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Micro Exam 4 Study GuideTranscriptionIntroductionoDNA to RNA to protein the central dogmaoRNA is often the final product of genes (nonprotein coding)oGene = sequence of DNA that is transcribed into RNA; some conventionsWe refer to the orientation of a gene based on the RNA that is produced (5’ to 3’)Technically Coding strand has the gene oriented properly on it… the template strand is what is used to actually transcribe the RNA in the proper orientation of the genePromoter is at the 5’ end of the gene and “upstream” of the start of the mRNATerminator at the 3’ end of the gene and “downstream” of the start of the mRNAGenes in organisms long string off alternating short exons and long intronsSome parts of the genome lack genesLots of DNA is ‘meaningless’From DNA to RNARNASingle stranded, can also be double strandedA, U (absence of methyl group from T), C, G ribonucleotidesG occasionally pairs with ULinked by phosphodiester bonds, covalentA and G purines (two rings)C and T/U pyrimidines (one ring)Made by DNA transcriptionOpen and unwind DNATemplate strand synthesized strand created by complementary base pairingDifference between transcription and replicationRNA strand does not remain hydrogen bonded to the DNA strandDNA helix reforms after RNA is displacedRNA molecules are shorter than DNAMost no more than a few thousand nucleotides longRNA polymerase carries out transcriptionRNA Poly. transcribes genes into (unprocessed RNAs in Euk.) RNAs from a DNA template ALL kinds of RNA are processed in→Euk. Mechanism is reminiscent of DNA polymeraseAll types RNA have posttranscriptional modificationsPrimase is an RNA polymerase
Promoter a DNA sequence that recruits the RNA polymerase complex and trigger the start of transcriptionTranscription proceeds through 3 stereotypes phases:Initiation ElongationTerminationMultiple RNA polymerases can transcribe one gene simultaneously Regulating RNA levels is one way to regulate protein levels Read Out = the actual amount of protein made Gene expression measured by how much protein is →made The level of transcription occurring is a major way of impacting gene expressionCatalyze formation of phosphodiester bondsUnwinds the DNA helix ahead of the active site to expose more of the template strand for complementary basepairingHas “helicaselike activity”5’ to 3’ direction RNA Polymerase is driven by the hydrolysis of pyrophosphatedue to the 3’ OH group. The template strand sits in RNA polymeraseThe orientation of RNA polymerase determines the strand which is synthesized An RNA polymerase that moves from left to right makes RNA by using the bottom strand as a template An RNA polymerase that moves from right to left by using the top strand as a template Transcription occurs at active genes (that is, at many places simultaneously)RNA polymerase complex in Eukaryotes is much more complex than the one in prokaryotesIn eukaryotes three RNA polymerases split the jobs of making rRNA (vast majority of cellular RNA), tRNA, and mRNA.RNA molecules can begin to be synthesized from the same gene before the previous RNA molecules are completedAlmost immediate release of RNA from DNATypes (There are 3 different types in Eukaryotes ONLY)RNA polymerase I: 5.8S, 18S, and 28S rRNA, tRNA, somesmall RNAsRNA polymerase II: all proteincoding genes, plus snoRNA genes, miRNA genes, siRNA genes, and most snRNA genesRNA polymerase III: tRNA genes, 5S rRNA genes, some snRNA genes and genes for other small RNAs
rRNAs are named according to “S” value, larger S value means larger rRNAThese three are only in eukaryotesDifferences between RNA and DNA polymeraseRNA links ribonucleotides not deoxyribonucleotidesRNA polymerase can unzip DNARNA polymerase can start RNA chain without a primerTranscription does not need to be as accurateMistake 1 in 10^4 nucleotides (DNA polymerase is 1 to 10^7)Mistakes are not permanently stored in the genetic information of cellsRNA polymerase is completely processive start and finish without dissociatingRNA have proofreading mechanismExcision in which water replaces pyrophosphate and a nucleoside monophosphate is released Although both contain a critical Mg2+ ion at the catalytic site both of the structures are very differentTwo different evolutionary lineagesCells produce different categories of RNA moleculesHumans produce on the order of 10,000 noncoding RNAsEnzymatic, structural, and regulatory components for cell processesTypesmRNAs: Messenger RNAs, code for proteinsrRNAs **mostly** Ribosomal RNAs, form the basic structure of the ribosome and catalyze protein synthesistRNAs: Transfer RNAs, central to protein synthesis as adaptors between mRNA and amino acidssnRNAs: Small nuclear RNAs, function in a variety of nuclear processes, including the splicing of premRNAsnoRNAs: Small nucleolar RNAs, help to process and chemically modify rRNAsmiRNAs: MicroRNAs, regulate gene expression by blocking translation of specific mRNAs and cause their degradationsiRNAs: Small interfering RNAs, turn off gene expression by directing the degradation of selective mRNAs and the establishment of compact chromatin structurespiRNAs: Piwiinteracting RNAs, bind to piwi proteins and protect the germ line from transposable elementslncRNAs: Long noncoding RNAs, many of which serve as scaffolds; they regulate diverse cell processes, including X chromosome inactivation
Transcription unit each transcribed segment of DNAEukaryotes: information of 1 geneBacteria/Prokaryotes: set of adjacent genes often transcribed as a unitSignals in DNA tell RNA polymerase where to start and stopPromoters often have conserved sequences (especially in prokaryotes: e.g. the “TATA box”)Genes have 1 functional strand (the coding strand) while promoters have twoBacteriaPromoter TATA Box →Sigma factor associated with the core RNA polymerase to help it read the signals in the DNA and tell it where to start transcriptionSigma Factors bind to TATA box (Promoter/35) to recruit RNA polymeraseTogether known as RNA polymerase holoenzymeAdheres weakly to bacteria unless hits a promoterRNA polymerase binds tightly to promoter due to sigma factor, opens the double helix to create a transcription bubble (transcription bubble = ~ 12 nucleotides)Bubble is stabilized as the sigma factor binds to the unpaired bases on one of the exposed strands →coding strand Other strand is the templatePolymerase moves down the DNA, breaking free of sigma factor when leaving the promoterTranscription bubble expands but also closes behindContinues transcription until encounters terminator (terminator =a sequence that forms a hairpin)Polymerase releases the new RNA and DNA templateFree polymerase then reassociates with free sigma factorAT nucleotide pairs and a hairpin structureHairpin causes the RNA polymeraseto fall off
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School: Pennsylvania State University
Course: Introductory Microbiology
Professor: Olanrewaju Sodeinde
Term: Fall 2016
Name: Micro Exam 4 Study Guide
Description: Covers the lecture notes, notes from the in class review, and comprehensive notes from the textbook.
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