear on the command line after you first click on the "pick coord" selection under the "settings" menu, and then click on the atom in the graphics HindoH.j [3“,EEE, 14?,“11, 2H1.h253 b- Hen:u:= Lh: interatomie di$tdh¢¢ h¢tH¢¢h th¢ H3 F¢$ltl¢n fit the guanine and the H9 position of the adenine in the EPA structure. 1c11ct on the 'pick distance" setting, then click on the two atoms] 3.345i c- What sort of interaction does the distance you measured in part h cussccpflnd Ln? [covalent. H—bond. electrostatic or van oer Whale] ‘u'an dc? Was I s 2— Using RneHul. brihg in the Dickerson ENE coceeamer [dietereon-12mer.pdh]- The two complementary chains are called A and E, each of which are 12 nucleotides long- NOTES: {1} In looking at individual nucleotides or atoms in a complicated structure, it helps to use the 11slab mode” under the “options'r menu- E? hflldlng dawn the control key dhd sliding the mouee downward, you can display thinner slahs or slices of the structure, or slide it upward to make the slab thicker. 42F Another helpful trick is to place the center of rotation of the molecule at an atom that you are focusing on. To do this, click on 'pict centre' in the "settings" menu- Then click on an atom, and it will ccntc: the Inltculc on the atom you clicked, and also use thflt atom for a rotation center when viewing. Unfortunately, the slab function does not re—center when you use "pick centre" — a clunky aspect of RasHol- u. Enuh in an LEE middle at th: dndecamer, and Iihfl tht N3 Fflfiltifln a! 1'? en the A chain [in the eemand minder-«r it should say "Atem: N3 111] Eire-up: T 'I' Chaimh'r. Then find the Ill atem ef m5 en the E chain. New measure the diatanee between the H3 us! 'I".' and the m. e1 1115. What kind of Iweak. interactien dens this distance correspond to? 2.79691; Harare-gen Bending 1:. Find the pheaphezrus atems belonging to T'? and TE, and measure their IntEIat-Dll-E distance- This value is near the maximum Feasible EI—EI dl=LHHE= In: ndjflttht hfl¢1¢¢tid¢$ in an RNA er UHF thlih. IE .2933. Che-Lin A 5.?efl Chain 5 humfihfiifilfihnmfilifium plflmliml'hirll cmfl'filammmdmufluflhhflh www.mwurmmmumxafl-mtu WWWLMHIEmflmnd-uflh. n3: 24mg 31',“ hf“. J— I-Iilll ‘LEA. I'll-#:55- ___——-;_'5 5'! Mlflmfi: J. flanthLlixu h" a.-.e.rrdcdmé-1LHM=-q finial-1.151,... .ll 5:! L.- ' sn- 1. 'sn * “was “"3 Pr“ mmhmMIiflfimflhMimemmd Criklhlhnmmdfininflwnfladnhkhdh? I. nflu‘fih III-Jen”, Elf Ind-F an” (ng-mmuhqg—rmdm-llamfii ' z, 3’31ou feflflj WITH“ “File M'fifflu‘nhr I: mmm‘m‘ mimmduflwfl Eur: [Irrenwhuhumhififl [uni Hlbldumfl: lumbar. i=1 Wmmm mammal: ins-min n} -.. d..- ..' ac, - hfl ‘J .i- "Fri-H! ::. eats-{amen "- fifigfiffiflj {eh-d} a} I. “-3331; I511; *zlilu-Tmfl-ru-‘l' J]. .-'_ ‘J'H'M. find—mm pin: 1i. -difis iii-Md i? din :- -,r.; 115151;.” If Hw-Iflifi-I'H—l' Wand arm-dame mmmflmmmm. me mmbqfliflnfilfi whtdnynlflint I: W? ham?“ '.|'.l|'.1 win-31mm: plwerflflnfm Mmhmmhnfim mmmnmmwmnmhmm Ewlinhfllfiflluidmhllflflu. €an III-Pfimhill}: flm'll _L~.f,_ Drug! 4—- ua ~11 .1 :. m+w¢ummm Maw ‘1 walk-H H-LthLqujmTfi‘nL-ufrwflwflfl-fihawr an“, a an: LL11! as... u an Half-.1 45.) hm- I‘n'l *JH‘IEI' 14nd”: m m ”Jun-Ll M mfl+ I-Ir (La. £311”: nun-link} fl hut-pulmflpfl 1mm. mum DHAJIIII'I'IhmflHI-uh. hulmpulnwhficufpfl'sifl autiiErI-I'n'u. If“ 'Lu-‘u'hufluw'! ' lat-Chi!“ 1. “h? ' film-ankllinm '0 E.&. H Li”! in.” H... P] d4"!- ...
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