Biology Of The Living Cell
Biology Of The Living Cell BIOL 23000
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BIOL 12100 - 001
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This 8 page Class Notes was uploaded by Gordon Beier Jr. on Saturday September 19, 2015. The Class Notes belongs to BIOL 23000 at Purdue University taught by Edward Bartlett in Fall. Since its upload, it has received 71 views. For similar materials see /class/207826/biol-23000-purdue-university in Biological Sciences at Purdue University.
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Date Created: 09/19/15
Review Sheet for Bio 230 Exam 4 2011 1 Which of the following statements are true a 3 to 5 exonuclease is part of DNA polymerase I b 3 to 5 exonuclease is part of DNA polymerase 111 c Base excision repair uses endonucleases and ligases d Nucleotide excision repair uses endonucleases and ligases e a and c f b and d g a c and d h b c and d 2 Describe one form of postreplicative DNA repair In nucleotide excision repair NER which occurs post replication the lesion is recognized by RNA polymerase or other proteins A transcription factor acts as a helicase to separate the damaged strand The segment containing the error is cut out by two endonucleases DNA polymerases put back the proper DNA sequence DNA ligase joins the newly synthesized ends In base excision repair which also occurs post replication DNA glycosylases recognize specific aberrant bases in the DNA The glycosylases cleave the glycosidic bond and remove the base only not nucleotide or nucleotide sequence as in NER Then endonucleases break the backbone next to baseless sugar phosphate to form a single strand nick A DNA polymerase puts back the proper DNA sequence DNA ligase joins the ends 3 Where does RNA polymerase bind to initiate transcription in prokaryotes or eukaryotes In the promoter region just upstream of the start site for transcription 4 In bacteria is RNA polymerase able to locate and bind to the promoter region Ifnot what enables the polymeraseDNA association It can bind but does so randomly It requires the sigma factor to bind specifically at the promoter Together the RNA polymerase and promoter form a holoenzyme 5 In mammals what is that forms to allow RNA polymerase to begin transcription Which part of this allows multiple RNA polymerase II molecules to rapidly create multiple mRNAs A pre initiation complex forms This consists of a series of proteins including TFIID that binds at the promoter RNA polymerase II and TFIIF TFIIH and TFIIE As long as TFIID is bound multiple RNA polymerase II can attach sequentially and transcribe 6 Describe two modi cations that are made to premRNAs to form mature mRNAs Possibilities includes addition of a 5 methylguanosine cap addition of a polyA tail on the 3 end of the mRNA or splicing out introns 7 3000 bp of DNA were transcribed to form a mRNA but the nal protein product consists of only 100 peptides Explain how this probably came about Given that 3 bp 1 amino acid we would expect 1000 potential amino acids in apeptide chain The fact that there are only 100 amino acids suggests that the mature mRNA is 300 bp or slightly more including stop codon 8 What is the open reading frame and how would you identify it in the following sequence 5 7 UGAUGCCCACC It is thefirstAUGfrom the 5 end 9 What serves as the intermediate between mRNA and protein tRNA 10 If the 3 end of the tRNA has been cleaved what part of translation will be affected Charging ofthe tRNA with an amino acid 1 1 How many amino acids does each codon code for Is the number of codons for each amino acid larger smaller or the same Each codon codes for 1 amino acid However there are generally multiple codons that code for each amino acid 12 What are the main steps in translation by the ribosome Small subunit binds mRNA rRNA recognizesAUG on mRNA tRNA Met enters P site and binds toAUG Large subunit binds GTP Second tRNA binds A site GTP Peptide bond peptide attached to 2nd tRNA Translocation by 1 codon towards 3 end GTP Release of st tRNA from E site Continue 5 8 until stop codon is reached 10 Stop codon inA site gt termination GTP Q9 d dii t 13 A space probe brings back a new life form It is carbonbased and its genetic material is similar to Earth DNA except that it uses 6 different nucleotide bases instead of 4 Its proteins are also similar to those on Earth but there are 28 amino acids instead of 20 You hypothesize about the genetic code for this organism How many quotlettersquot would you propose in each codon of the genetic code for this organism The code should be unambiguous and may be degenerate Since there are 36 possible codons ifeach codon contains two letters a two letter codon would be possible It would allow for some degeneracy and stop signals 14 Which steps in translation require ATP hydrolysis Which steps require GTP hydrolysis None requireATP Stabilizing large subunit binding tRNA binding inA site translocation termination of translation after reaching a stop codon in theA site all require GT P hydrolysis 15Youhave enuenren i methods After the fragments in each ofyour fourtesl tubes have been separated and visualized with autoradiography The patterns in the diagram below are s ddG ddA ddC ddT u u certain to label the 5 and 3 ends ofthe sequence The Sequenczfmm the gel 15 5 CATGAGCL 3 Cumplzmemary SEqMEVLCE 3 GTACTCGA a 5 16 The inducer A combines with arepressor and prevents it from binding to the promoter B CummeS thh a repressm ohttprevehts ztfmm hththhg a the uperatm r u i u L39AAAL ii Eii i 17 n 439 an quot expression what elements would you need DNAn repressm 7a I able to bmd he mdltcer and he uperamr regmrt and art mdltcer that z able to bmd he 18 Why might you choose an inducible operon over arepressible operon ifyou were designing a gene regulation network o I M wzll 111qu he eg but 710 M In a a me D the pmmater ahd step trahscrzptmh 19 You are investigating a bacterial operon that controls intracellular sodium levels by transcribing sodium pump genes You have identi ed sodium as an inducer but the genes for sodium pumps do not become activated unless MAP kinase or one of its targets the transcription factor Elkl are also activated What is a likely explanation A A Gprotein coupled receptor provides positive control of transcription B A Gprotein coupled receptor provides negative control of transcription C A receptor tyrosine kinase provides positive control of transcription D A receptor tyrosine kinase provides negative control of transcription E None of the above 20 How does a repressor control operon expression A repressor controls operon expression by binding to the operator sequence that is usually upstream of the transcription start This prevents the holoenzyme sigma factor RNA polymerase from binding at the promoter Transcription cannot be initiated in this case so the genes in the operon will not be expressed 21 In a repressible operon how would you cause the repressor to inactivate A Increase the inducer B Decrease the inducer C Increase the corepressor D Decrease the corepressor E None of the above 22 Alternative splicing of mRNA is an example of A transcriptionlevel control B processing level control C translationlevel control D None of the above 23 What is the principle that allows cDNAs to be recognized in microarrays What were the cDNAs formed from and what can they tell us about the cell Base sequence complementarity The cDNAs were formed from either DNA or mRNA and can tell us either which genes were present or which genes were expressed and potentially their concentrations 24 What is the general function of transcription factors in cells and how do they accomplish this function Transcription factors are small proteins that regulate the transcription of genes by binding to the DNA at specific sequences This can result in turning on turning off upregulating or downregulating gene expression 25 Every cell with a nucleus within a multicellular organism contains the same DNA within its nucleus Describe how the major differences between cell types originates meaning how does the same genome lead to many different cell types The differentiation of eukaryotic cells is due to the di quoterential expression of genes and their translated proteins at different times and in different combinations 26 Which technique below provides the most direct evidence of widescale transcriptional level control This technique allows the transcription levels of thousands of genes to be monitored in a single experiment a DNA PCR b DNA microarrays actually cDNA microarrays would be more precise c two dimensional gel electrophoresis d affinity chromatography e Proteomic assays 27 What is one function of the translocon The translocon is involved in bringing a forming polypeptide into the ER lumen and it is involved in orienting a membrane protein properly in the membrane 28 List in order the intracellular traf cking components that a protein destined for the plasma membrane will pass through ER to ERGIC to cis Golgi to trans Golgi to vesicle Note that we did not discuss the ERGIC which is a transitional complex between the ER and Golgi so that will not be on the exam 29 As transmembrane proteins pass through the Golgi network what allows other molecules to recognize what will ultimately be their intracellular versus extracellular sides One means to identify their extracellular sides is by glycosylation In addition the portion of the protein that is in the Golgi or vesicle lumen will generally become the extracellular portion 30 What determines whether a vesicle will be transported retrogradely towards the nucleus or anterogradely towards the plasma membrane The coat protein surrounding a vesicle determines its direction of transport C OPH coated vesicles will be transported anterogradely from ER towards the trans Golgi COP coated vesicles will be transported retrogradely from trans Golgi ER towards the ER 31 Which of the following changes would be most likely to lead to a nonsense mutation 2 pts A UAC to AAC B UAA to AAA C GGA to AGA D CGA to UGA because itforms a stop codon E UAA to UGA 32 The TATA box and Pribnow box TATAAT are examples of 2 pts A repressor sequences that are involved in transcription B promoter sequences that are involved in transcription C repressor sequences that are involved in translation D promoter sequences that are involved in translation E none of the above 33 What controls which proteins enter the nucleus A nucleolus and nuclear localization signal B nucleolus and signal recognition particle C nuclear pores anal nuclear localization signal D nuclear pores and signal recognition particle 34 What is the main function of histones A Facilitate entry of materials into the nucleus B Packaging mRNA C Compaction of DNA D Unwinding DNA 35 Describe the histone code The histone code is a series of modi cations including methylation acetylation anal phosphorylation to specific amino acids in histone protein subunits that can permit block or alter transcription 36 How does a repressor control operon expression 2 pts A If it binds to the operator it shields the promoter from RNA polymerase B Ifit binds to the operator it prevents transcription of operon structural genes C It denatures RNA polymerase D It synthesizes RNA E A anal B 37 In a repressible operon how would you cause the repressor to inactivate A Increase the inducer B Decrease the inducer C Increase the corepressor D Decrease the corepressor E None of the above 38 The amount of protein expressed and when a protein is expressed is determined by A Amount and when transcription occurs B Amount anal when translation occurs though one could potentially make the argument that some amount of transcription must occur prior to translation The main point is that the presence of mRNA by itself does not determine the level of protein expression C Amount and when replication occurs D A and B E A B and C 39 Which of the following rely on sequence complementarity for proper functioning A DNA microa1rays B transcription C translation D A and B E A B anal C C is true because oftRNA recognition omeNA
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