Transcription. Outline. RNA Structure. Transcription: Key Questions. Chapter 13

Transcription

1 Transcription Chapter 13 GENOTYPE PHENOTYPE Outline Key Questions Structure of RNA Types of RNA Ingredients for Transcription Bacterial Transcription Initiation, Elongation, Termination Eukaryotic Transcription Initiation, Elongation, Termination Transcription: Key Questions RNA Structure What ingredients are required? Where does transcription start? How does transcription proceed? Where and why does it stop? 2 Carbon Atom 1

2 Wow! This must be IMPORTANT!!! Prokaryotes and Eukaryotes Eukaryotes only Transcription: SELECTIVE synthesis of RNA Ingredients rntps DNA Template Enzymes 2

3 DNA Template Transcription is highly selective RNA is synthesized from one DNA strand (the TEMPLATE STRAND) RNA is synthesized complementary and antiparallel to template strand Template Strand(s) The Transcription Unit Stretch of DNA that codes for an RNA molecule and the sequences necessary for transcription How does the transcription apparatus know which strand to read, where to start, and where to stop? The Transcription Unit Stretch of DNA that codes for an RNA molecule and the sequences necessary for transcription 3 critical regions: PROMOTER RNA CODING REGION TERMINATOR The PROMOTER is a DNA sequence that is recognized and bound by the transcription apparatus. It indicates the template strand, and the direction of transcription. -Y +1 +X 3

4 Transcription Apparatus RNA Polymerase Bacterial Transcription Apparatus Sigma factor (involved in promoter recognition) Holoenzyme (core RNA Pol + Sigma) Rho (involved in termination) Eukaryotic Transcription Apparatus RNA Pol I: Large rrna RNA Pol II: Pre-mRNA, some snrna, snorna RNA Pol III: trna, small rrna, snrna Many accessory proteins (transcription factors) Ribonucleoside triphosphates (rntps)) are substrates used in RNA synthesis Many bacteria have multiple types of sigma factors, which help in the recognition of multiple classes of promoters. The bacterial RNA polymerase Bacterial Transcription: Initiation Promoter Recognition Formation of Transcription Bubble Bond creation between rntps Escape of transcripton apparatus from promoter Promoters and Consensus Sequences A Consensus Sequence is a short stretch of DNA that is conserved among promoters of different genes. There are two consensus sequences upstream of the start site, at approximately -10 and -35. Gene Sequence AATAAA TTTAAT TATTTT TAAAAT Consensus TATAAT 4

5 Pribnow Box Bacterial Initiation Bacterial Transcription: Elongation RNA polymerase unwinds DNA ahead of it, and rewinds the DNA at the end of transcription. Transcription occurs in the Transcription bubble Bacterial Transcription: Termination Transcription ends after a terminator is transcribed Two types of terminators in bacteria: Rho-dependent terminators Rho-independent terminators Rho-independent Termination 1) Two inverted repeats in the DNA sequence are transcribed 2) A string of ~6 Adenines follows the second inverted repeat 3) The inverted repeats form a hairpin structure pausing the polymerase 4) The A-U bonds break and the RNA molecule separates from the template 5

6 Rho-dependent Termination The Hindenberg Lecture 1) Rho binds a stretch of DNA that encodes RNA upstream of the terminator. 2) DNA causes a pause in transcription and Rho catches up. 3) Rho unwinds DNA-RNA hybrid using helicase activity Eukaryotic Transcription Eukaryotic Transcription is Horribly Complicated! Three different polymerases Multiple promoter types Many proteins required for promoter recognition Eukaryotic Initiation Promoters Always found adjacent to gene a fixed number of nucleotides away from start site Enhancers Can be thousands of nucleotides away, and exact location can be variable Increase the rate of transcription Promoter recognition accomplished by accessory proteins that recruit the appropriate Polymerase RNA Polymerase II (PROTEINS) Core promoter Immediately upstream of the gene Includes one or more consensus sequences (most common is the TATA box: TATAAA) Located -25 to -35 Basal Transcription Apparatus Consists of general transcription factors, RNA polymerase, Mediator Binds to DNA near start site Is necessary for transcription at minimal levels Additional proteins (transcriptional activators) bind to other promoters and enhancers affecting the RATE of transcription. 6

7 Figure Figure Figure ZZZZZZZ TATA Binding Protein Transcription factors RNA Polymerase I (Large rrnas) Same idea: transcription factors bind to consensus sequence and recruit RNA Polymerase I. RNA Pol I promoters have 2 key elements Core element, surrounds start site and is sufficient to initiate transcription Upstream control element increases efficiency 7

8 RNA Polymerase I Promoters Figure RNA Polymerase III (trna,, small rrna, snrna) Recognizes several types of promoters Several contain consensus sequences and are also used by RNA pol II (including the TATA box) Promoters for rrna and trna Contain internal promoters downstream of transcription site Figure Eukaryotic Termination Three RNA Polymerases use different mechanisms for termination RNA pol I: requires a termination factor RNA Pol II: termination can end at multiple sites (Chapter 14) RNA Pol III: requires transcription of a string of Uracils (hairpin not required) Summary Transcription: making RNA from a DNA template to transfer information from the genome Ingredients: rntps, DNA template, Transcriptional Apparatus Stages: Initiation, Elongation, Termination Bacteria vs. Eukaryotes: Compare and Contrast (Problem Set) Archea, Eubacteria,, and Eukaryotes Transcription has strong similarities between Archea and Eukaryotes Archea have TBP Archea have TFIIB Both of these are not in Eubacteria 8

9 What are the major similarities and differences between bacterial and eukaryotic transcription, and why should I care? 9