Assembly of RNA Polymerase-II Initiation Complex

Nov 14, 2014

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TBP. TAFs. Inhibitor. TAFs. TBP. TFIIF. RNA Pol-II. TAFs. TFIIA. TFIIF. TBP. TFIIE. TFIIH. TFIIJ. RNA Pol-II. TAFs. 2009 ProteinLounge.com. TFIIA. TFIIA. TFIIA. TFIIF. TBP. TBP. TFIIB. TFIIB. TFIIB. TFIIE. TFIIH. TFIIJ. RNA Pol-II. TATA Box. Transcribed Region.

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Assembly of RNA Polymerase-II Initiation Complex

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TBP TAFs Inhibitor TAFs TBP TFIIF RNA Pol-II TAFs TFIIA TFIIF TBP TFIIE TFIIH TFIIJ RNA Pol-II TAFs 2009 ProteinLounge.com TFIIA TFIIA TFIIA TFIIF TBP TBP TFIIB TFIIB TFIIB TFIIE TFIIH TFIIJ RNA Pol-II TATA Box Transcribed Region TAFs TFIID TBP Assembly of RNA Polymerase-II Initiation Complex Inhibitor TAFs TFIIB C

Activities of RNA Polymerase

Activities of RNA Polymerase. sequence specific DNA binding -promoters melts DNA to reveal the template strand selects ribonucleotide (not deoxynucleotides) that anneals to template strand polymerizes RNA strand translocates on DNA template, during which it must:

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RNA-directed Viral Assembly

I ) Self-Assembly and Free Energy Minimization. RNA-directed Viral Assembly. II) Fundamental Interactions. III ) Self-Assembly Empty Capsids. IV) Condensation of RNA genome molecules. V) Free Energy Landscape Viral Assembly. I ) . (1995, Scientific American). “Mark I” Self-Assembly

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Part II Initiation

Part II Initiation. During the “Initiation” phase, the hero learns how to live in the new world. A. The Road of Trials. The hero learns that life in the world of adventure can be difficult. B. Meeting with the Goddess/God/Mentor. A wise or magical being gives guidance or advice to the hero.

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Regulatory effects on RNA polymerase

Regulatory effects on RNA polymerase. Binding constants Rate constants Measuring K B. Multiple steps in initiation and elongation by RNA polymerase are targets for regulation. RNA Polymerase has to * bind to promoters, * form an open complex, * initiate transcription,

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89 - RNA polymerase 1 Subunit C

90 - Putative DNA primase # GfIV-C20 ORF1. 92 - ALI-like protein. 95 - Zinc finger protein. 89 - RNA polymerase 1 Subunit C. 91 - Unknwon GfV-like protein. 93 - D5 pox-like protein # CIV 184R & GfIV-C20 ORF1. 94 - Putative chromosomal replication protein. 1. 5. 10. 13.

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E. coli RNA polymerase (redux)

E. coli RNA polymerase (redux). Functions of other subunits: α - binds the UP element upstream of very strong promoters (rRNA), and some protein activators. β - active site of Pol, also binds  , nascent RNA, RNA-DNA hybrid, and DS DNA in front of bubble.

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De novo assembly of RNA

De novo assembly of RNA. Steve Kelly www.stevekelly.eu Slides are available at: http://bioinformatics.plants.ox.ac.uk/EBI_2014/EBI_2014.ppt Example data is available at: http://bioinformatics.plants.ox.ac.uk/EBI_2014/reads.zip. What is a de novo transcriptome?.

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RNA polymerase II The central enzyme of gene expression

TF. TBP. TATA. Promoter. RNA polymerase II The central enzyme of gene expression. Enzymatic function. Enzymatic reaction: NTP  RNA + PPi (1969) RNA n + NTP + (Mg ++ + templat) = RNA n+1 + PP i Processive - can transcribe 10 6 bp template without dissociation

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RNA Sequence Assembly

RNA Sequence Assembly. WEI Xueliang. Overview. Sequence Assembly Current Method My Method RNA Assembly To Do. Sequence Assembly. Goal : get the DNA/RNA sequence. Machine cannot read whole genomes in one go, but rather small pieces between 20 and 1000 bases. Define: Read = Tag = Fragment.

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a. DNA ligase b. DNA polymerase c. RNA polymerase d. Restriction enzyme

a. DNA ligase b. DNA polymerase c. RNA polymerase d. Restriction enzyme e. Reverse transcriptase f. Transformation 1. Enzyme found in retroviruses that produce DNA from an RNA template. 2. Enzyme used during replication to attach Okazaki fragments to each other.

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Molecular basis of rna -dependant rna polymerase II activity

Molecular basis of rna -dependant rna polymerase II activity. Elisabeth Lehmann et. al. Introduction. Catalyses DNA-Dependant RNA synthesis Structure has 12 subunits ~ 550 kDa Key polymerase in transcription. Introduction. Error Rate : 10 -3

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Eukaryotic RNA polymerase 18S+ 30 proteins= 40S

Initiation of rDNA transcription Two transcription factors, UBF and SL1, bind cooperatively to the rDNA promoter and recruit RNA polymerase I to form an initiation complex. One subunit of SL1 is the TATA-binding protein (TBP) and the other is TBP- associated Factor (TAF).

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II. RNA

II. RNA. Ribonucleic Acid Function – makes proteins. A. Differences between RNA and DNA. -- DNA RNA -- 2 strands 1 strand -- deoxyribose ribose sugar -- thymine uracil. B. 3 types of RNA. 1. Messenger RNA (mRNA) - straight strand

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Formation of RNA Polymerase II pre-initiation complex

Formation of RNA Polymerase II pre-initiation complex. IID contains TBP that binds TATA box. IIA stabilizes IID binding to promoter. IIB binds initiation sequence. Pol II binds IIB. IIE stimulates transcription. IIH has kinase and helicase activity. RNA Synthesis in E. Coli. Transcription

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E. coli RNA Polymerase

E. coli RNA Polymerase. M.Prasad Naidu MSc Medical Biochemistry, Ph.D.Research Scholar. RNA Polymerase. Catalyzes the formation of the phosphodiester bonds between the nucleotides (sugar to phosphate) Uncoils the DNA, adds the nucleotide one at a time in the 5’ to 3’ fashion

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RNA pol II

P. AID. 70. 32. 14. Supplementary figure 7. RGYW. S REGION/ V GENE. B CELL SPECIFIC ACTIVATION. TRANSCRIPTION. (other modifications?). AID. P. AID. 70. STABILIZATION OF ssDNA IN TRANSCRIPTION BUBBLES. 32. 14. RNA pol II. P. DEAMINATION. AID. UNG. 70. 32. 14. NHEJ.

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RNA Polymerase

RNA Polymerase. mRNA being formed from a strand of DNA by proteins. HUMAN ATGCTTCCGGGCACATT...ACGAG CHIMP ATGCTTCCGGGCACATT...ACGAG RAT AT A.. TC G G A G T ACAT CGCA ACGA A HUMAN C.TCAGTGCCTGCCGGAAATCTCCC CHIMP C.TCAGT AT CTGCCGGAAATCTCCC RAT C A T TG GTGCCT TTT G C A TG T T T G CC

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RNA Polymerase binding

RNA Polymerase binding. *Constitutive or basal level transcription. Allosteric activation of RNA polymerase. Inhibition of transcription. DNA-protein interactions. Negative Control of the lac Operon. Proposed CAP-cAMP Activation of lac Transcription. Transcription in Eukaryotes.

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ECOLI RNA POLYMERASE

BIOCHEMISTRY

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Formation of RNA Polymerase II pre-initiation complex

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Chapter 11: Assembly of the Transcription Initiation Complex

Chapter 11: Assembly of the Transcription Initiation Complex. Transcription is more complex than once assumed. 11.1 DNA-binding proteins and their attachment sites. Direct readout. 11.1.1 The special features of DNA-binding proteins. X-ray crystallography

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RNA polymerase II The central enzyme of gene expression

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