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(1987) Molecular Biology of the Gene, 4th edn, The Benjamin/Cummings Publishing Company, Menlo Park, CA.DNA-Directed RNA SynthesisConaway, J.W. & Conaway, R.C. (1991) Initiationof eukaryotic messenger RNA synthesis. J. Biol.Chem. 266, 17721-17724.A good minireuiew.McClure, W.R. (1985) Mechanism and control oftranscription initiation in prokaryotes. Annu. Rev.Biochem. 54, 171-204.Platt, T. (1986) Transcription termination and theregulation of gene expression. Annu. Rev.
Biochem.55, 339-372.Sawadogo, M. & Sentenac, A. (1990) RNA polymerase B (II) and general transcription factors.Annu. Rev. Biochem. 59, 711-754.A good review of eukaryotic RNA polymerase II.RNA ProcessingBreitbart, R.E., Andreadis, A., & Nadal-Ginard,B. (1987) Alternative splicing: a ubiquitous mechanism for the generation of multiple proteinisoforms from single genes. Annu.
Rev. Biochem.56, 467-495.Cech, T.R. (1986) RNA as an enzyme. ScL Am. 255(November), 64-75.Cech, T.R. (1987) The chemistry of self-splicingRNA and RNA enzymes. Science 236, 1532-1539.Deutscher, M.P. (1990) Ribonucleases, tRNA nucleotidyltransferase, and the 3' processing oftRNA. Prog.
Nucleic Acid Res. Mol. Biol. 39, 209240.A good overview of tRNA processing reactions.Green, M.R. (1986) Pre-mRNA splicing. Annu.Rev. Genet. 20, 671-708.McCorkle, G.M. & Altman, S. (1987) RNAs as catalysts: a new class of enzyme. J. Chem. Educ. 64,221-226.Pace, N.R. & Smith, D. (1990) Ribonuclease P:function and variation. J.
Biol. Chem. 265, 35873590.Ross, J. (1989) The turnover of messenger RNA.ScL Am. 260 (April), 48-55.Sharp, P.A. (1987) Splicing of messenger RNA precursors. Science 235, 766-771.Wahle, E. & Keller, W. (1992) The biochemistry of3'-end cleavage and polyadenylation of messengerRNA precursors. Annu. Rev. Biochem. 61,419-440.Wickens, M. (1990) How the messenger got its tail:addition of poly(A) in the nucleus. Trends Biochem.Sci. 15, 277-281.RNA-Directed RNA or DNA SynthesisBelfort, M. (1991) Self-splicing introns in prokaryotes: migrant fossils? Cell 64, 9-11.A discussion of the evolutionary significance ofprokaryotic introns.Bishop, J.M.
(1991) Molecular themes in oncogenesis. Cell 64, 235-248.A good overview of oncogenes; it introduces a seriesof more detailed reviews included in the same issueof Cell.Blackburn, E.H. (1991) Telomeres. Trends Biochem. Sci. 16, 378-381.Blackburn, E.H. (1992) Telomerases. Annu.
Rev.Biochem. 61, 113-129.Boeke, J.D. (1990) Reverse transcriptase, the endof the chromosome, and the end of life. Cell 61,193195.The possible role oftelomerase in regulating the lifespan of an organism.Chapter 25 RNA MetabolismDorit, R.L., Schoenbach, L., & Gilbert, W.
(1990)How big is the universe of exons? Science 250,1377-1382.Interesting speculation on the origin and functionof exons.Gallo, R.C. & Montagnier, L. (1988) AIDS in 1988.Sci. Am. 259 (October), 40-48.The introductory article to an entire ScientificAmerican issue devoted to AIDS.Kingsman, A.J. & Kingsman, S.M.
(1988) Ty: aretroelement moving forward. Cell 53, 333-335.Describes a well-studied yeast transposon related toretrouiruses.891Perlman, P.S. & Butow, R.A. (1989) Mobileintrons and intron-encoded proteins. Science 246,1106-1109.This article describes a special class of introns capable of colonizing homologous genes that lackintrons.Temin, H.M.
(1976) The DNA provirus hypothesis:the establishment and implications of RNAdirected DNA synthesis. Science 192, 1075-1080.A discussion of the original proposal for reversetranscription in retroviruses.Varmus, H. (1987) Reverse transcription. Sci. Am.257 (September), 56-64.Pace, N.R. (1991) Origin of life—facing up to thephysical setting. Cell 65, 531-533.A discussion of the conditions believed to have existed when life began evolving.Varmus, H.E. (1989) Reverse transcription in bacteria. Cell 56, 721-724.1. RNA Polymerase How long would it take for theE.
coli RNA polymerase to synthesize the primarytranscript for E. coli rRNAs (6500 bases)?What enzyme would such a (-) strand virus needto include in the virus particle to successfully invade a host cell?2. Error Correction by RNA Polymerases DNApolymerases are capable of editing and error correction, but RNA polymerases do not appear tohave this capacity. Given that a single base errorin either replication or transcription can lead to anerror in protein synthesis, can you give a possiblebiological explanation for this striking difference?6. The Chemistry of Nucleic Acid Biosynthesis Describe three properties common to the reactionscatalyzed by DNA polymerase, RNA polymerase,reverse transcriptase, and RNA replicase.3. The Rate of Transcription From what you knowof the rate at which E. coli RNA polymerase synthesizes RNA, predict how far the transcription"bubble" formed by RNA polymerase will movealong the DNA in 10 s.8.
Telomerase Assuming that the RNA componentof telomerase is fixed within the protein structure,in what respect might the active site of this enzyme differ from the active site of reverse transcriptases, RNA polymerases, and DNA polymerases? (Hint: The latter three enzymes add onenucleotide at a time.)Problems4. RNA Posttranscriptional Processing Predictthe likely effects of a mutation in the sequence(5')AAUAAA in a eukaryotic mRNA transcript.5. Coding vs.
Template Strands The RNA genomeof phage Q/3 is the nontemplate or ( + ) strand, andwhen introduced into the cell it functions as anmRNA. Suppose the RNA replicase of phage Q/3synthesized primarily ( —) strand RNA anduniquely incorporated it into the virus particles,rather than ( + ) strands. What would be the fate ofthe (-) strands when they entered a new cell?7. RNA Splicing What is the minimum number oftransesterification reactions needed to splice anintron from an mRNA transcript? Why?9.
RNA Genomes The RNA viruses have relatively small genomes. For example, the singlestranded RNAs of retroviruses have about 10,000nucleotides and the Q/3 RNA is only 4,220 nucleotides long. Given the properties of reverse transcriptase and RNA replicase described in thischapter, can you suggest a reason for the small sizeof these viral genomes?.
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