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Gene expression

DNA  RNA  Protein


DNA
Replication
Initiation
DNA
Elongation
Transcription Processing
Degradation
Export
RNA
Translation Initiation
Degradation Elongation
Protein Processing
Targeting
Chapter 6
• Transcription
• Sections
• From DNA to RNA
– The start of the chapter to the end of “Mature eucaryotic
mRNAs are selectively exported from the nucleus”
RNA structure

RNA is single stranded polymer of C, G, A, U

Can have secondary structure but typically not a


double helix (Fig. 6-6)
RNA structure

many types of RNA made:

•mRNA: encodes proteins,

•snRNA: RNA processing

•snoRNA: rRNA processing

•tRNA: translation

•rRNA: translation
Transcription initiation

DNA acts as a template for RNA synthesis (Fig 6-


9)
Transcription initiation

DNA acts as a template for RNA synthesis


Synthesis by RNA polymerase -RNA Pol

RNA Pol I makes tRNA and rRNA

RNA Poly II makes mRNA in nucleus


Control of transcription

Transcription initiation by RNA Pol II requires


general transcription factors (Fig 6-16)
Control of transcription
(Fig. 6-16)

Transcription start site usually a TATA box (not


always)

TBP (TATA-binding protein) binds, changing DNA


structure (Fig 6-18).

Recruits transcription factor II proteins (TFIIA,


B, …) then RNA Pol II

Collectively the transcription initiation complex


Control of transcription

Since DNA is wrapped around histones, how does


RNA Pol gain access to the promoter?

How does RNA Pol know where to bind?


Control of transcription
(Fig. 6-19)

Transcription initiation also requires:


•activators
•mediators (or co-activators),
•chromatin-remodeling proteins

Activators increase the likelihood of successful


transcription initiation

Mediators allow activators to communicate with


RNA Pol II
Transcription factors

• DNA-binding proteins associate with


specific regions on DNA (elements)

• Elements may be as small as 6 nucleotides

• Subtle differences in DNA 3 dimensional


structure alter the ability of proteins to
bind
RNA processing

Newly synthesized transcripts (mRNA) are processed


(Fig. 6-21):

•Splice out intervening sequences (=introns) leaving


expressed sequences (exons)

•“Cap” 5’ end of RNA

•Poly-adenylate 3’ end (Poly A+ tail)


RNA processing

Introns are removed in spliceosomes ( a complex


of proteins and snRNA)

cut and paste RNA at specific sites (Fig 6-26, 6-


29)

Requires ATP
Transcript processing

3’ end is also processed


cut downstream from poly-adenylation site (AU-
rich region)

Poly A polymerase adds 100’s of ATPs

Length of poly A+ tail influences half-life


(degradation rate)
Transcript export

Proteins associated with mRNA mark it for export

Only mature mRNA is exported from nucleus

Exit via nuclear pore complexes