LIFESCI 3 Spring 2006 Exam 1

LIFESCI 3 Spring 2006 Exam 1 - INTRODUCTION OF MOLECULAR...

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Unformatted text preview: INTRODUCTION OF MOLECULAR BIOLOGY LS3 EXAM 1 ' 5/4/06 6:00 TO 9:00 PM Name_ ID# Discussion Section Part 1: Multiple Choice Question 6 O / i O 0 Total of 25 questions (4 points for each question) Part II: Short Answer Questions SAQ 1 (20 Points) 7/0 gsAQ 2 (20 Points) [fl SAQ 3 (20 Points) “‘0 SAQ 4 (20 Points) )3 SAQ 5 (20 Points) 4 .5 Total Points: 200 I g y 9 I . ; SHOW ALL WORK FOR FULL CREDIT. GOOD LUCK! n 2.0 Multiple Choice Questions (100 Points) Name 2 = ' 1. Hydrogen bond forms when a hydrogen atom is “sandwiched” between two electron- attracting atoms: . M H 1AM?“ , A) Qxygenandfiulfur 045$” [aft/>Utcl'rt7fii‘961illili'l «h B) Qarbon and Qxygen P ' 7 1, (if ' ,- “\ Ehosphorus and Nitrogen Ci M Qxygen and Nitrogen —-——-:) mask immanent 1 (as/ad M Dfi/d . i All the above ., .1 H A} l .um‘i'j; __ 2. Which of the following amino acids is NOT involved in glycosylation? O 3 _, A) ASparagine "‘ 3" 1d r0 rhtlh :2 E Tyrosine .. 41d.“ “loin“ C) Serine —' l-pjaraplhll‘u D) Threonine '3" 5“]de ’10 in» B) All the above 0 1,1le of L... 3. Which amino acid can be phosphorylated by a kinase? A Phenylalanine L\ Histidine ) Cysteine I (3 Tryptophan None of the above I 4. Which amino acid is mOSt likely located on the surface of a native protein in aqueous solution? -—-"’" A) Phenylalanine \if B) Isoleucine WW? N Lift” “74 rag-h .H t L @' Asparagine D) Tryptophan 3,2, «‘3‘!— E) None of the above ; " (E) K 5. What is the function of Chaperone? A) Chaperone is a protease that involved in protein cleavage. B) Chaperone can stabilize unwinded DNA during DNA replication. © Chaperone is involved in protein folding. D) Chaperone is mainly involved in transcription termination. E) None of the above Name 6. Protein solution absorbing 280 nm light is mainly due to: A , Lysiner b.1120 , I ‘\ TTYPtophan ‘3 h4df°€bhw to L’\ ) ethionine - w / Moline - Cflollv _ > E) Giutamine~ Md rain; ttw 7. Which of the following statement is m true for an enzyme? A) Enzyme does not change AG B) Enzyme functions by lowering the activation energy of the reaction 9 The greater the Km the greater the affynity for an enzyme to its substrate The greater the Vmax the greater the activity of an enzyme. E) Enzyme converts a substrate to a product without changing itself 8. Which of the following methods can be used to determine protein sequences? A) X—ray crystallography Mass Spectrometry C) 6 N HCl protein degradation \,\ D) SDS-PAGE Electrophosis / M all of the above 9. The following statements for the two isotopes 32F and 31F are true except 32F and 3 IP have different numbers of protons ). 32F and 311’ have the same number of electrons % O 32F is radioactive, 31F is not a radioactive isotope . P and 3 IP have the identical chemical properties . 32F can be used to label DNA ,‘i 10. During DNA replication of a bacterium ( 1st generation), an A (instead of a C ) is accidentally incorporated into one of the newly synthesized DNA strand (2nd generation). This error is not corrected by the proofreading activity of DNA polymerase, but it has no effect of the progeny to grow and reproduce. What proportion of that bacterium’s progeny would you expect to contain the mutation afier three generations? A) 100% 50% j 25% .« O f ) 12.5% '9 E) 6.25% I?) g 3 D J {9&9 a, 5') an 8/343 Name r 11. In the regulation of the lac operon, Cyclic AMP (CAMP) ,é)’ can inhibit the transcription of the lac operon :3)“ increases in the presence of glucose almost? itumfnb 9 increases in the absence of glucose ) increases in the presence of lactose '3’ I.) i. a“ ‘1’ i (am f l B) increases in the absence of lactose (MMFT NF 0“” 12. What is the function of Rho? ,Xf Rho is involved in transcription termination in eukaryotic cells. @ Rho is involved in transcription termination in prokaryotic cells. Rho is involved in transcription initiation in eukaryotic cells. D) Rho is involved in transcription initiation in prokaryotic cells. E) Rho is involved in DNA replication in prokaryotic cells. ‘1“ (finding/:5 ('hwmufiridf '--') ace-wan:- 13. Generally speaking, histone acetylations “/7 59f H C J 4 r“ ' ‘7'" "" ’1 L 'O"“jl/2 ENE ID/J/I' " (6 Increase transcription in both prokaryotic and eukaryotic cells a t : f'ku Decrease transcription in both prokaryotic and eukaryotic cells 6 Increase transcription only in eukaryotic cells J» Decrease transcription only in eukaryotic cells / “E y Do not affect transcription 14. Under high pH (Alkaline) condition, . EAL NA will be hydrolyzed to small pieces RNA will be hydrolyzed to small pieces Double strand DNA will be denatured into single strand —-—7 ) d‘ -- All of the above / B & C only. 15. A difference between a prokaryotic gene and an eukaryotic gene is that prokaryotic genes are polycistronic, so each gene may have more than one promoter The termination of transcription is more heterogeneous for eukaryotic genes than one prokaryotic gene can encode more than one protein, so each gene may have more than one Shine Dalgarno sequence \Q Transcription of a prokaryotic gene requires a primer whereas transcription of an eukaryotic gene does not require a primer. \.\ for prokaryotic genes / yrokaryotic genes need to be transported from the nucleus to the cytosol \ t. Name___. / [e (‘10 16. The statement that “genes can be in either direction of the genomic DNA” means: A) a gene can be transcribed in either S’—>3’ or 3’——+5’ direction. either strand of the genomic DNA may be used as the template for transcription ) the two ends of a chromosome always contain active genes D) None of the above E) both A and B are correct 17. Which of the following protein(s) can unwind double strand DNA? A) Sigma factor fl, Helicase C TFIIH All of above 13) A and B only 18. If four related transcription factors in the same family can randomly form homodimers or heterodimers, how many sets of genes they can maximally regulate? (Assuming that each gene is regulated by only one cis element) A) 3 \ 1 23 M “H @ 10 I 1‘) 23 C) 12 l 1 n, D) 16 x 3 E)‘ 20 1 t) 19. The following features are common between the process of DNA replication and RNA trasncription EXCEPT _ WBOflI require RNA polymerases ”’7 Wm B) Both involve phosphodiester bond Both use ribonucleotide triphosphate as substrates ‘3 N Pr P ""W’Lf Both use DNA as template \E) Both happenin the nucleus 20. If the Guanine content of a DNA genome is 36%, what percentage of bases in this genome will be Thymine? A) 36% A) 18% ' (a C *3 77, C) 64% . , , D) 72% RT licb/IIL ’ W ® None of the above We 21. A double strand DNA solution contains 0.5 units of Absorption at 260nm UV light. During heat denaturation, the Absorption at 260nm UV light will: ® 13) C) D) E) 22. Antibody is a hetero—tetramer contains two identical 25 KD light chains and two identical 55 KD heavy chains linked by intra- and inter-chain disulfide bonds. If a purified antibody was denatured in a non-reducing condition (in the absence of [3- mercaptoethanol, or DTT), run through a Name Increase Decrease Remain unchanged Become zero Non 5f the above number(s) of hands you can see on the gel.“ ”—‘V %) One \{4 ) Two W, Nod/m C) Three law {3 J. is D) Four A“ I \4' E) Eight ‘ 23. DNA replication requires: A) B) C) “IE? RNA polymerase ' 'L dATP “3 ATP Kiri Wt} All the above Q59 A and B only 24. Transcription requires: A) B) 3‘ DNA UTP dUTP All the above A and B only 25. HIV carries a reverse transcriptase that can: A) B) s? use DNA as a template to make RNA use DNA as a template to make DNA use RNA as a template to make RNA use RNA as a template to make DNA use RNA as a template to make protein ‘u.’ -PAGE gel and stained, predict the 162110 SAQ 1 (Total 20 points) Your Name You have the following 4 proteins mixed in a solution at PH 7.0: Protein Molecular Weight (kD) PI (Isoelectric point) P1 120 4 N 7 = WWW P2 120 10 P " > P3 40 4 “*3 P4 40 10 p as *VA) In experiment A, if you pass the above samples through a column with positively charged ion-exchange beads, which proteins will be bound to the column? (4 points) fl awév 93 *‘f B) In experiment B, if you pass the above samples through a gel filtration column, which proteins will come out of the column first? (4 points) ?, and RL 4’ K1‘4?) In experiment C, you first pass through an affinity column with beads covalently attached to an antibody specific for proteinfll. Then, you take the flow through (unbound materials) fractions and pass them through a column with negatively charged ion- exchange beads at pill. What protein will you expect to come out of the ion—exchange column? (4 points) {3 3 ’rg/F) If you run the above four proteins with 2-D Gel Electrophoesis. Indicate the final locations of P1, P2, P3 and P4 onto the right gel. (8 points) pH4.0 pH7.0 pH10 80 kD 40 kD SAQ 2 (Total 20 points) Your Name 4 . ' ' Shown below is a real 3D structure of a protein called Interleukin 8. A. What is the secondary structure shown in “A”? How many amino acid residues per 5 turn? Are the hydrogen-bonds perpendicular or parallel to the axis of the helix? (8 points) («A km a - figmflduc’) {Pér lam —- 37,: my 1/1 , by ad ) B. What IS the secondary structure shown In “B”? Are the hydrogen bonds formed within the same strand or between two adjacent strands? (6 points) _: I [email protected] beta P‘f («are é 5 mes / " ‘ H rbané/j \p/g Z qel 3 a cam .sc 9 Hang; r——-———~—————-———""“ m g C. What is the secondary structure shown in “C”? Which amino acid is most likely involved in bends in protein chains? (6 points) fig” 1103.. SAQ 3 (Total 20 points) Your Name . . _ I. The figure below is a replication fold during DNA replication. Feel 5’ or 3’ in the box next to the arrow to indicate the orientation of the template DNA based on the information of the leading and lagging strands of the newly synthesized DNA. (4 points) Primase Single-strand- binding protein (88 B) 2. Use one sentence to describe the fimction of topoisomerase during DNA replication. (4 pomts) _ Adi “my“ "E‘ “WW I MW in. 4-H: Asa-me "Shawna! F ~.\ Ain‘t LID-(,{Ui‘e ITLPHCMIHQQ) Jlé‘r‘ei‘iirx‘r gd?€f69"8\\ .\ . ku.¢;7kmn_"_ . ‘ -v’) ( (:am {arming 3. What are the three enzymes involved in removal of RNA primers and fill the gaps between Okazaki fragments. (9 points) a ( IQAJA {9 r M w ’4? Mix .. " V‘lmauu5 audit UH manage _LH"_ €0§lcr~vnuutc¢fc [upbf-LJ‘I‘} dc; @614; .3 in”) ”‘ 3'1““) Wtflmgmmfi 4 Which enzymatic activity of E. coli DNA polymerase III 15 responsible for proofread1ngto_ reduce “spontaneous” mutations during DNA replication. (3 points) ( 3:75 KXJnULlectSF \k..., H...“ «vs SAQ 4 (Total 20 points) Your Name I J_____ A). In eukaryotic cells, which RNA polymerases are responsible for the synthesis of rRNA, mRNA, tRNA and SnRNA? (4 points) Arm“ s»).~.-+msw,¢<{ b1 Pche‘raéfi f— )? . xymfl/Uc‘l :1 1r pei1m¢rq$( I]: w -—-—7 {- lZ/VA } San [2M4 \Sy-nd—mgrzgcl b] (pal/MCWGSC E B). Where are rRNA, mRNA, tRNA and SnRNA initially synthesized and where are their final locations in typical eukaryotic cells? (6 points) ’ €1n-ihé5ifi-‘-A FW'NK‘l lU(¢:+tvI\ \/® [‘RMA' n»! {ILLVB -C"f r090: milk/l. HuLtge$ ”TVS“ l' 115’” nJOl-W) (3wawa\_ . . ‘ . .5‘ JA RM? fiqblCVfi @dfww\ Y“ {\er C). Describe the PULSE-CHASE experiments to determine the place of RNA synthesis and their final locations. Be sure to indicate which radioactive nucleotide you plan to use, your prediction and explanation of both the PULSE and CHASE experiments. (10 points) “We Pew: showman-r thaws mu: limo u; «mhuuj 67“Crhe§;26‘£ m The haugug’. {,r c545 r-almctehue 17¢ FD C-pr‘ar H11. ”MW/)9; aHmS "‘ ”Fwd," 'i‘5 h” R‘HU” \MJEr 9‘" Km1 {'0 Pmi W total/Lon oé “WM Cbm'finaimwum flwchm swam hm mm; fix/f4 flu cl ' . . . j j( «and ”MIL" 1H“ ,‘jr‘qtm 6119'“ la align: eff? OUMIDIMC’ l' I" - . . ‘- 7:112 '. tvnbfwr'u (‘t ij fun pk} .0J7h flu Arr“? 5196”” 'J... .- , , - 9am) “mg 1‘11: “fl/45 "“1/ [)95,/,O.7 rl' awaéaf'g Hy. ”HM/fl: ad: .- ’ ~ = 3 " . d an-wz nucw-JFMe ,.;— flue/(add 5"" 19"? (fa fir/11m“ wi/f ' £6 W‘chwaL/iv’c’ "‘ 7&1 0‘15? . 15 Jjn(}’h’(3‘lf,guk W mick” and bfi ””5 e fut/4 SAQ 5 (Total 20 points) Your Name _ , As shown in the diagram below, both the green fluorescent protein (GFP) gene and the red fluorescent protein (RFP) gene are located in the same cells under the control of LAC operons. Both operator 1 (01) and operator 2 (02) share the same nucleotide sequences and can be bound by the lac repressor protein from the 11 and/or 12 gene in the absence of lactose to stop transcription. If only GFP is expressed, the cells show green color under UV light. If only RFP is expressed, the cells show red color. If both GFP and RFP are co-expressed, the cells show yellow color. On the other hand, if neither GFP nor RFP is expressed, the cells show no color. . If there is a mutation abolishing the fimction of 01, what color will the cells be in the bs cc and presence of lactose? Explain why. (10 points) _ 9mm “A“; tau/“25¢ (la-5 may Plug anj any) .4 Hm hbflflf‘ Ci [atfi'gfi rhfl‘c w! be h‘ ' or- game no (Arrays t5 ,Wfii‘fl" {he f‘fpnsgar from (1 will in: pc'gpanfgfrermrrh? RFP erfrvggiJn. GFP [anneal be cy‘f‘flgguf W/v‘~H ‘1 fwf’irt.’ P‘dnbf-thnt/l? riparian-FR“ (A firm frzb’xmzd 0‘ Lit-twat f'He (Lap-19:,“- will hm; A) (uni-vii, uné +rhn$flf\Ff'I-n’i (an Eonrmda. 12?? Will £0 4;.“ P/Sjcd Ana “M ('tltlj w.” b‘( rid, GP], Dnflé “(j ‘tln (Ll/load; {ZviflL}IJO,— B). If there is a mutation abolishing the function of the 11 gene product, what color will the cells be in the absence and presence of lactose? Explain why. (10 points) n 'n “at 51531;:ng 0!; {gnu FM (“I5 wit} LL r‘ - gm! ”7:! (,F': ClIJPCpHSgJ,» [5 ’13:} (outrun-.4“? OI will ‘lr‘anégmbf tii'é bag,“ (gdl 6 an; (95:? will be, Mcrrgsgggm l1 fidmbdhmmj ta.“ ,6 /)(/\G LupraSLqu a? {Ll’i’k 91nd il-wili flair lo: (3. _ , ‘ or Jattas- -- ”“55““ ‘* “5 P~r$enct L {ht “I“ IV-ll “PPM” V'gilofl, (“712? U," ' ll~ (#:an 5C humid ”‘1‘“ (AAA H . irc 559115566! htt'i‘vd$( ””54 W"! 10"”? 4'0 m [a ”Paw-2r £004 15:“er 0 {-1) 5. , . {I JLLfésLVH.) + g_ Ra _ rum b f‘ a N!" Lt Expnislw‘ or: { Few 80'}Yl_ {Si’P‘incl RFP f‘flu it”: 11 ...
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