Transcription of Prokaryotes and Eukaryotes PDF

2/5/24 Transcription https://cdn1.byjus.com/wp-content/uploads/2018/11/Central-Dogma-DNA-to-RNA-to-Protein.png 1...

2/5/24 Transcription https://cdn1.byjus.com/wp-content/uploads/2018/11/Central-Dogma-DNA-to-RNA-to-Protein.png 1 2 RNA Transcription The synthesis of RNA molecules using DNA strands as the templates so that the genetic information can be transferred from DNA to RNA. http s://la b ster-im a g e- m a na g er.s3.a m a zo na w s.c o m /6ee6b524-69d1-4937-b0c6- 5253fcc6a9ff/PSL_D N A to Pro tein.en.x512.p ng https://ib.bioninja.com.au/_Media/dna-vs-rna-structure_med.jpeg 3 4 1  2/5/24 Structural DNA regions that can be genes transcribed into RNA Molecular Biology of the cell, 7th ed, 2022 http s://s3-us-w est-2.a m a zo na w s.co m /co urses-im a g es/w p - co ntent/up lo a d s/sites/1094/2016/11/03164740/O SC _M icro b io _11_07_O p ero n.jp g 5 6 Is the strand from which the Is the strand whose base sequence Template strand RNA is actually transcribed. Coding strand specifies the amino acid sequence of the encoded protein. http s://i0.w p.c o m /m ic ro b e o nline.c o m /w p -c o nte nt/up lo a d s/2022/07/te m p la te -stra nd.p ng ? ssl= 1 http s://i0.w p.co m /m icro b e o nline.co m /w p -co nte nt/up lo a d s/2022/07/te m p la te -stra nd.p ng ?ssl=1 7 8 2  2/5/24 RNA-pol of E. Coli RNA polymerase The enzyme responsible subunit function for the RNA synthesis Determine the DNA to be a transcribed In E. coli is consists of 5 different subunits: a2 b b¢ b Catalyze polymerization ws. b¢ Bind & open DNA template - Recognize the promoter s http s://ved ip hlie-a w s.s3.a p -so uth- for synthesis initiation 1.a m a zo na w s.c o m /Struc ture_o f_C o re_RN A _p o lym era se_a nd _RN A _p o lym era se_ho lo enzym e_3d 7462a 85a.PN G www.fppt.info 9 10 Recognition of Origins Rifampicin Each transcriptable region is called Drug for operon. tuberculosis, can bind specifically to One operon includes the b subunit of several structural RNA-pol and inhibit genes and upstream the RNA synthesis. regulatory sequences. https://tajgenerics.com/wp-content/uploads/Rifampicin-Capsules-USP-300-mg- http s://rb rlife scie nce.co m /w p -co nte nt/up lo a d s/2022/01/o p e ro n-structure -p ro ka ryo te s.p ng specifications-scaled.jpg 11 12 3  2/5/24 Bacterial Promoter Pribnow region Is the DNA sequence that RNA-pol can bind. Promoter Is a region of DNA where transcription of a gene is initiated. http s://cd n.ka sta tic.o rg /ka -p e rse us-im a g e s/a 1541486673e 01a 5ce 609108061d 3a 205d 0897ca.p ng 13 14 Eukaryotic promoter Transcription Process https://cdn.kastatic.org/ka-perseus-images/d8f337cfb9d80ad3576e26877c766626ede50b1d.png 15 16 4  2/5/24 §2.1 Transcription of Prokaryotes a. Initiation Initiation phase: RNA-pol recognizes the promoter and starts the transcription. The first nucleotide on RNA transcript Elongation phase: the RNA strand is is always purine continuously growing. triphosphate. Termination phase: the RNA-pol stops GTP is more often synthesis, and the nascent RNA is than ATP. separated from the DNA template. https://www.researchgate.net/publication/340292351/figure/fig1/AS:875013934686219@1585630987807/Graphic- representation-of-the-bacterial-transcription-process-Transcription-begins-with.png 17 18 c. Termination b. Elongation Where the nascent RNA is released from its Free nucleotides complex with RNA pol triphosphates are added sequentially and template to the 3’OH of the nascent RNA strand. Two types of termination in bacteria: intrinsic and rho-dependent https://www.researchgate.net/publication/340292351/figure/fig1/AS:875013934686219@1585630987807/Graphic- representation-of-the-bacterial-transcription-process-Transcription-begins-with.png https://www.researchgate.net/publication/340292351/figure/fig1/AS:875013934686219@1585630987807/Graphic- representation-of-the-bacterial-transcription-process-Transcription-begins-with.png 19 20 5  2/5/24 Rho-dependent r-independent termination termination Depends on rho factor, no formation of hairpin structure Termination is determined by specific sequences (termination sites) Rho factor is a protein that binds to nascent RNA and tracks along the RNA to interact with RNA polymerase and release it from Termination sites consist of 3 the elongation complex. features: Inverted repeats, rich in G:C Rho is a hexameric and ATP-dependent which form a stem-loop RNA translocase, that terminates structure (hairpin) in RNA transcription at certain specific genomic transcript sites called a rut (rho utilization). Series of 7 U residues following the hairpin stem http://www.researchgate.net/publication/351426601/figure/fig1/AS:114312811 16727968@1675306442157/Graphic-representation-of-Rho-dependent- transcription-termination-During-the-elongation.pngs https://img.freepik.com/premium-vector/intrinsic-termination-transcription-prokaryotes-vector-illustration-infographic-diagram_683773-687.jpg 21 22 r-independent termination https://microbiologynotes.org/wp-content/uploads/2020/12/Intrinsic-Termination-of-Transcription.jpg © 2002 by Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter. 23 24 6  PX?|“%;Z)]W0BMWz;-%­7“|”7WkkW(|”W­|q%W”Z“X]ZX“|-W”)­)-|“)Z)7”WZ;W[|]Z7“)|-W 0BMWz;-%­7“|”7Wn(Q6j^:LuCs-&yWDXZWZ(7“7W|“7W”7'7“|-W)­z;“Z|qZW4)667“7q]7”W)qWZ(7W ^|%W)qW^()](WZ(7W[|]Z7“)|-W|q4W7X?|“%;Z)]W7q+%­7”W6Xq]Z);qpWZ^;W;6W^()](W];qa ]7“qWX”W)­­74)|Z7-%y 2/5/24 byWE()-7W[|]Z7“)|-W0BMWz;-%­7“|”7W“7 X)“7”W;q-%W|W”)q8-7WZ“|q”]“)zZ);qa )q)Z)|Z);qW6|]Z;“WnHR&WZ;W[78)qWZ“|q”]“)zZ);qpW7X?|“%;Z)]W0BMWz;-%­7“|”7”W “7 X)“7W­|q%W”X](W6|]Z;“”pW];--7]Z)'7-%W]|--74WZ(7WF)K)JI~MOJIK/5J89O8°KW jI5O°J/y eyWPX?|“%;Z)]WZ“|q”]“)zZ);qW)q)Z)|Z);qW­X”ZWZ|?7Wz-|]7W;qWvBMWZ(|ZW)”W z|]?|874W)qZ;WqX]-7;”;­7”W|q4W()8(7“a;“47“W6;“­”W;6W](“;­|Z)qW”Z“X]a ZX“7Wn47”]“)[74W)qWH(|zZ7“Wd&pW67|ZX“7”WZ(|ZW|“7W|[”7qZW6“;­W[|]Z7“)|-W ](“;­;”;­7”y 2X*S2X!**Szm.SF[+f°*!)a*aSK=SPp/)!f[tKqS&*++a 2f]*S[ZS][+f°*!)a*SY*=*aSt!)=aq!K0*x -1PT‘’q\j0”3?0TU nbh6ATRh6AT3QzTah6T”-1PTa0Q0? -1PT‘’q\j0”3?0TUU PqqT‘”’+0lQl:’zlQaTa0Q0?AT‘qp?T?Q’-1PTa0Q0?ATjl-1PTa0Q0?AT ?l-1PTa0Q0?ATqQ:-1PTa0Q0?AT3QzTj’?+T?Q-1PTa0Q0? Transcription of Eukaryotes -1PT‘’q\j0”3?0TUUU +-1PTa0Q0?ATn6T”-1PTa0Q0?AT?’j0T?Q-1PTa0Q0?AT3QzT a0Q0?Tt’”T’+b0”T?j3qqT-1P? (b0T”-1P?T_0”0TQ3j0zT3::’”zlQaT+’T+b0l”T*6&T—3qp0?AT_bl:bT”0t0”T+’T+b0l”T”3+0T’tT?0zlj0Q+3+l’QT lQT3QTpq+”3:0Q+”ltpa0bT(b0Tq3”a0”T+b0T6T—3qp0AT+b0Tq3”a0”T+b0T”-1Pb 25 26 RNA-pol of eukaryotes RNA-pol I II III 5S rRNA products 45S rRNA hnRNA tRNA Initiation snRNA Sensitivity No high moderate to Amanitin Amanitin is a specific inhibitor of RNA-pol. 27 28 7  2/5/24 are the specific sequences on Cis-acting element the DNA template that regulate the transcription of one or more genes. cis-acting element structural gene GCGC CAAT TATA exon intron exon start TATA box (Hogness box) enhancer CAAT box GC box https://preuniversity.grkraj.org/html/10_MOLECULAR_BIOLOGY_files/image019.jpg 29 30 Pre-initiation complex (PIC) TBP (TATA binding proteins) 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 Molecular Biology of the cell, 7th ed, 2022 31 32 8  2/5/24 Pre-initiation complex (PIC) RNA pol II Activators TF II F TF II E Gene regulatory TF II TBP TAF proteins that help TF II A TATA B RNA pol, the general TF II H DNA factors, and the mediator all to assemble at the promoter TF II H is of protein kinase activity to phosphorylate CTD of RNA-pol. (CTD is the C-terminal domain of RNA-pol Molecular Biology of the cell, 7th ed, 2022 33 34 Mediators Elongation Similar to that of prokaryotes Allows the activator There are elongation factors proteins to (Spt4, Spt5, and Elf) that communicate stabilizes RNA pol properly with the Pol II and with the general The transcription and transcription factors. translation do not take place simultaneously since they are separated by nuclear membrane Molecular Biology of the cell, 7th ed, 2022 Molecular Biology of the cell, 7th ed, 2022 35 36 9  2/5/24 DNA topoisomerase Termination Enzymes that rapidly remove superhelical tension in DNA The termination sequence is AATAAA followed DNA gyrase by GT repeats A specialized topoisomerase in bacteria that Uses the energy of ATP hydrolysis to pump supercoils continuously Termination may into the DNA, thereby maintaining the DNA under constant be Rho factor tension dependent or independent, https://assets-global.website-files.com/621e95f9ac30687a56e4297e/64a8d6fb7e08150d04ef0f44_V2_1675775972286_6dfdb766-c766-4a5d-8f44- 36109b991b94.png 37 38 Post- transcriptional modifications https://search-static.byjusweb.com/question-images/byjus/infinitestudent- images/ckeditor_assets/pictures/291311/content_115.jpg 39 40 10  2/5/24 Modification of hnRNA a. Capping at the 5¢- end Primary transcripts of mRNA are called as heteronuclear RNA The capping process (hnRNA). occurs in nuclei. The cap structure of mRNA Modification includes will be recognized by the Capping at the 5¢- end cap-binding protein Tailing at the 3¢- end required for translation. mRNA splicing http s://c d n.le c turio.c o m /a sse ts/Sum m a ry-o f-p o st-tra nsc rip tio na l-m o d ific a tio ns-o f-hnRN A.jp g The capping occurs before the splicing. https://plantlet.org/wp-content/uploads/2019/10/Capture-4.png 41 42 b. Poly-A tailing at 3¢ - end Increased mRNA stability. Increased translational efficiency c. Splicing Splicing of the last intron http s://slid e p la ye r.c o m /slid e /6303472/21/im a g e s/54/Func tio n+ o f+ p o ly% 28A % 29+ ta il.jp g 43 44 11  2/5/24 A gene consisting of introns Split gene and exons. Exons are the coding sequences that appear on split genes and primary transcripts, and will be expressed to matured mRNA. https://cdn.britannica.com/96/114896-050-3F22219B/Genes-promoter-regions-production-introns-exons-gene.jpg https://cdn.britannica.com/96/114896-050-3F22219B/Genes-promoter-regions-production-introns-exons-gene.jpg 45 46 the large assembly of small nuclear Spliceosome RNA(snRNAs) and protein molecules that Introns performs pre-mRNA splicing in the cell. are the non-coding sequences that are transcripted into primary mRNAs, and will be cleaved out in the later splicing process. https://cdn.britannica.com/96/114896-050-3F22219B/Genes-promoter-regions-production-introns-exons-gene.jpg https://www.frontiersin.org/files/Articles/1158965/fpls-14-1158965-HTML/image_m/fpls-14-1158965-g001.jpg 47 48 12  2/5/24 RNA editing Changes (insertion, deletion, base substitution) to specific nucleotide sequences within an RNA molecule after it has been generated. http s://d ire c to rsb lo g.nih.g o v /w p -c o nte nt/up lo a d s/2013/08/he la -ii.jp g Significance: multiple functions of gene, localization and stability of RNAs, has been linked to human diseases http s://inno p ro t.c o m /w p -c o nte nt/up lo a d s/2019/04/linte rna -he la -1.jp g https://media.springernature.com/lw685/springer-static/image/art%3A10.1186%2Fs12967-019-2071-4/MediaObjects/12967_2019_2071_Fig1_HTML.png?as=webp 49 50 Prokaryotes vs. Eukaryotes Prokaryotes Eukaryotes mRNA transcribed mRNA undergoes several immediately translated post-transcriptional without any modification modifications like 5 methyl capping, poly A tail, splicing in the nucleoplasm 51 13