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Chapter 19: Eukaryotic Genomes: Organization, Regulation & Evolution

Chapter 19: Eukaryotic Genomes: Organization, Regulation & Evolution1. How is chromatin structured on a chromosome?

2 nm

10 nm

DNA double helix

Histonetails

His-tones

Linker DNA(“string”)

Nucleosome(“bead”)

Histone H1

(a) Nucleosomes (10-nm fiber)

Nucleosome

Protein scaffold

30 nm

300 nm

700 nm

1,400 nm

(b) 30-nm fiber

(c) Looped domains (300-nm fiber)

(d) Metaphase chromosome

Loops

Scaffold

Chapter 19: Eukaryotic Genomes: Organization, Regulation & Evolution1. How is chromatin structured on a chromosome?2. How is gene expression regulated?

- DNA level – Chromatin changes- DNA demethylation

- Histone acetylation

Signal

NUCLEUS

Chromatin

Chromatin modification:DNA unpacking involvinghistone acetylation and

DNA demethlation

Gene

DNAGene availablefor transcription

RNA Exon

Transcription

Primary transcript

RNA processing

Transport to cytoplasm

Intron

Cap mRNA in nucleus

Tail

CYTOPLASM

mRNA in cytoplasm

Degradationof mRNA

Translation

Polypetide

CleavageChemical modificationTransport to cellular

destination

Active protein

Degradation of protein

Degraded protein


- DNA level – Chromatin changes- DNA demethylation

- 5% of Cytosines have –CH3

- Demethylase removes –CH3

- Histone acetylation

Chromatin changes

Transcription

RNA processing

mRNA degradation

Translation

Protein processingand degradation

Histonetails

DNAdouble helix Amino acids

availablefor chemicalmodification

(a) Histone tails protrude outward from a nucleosome

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

Unacetylated histones Acetylated histones



- DNA level – Chromatin changes- DNA demethylation- Histone acetylation

- RNA level- Activation of transcription

Signal

NUCLEUS

Chromatin


DNA demethlation

Gene


RNA Exon

Transcription

Primary transcript

RNA processing


Intron

Cap mRNA in nucleus

Tail

CYTOPLASM

mRNA in cytoplasm

Degradationof mRNA

Translation

Polypetide


destination

Active protein


Degraded protein

Enhancer(distal control elements)

Proximalcontrol elements

DNA

UpstreamPromoter

Exon Intron Exon Intron

Poly-A signalsequence

Exon

Terminationregion

Transcription

Downstream

Poly-Asignal

ExonIntronExonIntronExonPrimary RNAtranscript(pre-mRNA)

5

Intron RNA

RNA processing:Cap and tail added;introns excised andexons spliced together

Coding segment

P P PGmRNA

5 Cap 5 UTR(untranslated

region)

Startcodon

Stopcodon

3 UTR(untranslatedregion)

Poly-Atail

Chromatin changes

Transcription

RNA processing

mRNAdegradation

Translation


Cleared 3 endof primarytransport

Figure 19.5 A eukaryotic gene and its transcript

-Proximal and distal control elements farther upstream from promoter-Enhancers (activators) or silencers may bind here

Distal controlelement

Activators

Enhancer

PromoterGene

TATAbox

Generaltranscriptionfactors

DNA-bendingprotein

Group ofMediator proteins

RNAPolymerase II

RNAPolymerase II

RNA synthesisTranscriptionInitiation complex

Chromatin changes

Transcription

RNA processing

mRNAdegradation

Translation


A DNA-bending proteinbrings the bound activators

closer to the promoter.Other transcription factors,

mediator proteins, and RNApolymerase are nearby.

2

Activator proteins bindto distal control elementsgrouped as an enhancer in the DNA. This enhancer hasthree binding sites.

1

The activators bind tocertain general transcription

factors and mediatorproteins, helping them form

an active transcriptioninitiation complex on the promoter.

3

Figure 19.6 A model for the action of enhancers and transcription activators

Why is this relevant??Who cares??

All somatic cells have the same DNA so…

Enhancer Promoter

Controlelements

Albumingene

Crystallingene

Liver cellnucleus

Lens cellnucleus

Availableactivators

Availableactivators

Albumingeneexpressed

Albumingene notexpressed

Crystallin genenot expressed

Crystallin geneexpressed

Liver cell Lens cell(a) (b)

How is cell-specific transcription controlled?

-cell-specific activators

-Non-active genes are heavily methylated

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- DNA level- DNA demethylation- Histone acetylation

- RNA level- Activation of transcription- RNA processing

- 5’ cap & 3’ poly-A tail- Alternative splicing- 75% of human genes

- mRNA transport to cytoplasm- mRNA degradation

Chromatin changes

Transcription

RNA processing

mRNAdegradation

Translation


Exons

DNA

PrimaryRNAtranscript

mRNA

RNA splicing or

Chromatin changes

Transcription

RNA processing

mRNAdegradation

Translation


Degradation of mRNAOR

Blockage of translation

Target mRNA

miRNA

Proteincomplex

Dicer

Hydrogenbond

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

1 An enzymecalled Dicer movesalong the double-stranded RNA, cutting it intoshorter segments.

2 One strand ofeach short double-stranded RNA isdegraded; the otherstrand (miRNA) thenassociates with acomplex of proteins.

3 The boundmiRNA can base-pairwith any targetmRNA that containsthe complementarysequence.

4 The miRNA-proteincomplex prevents geneexpression either bydegrading the targetmRNA or by blockingits translation.

5

Figure 19.9 Regulation of gene expression by microRNAs (miRNAs)


- DNA level- DNA demethylation- Histone acetylation

- RNA level- Activation of transcription- RNA processing- mRNA transport to cytoplasm- mRNA degradation

- Protein level- Translation - Cleavage

- signal peptide - Inactive “-ogen” proteins

- Chemical modification – Carbs, lipids- Transport to organelles- Protein degradation

Signal

NUCLEUS

Chromatin


DNA demethlation

Gene


RNA Exon

Transcription

Primary transcript

RNA processing


Intron

Cap mRNA in nucleus

Tail

CYTOPLASM

mRNA in cytoplasm

Degradationof mRNA

Translation

Polypetide


destination

Active protein


Degraded protein

Chromatin changes

Transcription

RNA processing

mRNAdegradation

Translation


Ubiquitin

Protein tobe degraded

Ubiquinatedprotein

Proteasome

Proteasomeand ubiquitinto be recycled

Proteinfragments(peptides)

Multiple ubiquitin mol-ecules are attached to a proteinby enzymes in the cytosol.

1 The ubiquitin-tagged proteinis recognized by a proteasome,which unfolds the protein andsequesters it within a central cavity.

2 Enzymatic components of theproteasome cut the protein intosmall peptides, which can befurther degraded by otherenzymes in the cytosol.

2

Protein entering aproteasome

Figure 19.10 Degradation of a protein by a proteasome

Chapter 19: Eukaryotic Genomes: Organization, Regulation & Evolution1. How is chromatin structured on a chromosome?2. How is gene expression regulated?3. How can proto-oncogenes become oncogenes?

Proto-oncogene

DNA

Translocation or transposition:gene moved to new locus,under new controls

Gene amplification:multiple copies of the gene

Point mutationwithin a controlelement

Point mutationwithin the gene

OncogeneOncogene

Normal growth-stimulatingprotein in excess

Hyperactive ordegradation-resistant protein



Newpromoter

Chapter 19: Eukaryotic Genomes: Organization, Regulation & Evolution1. How is chromatin structured on a chromosome?2. How is gene expression regulated?3. How can proto-oncogenes become oncogenes?4. How can disruptions of cell growth pathways lead to cancer?

1 Growthfactor MUTATION

2 Receptor

ppp p

pp

GTP

Ras

3 G protein

Ras

GTP

HyperactiveRas protein(product ofoncogene)issues signalson its own

4 Protein kinases(phosphorylationcascade)

5 Transcriptionfactor (activator)

NUCLEUS

DNA

Gene expression

Protein thatstimulatesthe cell cycle

2 Protein kinases

UVlight

DNA damagein genome

1

DNA

3 Activeformof p53

Defective ormissingtranscriptionfactor, such asp53, cannotactivatetranscription

MUTATION

Protein thatinhibitsthe cell cycle

EFFECTS OF MUTATIONS

Proteinoverexpressed

Cell cycleoverstimulated

Increased celldivision

Cell cycle notinhibited

Protein absent

(a) Cell cycle–stimulating pathway.This pathway is triggered by a growthfactor that binds to its receptor in theplasma membrane. The signal is relayed to a G protein called Ras. Like all G proteins, Rasis active when GTP is bound to it. Ras passesthe signal to a series of protein kinases.The last kinase activates a transcriptionactivator that turns on one or more genes for proteins that stimulate the cell cycle. If amutation makes Ras or any other pathway component abnormally active, excessive celldivision and cancer may result.

12

4

3

5

(b) Cell cycle–inhibiting pathway. In this

2pathway, DNA damage is an intracellularsignal that is passed via protein kinasesand leads to activation of p53. Activatedp53 promotes transcription of the gene for aprotein that inhibits the cell cycle. Theresulting suppression of cell division ensuresthat the damaged DNA is not replicated.Mutations causing deficiencies in anypathway component can contribute to thedevelopment of cancer.

1

3

(c) Effects of mutations. Increased cell division,possibly leading to cancer, can result if thecell cycle is overstimulated, as in (a), or notinhibited when it normally would be, as in (b).

Figure 19.12 Signaling pathways that regulate cell division

Chapter 19: Eukaryotic Genomes: Organization, Regulation & Evolution1. How is chromatin structured on a chromosome?2. How is gene expression regulated?3. How can proto-oncogenes become oncogenes?4. How can disruptions of cell growth pathways lead to cancer?5. What are the differences between prokaryotic & eukaryotic DNA?

Prokaryotic EukaryoticNo introns Introns More mutations Few mutations (proofreading)Circular chromosome Several linear chromosomesNot in a nucleus In a nucleusCoupled transcription Separate transcription

& translation & translationMostly coding Mostly “filler”

Exons (regions of genes codingfor protein, rRNA, tRNA) (1.5%)

RepetitiveDNA thatincludestransposableelementsand relatedsequences(44%)

Introns andregulatorysequences(24%)

UniquenoncodingDNA (15%)

RepetitiveDNAunrelated totransposableelements(about 15%)

Alu elements(10%)

Simple sequenceDNA (3%)

Large-segmentduplications (5–6%)

Figure 19.14 Types of DNA sequences in the human genome

- Tandomly repetitive DNA (satellite DNA) – 15% - …GTTACGTTACGTTACGTTACGTTAC…- Found in telomeres & centromeres

- Interspersed repetitive DNA – 44%- repeats scattered throughout the genome

Chapter 19: Eukaryotic Genomes: Organization, Regulation & Evolution1. How is chromatin structured on a chromosome?2. How is gene expression regulated?3. How can proto-oncogenes become oncogenes?4. How can disruptions of cell growth pathways lead to cancer?5. What are the differences between prokaryotic & eukaryotic DNA?6. How do eukaryotic transposable elements become repetitive?

TransposonNew copy oftransposon

Transposonis copied

DNA of genome

Insertion

Mobile transposon

(a) Transposon movement (“copy-and-paste” mechanism)

RetrotransposonNew copy of

retrotransposon

DNA of genome

RNA

Reversetranscriptase

(b) Retrotransposon movement

Insertion

Figure 19.16 Movement of eukaryotic transposable elements

Figure 19.15 The effect of transposable elements on corn kernel color


1. How is chromatin structured on a chromosome?2. How is gene expression regulated?3. How can proto-oncogenes become oncogenes?4. How can disruptions of cell growth pathways lead to cancer?5. What are the differences between prokaryotic & eukaryotic DNA?6. How do eukaryotic transposable elements become repetitive?7. What are gene families?

- Collection of identical or very similar genes that are clustered or dispersed throughout the genome

DNA RNA transcripts

Non-transcribedspacer Transcription unit

DNA18S 5.8S 28S

rRNA5.8S

(a) Part of the ribosomal RNA gene family

28S

18S

Heme

Hemoglobin

-Globin

-Globin

-Globin gene family -Globin gene family

Chromosome 16 Chromosome 11

21

2 1 G A

EmbryoFetus

and adult Embryo Fetus Adult

(b) The human -globin and -globin gene families

Figure 19.17 Gene families

Eukaryotic version of an operon.- controlled by 1 promoter

Chapter 19: Eukaryotic Genomes: Organization, Regulation & Evolution1. How is chromatin structured on a chromosome?2. How is gene expression regulated?3. How can proto-oncogenes become oncogenes?4. How can disruptions of cell growth pathways lead to cancer?5. What are the differences between prokaryotic & eukaryotic DNA?6. How do eukaryotic transposable elements become repetitive?7. What are gene families?8. How do genes get duplicated or deleted?

Figure 19.18 Gene duplication due to unequal crossing over

Nonsisterchromatids

Transposableelement

Gene

Incorrect pairingof two homologuesduring meiosis

Crossover

and

Chapter 19: Eukaryotic Genomes: Organization, Regulation & Evolution1. How is chromatin structured on a chromosome?2. How is gene expression regulated?3. How can proto-oncogenes become oncogenes?4. How can disruptions of cell growth pathways lead to cancer?5. What are the differences between prokaryotic & eukaryotic DNA?6. How do eukaryotic transposable elements become repetitive?7. What are gene families?8. How do genes get duplicated or deleted?9. How did the globin gene family evolve?

Ancestral globin gene

21

2 1 G A

-Globin gene familyon chromosome 16

-Globin gene familyon chromosome 11

Evo

lutio

nary

tim

e

Duplication ofancestral gene

Mutation inboth copies

Transposition todifferent chromosomes

Further duplicationsand mutations

Figure 19.19 Evolution of the human -globin and -globin gene families

Chapter 19: Eukaryotic Genomes: Organization, Regulation & Evolution1. How is chromatin structured on a chromosome?2. How is gene expression regulated?3. How can proto-oncogenes become oncogenes?4. How can disruptions of cell growth pathways lead to cancer?5. What are the differences between prokaryotic & eukaryotic DNA?6. How do eukaryotic transposable elements become repetitive?7. What are gene families?8. How do genes get duplicated or deleted?9. How did the globin gene family evolve?10. How do new genes evolve?

- Exon shuffling

EGF EGF EGF EGF

Epidermal growthfactor gene with multipleEGF 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“kringle” exon (blue)

Portions of ancestral genes TPA gene as it exists today

Figure 19.20 Evolution of a new gene by exon shuffling

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Students -Get handout - FRQs -Pull out Learning Logs for check -Thursday – Test – Learning logs due -Friday – Test corrections -Cell phones in bins….off