module 4 lecture 2 - RNA polymerases
Page 1: Title and Module Information
Course: BIOL10221 "Molecular Biology"
Lecturer: Dr. David Boam
Module 4: From DNA to RNA
Lecture 2: RNA polymerases
Page 2: Aims of the Lecture
Objectives:
Discuss differences in complexity and organization between prokaryotic and eukaryotic transcriptional apparatus.
Explore RNA polymerases used in prokaryotes and eukaryotes.
Review RNA polymerase-associated general factors.
Page 3: Transcription Initiation by Prokaryotic RNA Polymerase
Strands:
Coding Strand (Sense): 5’ to 3’
Template Strand (Antisense): 3’ to 5’
Key Promoter Elements:
-35 and -10 regions.
RNA Polymerase Holoenzyme Components:
Sigma (σ) - Important for promoter recognition.
2 x Alpha (α) - Assembly and activation functions.
2 x Beta (β + β’) - Catalysis and termination.
Omega (ω) - Assembly and folding, required for some genes.
Page 4: Transition from Initiation to Elongation
holoenzyme Formation:
After σ is released, core enzyme (α2ββ’) becomes competent for elongation.
Page 5: Types of RNA Polymerases
Types of RNA and Corresponding Polymerases:
Prokaryotic: One RNA polymerase for all types of RNA.
Eukaryotic: Three types of RNA polymerases:
Pol I: Ribosomal RNA genes (rRNA).
Pol II: Protein coding genes (mRNA), small nuclear RNA (snRNA).
Pol III: Transfer RNA (tRNA), rRNA, and snRNA.
Page 6: Assembly of the RNA Polymerase II Complex - Part 1
Key Components:
TFIID: Contains TATA binding protein (TBP) + TBP-Associated Factors (TAFs).
TBP promotes specific DNA-protein interactions.
Functions of Additional Factors:
TFIIA: Assists in TFIID binding.
TFIIB: Sets distance from TATA element to transcription start site.
Page 7: TBP-DNA Complex Structure
Complex View:
Head-on view of TBP and DNA barrel.
Structure has a saddle shape; 'b-sheet' surface contacts the DNA minor groove.
Page 8: TBP-TFIIB-DNA Complex
Details on how TBP and TFIIB interact with DNA.
Page 9: TBP-TFIIA-DNA Complex
Notes on the interaction dynamics of TBP and TFIIA with DNA.
Page 10: Assembly of RNA Polymerase II Initiation Complex - Part II
Components:
IID, IIB, RNA polymerase II (10 subunits).
Functions:
TFIIE, F, H, J, K assist in recruitment of polymerase II.
Prevents non-specific binding of polymerase II to DNA like σ does.
Functions in promoter clearance, helicase activity, processivity, and transcription-coupled DNA repair.
Page 11: RNA Polymerase I Complex
Process of Initiation:
Upstream Binding Factor (UBF) binds to UCE and core element of DNA.
SL1 = TBP + Pol I-specific TAFs; initiates transcription.
Page 12: RNA Polymerase III - tRNA Genes
Mechanism:
Promoter located within the coding region.
TFIIIC binds to B box, TFIIIB is recruited upstream of start site.
TFIIIB composed of TBP + 2 Pol III-specific TAFs.
Page 13: Other RNA Polymerase III Genes
5S rRNA Genes:
Similar to tRNA genes, utilize additional factor TFIIIA to recruit TFIIIC.
snRNA Genes:
Structured like Pol II genes, include upstream promoter and TATA box.
Page 14: Summary of Key Concepts
Differences in complexity and organization between prokaryotic and eukaryotic transcriptional apparatus.
RNA Polymerases as macromolecular complexes:
Prokaryotes: One polymerase.
Eukaryotes: Three specialized, gene-type-specific polymerases.
Page 15: Intended Learning Objectives
Understanding the nature of RNA Polymerases as macromolecular complexes.
Grasping distinctions between prokaryotic and eukaryotic systems.
Appreciating gene-type specificity of eukaryotic RNA polymerases.
Comprehension of transcription initiation process in prokaryotes and similarities in eukaryotes.
Identifying and understanding functions of general transcription factors in eukaryotic RNA polymerases.
Keywords
RNA polymerase, Recruitment, Multi-protein complex, Sigma, TBP, TFIIA-J, tRNA promoter, rRNA promoter, mRNA promoter.