EUKARYOTIC RNA POLYMERASES Based on their elution order from ion-exchange chromatography purification, the eukaryotic RNA polymerases were given the names I, II, and II. They can also be distinguished by their a-amanitin and related amatoxin-family mushroom poison sensitivity. RNA Pol has a core promoter and an upstream promoter element (UPE). RNA Pol is the most studied RNA polymerase and transcribes DNA into precursors mRNA, while RNA Pol has been observed to use both upstream and internal promoters.

EUKARYOTIC RNA POLYMERASES Based on their elution order from ion-exchange chromatography purification, the eukaryotic RNA polymerases were given the names I, II, and II. They can also be distinguished by their a-amanitin and related amatoxin-family mushroom poison sensitivity. RNA Pol has a core promoter and an upstream promoter element (UPE). RNA Pol is the most studied RNA polymerase and transcribes DNA into precursors mRNA, while RNA Pol has been observed to use both upstream and internal promoters.

Biochemistry

6th Edition

ISBN:9781305577206

Author:Reginald H. Garrett, Charles M. Grisham

Publisher:Reginald H. Garrett, Charles M. Grisham

Chapter29: Transcription And The Regulation Of Gene Expression

Section: Chapter Questions

Problem 3P: Substrate Binding by RNA Polymerase RNA polymerase has t binding sites for ribonucleoside...

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88Sequential binding of RNA polymerase II-TFIIF complex, TFIIE, and TFIIH completes ___________________ formation. A.pre-initiation complexb.TF recognition elementc.pre-elongation complexD.TATA binding complex 89Which of the following is the GDP-GTP exchange protein?A.EF-Tub.none of the abovec.EF-TsD.EF-G 90RNA polymerase II has 14 subunits. Yesorno
73Dicer catalyzes Sequence-dependent single-stranded RNA cleavage. Yesorno 74Amino acid-coding regions within eukaryotic genes may be interrupted by ___________ regions. A.noncodingb.long terminal repeatc.split geneD.enhancer 75Which of the following cleaves the N-terminal methionine from polypeptides?A.Methionine isomeraseb.Methionine aminopeptidasec.Methionine carboxylaseD.Methionine transferase
Briefly explain WHY a 5 7-methylguanosine cap is only added to mRNA, not to tRNA orrRNA. (Please note that I am not looking for the function of the 5’ cap, but for the mechanismrestricting capping to messenger RNA.)
Please help with all parts of A, B, C, D 2. You are studying the function of a messenger RNA named Genetixrox and want to label themRNA with a radioactive atom. Assume the mRNA is long and contains all four standardRNA bases. Assume that the cell cannot convert ribonucleotides to deoxyribonucleotides (orvice versa).A. Will you generate radioactive Genetixrox mRNA with 3H-threonine? Threonine is an aminoacid. Answer yes or no, and provide a one sentence rationale.B. Will you generate radioactive Genetixrox mRNA with 3H-adenosine triphosphate? Answeryes or no, and provide a one sentence rationale.C. Will you generate radioactive Genetixrox mRNA with 3H-deoxyadenosine triphosphate?Answer yes or no, and provide a one sentence rationale.D. Will you generate radioactive Genetixrox mRNA 12C-with adenosine triphosphate? Answeryes or no, and provide a one sentence rationale
34The crystal structure has been determined for the complete 12-subunit yeast RNA polymerase II bound to a transcription bubble and product RNA. Yesorno 35 ( ) can be used to purify transcription activator proteins 36A mutation that adds or deletes a base pair in the open reading frame and is termed a ( ) mutation.
The human α-tropomyosin gene is alternativelyspliced to produce different forms of α-tropomyosinmRNA in different cell types (Figure Q6–3). For all forms ofthe mRNA, the protein sequences encoded by exon 1 arethe same, as are the protein sequences encoded by exon10. Exons 2 and 3 are alternative exons used in differentmRNAs, as are exons 7 and 8. Which of the following state-ments about exons 2 and 3 is the most accurate? Is thatstatement also the most accurate one for exons 7 and 8?Explain your answers.A. Exons 2 and 3 must have the same number ofnucleotides.B. Exons 2 and 3 must each contain an integral num-ber of codons (that is, the number of nucleotides dividedby 3 must be an integer).C. Exons 2 and 3 must each contain a number ofnucleotides that when divided by 3 leaves the sameremainder (that is, 0, 1, or 2).
Before the technology existed to synthesize RNAmolecules of defined sequence like those in Fig. 8.5,similar experiments were performed with syntheticmRNAs of undefined sequence. For example, RNAsconsisting only of Us and Gs could be synthesized invitro, but they would have random sequences. Supposea pool of random-sequence RNAs was synthesized ina reaction mixture containing three times as much UTPas GTP, and that the resulting RNAs were translatedin vitro.a. How many different codons exist in the RNAs?b. How many different amino acids would you find inthe polypeptides synthesized?c. Why are your answers to (a) and (b) not the same?d. How often would you expect to find each of thecodons in (a)?e. In what proportions would you expect to find eachof the amino acids in the polypeptides?f. If you did this experiment—that is, synthesizedrandom-sequence RNAs containing a 3:1 ratio ofU:G, and quantified the amount of each amino acidin the polypeptides produced—prior to knowledgeof the genetic…
In bacteria, a transcription experiment in vitro with purified RNA polymerase holoenzyme is fairly straightforward. In eukaryotes, it is not. Explain this observation, including what would be meant by the term “holoenzyme” for a eukaryotic RNA polymerase.
The RNA polymerase from bacteriophage T7 diff ers structurally from prokaryotic and eukaryotic RNAPs and is extremely specifi c for its own promoter. Why do these properties make T7 RNAP useful in experiments with recombinant DNA?
A doctoral student in biology, Esther Mensah, is reviewing primary literature over RNAi interference as part of her literary research for her proposal on decreasing the amount of abnormal white blood cell growth associated with acute myeloid leukemia (AML) using a murine (mouse) model. She is being provided with 10 AML mice courtesy of her mentor. Can you help her out with her proposal? 1) Esther has located the coding strand of cDNA from the AML gene that she wants to target for her RNA interference: ATG CCC GGT AAT CGC TTA TGC CTC. What will be the sequence of her siRNA? a AUG CCC GGU AAU CGC UUA UGC CUC. b TAC GGG CCA TTA GCG AAT ACG GAG. c CTC CGT ATU CGC TAA GGU CCC GUA. d UAC GGG CCA UUA GCG AAU ACG GAG. 2) RNAi works by inteferring with mRNA. Esther decides to design her RNAi strand using genomic DNA (gDNA) information. What is your opinion on her approach? a Smart move! You got this, girl! b It would be better if she designs…
Many uridine molecules are inserted into some mitochondrial mRNAs in trypanosomes. The uridine residues come from the poly(U) tail of a donor strand. Nucleoside triphosphates do not participate in this reaction. Propose a reaction mechanism that accounts for these findings. (Hint: Relate RNA editing to RNA splicing.)
EF-Tu binds all aminoacyl–tRNAs with approximately equal affinity so that it can deliver them to the ribosome with the same effi ciency. Based on the experimentally determined binding constants for EF-Tu and correctly charged and mischarged aminoacyl–tRNAs (see table), explain how the tRNA–EF-Tu recognition system could prevent the incorporation of the wrong amino acid during translation.