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 sequences 100’s have been identified Either 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 homeostasis Compensate for physiological changes Growth 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 domain Functionally 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 repressor Presence 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 General Necessary for assembly of transcription apparatus Recruitment 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 domain Activating domain (interacts with transcription apparatus) Interchangable

Binding sites Promoters Enhancers Binding sites for general transcription factors Mediated binding of RNA pol II Enhancers Binding sites for specific transcription factors Act over large distances DNA forms a loop

In Summary Activators: Coactivators: General factors 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 Methylation Addition of methyl group (CH4) to cytosine Found on most inactive mammalian genes Blocks “accidental” transcription of inactive genes Prevents 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 interference Double stranded RNA Gene silencing: Strong inhibition of genes

Dicer miRNAs: bind directly to mRNA and prevent translation

Alternative slicing Different tissues Different timing in cells Calcitonin CGRP Different tissues, different functions, same transcription unit

RNA editing Apolipoprotein B 5-HT Serotonin 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 life 3 min: prokaryotic mRNA transcripts 10 hours: eukaryotic B-globin transcripts 1 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