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Chapter 11

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BIOL 1090
Andrew Bendall

Bio 1090 Chapter 11 p.256-273 Transcription and RNA processing Storage and transmission of information with simple codes - computer uses a binary code 1) Transfer of genetic information: The central Dogma  Genetic information flows from: - DNA to DNA during its transmission from generation to generation - DNA to protein during its phenotypic expression in an organism 1. Transcription: transfer of the genetic information from DNA to RNA (reversible) 2. Translation: transfer of information from RNA to protein (irreversible)  During replication of RNA viruses; info is transmitted from RNA to RNA  Genetic information flows from RNA to DNA during the conversion of the genomes of RNA tumor viruses to their DNA proviral form Transcription and translation - During transcription; one strand of DNA of a gene is used as a template to synthesize a complementary strand of RNA called the gene transcript - During translation the sequence of nucleotides in the RNA transcript is converted into the sequence of amino acids in the polypeptide gene product (Conversion governed by the genetic code; specification of amino acids by nucleotide triplets codons in the gene - translation takes place on intricate macromolecular machines; ribosomes (composed of 5 RNA molecules and 50 to 90 different proteins), requires participation of other macromolecule - RNA translated on ribosomes  messenger RNAs (mRNAs) - In prokaryotes, product of transcription; primary transcript (= to the mRNA molecule) - In eukaryotes, primary transcript precursors to mRNAs  pre-mRNAs - Nuclear gene in higher eukaryote and some in lower contains noncoding sequences  introns that separate the expressed sequences or exons of these genes (entire sequences of these split gene are transcribed in pre-mRNA and noncoding intron sequences removed by splicing reactions carried out on spliceosomes) Five types of RNA molecules - Messenger RNAs  carry out genetic information from DNA to the ribosomes where proteins are synthesized - Transfer RNAs (tRNAs)  small RNA molecules that function as adaptors between amino acids and the codons in mRNA during translation - Ribosomal RNAs (rRNAs) structural and components of the ribosomes, the intricate machines that translate nucleotide sequences of mRNAs into amino acid sequences of polypeptide - Small nuclear RNAs (snRNAs)  structural components of sliceosomes, the nuclear organelles that excise introns from gene transcripts - Micro RNAs (miRNAs)  short 20- 22 nucleotide single-stranded RNAs that are cleaved from small hairpin- shaped precursors and block the expression of complementary or repressing their translation mRNAs by either causing their degradation or repressing their translation - all produced by transcription - mRNAs specify polypeptide, final products tRNA, rRNA, snRNA and miRNA genes are RNA molecules - transfer RNA, ribosomal RNA, snRNA and miRNA molecules are not translated The process of gene expression An mRNA intermediary - genetic information stored in the sequences of nucleotide must be transferred to the sites of protein synthesis in the cytoplasm - messenger needed to transfer genetic information from the nucleus to the cytoplasm General features of RNA synthesis - RNA synthesis 1. precursors are ribonucleoside triphosphates rather than deoxyribonucleoside triphosphate 2. only on strand is used as a template for the synthesis of a complementary RNA chain in any given region 3. RNA chains can be initiated de novo, without any requirement for a preexisting primer strand - RNA molecule produced; complementary and antiparallel to the DNA template strand and identical to the DNA nontemplate strand (uridine replace thymidines) - If RNA is mRNA specify amino acids in the protein gene product (coding strands of RNA or sense strands of RNA because nucleotide sequences make sense) - Antisense RNA RNA molecule that is complementary to an mRNA - Synthesis of RNA chains, like DNA chains occurs in the 5’3’ direction, with the addition of ribonucleotides to the 3’- hydroxyl group at end of each chain (nucleophilic attack by the 3’-OH on nucleotidyl phosphorus of RNA precursor with elimination of pyrophosphate: catalyzed by enzymes called RNA polymerases) ** n(RTP) DNA template ---------------> (RMAP)n + n(PP) RNA polymerase - n is the number of moles of ribonucleotide triphosphate (RTP) consumed, ribonucleotide monophosphate (RMP) incorporated into RNA and pyrophosphate (PP) produced - RNA polymerase binds to specific nucleotide sequences promoters and with transcription factors. Initiate the synthesis of RNA molecules at transcription start sites - Promoter in eukaryotes are more complex than those in prokaryotes - In prokaryotes, single RNA polymerase carries out all transcription and 5 different RNA polymerase are present in eukaryotes (responsible for synthesis of a distinct class of RNAs) - RNA synthesis takes place in unwound segment of DNA; transcription bubble, produced by RNA polymerase - Nucleotide sequence of RNA complementary to DNA template strand and RNA synthesis governed by same base-pairing rules as DNA synthesis  Origin of RNA transcript can be determined by hybridization of DNAs from different sources Transcription in prokaryotes - transcription unit: segment of DNA that is transcribed to produce one RNA molecule (may be equivalent to individual genes or may include several contiguous genes), large transcript that carry coding sequence common in bacteria 1. Initiation: new RNA chain 2. Elongation: of the chain 3. Termination: of transcription and release of the nascent RNA molecule (upstream and downstream  region located toward the 5’ end and the 3’ end, in DNA sequence) RNA polymerase: complex enzymes - RNA polymerase that catalyze transcription are complex, multimeric proteins - Complete RNA polymerase molecule; the holoenzyme has composition (a2BB’o), a involved in assembly of tetrametric core of RNA polymerase, B contains RNA binding site and B’ harbors DNA template-binding region - Sigma factor; involved only in initiation (is release after), recognize and bind RNA polymerase to the transcription initiation or promoter sites in DNA - Chain elongation catalyze by core enzyme (catalyze RNA synthesis from DNA templates in vitro, initiate RNA chains at random sites on both strands of DNA - Holoenzyme initiates RNA chains in vitro only at sites used in vitro Initiation of RNA chains (1) binding of RNA polymerase holoenzyme to a promoter region in DNA (2) localized unwinding of the two strands of DNA by RNA polymerase, providing a template strand free to base-pair with incoming ribonucleotides (3) formation of phosphodiester bonds between the first few ribonucleotides in the nascent RNA chain. The holoenzyme remains bound at the promoter region during the synthesis of the first 8 or 9 bonds, then sigma factor release and core enzyme begins the elongation phase of RNA synthesis - short chains of 2 to 9 ribonucleotide are synthesized and released, stops when 10 or + have been synthesized - nucleotide pairs numbered to the transcript initiation site (+1) and base pairs preceding the initiation site are given – prefixes, those following initiation site + - upstream sequence: nucleotide sequences preceding the initiation site - downstream sequences: the ones following the initiation site - 10-sequence  nontemplate strand is TATAAT and 35-sequence TTGAGA (vary from gene to gene), consensus sequence present in these conserved genetic elements - sigma recognize and binds to the 35 sequences: recognition sequence. Distance between the 2 conserved in E coli promoters - AT-rich 10 sequence facilitates the localized unwinding of DNA (needed for synthesis of new RNA chain) Elongation of RNA chains - catalyzed by the RNA polymerase core enzyme after the release of the sigma subunit - covalent extension of RNA chains takes place within the transcription bubble, unwound segment of DNA - RNA polymerase contains DNA unwinding and DNA rewinding activities, unwinds the DNA double helix and rewinds the complementary DNA strands (+ length in E coli is 18 nucleotide pairs and 40 ribonucleotide) - Nascent RNA chain displaced from DNA template strand as RNA polymerase move along DNA molecule, short; 3 base pairs in length - stability of transcription complex maintained by binding of DNA and growing RNA chain to RNA polymerase Termination of RNA chains - RNA polymerase encounters termination signal, transcription complex dissociates releasing the nascent RNA molecule Type 1: results in termination only in the presence of a protein called rho (p); rho-depen
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