transcription and mRNA processing

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template strand runs which direction

3’→5’

5’→3’

non-template strand run which direction

5’→3’ (follows template strand)

RNA is made in which direction

where the RNA is being produced

what is the transcription bubble

+1

what signifies the transcriptional start site?

0 (zero)

unlike a usual number line what does DNA NOT have?

RNA polymerase 2

what protein synthesizes mRNA

bacteria

what only uses one RNA polymerase for transcription?

-35: TTGACA

-10: TATAAT

what are the 2 main consensus sites?

bacteria (during bacterial transcription)

core RNA pol+sigma factor=RNA pol holoenzyme is found where

sufficient to produce mRNA

Core RNA polymerase

allows RNA pol to bind the -10 and -35 sites which positions RNA pol to start transcription at +1

Sigma Factor

higher with core pol

overall affinity for DNA

higher with sigma factor

specific affinity for DNA

eukaryotes have introns and exons

Eukaryotic difference from prokaryotes

• modulate rate of transcription

• can be ‘activators’ or ‘repressors’

• must have DBD and interaction domain

• have specific binding sites

characteristics of eukaryotic transcription factors

DNA binding domain

DBD

carries out the activation or repression

interaction domain

required by DNA pol 2 for all transcription events

• ex: TBP →TATA binding protein

Basal (general) Transcription Factors

unique to activate or repress at specific genes or in specific circumstances

Specific transcription factors

region immediately upstream of transcription start site

this is also the site of RNA pol binding

promoter region

zinc

transcription depends on

DNA + associated proteins

chromatic

modification of interactions between histones and DNA

chromatin remodeling

“closed chromatin”

regions of condensed DNA that is NOT transcribed

heterochromatin

“open chromatin”

regions of actively expressed DNA with loose histone DNA interactions

euchromatin

created by the differences of eu- and heterochromatin when they are stained

banding patterns

acetyl groups neutralize histone tail charge and loosen their interactions with DNA

modification of histone tails

acetylation

modification occurs by

acetyl groups→positive charge

histone tails→negative charge

if acetyl groups neutralize the charge of the histone tails, what is the charge of acetyl groups and histone tails if DNA has a negative charge?

created euchromatic (turns genes on)

acetylation

eukaryote

prokaryotes do not have histones

histones indicate