Exam 3 Gene Control

Activation domain

Protein region that activates transcription by interacting with other factors.

How are activation domains identified?

Domain-swapping experiments.

Types of activation domains

Acidic, glutamine-rich, proline-rich.

Mediator

Large complex linking activators to RNAP II; regulates initiation & elongation.

Co-activator

Protein that does not bind DNA but bridges activator to transcription machinery; example CBP/p300.

Repressor

Protein that inhibits transcription by blocking activators or recruiting co-repressors.

Lampbrush chromosome

Meiotic chromosome with active transcription loops showing “Christmas tree” RNA.

HIV Tat function

Binds TAR RNA, recruits pTEFb, promotes elongation.

5' Cap chemical structure

7-methylguanosine linked by 5’-5’ triphosphate bond.

Cap functions

Protects RNA, required for translation, export, and splicing.

CBP vs eIF4E

CBP binds cap in nucleus; eIF4E binds cap in cytoplasm for translation.

PolyA signal sequence

AAUAAA.

CPSF role

Binds AAUAAA signal to initiate 3' end processing.

PAP role

Adds polyA tail.

PABP role

Binds polyA tail; stabilizes and promotes translation.

snRNP U1

Binds 5' splice site.

snRNP U2

Binds branch point A.

Lariat formation

Branchpoint A attacks 5' splice site forming loop.

SR proteins

Promote exon recognition and recruit spliceosome.

Nuclear export requirements

SR proteins, EJC, CPSF, CBC, PABP.

Eukaryotic ribosome size

80S = 40S + 60S.

Translation initiation

eIF4E binds cap, scanning to AUG, 60S joins.

Translation termination

eRF binds stop codon.

Polyribosome

Multiple ribosomes translating a single mRNA.

Circular mRNA mechanism

PABP interacts with eIF4G/eIF4E to loop mRNA.

NMD trigger

Premature stop codon upstream of EJC.

Alternative splicing regulators

SR proteins, EJC, transcription rate.

CLIP

Experimental method mapping protein-RNA interactions.

CstF and polyA switching

High CstF causes proximal site usage.

RNA editing C→U

Cytidine deaminase.

RNA editing A→I

ADAR; I read as G.

mRNA localization example

Bicoid/Nanos.

Translation regulation: eIF2 phosphorylation

Global translation shut down.

IRES

Cap-independent translation initiation.

Ferritin regulation

5' UTR hairpin inhibits translation unless iron present.

Transferrin receptor regulation

3' UTR stabilized under low iron.

siRNA vs miRNA

siRNA degrades mRNA; miRNA represses translation.

miRNA production

Drosha → Dicer → RISC.

Hydrophilic vs hydrophobic ligands

Hydrophilic bind surface receptors; hydrophobic bind intracellular.

JAK-STAT

Cytokine → JAK → phosphorylates STAT → nuclear entry.

GPCR-cAMP-CREB

cAMP activates PKA which phosphorylates CREB → CBP recruitment.

NFκB activation

IκB degraded, NFκB enters nucleus.

Glucocorticoid receptor

Cytoplasmic receptor that moves to nucleus when hormone binds.