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Housekeeping proteins
•common to all cells (RNA polymerases, ribosomal proteins, metabolic proteins, repair proteins, cytoskeletal proteins)
Points at which gene expression is regulated
1.When a given gene is transcribed and how often 2.How RNA transcript is spliced or processed 3.Selecting which mRNAs are exported into the cytosol 4.Selectively degrade certain mRNA molecules 5.Selecting which mRNAs are translated by ribosomes 6.Selectively activating or inactivatin…
Order of events leading to Eukaryotic transcription
•Chromatin remodeling, activator proteins, general transcription factors and RNA polymerase II work together to turn gene expression on and off
The promoter
•is the DNA sequence (surrounding the TATA box) where the general transcription factors and RNA polymerase II assemble
The regulatory sequences
•(elements) serve as binding sites for gene regulatory proteins whose presence on the DNA affect the rate of transcription initiation
Regulatory sequences can be located
•adjacent to the promoter, far upstream of it, or even within introns or downstream of the gene
Transcriptional regulators (Transcription Factors
•proteins which recognize regulatory DNA sequences - Bind to DNA and effect the rate of transcription (either stop or speed up!) •Allow “fine tuning” gene expression •Bacteria have several 100, human several 1,000!! •Regulators bind VERY specifically into a defined shape via h-bo…
Regulator DNA sequences
•areas on the DNA recognized by regulatory factors
Activator
•a protein that binds to a specific regulatory region of DNA to activates (turn on!) transcription of an adjacent gene
Repressor
•a protein that binds to a specific regulatory region of DNA to repress (turn off!) transcription of an adjacent gene
Repressors and Activators
•Can work upstream or downstream from the promoter •Can work from thousands of nucleotides away from promoter –How does this work?
On-off switch of transcription is
dynamic and involves activators, repressors and chromatin remodeling
TURNING GENES ON!
-Chromatin must be opened -Activators must bind -General transcription factors must bind
Activators
Activators can be “constitutive” or activated by second messengers (see chapter 16 for example of second messengers) The activity of activators can be altered by phosphorylation (turned on or off)
Activator protein binding....
triggers formation of the pre-initiation complex
In eukaryotes, gene activation occurs at...
a distance -activator proteins can enhance transcription even when they are 1,000s of base pairs away! -activator proteins can be bound upstream or downstream from the gene! -mediator: between activator and transcription complex
Many activators need to...
bind to the promoter
Tissue-specific activators or transcription factors
•interact with more ubiquitous activators expressed in every cell
Hydrophobic hormones can...
regulate transcription directly
TURNING GENES OFF!
-Chromatin must be tight/condensed -repressors prohibit GTFs binding
Repressors block
binding of RNA polymerase
Some repressors are
“constitutive” or “always active”
The activity of repressors
can be altered by phosphorylation (turned on or off)
Gene expression can be controlled....
in response to the cells metabolic needs!
in response to the cells metabolic needs!
attach acetyl group to lysines “opens DNA”
Histone Deacetylases (HDACs)
remove acetyl group from lysines decrease accessibility “closed DNA
A single transcription regulator is able to...
•switch whole groups of genes on or off, •As long as different genes contain the DNA sequence for the transcription factor –Both activators and repressors
Combinatorial Control
•Typical gene controlled by dozens of transcription regulators –Both repressors and activators –Help determine the final level of expression for a gene
Combinatorial control
•groups of regulatory proteins work together to determine the final rate of transcription initiation
Combinatorial control can
create different cell types
how does a cell remember which genes it needs to turn on and when?
1.Positive feedback loop –Key transcriptional regulator activates transcription of own gene 2.Propagation of condensed chromatin structure from parent to daughter cell (epigenetics are heritable!) 3. DNA methylation patterns (also heritable)
Positive feedback loop
–Key transcriptional regulator activates transcription of own gene
Maintenance methyltransferase
guarantees that once has pattern of methylation has been established, it is inherited by progeny DNA
Formation of an entire organ
can be triggered by a single transcription factor
Post-transcriptional controls
Alternative splicing UTR regions – shape of UTR effects binding of activators/repressors Small regulatory RNAs – cause degradation of mRNA Protein degradation – the proteosome
DICER
•nuclease that cleaves the double-stranded RNA into shorter fragments
RNA interference (RNAi)
•Degrade foreign RNA molecules – double-stranded RNA •Attract DICER - nuclease that cleaves the double-stranded RNA into shorter fragments –Small interfering RNAs – siRNAs •Incorporated into RISCs (RNA-induced silencing complex) - discards one strand of siRNA and uses remaining to loc…
Proteolysis
process where enzymes break proteins down into their constituent amino acids
Enzymes = Protease
hydrolyze the peptide bonds between amino acids 1.Rapidly degrade proteins with short lifetimes 2.Eliminate misfolded or damaged proteins
Stoppers
bind the proteins to be digested
Proteasomes
- location where most proteins are broken down
Proteins are marked for degradation by
covalent addition of ubiquitin
Protein production requires many
steps; each step can be controlled to maintain perfect function

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