Molecular Biology
Chapter 11a Outline
Class II preinitiation complex:
· Nomenclature for class II factors; order of factor binding (F11.1, F11.2); where preinitiation factors bind to DNA (F11.3, F11.4, F11.5).
TFIID:
· TBP
a) C-terminal 180 aa binds to the TATA box (F11.6); TBP binds via the minor groove; structure of the TBP-DNA complex (F11.10).
b) TBP functions with all three RNA polymerases (F11.11).
· TAFs
a) Nomenclature and number of TAFs (F11.12); function of TAFs in promoters with initiator/downstream elements (F11.14); TAFs that bind the TATA box (F11.15, F11.16); photo-cross-linking.
b) Function of TAFs in non-TATA box containing promoters (F11.17, F11.18); requirement for TAFII110 in Sp1 activated promoters (F11.19); Function of TAFs with other gene-specific transcription activators (F11.20).
c) TAFs are not required for all transcription (T11.1); TBP is not required for all transcription (F11.21, F11.22).
TFIIA and TFIIB
· TFIIA is essential in vivo; TFIIA binds to TBP and stabilizes its binding to DNA (F11.1).
· TFIIB binds after TFIIA/TFIID (F11.2); TFIIB is essential for TFIIF/RNAPolII binding downstream.
TFIIF, TFIIE and TFIIH
· TFIIF is comprised of two subunits; TFIIF is similar to sigma factor from prokaryotes since it binds to RNA polII and directs it to promoters with DAB preinitiation complexes (F11.24).
· TFIIE is comprised of two subunits and four total proteins; TFIIE binds to the DABPolF complex (F11.25) and stimulates transcription (F11.26).
· TFIIH is the last factor to join the preinitiation complex (F11.27); TFIIH phosphorylates PolII (F11.28, F11.29), switching it from the PolIIA to PolIIO (F10.17); PolII phosphorylation occurs on the C-terminal domain (CTD) (F11.30); TFIIH is comprised of a 4 subunit kinase domain and a 5 subunit core domain with an ATP dependent helicase activity (F11.31); TFIIH helicase is required for transcription (F11.32); TFIIH helicase unwinds the DNA strands and is required for promoter clearance (F11.33).
TFIIS and PolII holoenzyme:
· TFIIS stimulates transcript elongation (F11.34, F11.35) and proofreading of transcripts (F11.37).
· RNA PolII holoenzyme contains many of the proteins involved in preinitiation complexes, which differ in their completeness depending on organism (F11.38).