Basics of Transcription

Question 1

Three stages of Transcription

Answer 1

1) Initiation: RNA pol binds to promoter and denatures DNA strands to initiate transcription
2) Elongation: RNA pol leaves promoter and synthesizes RNA strand using 1 DNA strand
3) Termination: RNA pol reaches terminator sequence and leaves DNA strand

Question 2

Prokaryotic RNA pol

Answer 2

RNA pol core made of 5 subunits; 6th sigma factor subunit binds to core to create holoenzyme; alpha subunits bind to regulatory sequences, beta units are for catalytic and DNA binding

Question 3

Sigma factor

Answer 3

Binds transiently to core and is responsible for promoter recognition by scanning for -35 and -10 regions (AT rich region upstream (-) of TSS); after sigma factor binds, RNA pol binds tightly to DNA (no more sliding)

Question 4

Prokaryotic Initiation

Answer 4

DNA strands are separated at -10 region to create open complex, once RNA synthesis begins, RNA pol leaves promoter to start elongation phase and sigma factor is released

Question 5

Prokaryotic elongation

Answer 5

Begins when RNA pol has left the promoter (promoter clearance); RNA pol binds tightly to template DNA strand

Question 6

Abortive initiation

Answer 6

binding and release of short RNA strands from DNA at early stages of transcription; after ~10 RNA nucleotides phosphodiester bonds, elongation continues until termination

Question 7

Eukaryotic RNA pols

Answer 7

RNA pol 1 makes most rRNA, RNA pol 3 makes all tRNA and some rRNA, RNA pol 2 makes all mRNA, micro and some noncoding RNA

Question 8

Eukaryotic RNA pol II

Answer 8

Uses 5 general transcription factors to recruit RNA pol II to promoter: TFIID - uses TATA binding protein to bind to TATA box in promoter (-30 position) - TBP associated factors recognize promoter and histone modifications & recruit TFIID to promoters without TATA box
TFIIB - binds to TBP with C terminal domain and RNA pol II with N terminal domain
TFIIF - bound to RNA pol II, helps it to interact with TFIIB at promoter
TFIIE & TFIIH - bind last and form preinitiation complex which turns into initiation complex when DNA is unwound

Question 9

TFIIH

Answer 9

uses helicase activity to form open complex and kinase activity to phsophorylate C terminal domain of RNA pol II to release H,E,B from core promoter

Question 10

Termination in Eukaryotes

Answer 10

RNA pol II is dephosphorylated so it can be recycled and transcribe other genes