4. control expresion of gene

7/28/2019 4. Control Expresion of Gene

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LOGO

4. Gene expression control


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Bacterial metabolism

Bacteria need to respond quickly tochanges in their environment

if have enough of a product,

need to stop production why? waste of energy to produce more

how? stop production of synthesis enzymes

if find new food/energy source,

need to utilize it quickly

why? metabolism, growth, reproduction

how? start production of digestive enzymes


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Reminder: Regulation of metabolism

Feedback inhibition product acts

as an allosteric

inhibitor of

1st enzyme in

tryptophan pathway

= inhibition-


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Another way to regulate metabolism

Gene regulation block transcription of

genes for all

enzymes in

tryptophan pathway saves energy by

not wasting it on

unnecessary protein

synthesis

= inhibition-


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Gene regulation in bacteria

Cells vary amount of specific enzymesby regulating gene transcription

turn genes on or turn genes off


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So how can genes be turned off?

First step in protein production? transcription

stop RNA polymerase!

Repressor protein binds to DNA near promoter region blocking

RNA polymerase

binds to operatorsite on DNA blocks transcription


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Jacob & Monod: lac Operon

Francois Jacob & Jacques Monod

first to describe operon system

coined the phrase operon

1961 | 1965

Francois JacobJacques Monod


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Genes grouped together

Operon genes grouped together with related functions

ex. enzymes in a synthesis pathway

promoter = RNA polymerase binding site

single promoter controls transcription of all genes in operon transcribed as 1 unit & a single mRNA is made

operator = DNA binding site of regulator protein


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operatorpromoter

Repressible operon: tryptophan

DNATATA

RNApolymerase

repressor

tryptophan

repressor repressor protein

repressortryptophan repressor protein

complex

Synthesis pathway modelWhen excess tryptophan is present,

binds to tryp repressor protein &

triggers repressor to bind to DNA

blocks (represses) transcription

gene1 gene2 gene3 gene4RNA

polymerase

conformational change inrepressor protein!


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operatorpromoter

Inducible operon: lactose

DNATATARNA

polymerase

repressor repressor protein

repressorlactose repressor protein

complex

lactose

repressor gene1 gene2 gene3 gene4

Digestive pathway modelWhen lactose is present, binds to

lacrepressor protein & triggers

repressor to release DNA

induces transcription

RNApolymerase

conformational change inrepressor protein!


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Operon summary

Repressible operon usually functions in anabolic pathways

synthesizing end products

when end product is present in excess,

cell allocates resources to other uses

Inducible operon

usually functions in catabolic pathways,

digesting nutrients to simpler molecules

produce enzymes only when nutrient is available

cell avoids making proteins that have nothing to do, cell

allocates resources to other uses


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The BIG Questions

How are genes turned on & off in eukaryotes?

How do cells with the same genes differentiate to

perform completely different, specialized

functions?


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Why turn genes on & off?

Specialization each cell of a multicellular eukaryote expresses

only a small fraction of its genes

Development

different genes needed at different points in lifecycle of an organism

afterwards need to be turned off permanently

Responding to organisms needs

homeostasis cells of multicellular organisms must continually

turn certain genes on & off in response to signalsfrom their external & internal environment


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Prokaryote vs.eukaryote genome

Prokaryotes small size of genome

circular molecule ofnaked DNA DNA is readily available to RNA polymerase

control of transcription by regulatory proteins

operon system

most of DNA codes for protein or RNA no introns, small amount of non-coding DNA

regulatory sequences: promoters, operators


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Prokaryote vs. eukaryote genome

Eukaryotes much greater size of genome

how does all that DNA fit into nucleus?

DNA packaged in chromatin fibers

regulates access to DNA by RNA polymerase

cell specialization need to turn on & off large numbers of genes

most of DNA does not code for protein

97% junk DNA in humans


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Points of control

The control of gene expressioncan occur at any step in thepathway from gene to functionalprotein

unpacking DNA transcription

mRNA processing

mRNA transport

out of nucleus through cytoplasm

protection from degradation

translation

protein processing

protein degradation


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DNA packing

How do you fit allthat DNA intonucleus? DNA coiling &

folding double helix

nucleosomes

chromatin fiber

looped domains

chromosome

from DNA double helix to

condensed chromosome


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Unpacking DNA control

Degree of packing of DNA regulates transcription tightly packed = no transcription

= genes turned off

darker DNA (H) = tightly packed

lighter DNA (E) = loosely packed


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Unpacking DNA control : histone acetylation

Acetylation ofhistones unwinds DNA loosely packed = transcription

= genes turned on

attachment of acetyl groups (COCH3) to histones

conformational change in histone proteins

transcription factors have easier access to genes


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Unpacking DNA control : DNA methylation

Methylation ofDNA blocks transcription factors attachment of methyl groups (CH3) to cytosine

C = cytosine

no transcription = genes turned off

nearly permanent inactivation of genes

ex. inactivated mammalian X chromosome


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Transcription control : initiation step

Control regions on DNA promoter

nearby control sequence on DNA

binding of RNA polymerase & transcription factors

base rate of transcription

enhancers distant control

sequences on DNA

binding of activatorproteins

enhanced rate (high level)of transcription


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Model for Enhancer action

Enhancer DNA sequences distant control sequences

Activator proteins bind to enhancer sequence &

stimulates transcription

Silencer proteins bind to enhancer sequence &

block gene transcription


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mRNA processing control

Alternative RNA splicing variable processing of exons creates a family

of proteins

RNA t t t l


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mRNA transport control :

mRNA degradation

Life span of mRNA determines pattern ofprotein synthesis

mRNA can last from hours to weeks

RNA t t t l


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mRNA transport control :

RNA interference

Small RNAs (sRNA) short segments of RNA (21-28 bases)

bind to mRNA

create sections of double-stranded mRNA

death tag for mRNA triggers degradation of mRNA

cause gene silencing even though post-transcriptional control, still turns

off a gene


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RNA interference

Small RNAs

double-stranded RNA

sRNA + mRNA

mRNA

mRNA degraded

functionally turns

gene off


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Translation control

Block initiation stage regulatory proteins attach to

5 end of mRNA

prevent attachment of ribosomal subunits & initiator

tRNA

block translation of mRNA to protein


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Protein processing & degradation control

Protein processing folding, cleaving, adding sugar groups,

targeting for transport

Protein degradation

ubiquitin tagging

proteosome degradation


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Ubiquitin

Death tag mark unwanted proteins with a label

76 amino acid polypeptide, ubiquitin

labeled proteins are broken down rapidly in"waste disposers"

proteasomes

1980s | 2004

Aaron Ciechanover

Israel

Avram Hershko

Israel

Irwin Rose

UC Riverside


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Proteasome

Protein-degrading machine cells waste disposer

can breakdown all proteins

into 7-9 amino acid fragments

4. control expresion of gene

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