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William Rainey Harper College *

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Physics

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Oct 30, 2023

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o AR a - A P Vr" { AR ST W30 Physics 132 -Lab# — Title Pre - laboratory Assignment Carefully read the lab manual 1. Describe in your own words the overall goals of the lab. .-—'r-" e 2 P : \ e ‘. ? | n A A-ON O 1 ) ) { O ‘ y i i | L e - i "* ! ) o ’ » i o & f "l . Q. P \ ¥ { 1A ‘ﬂJ~ : , + i : d . i M N AL Ay A \‘ { i /‘ w T vt Jf} ’ - f \ \ ’ : 1 7 ¢ e ¥ R \ 1 3 ' F &3 » i » ¥ [ b= » | ‘/ = ™ -.”( 2. Identify the physics concepts that you will learn about or test in the lab. : \ (" : - ) i ’;.. A L W losan almar e Aciondoswy feerthiin -t . D! b I'J’F\ 9‘\,&%\ A ‘%ﬂ 'J)&qu“’q C IR WAL , O M U}ﬂlgq, f«\s_ é‘“m Qf }\Q“:j (‘ﬂfj }U*\/ . ¢ 0 4" H (¢ A\ k,(l et szj ""'19’ ! \4.&7(\ 4 &N ‘ AL i M._ - ‘} A A | | reondony AdswihAe f b @ UD. Page 1 0of 2

I R UIC Physics Beparunent '3 Describe briefly what you will measure in the ] outcomes of the experiment. Physics 132 ab and make your prediction of the most impo ¥ VR | B § ki 1 ) A \ Y Lj\_;"“"c‘ AL L "' <34y k e / J TS AN 4 s, | } ) !'/‘ AD S - Ps ~r 3 - % - Dy N RIVA yWwropruwle o 2 o ¥ 4% ’\/«J,_»j Senn o A ~ 14 Voo % r. Ll p TN \ ¢ Pt WAl e YaosSie (Qleng R T B " A Q "()‘pi—l’;l A ' L et A O o -y 7 14O ; o ol Vo Pre-Laboratory Assignment rtant . Page2of 3

n A . a R ‘\(W!‘\..;q'# {3 ;;il,‘\' \”Hq””(‘“Y"‘ﬂhi“(“! (Computing and Data Analysis) ‘“ '“‘ t of the lab must be completed entirely independently of your lab partner(s) ol other students i 1Y I vOt 5 el i ithaov 1 A ( hat .l.. d unauthorized collaboration and plagiarism. All su pected violation of the tandards of Conduct will be referred to Student Judicial Affairs Lab Section (Day & Time) Name: A\ A ‘ Station#: ' Part 1. Manual Prediction of Secondary Structure You will be provided with a file named "PDB ID”_tRNA.pdf containing PDB 1D of a tRNA, short name of the tRNA (tRNAY, where X is the name of amino acid carrying by this tRNA), entire . sequence of the tRNA and a short fragment of the sequence o representing one of the structural motifs of the tRNA. ]‘ 1. Copy the sequence PDB 1D, name (including amino acid code, ( ' ) X, carrying by this tRNA), {he motif sequence and entire { » [ sequence of the tRNA in the box provided below: ‘ LT - 1 » 4 | | nasa, £ | PDB ID: Sequence Name: ", | | ) (s —— 1 : i ; f - v TG AL e | | (A el | || - | { - Sequence: . el ‘ ' \ ',uCCuu’frluf\.f/u')uLL:';&&'JFP\/P*P;A A | 1 f ! ; b atatatla O U L GeeptrRYS GG - P by rf\JU,Ap,JxJrf'.((,ucocur-’,f’t:'?' i | Motif: ‘ i (‘A/ C | i S , ~r i e RN Y AN ALY AUUCC-D S | | at i Ay e o —— e e i i e e Ak 2. First, let’s predict the secondary structure formed by the tRNA motif: - $ In the motif sequence above, draw lines connecting complementary base pairs forming the stem of ) ' the secondary structure. * » Draw the predicted seconday stucture in the box titled “Secondary Structure”, label the nucleotides in the structure and indicate the 5’ and 3’ ends. 3. Find and mark the structural motif in bold within the entire tRNA sequence. RNA Secondary Structure Prediction Page 4 0f 9 ™ e .‘.\':I ) . » , - B B B LS. oA 1 o= e B e = B - . = B . g - vhien NP o P T Y ’ B LI ; L -l (e .y r..\ ._!:'-I‘ - ' |I'. ] n = . r- =d = Ny - & nr. . : 5 e B .i'_!r g i adss e = . ' o Ry v o | g ALCRES Y , he s ’ . E g ; PR i XS Sl &t MR - 4 W - e "y s S i A : K : ; k- e ' .= PR SR LS L B iy o 4 , , A Ly Al A B o & ¥ { g g , e ¥ Y E s 3 ] y . e, S ] i 3 = i = 4 i » ¥ i ' -, » ) Y " 0 \ RIS, T '. . ! . L o € E ¢ 4 X > » g E Y | o , , ¢ > ‘ v 3 o + a 2 % ~

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- —— _ . ” [ s \! i S \:A i " 3 i ” y TS AT Part 2. Using Free Enery Minimization Procedure to Predict RNA Secondary Structure t 1 lab, y yoly free energy minimiz tion by usir ;;‘1142‘\A~L Mm,nu,.\«p.‘.‘75_'{1;.17\iOC‘U‘“‘“V I \ {ynamic paramets jssociated ith the RNA mot f used in the fix tp 'q‘,l{,fth‘“u%h Jl‘ndLUl“PJ‘K‘ i Cthe one that you drew on previots page, ynd then, you will repeat the same calculations for the entirt tHNA eauen o do thn 4. Double click on icon on your taskbar to load the program I'hen » (o to 1~ Sing nee (or just press Ctrl+P) A new window nday Structure will appear. In Seq submen, » Select RNA under Nucleic Acia 1ypt % (Click Enter Sequence relow under Sequence Source Partl in) ritle box, enter the sequence name (something like “PDB 1D used in part 1 in the box called (Enter Sequence We will use default values listed in Options and Constraints submenues » Copy the sequence name (something like “PDB lD"_Panl‘out) in the ' jcon and select Desktop as the location for output file » In Seguence ), without 5'- and -3’ » Copy the RNA sequence box named OQutput File then chick on » Click Start button to perform calculations. Evaluating the Folding Results A new window Results of Structure prediction Calculation will appear. 5. To visualize the structure with the lowest free energy: e predicted 2D structure of the sequence. » Click on MFE Structure + Probabilities to visualize th leotide is either base paired or not. Different colors indicate the probability thata given nuc » Copy (or draw) the structure in the box at the top left corner of the next page. 6. To calculate the thermodynamic parameters: RNA, then click on Efn2 RNA (or just press Ctrl+P) “ppB ID”_Part1_out_Fold.ct file and click Open. » In main menu, go to » For CT file, click on L—__J and select » Check box Write Thermodynamic Details File and click Start. The thermodynamic parameters of the sequence you can find in the “PDBID on your Desktop. Use Notepad app to open the file. » Then, select the whole set of parameters and copy (0 the next page » Repeat the same calculations for structure with the lowest free en copy (or write) its thermodynamic "_Partl_out_Fold.out file stored r write) it in the box at the top right corner of the entire tRNA* sequence. Then copy (or draw) the predicted ergy in the box on the bottom left corner of the next page. Next details in the box at the bottom right corner of the next page. idary Structure Prediction RNA Secot

i | { \ i e 1 W , w w_ —————————- e Structure Pr ediction RNA Secondary - B e - . e AW il = % ' - . [ . X s P’ . - . N L5 b o [ 3 i « ¥ e N f ' TN & N 2 & 15 : = i b i e X - % o L* .., * A - o m \< " = ¥ L s ¥ F it 4 - L Y %3 . A" & b ‘._.J“N. A e e ™ . T .z\ 1 K - » T B 3 i , b . pe & ). f,. . - o - ..f,. E R A A o B 8 'y . . - . e - % 3 = - %l 3 Rl 4 e Jr _,.,,

[=hairpin Anticodon arm and 1)-haiy Bt o 7. Record the free enei ww AG, for e ;‘hhwu‘!w ycture beloy A 4 Imol kcal Hll'] \G(T-arm) } i /m \G(acceptor stem) AG(anticodon arm) = kcal /mol AG(D-arm) kcal/mol Question 1. Is the motii used in the first part act eptor stem, [-arm, anticodon arm o1 D-arm R, ‘ ! » / 2 2 Question 2. In the first part, how does the 2D structure prc(hr:lvd by RNAstructure pt ogram compare 10 ! |‘} : e your manual prediction? iy a1 @ { el W 1\ ¢ R . ’ h | 5 L \ .,‘ /’»‘(','-’ {‘ & { 4 1 &\ & i \:_ , K Al : 4 i \ ﬂ; Question 3. Does the structural motif by itself and integrated into the structure of tRNA* have the same F vy \% B | i ’ stability? ‘ o | Jx e b ‘o 20 & ))/’{ i N O B L OMYS S, WAL (oY) " -—) o . \‘4\,1».-:\ oot - O A AGAP e } ey Question 4. Based on the thermodynamic parameters predicted by RNAstructure program for tRNA* which e y base pair, G-C or A-U, are more stable? Explain your reasoning. _ i " A — ¥ & - \ [fi ‘ 3 4 : - 3 ; ; MQAp rapoXe Al eneoand PUNTIIN LSO VARl S g1 | h . S . : 2 p % % ok i -C .,\}C*?,i \{r« o, I L SRR Or 9 2 vo) Acnn (e HAy Q0o *‘»,& F La \V_l ! : v 104 faate &g A by ] | Numerous experimental studies indicate that the structural stability of tRNA motifs is mainly determined g E by the relative content of G-C base pairs. > Question 5. By comparing the G-C contents with the thermodynamic parameters for T- and anticodon arm, i which structural motif is more stable? =k | AnR. lodon aoun A oot el Aeag Wi X r» - \ | - woehe (-Co fose Qcm,ul A Mg TO L W t9 RNA Secondary Structure Prediction Page 7 of 9

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P — 54 . AR 3 Tl \' ) ¥ v N % . 1 Al \ i & 1A !5 \l 5 L ructul 3 \ , " L Leg Tl Tadi [t Ll ) Y 4 3 . b s : s % (3 1 \ \ Lriad \ - P iy : A pro ) th ) i ) (8] Y ta %4 : measuienis § » & - 5\ yig iy ' WinT N 3 % A Y“““"t“'“!'““‘ dhe I wit L THe nam d : containin a diagraml I"“l Wing *T ‘| y I‘ whic h|),1:|;,.1!(;|v“ wetually form hydrog on bonds together ind define th econdary AKI*‘\H('(N"H tRNA ¥ S sequence used in the lab : cture #1 (see page 6H) cdhagram and the set ol thermodynamic p wwameters mm\u\w\ tor the stru 8. Use this to estimate the accuracy of the prediction, Show your work below. Ay 4 s eata i 1t ’ - ) 4 N A “,l ~P ‘\f ' g 7 ) b 2 0> | O - L8 A L)‘} \ I'JI ) k" ! > ‘»"3((/ N e ) » ® Rar J Sy LG POV Q('{‘(‘(l‘ & TR A7A ) ) 2 ( ) g, 1 ; . R, i p 3 A ¥) fi.)‘(f -{'(_9 :) 9 D A A ) \ 3 . Io® ok i = R &9 e bom \ ".‘F) ) \‘\ )Za@_,k, Lt (/,/ . Q19 Lol 5’~}-;;)l'.‘-;,- 3 Ny . ) > e LAY Mo Wie = < ’J/a 1N ‘T/u’ y LA AR N L2 gl ) £ oA 247 e A0 K . fr‘, C)Fs‘;)) O ! ‘ e 2 By e g X 2 w73, e 13 conday Structure with Suboptimal Structure 2 Part 4. A Comparison of Optimal Se % Prediction to a Crystal Structure here are practically always two or more secondary structures predicted by For the structure like tRNA, t i RNAstructure. and click on Generate all Suboptimal RNA Structures. 9, If not, then go to RNA in the main menu, » For Sequence File, click on [__ l select “PDB ID"_tRNA.fasta file and click Open. File will be generated automatically Energy Difference and 1 kcal/mol as the start point. Con h param | RNA structures will be generated. To visualize alternative structures, go to Draw (in main menu) and clickon Go to Structures. A new window Go to Structures will appear. Now you can switch between different predicted structures if there are. ary Structure Prediction Page 8 0f 9 . » The file name in CT tinue increasing these L » Use 10% for Max % : At eters until the suboptima BT i S ———— RNA Second R AT

M-«.w-«wv’ i e e : RNA Secondary Stn “ RPTE PR U Jite | " " 1{); {J_:L} mny seconaary strue b es #1 /A*"if"' poer B h) 3 " ”, 1 AN uld hay “.(“tl ent oy worse thain 5 6 ot Pt Ut " s v than the structure #1) in ot responding boxes provided below || T es between these twWo structures. Could som AP L e ey e 11. Give a brief description of the main differenc alternate structures be the functional one (or ones)? Explain your reasoning. LRk /M_ VX mfi;\i OJFQ}&,\-) Ofi Ay AL y 8 -2 A0 ()‘/Q ‘/$\ D\t), JS N} />‘f-u) “$fj_j} . Uk Con 5 oD UL N IR S AR NI o L ESRYS) g w2 M o lfi»\pm e B Pys . A Nad N cr B il Qc[fik@ Mo f.}?«\wfrﬂ X e -W’-"‘-N-AM wcture Prediction Q}ﬂmr\_\x}gfi T v 4 5. KOy JUCES XS od Al At 061 52 Xeod { i \ { e of these