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 TAF_II110 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).