Control of Gene Expression

Chapter 16

Many levels of control

Transcription initiation (most common) Post transcription modification Pre-translation Protein degredation

Translation initiation

RNA must be able to bind to DNA at the gene promotor

Regulatory proteins Bind to specific sequences100’s have been identifiedEither block transcription or stimulate it

Prokaryotes vs. Eukaryotes

Prokaryotes: Regulation is a direct function of the need to adjust to changing environment

Eukaryotes: Maintenance of homeostasisCompensate for physiological changesGrowth and development regulation (fixed

genetic program)Apoptosis

Major Groove

•The nucleotides hydrogen donors and acceptors are accessible through the major groove

DNA Binding motifs

DNA binding domainFunctionally distinct region in the DNA binding

motif the specifically bind to DNA in a set location

Helix-Turn-Helix

Homeodomain motif

Zinc Finger

Leucine Zipper Motif

Prokaryotic regulation Positive control: increases frequence of initiation

Activators Stimulate initiation of transcription

Negative control: decreases frequency of initiation Repressors Bind to operators Require effector molecules Allosteric proteins Active site binds to DNA; allosteric site binds to effector

Operons

Multiple genes Single transcription

unit Often same metabolic

pathway

Repression

lac operon: negatively regulated by lac repressor presence of lactose causes removal of

repressor from lac operon trp operon: positively regulated by trp

repressorPresence of tryptophan causes the binding of

repressor from trp operon

lac operon

Effector: allolactose

Glucose repression

Prevents repressor from binding Allows repressor binding

trp operon

Eukaryotic gene regulation Complicated by chromatin structure Amount of DNA Complex developmental programs Multiple tissues

Transcription factors

GeneralNecessary for assembly of transcription

apparatusRecruitment of RNA polymerase II to a

promoter Initiation complex

TFIID (recognizes and binds to TATA box)Several other transcription factors and

transcription-associated factors (TAFs)

Specific transcription factors

Tissue or time dependent Stimulate higher levels of transcription Have a domain organization

DNA Binding domainActivating domain (interacts with transcription

apparatus) Interchangable

Binding sites

PromotersBinding sites for general transcription factorsMediated binding of RNA pol II

EnhancersBinding sites for specific transcription factorsAct over large distancesDNA forms a loop

In Summary

Activators: Specific transcription factors Bind to enhancers at distance sites Increase rates of transcription

Coactivators: Transmit signals from activators proteins to the general

factors

General factors Position RNA polymerase at start of protein coding

sequence

Eukaryotic Chromatin structure

Nucleosomes may block binding of transcription factors

Histone modifications Modified to block promotors Chromatin remodeling complex

Large complexes of proteins Modify hitsones and DNA Changes chromatin

Repositions nulceosomes

Histone modifications

MethylationAddition of methyl group (CH4) to cytosineFound on most inactive mammalian genesBlocks “accidental” transcription of inactive

genesPrevents transcription activators from binding

to DNA

Histone Modifications

Acetylation Makes DNA

accessible to transcription factors

“Histone code” Control of chromatin

structure Access to transcription

sequences on DNA

Post-transcription Regulation

RNA interferenceDouble stranded RNAGene silencing: Strong inhibition of genes

Dicer

miRNAs: bind directly to mRNA and preventtranslation

Alternative slicing Different tissues Different timing in

cells

Calcitonin CGRP

Different tissues, different functions, same transcription unit

RNA editing

Apolipoprotein B APOB100: only in the liver

LDL

APOB48: only in small intestine “edited” form of APOB100 Alteration of mRNA changing a codon for glutamine to stop

5-HT Serotonin Multiple edits 12 different isoforms

mRNA transport

mRNA transcript cannot move through nuclear pore while splicing enzymes are attached

Transcript must be recognized by nuclear pore receptors Poly A tail

Only 5% of total mRNA transcripts reach cytoplasm

Degradation of mRNA

mRNA half life3 min: prokaryotic mRNA transcripts10 hours: eukaryotic B-globin transcripts1 hour: eukaryotic regulatory genes

Targeted for degradation Enables levels of regulatory proteins to be altered

quickly in response to changes

Protein degradation Turnover of eukaryotic proteins is essential to

cell function Chemical alteration Incorrect folding Aggregation into complexes

Parkinson’s disease Mad cow disease Alzheimer dementia

Decreased need for particular protein

Proteases

Breaking peptide bonds Lysosome

Nonspecific Need to protect necessary proteins;

remove “bad” proteins

Ubiquitin

Added in chain to target protein Ubiquitin ligase Requires ATP Polyubiquinated: signal for destruction

Proteasome

Nonmembrane organelle