Il differenziamento cellulare dipende da meccanismi di regolazione
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1 Il differenziamento cellulare dipende da meccanismi di regolazione dell espressione genica
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5 Trascrizione sintesi di tutti gli RNA cellulari
6 RNA Ribonucleotidi monofosfato uniti a formare una catena polinucleotidica
7 Formazione del legame fosfodiesterico
8 I precursori della sintesi sono i ribonucleotidi trifosfato. L energia che occorre per la formazione del legame fosfodiesterico è data dall eliminazione del pirofosfato per idrolisi del legame.
9 La direzione di sintesi è 5-3
10 La sequenza nucleotidica dell RNA è dettata dalla sequenza nucleotidica del DNA
11 L enzima che catalizza l unione dei ribonucleotidi è l RNA polimerasi
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13 RNA polimerasi sintetizza RNA in direzione 5 3 E in grado di iniziare la sintesi. Non necessita di un innesco Utilizza ribonucleosidi 5 -trifosfato (ATP, GTP, UTP e CTP) e richiede Mg++ Il 3 OH agisce da nucleofilo sul gruppo fosfato in 5 del ribonucleoside trifosfato entrante e si ha liberazione di PPi (NMP)n + NTP = (NMP)n+1+ PPi PPi2Pi Ogni nucleotide è selezionato in base alle regole della complementarietà A:U e G:C
14 closed promoter complex Transcription RNA polymerase open promoter complex initiation elongation termination RNA product
15 Legame al promotore della RNA polimerasi Apertura della doppia elica Inizio della sintesi Allungamento Terminazione
16 Direzione della sintesi Filamento senso Filamento antisenso
17 5' G C A G T A C A T G T C 3' coding strand 3' C G T C A T G T A C A G 5' template strand transcription 5' G C A G U A C A U G U C 3' RNA
18 5..AGAAGATG ATGTCGGGCCAAACGCTCACGGATCGGATCGCCGCCGCTCAGTACAGCGTTACAGGCTCTGCTGT AGCAAGAGCGGTCTGCAAAGCCACTACTCATGAAGTAATGGGCCCCAAGAAAAAGCACCTGGACTATTTGATCCAGGC TACCAACGAGACCAATGTTAATATTCCTCAGATGGCCGACACTCTCTTTGAGCGGGCAACAAACAGTAGCTGGGTGGTT GTGTTTAAGGCTTTAGTGACAACACATCATCTCATGGTGCATGGAAATGAGAGATTTATTCAATATTTGGCTTCTAGAAA TACACTATTCAATCTCAGCAATTTTTTGGACAAAAGTGGATCCCATGGTTATGATATGTCTACCTTCATAAGGCGCTATA GTAGATATTTGAATGAAAAGGCTTTTTCTTACAGACAGATGGCCTTTGATTTTGCCAGGGTGAAGAAAGGGGCCGATGG TGTAATGAGGACAATGGCTCCCGAAAAGCTGCTAAAGAGTATGCCAATACTACAGGGACAAATTGATGCACTGCTTGAA TTTGATGTGCATCCAAATGAACTAACAAATGGTGTCATAAATGCAGCATTTATGCTTCTTTTCAAAGATCTTATCAAACTT TTTGCTTGCTACAATGATGGTGTTATTAACTTACTCGAAAAGTTTTTTGAAATGAAGAAAGGACAATGTAAAGATGCTCTA GAAATTTACAAACGATTTCTAACTAGAATGACACGAGTGTCTGAATTTCTCAAGGTTGCAGAGCAAGTTGGTATTGATAA AGGTGACATTCCTGACCTCACACAGGCTCCCAGCAGTCTTATGGAGACGCTTGAACAGCATCTAAATACATTAGAAGGA AAGAAACCTGGAAACAATGAAGGATCTGGTGCTCCCTCTCCATTAAGTAAGTCTTCTCCAGCCACAACTGTTACGTCTC CTAATTCTACACCAGCTAAAACTATTGACACATCCCCACCGGTTGATTTATTTGCAACTGCATCTGCGGCTGTCCCAGTC AGCACTTCTAAACCATCTAGTGATCTCCTGGACCTCCAGCCAGACTTTTCCTCTGGAGGGGCAGCAGCAGCCGCAGCA CCAGCACCACCACCACCTGCTGGAGGAGCCACTGCATGGGGAGACCTTTTGGGAGAGGATTCTTTGGCTGCACTTTCC TCTGTTCCCTCTGAAGCACAGATTTCAGATCCATTTGCACCAGAACCTACCCCTCCTACTACAACTGCTGAAATTGCAAC CACTACTGCTGCCACCGCCGCTGCCACCACCACTACCATTCATCTCTTGCCAGCTTAGTAGGCAATCTTGGAATTTCTG GTACCACAACAAAAAAGGGAGATCTTCAGTGGAATGCTGGAGAGAAAAAGTTGACTGGTGGAGCCAACTGGCAGCCTA AAGTAGCTCCAGCAACCTGGTCAGCAGGCGTTCCACCAAGTGCACCTTTGCAAGGAGCTGTACCTCCAACCAGTTCAG TTCCTCCTGTTGCCGGGGCCCCATCGGTTGGACAACCTGGAGCAGGATTTGGAATGCCTCCTGCTGGGACAGGCATG CCCATGATGCCTCAGCAGCCGGTCATGTTTGCACAGCCCATGATGAGGCCCCCCTTTGGAGCTGCCGCTGTACCTGGC ACGCAGCTTTCTCCAAGCCCTACACCTGCCAGTCAGAGTCCCAAGAAACCTCCAGCAAAGGACCCATTAGCGGATCTTA ACATCAAGGATTTCTTGTAAACAATTTAAGCTGCAATATTTGTGACTGAATAGGAAAATAAATGAGTTTGGAGACTTCAAA TAAGATTGATGCTGAGTTTCAAAGGGAGCCACCAGTACCAAACCCAATACTTACTCATAACTTCTCTTCCAAAATGTGTA ACACAGCCGTGAAAGTGAACATTAGGAATATGTACTACCTTAGCTGTTATCCCTACTCTTGAAATTGTAGTGTATTTGGA TTATTTGTGTATTGTACGATGTAAACAATGAATGGATGTTACTGATGCCGTTAGTGCTTTTTTGGACTTCACCTGAGGAC AGATGATGCAGCTGTTGTGTGGCGAGCTATTTGGAAAGACGTCTGTGTTTTTGAAGGTTTCAATGTACATATAACTTTTG AACAAACCCCAAACTCTTCCCATAAATTATCTTTTCTTCTGTATCTCTGTTACAAGCGTAGTGTGATAATACCAGATAATA AGGAAAACACTCATAAATATACAAAACTTTTTCAGTGTGGAGTACATTTTTCCAATCACAGGAACTTCAACTGTTGTGAGA AATGTTTATTTTTGTGGCACTGTATATGTTAA..3
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20 Holoenzyme The holoenzyme of RNA-pol in E.coli consists of 5 different subunits: α 2 β β σ. holoenzyme core β σ β α α
21 RNA-pol of E. Coli subunit MW function α Determine the DNA to be transcribed β Catalyze polymerization β β Bind & open DNA template σ Recognize the promoter for synthesis initiation
22 Prokaryotic promoter 5' 3' region T T G A C A A A C T G T -10 region T A T A A T A T A T T A (Pribnow box) Consensus sequence start 3' 5'
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26 c. Termination The RNA-pol stops moving on the DNA template. The RNA transcript falls off from the transcription complex. The termination occurs in either ρ - dependent or ρ -independent manner.
27 ρ-independent termination The termination signal is a stretch of nucleotides on the RNA transcript, consisting of many GC followed by a series of U. The sequence specificity of this nascent RNA transcript will form particular stem-loop structures to terminate the transcription.
28 rpll protein DNA 5 TTGCAGCCTGACAAATCAGGCTGATGGCTGGTGACTTTTTAGGCACCAGCCTTTTT TTGCAGCCTGACAAATCAGGCTGATGGCTGGTGACTTTTTAGTCACCAGCCTTTTT... 3 RNA UUUU... UUUU...
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30 The human RNA polymerases Polymerase Location Product RNA polymerase I nucleolus 18S, 28S, 5.8S rrna RNA polymerase II nucleoplasm hnrna/mrna, U1, U2, U4, U5 snrna RNA polymerase III nucleoplasm mitochondrial RNA polymerase trna, 5S RNA, U6 snrna, 7SL RNA mitochondrion all mitochondrial RNA
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32 b). Gene structure promoter region exons (filled and unfilled boxed regions) +1 introns (between exons) transcribed region mrna structure 5 3 translated region
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34 Sequence elements within a typical eukaryotic gene 1 1 based on the thymidine kinase gene octamer transcription element promoter +1 ATTTGCAT GC CAAT GC TATA TATA box (TATAAAA) located approximately bp upstream of the +1 start site determines the exact start site (not in all promoters) binds the TATA binding protein (TBP) which is a subunit of TFIID GC box (CCGCCC) binds Sp1 (Specificity factor 1) CAAT box (GGCCAATCT) binds CTF (CAAT box transcription factor) Octamer (ATTTGCAT) binds OTF (Octamer transcription factor)
35 TATA box
36 Proteins regulating eukaryotic mrna synthesis General transcription factors TFIID (a multisubunit protein) binds to the TATA box to begin the assembly of the transcription apparatus the TATA binding protein (TBP) directly binds the TATA box TBP associated factors (TAFs) bind to TBP TFIIA, TFIIB, TFIIE, TFIIF, TFIIH 1, TFIIJ assemble with TFIID RNA polymerase II binds the promoter region via the TFII s Transcription factors binding to other promoter elements and transcription elements interact with proteins at the promoter and further stabilize (or inhibit) formation of a functional preinitiation complex 1 TFIIH is also involved in phosphorylation of RNA polymerase II, DNA repair (Cockayne syndrome mutations), and cell cycle regulation
37 Nome Alias Chromosoma TAF1 250 Xq13.1 TAF1L 250like 9p21.1 TAF q24.12 TAF p15.1 TAF q13.33 TAF4B q11.2 TF2D TBP + TAF TAF q24-10q25.2 TAF6 80 7q22.1 TAF6L 11q12.3 TAF7 55 5q31 TAF7L 50 Xq22.1 TAF8 43 6p21.1 TAF9 32 5q11.2-5q13.1 TAF p15.3 TAF p21.31 TAF p35.3 TAF p13.3 TAF q11.1-q11.2
38 Binding of the general transcription factors E F TAFs B TFIID H A TBP J TFIID (a multisubunit protein) binds to the TATA box to begin the assembly of the transcription apparatus the TATA binding protein (TBP) directly binds the TATA box TBP associated factors (TAFs) bind to TBP TFIIA, TFIIB, TFIIE, TFIIF, TFIIH, TFIIJ assemble with TFIID
39 Binding of RNA polymerase II E F B TFIID H A TBP J RNA pol II RNA polymerase II (a multisubunit protein) binds to the promoter region by interacting with the TFII s TFs recruit histone acetylase to the promoter
40 TATA BOX BINDING PROTEIN TBP Saddle-like domain TATA BOX DNA BINDING
41 TAF5 stabilizes TAFs interaction, specially histonelike ones (TAF6, TAF9) TAF1: Acetyl transferase activity Interaction with TFIIF TAF6 TAF11 TAF4 TAF12 TAF9 TAF13 TAF3 TAF12 TAF8 TAF4 TAF10 TBP TAF7 TAF5 TAF5 TAF11 TAF8 TAF3 TATA BOX TAF13 TAF6 TAF9TAF10
42 DNA BENDING
43 TFIID
44 Pre-initiation complex (PIC) RNA pol II TF II A TBP TAF TATA TF II F TF II B TF II E TF II H DNA
45 Pre-initiation complex (PIC) TBP of TFII D binds TATA TFII A and TFII B bind TFII D TFII F-RNA-pol complex binds TFII B TFII F and TFII E open the dsdna (helicase and ATPase) TFII H: completion of PIC
46 Phosphorylation of RNA-pol TF II H is of protein kinase activity to phosphorylate CTD of RNA-pol. (CTD is the C-terminal domain of RNA-pol)
47 b. Elongation The elongation is similar to that of prokaryotes. The transcription and translation do not take place simultaneously since they are separated by nuclear membrane.
48 c. Termination The termination sequence is AATAAA followed by GT repeats. The termination is closely related to the post-transcriptional modification.
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50 Structure of eukaryotic mrna 5 Cap 7mGppp 5 untranslated region initiation AUG translated region 3 untranslated region UGA termination polyadenylation signal AAUAAA (A) ~200 poly(a) tail all mrnas have a 5 cap and all mrnas (with the exception of the histone mrnas) contain a poly(a) tail the 5 cap and 3 poly(a) tail prevent mrna degradation loss of the cap and poly(a) tail results in mrna degradation 3
51 Steps in mrna processing (hnrna is the precursor of mrna) capping (occurs co-transcriptionally) cleavage and polyadenylation (forms the 3 end) splicing (occurs in the nucleus prior to transport) exon 1 intron 1 exon 2 cap Transcription of pre-mrna and capping at the 5 end Cleavage of the 3 end and polyadenylation cap cap poly(a) Splicing to remove intron sequences cap poly(a) Transport of mature mrna to the cytoplasm
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53 The 5 - cap structure is found on hnrna too. The capping process occurs in nuclei. The cap structure of mrna will be recognized by the cap-binding protein required for translation. The capping occurs prior to the splicing.
54 b. Poly-A tailing at 3 - end There is no poly(dt) sequence on the DNA template. The tailing process dose not depend on the template. The tailing process occurs prior to the splicing. The tailing process takes place in the nuclei.
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56 Polyadenylation cleavage of the primary transcript occurs approximately nucleotides 3 -ward of the AAUAAA consensus site polyadenylation catalyzed by poly(a) polymerase approximately 200 adenylate residues are added cleavage AAUAAA mgpppnmpnm mgpppnmpnm AAUAAA A A A polyadenylation A A A 3 poly(a) is associated with poly(a) binding protein (PBP) function of poly(a) tail is to stabilize mrna
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60 Splicing Rimozione di un introne attraverso due reazioni sequenziali di trasferimento di fosfato, note come transesterificazioni. Queste uniscono due esoni rimuovendo l introne come un cappio
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65 Chemistry of mrna splicing two cleavage-ligation reactions transesterification reactions - exchange of one phosphodiester bond for another - not catalyzed by traditional enzymes branch site adenosine forms 2, 5 phosphodiester bond with guanosine at 5 end of intron intron 1 Pre-mRNA 2 OH-A branch site adenosine exon 1 exon 2 5 G-p-G-U - A-G-p-G 3 First clevage-ligation (transesterification) reaction
66 ligation of exons releases lariat RNA (intron) intron 1 U-G-5 -p-2 -AA Splicing intermediate exon 1 exon 2 5 G-OH 3 A-G-p-G A - 3 Second clevage-ligation reaction intron 1 Lariat U-G-5 -p-2 -A Spliced mrna 3 G-A exon 1 exon 2 5 G-p-G 3
67 Recognition of splice sites invariant GU and AG dinucleotides at intron ends donor (upstream) and acceptor (downstream) splice sites are within conserved consensus sequences donor (5 ) splice site branch site acceptor (3 ) splice site G/GUAAGU... A... YYYYYNYAG/G U1 U2 small nuclear RNA (snrna) U1 recognizes the donor splice site sequence (base-pairing interaction) U2 snrna binds to the branch site (base-pairing interaction) Y= U or C for pyrimidine; N= any nucleotide
68 intron 1 Step 2: binding of U4, U5, U6 2 OH-A exon 1 exon 2 U5 5 G-p-G-U - A-G-p-G 3 U1 U2 U4 U6 intron 1 Step 3: U1 is released, then U4 is released 2 OH-A exon 1 exon 2 U5 U6 U2 5 G-p-G-U - A-G-p-G 3
69 Step 4: U6 binds the 5 splice site and the two splicing reactions occur, catalyzed by U2 and U6 snrnps intron 1 mrna 3 G-A U6 2 OH-A U2 U-G-5 -p-2 -A U5 5 G-p-G 3
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73 Trans-splicing Nei protozoi e in un nematode
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76 Differenti molecole di mrna dallo stesso gene Splicing alternativo Uso di promotori alternativi Uso di segnali di poliadenilazione alternativi
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80 d. mrna editing Taking place at the transcription level One gene responsible for more than one proteins Significance: gene sequences, after post-transcriptional modification, can be multiple purpose differentiation.
81 Different pathway of apo B Human apo B gene hnrna ( base) CAA to UAA At 6666 liver apo B100 (500 kd) intestine apo B48 (240 kd)
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83 Structure of prokaryotic messenger RNA 5 Shine-Dalgarno sequence PuPuPuPuPuPuPuPu 3 AAU termination translated region initiation AUG The Shine-Dalgarno (SD) sequence base-pairs with a pyrimidine-rich sequence in 16S rrna to facilitate the initiation of protein synthesis
84 Il gene dei procarioti è policistronico
85 Enhancers Nei geni degli eucarioti gli enhancers possono distare dalla regione codificante anche più di 50 Kb.
86 Regolazione dell espressione genica Organizzazione della cromatina Punto 1 Inizio della trascrizione
87 Meccanismi di Regolazione dell espressione genica Fase Nucleare Scelta del gene che deve essere espresso Maturazione dell RNA Trasferimento Nucleo Citoplasma Fase Citoplasmatica Sintesi delle catene polipeptidiche Modificazioni post-traduzionali Trasferimento delle proteine nelle sedi di competenza
RNA. Ribonucleotidi monofosfato uniti a. formare una catena polinucleotidica
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