Gene Regulation Flashcards
Reverse transcriptase
Rna to DNA
Functional RNA
Ribozymes, long non-coding RNAs, miRNAs
Start codon of translation
ATG (DNA)
AUG (RNA)
Stop codon
UAA, UAG, UGA (RNA)
TAA, TAG, TGA (DNA)
Introns
Removed
Cleae-polyadenylation site
Cut at the 3’ end and a bunch of A’s are added…defines end of last exon included
Why is mRNA longer than protein?
5’ and 3’ UTR regions
Enhancer/promoter location
Promoter - only at beginning
Enhancer - can be anywhere
Upstream vs. downstream
Upstream - 5’
Downstream - 3’
What controls expression of genes?
Trans-acting transcription factors and cis-acting DNA sites
Cis
DNA motifs
Structurally linked to gene
Do not encode proteins but serve as docking sites for trans-acting genes
Trans
Protein factors that regulate transcription of target genes…non covalentlybind to cis acting sites in a sequence specific manner
Promoter
Adjacent to transcription start site…contains cis-acting site that assembles with RNA polymerase 2 complex…may interact with others
Enhancer
Bind trans-acting transcription factors that positively influence chroomatin
Silencer
Opposite of enhancer
Trans-acting factor structure
Bipartite structure
Activation domain and DNA-binding domain
Changes in amino acid sequence of trans-acting
Change affinity of binding to DNA
Changes in nucleotides of cis-site
Increase or decrease affinity to protein
Enhancers are a cluster of
Transcription factor binding sites
Enhancers can
Alter chromatin or influence the recruitment of RNA poly 2 complex
Enhancers are DNA elelments that are linked to
Increasing rate of transcription initation from a linked promoter
Co-activator example
CBP/p300
HAT
Co-activator
Interact with transcription factors (do NOT bind DNA)
Co-activators may act as
Bridge between DNA binding proteins and Pol 2 transcription initiation complex
Co-repressor example
HDAC
Co-repressors
May block bridges between DNA binding proteins and Pol 2 transcription initiation complex
Transcription facotrs can
Influence assempy of RNA polymerase 2 and associated factors on a promoter
Influence rate of transcription initiation
Interact with cis-acting site that are large distance away from promoters
Combinatorial model of gene regulation
Interaction of multiple trans-acting transcription factors with multiple cis-acting binding sites will ultimately determine specificity, timing, and level of gene expression
One TF can control
Multiple target genes
Nuclear receptor superfamily of TFs conserved doamin
DNA-binding domain
Generalized domain structure of nuclear receptors
Transactivation
DNA binding (Zn)
Ligand binding
Orphan receptors
Nuclear receptors for which a ligand has not been ID’d
Type 1 NR
In absence of ligand, in cytosol as a monomer with chaperone proteins…In presence of hormone, NR dissociates from chaperone, dimerizes, enters nucleus, binds to cis-acting sites of target genes and recruits co-activators and RNA polymerase to activate transcription
Type 1 NR cis-binding
HRE - Hormone response element
Type 2 NR
In absence of ligand, heterodimer bound to HRE and associated with co-repressors that repress…in presence of ligand, co-receptors dissociates, co-activators bind NR and recruits RNA polymerase to increase transcription
Stays associated the whole time
What do type 1 and 2 NR have in common?
Both do not require protein synthesis and are fialry rapid response
HNF-4alpha
Hepatocyte nuclear factor 4alpha
Orphan receptor controls expression in liver, pancreas, and kidney
Nuclear factor kB complexes
IKK - IKKgamma/NEMO, IKKalpha, IKKbeta
NFKB - p50:relA heterodimer (others exist)
IkB
Nuclear factor kB pathway
Stimulus activates IKK complex
IKK complex phosphorylates IkB
Phosphorylated IkB is polyubiquitnated
Polyubiquitanted IkB is degraded by 26s protesosome
NFkB translocates to nucleus and binds cis acting site
RNA pol 2 and associated factors recruited to promoter and transcribe gene
Binding site of NFkB on DNA
NFkB RE
NF-kB effect
Pro-survival
No proetin syntesis required
Regulation of NF-kB
targets IkB…this provides feedback mechanism that can inhibit the NFkB complex
