AP Biology 2007-2008

Chapter 19:Control of

Eukaryotic Genes

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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? Differential gene expressions

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How do you fit all that DNA into nucleus?

DNA coiling & folding double helix nucleosomes chromatin fiber looped

domains chromosome

from DNA double helix to condensed chromosome

1. DNA packing

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Nucleosomes “Beads on a string”

1st level of DNA packing histone proteins

8 protein molecules positively charged amino acids bind tightly to negatively charged DNA

DNA packing movie

8 histone molecules

https://www.youtube.com/watch?v=gbSIBhFwQ4s&list=PLAD3DE96CA98E831E&index=3

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DNA packing as gene control Degree of packing of DNA regulates transcription

tightly wrapped around histones no transcription genes turned off Heterochromatin (Interphase)

darker DNA (H) = tightly packed euchromatin

lighter DNA (E) = loosely packed

H E

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Points of control The control of gene

expression can occur at any step in the pathway from gene to functional protein1. packing/unpacking DNA

2. Transcription (most common)

3. mRNA processing

4. mRNA transport

5. translation

6. protein processing

7. protein degradation

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Histone Modification Chemical modification of histone tails

Can affect the configuration of chromatin and thus gene expression

Figure 19.4a (a) Histone tails protrude outward from a nucleosome

Chromatin changes

Transcription

RNA processing

mRNA degradation

Translation

Protein processingand degradation

DNAdouble helix

Amino acids (N-terminus)available

for chemicalmodification

Histonetails

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Histone acetylation Acetylation of histones unwinds DNA

loosely wrapped around histones enables transcription genes turned on

attachment of acetyl groups (–COCH3) to postive charged lysines

Neutralized (+) charged tails no longer bind to neighboring nucleosomes

transcription factors have easier access to genes

(b) Acetylation of histone tails promotes loose chromatin structure that permits transcription

Unacetylated histones Acetylated histones

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DNA methylation Methylation of DNA blocks transcription factors

no transcription genes turned off attachment of methyl groups (–CH3) to cytosine

C = cytosine nearly permanent inactivation of genes

ex. inactivated mammalian X chromosome = Barr body Ex. Epigenetic inheritance

Inheritance of traits by mechanisms not involving the nucleotide sequence

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Regulation of Transcription Initiation

Chromatin-modifying enzymes provide initial control of gene expression By making a region of DNA either more or

less able to bind the transcription machinery

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2. Transcription initiation Noncoding control regions on DNA

promoter nearby control sequence on DNA binding of RNA polymerase & transcription factors

proximal control elements UTR located close to the promoter

enhancer distant control

sequences on DNA binding of activator

proteins “enhanced” rate (high level)

of transcription

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Organization of a Typical Eukaryotic Gene

Figure 19.5

Enhancer(distal control elements)

Proximalcontrol elements

DNA

UpstreamPromoter

Exon Intron Exon Intron

Poly-A signalsequence

Exon

Terminationregion

Transcription

Downstream

Poly-Asignal

ExonIntronExonIntronExonPrimary RNA

transcript(pre-mRNA)

5

Intron RNA

RNA processing:Cap and tail added;introns excised and

exons spliced together

Coding segment

P P PGmRNA

5 Cap5 UTR

(untranslatedregion)

Startcodon

Stopcodon

3 UTR(untranslated

region)

Poly-Atail

Chromatin changes

Transcription

RNA processing

mRNAdegradation

Translation

Protein processingand degradation

Cleared 3 endof primarytransport

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Model for Enhancer action

Enhancer DNA sequences distant control sequences

Activator proteins bind to enhancer sequence &

stimulates transcription Silencer (repressor) proteins

bind to enhancer sequence & block gene transcription

Turning on Gene movie

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Transcription complex

Enhancer

ActivatorActivator

Activator

Coactivator

RNA polymerase II

A

B F E

HTFIID

Core promoterand initiation complex

Activator Proteins• regulatory proteins bind to DNA at

distant enhancer sites• increase the rate of transcription

Coding region

T A T A

Enhancer Sitesregulatory sites on DNA distant from gene

Initiation Complex at Promoter Site binding site of RNA polymerase

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Combinatorial Control of Gene Activation

A particular combination of control elements Will be able to activate transcription

only when the appropriate activator proteins are present

Enhancer Promoter

Controlelements

Albumingene

Crystallingene

Liver cellnucleus

Lens cellnucleus

Availableactivators

Availableactivators

Albumingene

expressed

Albumingene not

expressed

Crystallin genenot expressed

Crystallin geneexpressed

(a) (b)Liver cell Lens cell

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Coordinately Controlled Genes

Unlike the genes of a prokaryotic operon Coordinately controlled eukaryotic genes

each have a promoter and control elements The same regulatory sequences

Are common to all the genes of a group, enabling recognition by the same specific transcription factors

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3. Post-transcriptional control Alternative RNA splicing

Different mRNA molecules produced from the same primary transcript

Depends on which RNA segments are treated as introns and exons

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4. Regulation of mRNA degradation Life span of mRNA determines amount of protein synthesis

mRNA can last from hours to weeks Ex. Long lived hemoglobin & short lived growth factor Determined by sequences towards the 3’ end UTR

Enzymatic shortening of poly A tail removal of 5’ cap nuclease degrades mRNA

RNA processing movie

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RNA interference Small interfering RNAs (siRNA)

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” post-transcriptional control turns off gene = no protein produced

siRNA

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RNA interference by single-stranded microRNAs (miRNAs)

Can lead to degradation of an mRNA or block its translation

Figure 19.9

5

Chromatin changes

Transcription

RNA processing

mRNAdegradation

Translation

Protein processingand degradation

Degradation of mRNAOR

Blockage of translation

Target mRNA

miRNA

Proteincomplex

Dicer

Hydrogenbond

The micro-RNA (miRNA)precursor foldsback on itself,held togetherby hydrogen

bonds.

12 An enzymecalled Dicer movesalong the double-stranded RNA,

cutting it intoshorter segments.

2 One strand ofeach short double-stranded RNA is

degraded; the otherstrand (miRNA) then

associates with acomplex of proteins.

3 The boundmiRNA can base-pair

with any targetmRNA that containsthe complementary

sequence.

4 The miRNA-proteincomplex prevents gene

expression either bydegrading the targetmRNA or by blocking

its translation.

5

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RNA interference1990s | 2006

Andrew FireStanford

Craig MelloU Mass

“for their discovery of RNA interference —gene silencing by

double-stranded RNA”

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5. Control of translation Block initiation of translation stage

regulatory proteins attach to 5' end of UTR of mRNA

prevent attachment of ribosomal subunits & initiator tRNA

block translation of mRNA to protein

Control of translation movie

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6-7. Protein processing & degradation Protein processing

folding, cleaving, adding sugar groups, targeting for transport

Protein degradation ubiquitin tagging proteasome degradation

Protein processing movie

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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 CiechanoverIsrael

Avram HershkoIsrael

Irwin RoseUC Riverside

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Proteasome Protein-degrading “machine”

cell’s waste disposer breaks down any proteins

into 7-9 amino acid fragments cellular recycling

play Nobel animation

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Cancer results from genetic changes

Growth factors can create cancers proto-oncogenes

normally activates cell division growth factor genes become oncogenes (cancer-causing) when mutated

if switched “ON” can cause cancer example: RAS (activates cyclins) 30% cancers

tumor-suppressor genes normally inhibits cell division if switched “OFF” can cause cancer example: p53 - more than 50% cancers

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Cancer & Cell Growth Cancer is essentially a failure

of cell division control unrestrained, uncontrolled cell growth

What control is lost? lose checkpoint stops gene p53 plays a key role in G1/S restriction point

p53 protein halts cell division if it detects damaged DNA options:

stimulates repair enzymes to fix DNA forces cell into G0 resting stage causes apoptosis of damaged cell

p53 discovered at Stony Brook by Dr. Arnold Levine

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DNA damage is causedby heat, radiation, or chemicals.

p53 allows cellswith repairedDNA to divide.

Step 1

DNA damage iscaused by heat,radiation, or chemicals.

Step 1 Step 2

Damaged cells continue to divide.If other damage accumulates, thecell can turn cancerous.

Step 3p53 triggers the destruction of cells damaged beyond repair.

ABNORMAL p53

NORMAL p53

abnormalp53 protein

cancercell

Step 3The p53 protein fails to stopcell division and repair DNA.Cell divides without repair todamaged DNA.

Cell division stops, and p53 triggers enzymes to repair damaged region.

Step 2

DNA repair enzymep53

proteinp53

protein

p53 — master regulator gene

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How Transposable Elements Contribute to Genome Evolution

Movement of transposable elements or recombination between copies of the same element Occasionally generates new sequence

combinations that are beneficial to the organism

“copy and paste” mechanism Typically noncoding sequences make up these

transposable elements

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Repetitive DNA probably arose by mistakes in DNA replication or recombination

The basis of change at the genomic level is mutation Accidents in cell division

Can lead to extra copies of all or part of a genome, which may then diverge if one set accumulates sequence changes

Ex: errors in meiosis can result in extra sets of chromosomes Ex: duplications of genes on one chromosome

Duplication and Divergence of DNA Segments

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Duplication and Divergence of DNA Segments Unequal crossing over during

prophase I of meiosis Can result in one chromosome with

a deletion and another with a duplication of a particular gene

Nonsisterchromatids

Transposableelement

Gene

Incorrect pairingof two homologues

during meiosis

Crossover

and

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Evolution of Genes with Related Functions: The Human Globin Genes

The genes encoding the various globin proteins Evolved from one common ancestral globin gene,

which duplicated and diverged

Ancestral globin gene

2 1

2 1 G A

-Globin gene familyon chromosome 16

-Globin gene familyon chromosome 11

Evo

lutio

nary

tim

e

Duplication ofancestral geneMutation inboth copies

Transposition todifferent chromosomes

Further duplicationsand mutations

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Evolution of Genes with Novel Functions•The copies of some duplicated genes

▫Have diverged so much during evolutionary time that the functions of their encoded proteins are now substantially different

▫Ex: similar amino acid sequence in lactalbumin and lysozyme enzyme

▫Lysozyme – enzyme that helps prevent infection

▫Lactalbumin – protein in milk production in mammals

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In exon shuffling Errors in meiotic recombination lead to the

occasional mixing and matching of different exons either within a gene or between two nonallelic genes

Figure 19.20

EGF EGF EGF EGF

Epidermal growthfactor gene with multiple

EGF exons (green)

F F F F

Fibronectin gene with multiple“finger” exons (orange)

Exonshuffling

Exonduplication

Exonshuffling

K

F EGF K K

Plasminogen gene with a“kfingle” exon (blue)

Portions of ancestral genes TPA gene as it exists today