Jan. 26

Exams = open book, open notes
Feb. 6 = lab re-write due!

possible question on 1st exam: long strand of DNA and we find DNA expression of certain gene? something like that?

  • know start codon for translation (AUG)
  • know what consensus promoter sequence looks like

Consensus promoter sequence: promoter sequence of bases that most genes have in common -> closer promoter sequence is to consensus promoter sequence (more closely RNApolymerase type II) more interaction btwn pol II and promoter
& thus, more transcription of genes w/ promoter sequences very similar to consensus

V. Steps of Transcription

a) DNA in normal state supercoiled and (in eukaryotes) wound around histones (proteins)

b) initiation of transcription starts w/ local unwinding of DAN, change interaction btwn DNA and protein —> its wound around
(chromatin remodeling)
i. TBP (TATA-box binging protein) binds to promoter sequence
*TBP bends DNA into L-shape
ii. this L-shaped conformation —> recruitment of transcription accessory proteins to transcription bubble
TFIIE: binds ~ 30 base pairs (bp) upstream of TATA box, recruits other accessory proteins, TFIIH (heliocase activity which upwinds DNA allows transcription bubble to form) and TFIIB which stabilzes transcription bubble so it doesn't just go right back together.
iii. RNA polymerase II (pol II) binds to DNA at transcription bubble
*pol II, many accessory proteins can transcribe naked DNA (isn't all wound up around proteins) w/o other protein

c) RNA polymerase moves down DAN, in 3' to 5' direction (so RNA synthesized in 5' to 3' direction)
*ATP *CTP energy release from
*GTP *UTP breaking phosphates off

—> pol II only in correct conformation to catalyze reaction —> sugar-phos. backbone formation when it has RNA base complementary-pairing w/ corresponding bases.

i. in prokaryotes - transcription stops at hairpin loops in DNA
ii. in eukaryotes - not as many shared sequences that stopping transcript as in prokaryotes so transript caused by termination proteins that interact with RNA polymrase II to stop transcription.

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