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exam 1 solutions

by: mythili venkateswaran

exam 1 solutions CHEM3330

mythili venkateswaran
Texas State
GPA 2.9
Physical Chemintry 1
Dr. Easter

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Physical Chemintry 1
Dr. Easter
Study Guide
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This 9 page Study Guide was uploaded by mythili venkateswaran on Thursday October 1, 2015. The Study Guide belongs to CHEM3330 at Texas State University taught by Dr. Easter in Fall 2014. Since its upload, it has received 35 views. For similar materials see Physical Chemintry 1 in Chemistry at Texas State University.

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Date Created: 10/01/15
CHEM 4360 Fall 2015 EXAM 100 5 bonus points NAME KEY Answer the questions in the spaces provided Some questions have multiple parts make sure that you answer ALL the parts Please write legibly lfl cannot clearly understand your answer it will be marked incorrect Bulleted answers are acceptable if the question does not otherwise specify for complete sentences As a Texas State student I pledge to uphold the principles of honesty and responsibility at our university Student signature SECTION 1 20 pts Multiple Choice Answers differ between exam forms Look at the answer not the letter Mark your answers on the line 2 pts each 1 Identify the correct complementary DNA strand for the DNA strand 539GCTAATCATAT339 5 GCTAATCATAT3 5 AUAUGAUUAGC3 5 CGATTAGTATA3 5 ATATGATTAGC3 5 TATACTAATCG3 W909 2 Pyrimidines A bind via the N1 atom to a pentose sugar B are homocyclic rings C all form three hydrogen bonds D are found only in DNA 3 What kind of catalytic mechanism is used by topoisomerase Acidbase catalysis Covalent catalysis Metalion catalysis Proximity and orientation effects Preferential binding of transition state complex W905 4 Which of the following sets of amino acids is more likely to be found in the ligandbinding groove of a DNAbinding protein A Val Leu lle Met and Phe B Ser Thr Asp Glu and Pro C Arg His Lys Tyr and Phe D All of the above E None of the above 5 Of the following mutations which do you expect to be least damaging to the assembly of a nucleosome A Thr9Cys B Lys Arg C Glu Phe D lle Trp 6 Which of the following groups of amino acids can all be phosphorylated K L l 7 Approximately how many nucleosomes could form on a 1000bp DNA strand A 5 B 15 3000bp 15 C 150 D This is not enough DNA to make one nucleosome 8 The order of histone core assembly is A Two H2AB dimers bind DNA and then a H3H4 tetramer binds B A H2AB tetramer binds DNA and then two H3H4 dimers bind C Two H3H4 dimers bind DNA and then a H2AB tetramer binds D A H3IH4 tetramer binds DNA and then two H2AIB dimers bind E The order is random 9 Which of the following is not necessary for a DNA polymerase reaction A template DNA B primer strand C ATP D dNTPs E Mg2 10 What is required to form the open complex in bacterial replication initiation A Binding of DnaB helicase to the single strands of the replication bubble B Binding of DnaC to the doublestranded ATrich repeat sequence which destabilizes the double helix C Binding of DnaA to the four 9mer consensus sequences which destabilizes the AT rich repeat sequence D The HU protein oligomerizes upon binding the origin and wraps the DNA around the oligomer SECTION 2 85pts Short Answer 5Guc3a 5AUA3 o o 1 6 pts Shown to the rIght IS a short oligonucleotide he 0 0130 NM I a Is this an RNA or a DNA oligonucleotide 3 J kua f N N C N C I a N N o 0 0H 9 OH b What is the sequence of this oligonucleotide Be 040 0quot sure to label 5 and 3 ends I IO 0 o l I f f see labels on right Cquot a W39 Hwy 0 of o a c Describe the secondary structure that you would expect from a longer sequence that contains alternate 4 quot repeats of the above sequence and the sequence 0 99 wt GACUAU you may include a sketch along with your N l description 139 T v j w N 4 CH N quot Hairpin Aform helix 0 3 W E I 2 8 pts Shown to the right is the structure of O N N zidovudineaciclovir a drug that inhibits DNA replication l gt NH L and IS used to treat human ImmunodefICIency varicella HZN N N zoster chicken pox and herpes simplex virus infections H gt HO l N 0 O O a What nucleotide does zidovudineaciclovir most closely resemble Mind your nomenclature NNN Ol Zidovudlne aCIclowr thymidine guanidine b ldentify at least two different kinds of intermolecular interactions that zidovudineaciclovir can expenence Both can experience hydrogen bonding dipoledipole TrTrlbase stacking zidovudine can additionally experience ionion and iondipole interactions through the azido group c Make a prediction for how zidovudineaciclovir prevents DNA replication and support your prediction with at least one piece of evidence Prevents formation of the 3 phosphodiester bond with n1 nucleotide Zidovudine no 3 OH aciclovir absence of ribose will compromise conformation of backbone 3 6pts You have identified a mutant strain of bacteriayeast that contain a temperaturesensitive defect in the Tus proteinorigin replication complex ORC Draw a FACS plot with two populations of cells one of a population grown at the permissive temperature and one of a population grown at the restrictive temperature Be sure to clearly identify which line corresponds toxvhich population l 8 wt Tus 8 H Mutant ORC ac 5 I G1 arrest 8 8 I a a I 5 mutant Tus 5 u no termination u f II F y lore DNAcell g E 39 E g amp DNA content DNA content 4 5 pts a How do DNA polymerases discriminate against ribonucleotidesincorrect basepairing rNTPs discriminator patch of amino acids in the active site of DNA polymerase sterically andor electronically clashes with 2 OH on ribose incorrect basepairing size and shape of active site sterically restricts conformation of pairs to correct WatsonCrick pairs b Explain why DNA synthesis uses dNTPs instead of dNDPs Addition using a dNTP releases pyrophosphate which is coupled to a strong energetically favorable reaction pyrophosphatasemediated hydrolysis that produces 2 molecules of inorganic phosphate thus preventing the reverse reaction Addition of a dNMP releases only a single inorganic phosphate which is not broken down and is available to be used as a reactant for the reverse reaction 5 6pts How do eukaryoticbacterial cells ensure a single round of replication per cell cycle Eukaryotes Cellcycledependent segregation of loading G1 phase and activation Sphase of Mcm27 helicase Bacteria Hemimethylated origin is preferentially bound by Squ which blocks Dam methylase action to fully methylate the daughter strand and enable binding by DnaA Partial credit for nucleotide exchange of DnaA ADP must be exchanged for ATP to reactivate DnaA 6 6pts What function is served by the 5937395 exonuclease activity of some DNA polymerases 5 93 Removal of RNA primer on lagging strand partial credit for DNA repair 3 95 Intrinsic proofreading activity to remove incorrect basepairs andlor rNMPs 7 12 pts A diagram of an active bacterial replication fork is shown below with individual molecules identified by a letter In the table provided write the names of each molecule and briefly describe its func on Molecule Name Function A DNA Polymerase Catalyze addition of dNMP to 3 end B Bclamp Increase processivity of DNA polymerase C clamp loader Assemble clamp on ds nucleic acid D helicase Unwind dsDNA E primase Synthesize RNA primer F Okazaki fragment Discontinuous synthesis of lagging strand G S39nglz39idesiglndmg Protect amp organize singlestranded DNA 8 6pts a Briefly describe why nucleosomes might need to be relocated along a strand of DNA Access to DNA for replication transcription andor repair Compaction for cell division b Briefly describe one mechanism that is used to reposition nucleosomes Be sure to include the names or categories of the molecules involved in this mechanism Ejection redistribution change in core histone composition Requires use of histonelnucleosome chaperones like CAF andor action of nucleosome remodeling complexes 9 5pts ln lab this week you forgot to take a picture of your sequencing gel You remember that the sequence of your original piece of DNA was 5 TGTCATGAAGC but your boss wants you to include a diagram of the result in your group meeting talk tomorrow Using the gel below draw a picture of the sequencing gel that would result from complete Sanger termination sequencing of the above sequence Be sure to indicate the electrodes label the wells and label all the DNA fragments dNTPs dNTPs dNTPs dNTPs Anode ddATP ddTTP ddCTP ddGTP 5 GCTTCATGACA3 Cathode 10 5pts On the way home from class you notice that leaves on one branch on a tree looks very different than the others You suspect that the tree might be a chimera which resulted from grafting the branch onto the tree To test this you sequence the genomic DNA isolated from the two different parts However you find that the sequences are identical You next hypothesize that there must be differential gene expression between the two parts Name and describe in detail an experiment that you could use to test that hypothesis Multiple options Core idea measure changes in global gene expression Two possibilities are ChlP the different tissues using antibodies against histone modifications associated with either closed or open chromatin to identify regions of active transcription in the genome RNAseq using RNA isolated from different tissues to make cDNA library for sequencing and directly identifying the transcriptome 11 9pts Name the molecules and describe the interactions that stabilize the compaction of DNA in the following structures a 30nm ber10 nm ber 10 nm fiber electrostatics between core histones and DNA beads on a string likely does not involve histone H1 but H1 may be present depending on ionic strength of solvent 30 nm fiber electrostatic interactions between Nterminal tails of neighboring histones to form either a solenoid or a zigzag organization of nucleosomes may or may not include histone H1 depending on ionic strength of solvent b condensed chromatids in metaphase SMC proteins including cohesin and condensin loop around DNA and connect it to a protein scaffold c nucleosome Electrostatic interactions between the positivelycharged core histones H2A HZB H3 H4 and the negativelycharged DNA 13 5pts We discussed the functional role of posttranslational modifications to histone tails by modifying enzymes a Give two examples of such modifications Methylation phosphorylation acetylation ubiqutinylation b How are these modifications involved in the regulation of gene expression Modified histones are recognized and bound by chromatin remodeling complexes which change the accessibility of the DNA to transcription factors and machinery thus controlling the level of transcription of nearby genes 14 6pts From our Molecular Biology Timeline choose 2 scientists other than the ones you presented For each of the 2 scientists you chose complete the chart below Who did you present Name of scientists Accomplishment or discovery Significance u u u u u u acu u u u 3 n 3 It ltOC Igtltm OOltUmmU mxgtlt 3


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