Prokaryotic eukaryoticgenome

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

The Genetics of Viruses and Bacteria

• Viruses called bacteriophages

– Can infect and set in motion a genetic takeover of bacteria, such as Escherichia coli


• Recall that bacteria are prokaryotes

– With cells much smaller and more simply organized than those of eukaryotes

• Viruses

– Are smaller and simpler still

Figure 18.20.25 m

Virus

Animalcell

Bacterium

Animal cell nucleus


• A virus has a genome but can reproduce only within a host cell

• Scientists were able to detect viruses indirectly

– Long before they were actually able to see them

Figure 18.3

For example: Tobacco mosaic disease stunts the growth of tobacco plants and gives their leaves a mosaic coloration


• In the late 1800s

– Researchers hypothesized that a particle smaller than bacteria caused tobacco mosaic disease

• In 1935, Wendell Stanley

– Confirmed this hypothesis when he crystallized the infectious particle, now known as tobacco mosaic virus (TMV)


Structure of Viruses

• Viruses

– Are very small infectious particles consisting of nucleic acid enclosed in a protein coat and, in some cases, a membranous envelope

• Viral genomes may consist of

– Double- or single-stranded DNA

– Double- or single-stranded RNA


Figure 18.4a, b

18 250 mm 70–90 nm (diameter)

20 nm 50 nm(a) Tobacco mosaic virus (b) Adenoviruses

RNADNACapsomere

Glycoprotein

Capsomereof capsid

Capsids and Envelopes

• A capsid

– Is the protein shell that encloses the viral genome

– Can have various structures


• Some viruses have envelopes

– Which are membranous coverings derived from the membrane of the host cell

Figure 18.4c

80–200 nm (diameter)

50 nm(c) Influenza viruses

RNA

Glycoprotein

Membranousenvelope

Capsid


• Bacteriophages, also called phages

– Have the most complex capsids found among viruses

Figure 18.4d

80 225 nm

50 nm(d) Bacteriophage T4

DNA

Head

Tail fiber

Tail sheath


General Features of Viral Reproductive Cycles

• Viruses are obligate intracellular parasites

– They can reproduce only within a host cell

• Each virus has a host range

– A limited number of host cells that it can infect


• Viruses use enzymes, ribosomes, and small molecules of host cells

– To synthesize progeny virusesVIRUS

Capsid proteins

mRNA

Viral DNA

HOST CELL

Viral DNA

DNACapsid

Figure 18.5

Entry into cell anduncoating of DNA

ReplicationTranscription

Self-assembly of new virus particles and their exit from cell


Reproductive Cycles of Phages

• Phages

– Are the best understood of all viruses

– Go through two alternative reproductive mechanisms: the lytic cycle and the lysogenic cycle


The Lytic Cycle

• The lytic cycle

– Is a phage reproductive cycle that culminates in the death of the host

– Produces new phages and digests the host’s cell wall, releasing the progeny viruses


• The lytic cycle of phage T4, a virulent phage

Phage assembly

Head Tails Tail fibersFigure 18.6

Attachment. The T4 phage usesits tail fibers to bind to specificreceptor sites on the outer surface of an E. coli cell.

1Entry of phage DNA and degradation of host DNA.The sheath of the tail contracts,injecting the phage DNA intothe cell and leaving an emptycapsid outside. The cell’sDNA is hydrolyzed.

2

Synthesis of viral genomes and proteins. The phage DNAdirects production of phageproteins and copies of the phagegenome by host enzymes, usingcomponents within the cell.

3Assembly. Three separate sets of proteinsself-assemble to form phage heads, tails,and tail fibers. The phage genome ispackaged inside the capsid as the head forms.

4

Release. The phage directs productionof an enzyme that damages the bacterialcell wall, allowing fluid to enter. The cellswells and finally bursts, releasing 100 to 200 phage particles.

5


The Lysogenic Cycle

• The lysogenic cycle

– Replicates the phage genome without destroying the host

• Temperate phages

– Are capable of using both the lytic and lysogenic cycles of reproduction


• The lytic and lysogenic cycles of phage , a temperate phage

Many cell divisions produce a large population of bacteria infected with the prophage.

The bacterium reproducesnormally, copying the prophageand transmitting it to daughter cells.

Phage DNA integrates into the bacterial chromosome,becoming a prophage.

New phage DNA and proteins are synthesized and assembled into phages.

Occasionally, a prophage exits the bacterial chromosome, initiating a lytic cycle.

Certain factorsdetermine whether

The phage attaches to ahost cell and injects its DNA.

Phage DNAcircularizes

The cell lyses, releasing phages.Lytic cycleis induced

Lysogenic cycleis entered

Lysogenic cycleLytic cycle

or Prophage

Bacterialchromosome

Phage

PhageDNA

Figure 18.7


Viral Envelopes

• Many animal viruses

– Have a membranous envelope

• The broadest variety of RNA genomes

– Is found among the viruses that infect animals

• Viral glycoproteins on the envelope

– Bind to specific receptor molecules on the surface of a host cell Table 18.1


RNA

Capsid

Envelope (withglycoproteins)

HOST CELL

Viral genome (RNA)

Template

Capsidproteins

Glyco-proteins

mRNA

Copy ofgenome (RNA)

ER

Figure 18.8

• The reproductive cycle of an enveloped RNA virus Glycoproteins on the viral envelope bind to specific receptor molecules(not shown) on the host cell, promoting viral entry into the cell.

1

Capsid and viral genomeenter cell2

The viral genome (red)functions as a template forsynthesis of complementary RNA strands (pink) by a viral enzyme.

3

New copies of viralgenome RNA are madeusing complementary RNAstrands as templates.

4

Complementary RNAstrands also function as mRNA,

which is translated into bothcapsid proteins (in the cytosol)and glycoproteins for the viral

envelope (in the ER).

5

Vesicles transportenvelope glycoproteins to

the plasma membrane.

6

A capsid assemblesaround each viral

genome molecule.

7

New virus8


• Retroviruses, such as HIV, use the enzyme reverse transcriptase

– To copy their RNA genome into DNA, which can then be integrated into the host genome as a provirus

Figure 18.9

Reversetranscriptase

Viral envelope

Capsid

Glycoprotein

RNA(two identicalstrands)


• The reproductive cycle of HIV, a retrovirus

Figure 18.10

mRNA

RNA genomefor the nextviral generation

Viral RNA

RNA-DNAhybrid

DNA

ChromosomalDNA

NUCLEUSProvirus

HOST CELL

Reverse transcriptase

New HIV leaving a cell

HIV entering a cell

0.25 µm

HIV Membrane of white blood cell

The virus fuses with thecell’s plasma membrane.The capsid proteins areremoved, releasing the viral proteins and RNA.

1

Reverse transcriptasecatalyzes the synthesis of aDNA strand complementaryto the viral RNA.

2

Reverse transcriptasecatalyzes the synthesis ofa second DNA strandcomplementary to the first.

3

The double-stranded DNA is incorporatedas a provirus into the cell’s DNA.

4

Proviral genes are transcribed into RNA molecules, which serve as genomes for the next viral generation and as mRNAs for translation into viral proteins.

5

The viral proteins include capsid proteins and reverse transcriptase (made in the cytosol) and envelope glycoproteins (made in the ER).

6

Vesicles transport theglycoproteins from the ER tothe cell’s plasma membrane.

7 Capsids areassembled aroundviral genomes and reverse transcriptase molecules.

8

New viruses budoff from the host cell.9


Evolution of Viruses

• Viruses do not really fit our definition of living organisms (no cellular structure)

• Viruses, viroids, and prions are formidable pathogens in animals and plants

• Diseases caused by viral infections

– Affect humans, agricultural crops, and livestock worldwide


Viral Diseases in Animals

• Viruses may damage or kill cells

– By causing the release of hydrolytic enzymes from lysosomes

• Some viruses cause infected cells

– To produce toxins that lead to disease symptoms


• Vaccines

– Are harmless derivatives of pathogenic microbes that stimulate the immune system to mount defenses against the actual pathogen

– Can prevent certain viral illnesses

• Emerging viruses

– Are those that appear suddenly or suddenly come to the attention of medical scientists


• Severe acute respiratory syndrome (SARS)

– Recently appeared in China

(a) Young ballet students in Hong Kong wear face masks to protect themselves from the virus causing SARS.

(b) The SARS-causing agent is a coronavirus like this one (colorized TEM), so named for the “corona” of glycoprotein spikes protruding from the envelope.

Outbreaks of “new” viral diseases in humansAre usually caused by existing viruses that expand their host territory


Viral Diseases in Plants

• More than 2,000 types of viral diseases of plants are known

• Common symptoms of viral infection include

– Spots on leaves and fruits, stunted growth, and damaged flowers or roots

Figure 18.12


• Plant viruses spread disease in two major modes

– Horizontal transmission, entering through damaged cell walls

– Vertical transmission, inheriting the virus from a parent


Viroids and Prions: The Simplest Infectious Agents• Viroids

– Are circular RNA molecules that infect plants and disrupt their growth

• Prions

– Are slow-acting, virtually indestructible infectious proteins that cause brain diseases in mammals

– Propagate by converting normal proteins into the prion version

Figure 18.13

Prion

Normalprotein

Originalprion

Newprion

Many prions


• Rapid reproduction, mutation, and genetic recombination contribute to the genetic diversity of bacteria

• Bacteria allow researchers

– To investigate molecular genetics in the simplest true organisms


The Bacterial Genome and Its Replication

• The bacterial chromosome

– Is usually a circular DNA molecule with few associated proteins

• In addition to the chromosome

– Many bacteria have plasmids, smaller circular DNA molecules that can replicate independently of the bacterial chromosome


• Bacterial cells divide by binary fission

– Which is preceded by replication of the bacterial chromosome

Replicationfork

Origin of replication

Termination of replication

Figure 18.14


Mutation and Genetic Recombination as Sources of Genetic Variation

• Since bacteria can reproduce rapidly

– New mutations can quickly increase a population’s genetic diversity


Mechanisms of Gene Transfer and Genetic Recombination in Bacteria

• Three processes bring bacterial DNA from different individuals together

– Transformation

– Transduction

– Conjugation


Transformation

• Transformation

– Is the alteration of a bacterial cell’s genotype and phenotype by the uptake of naked, foreign DNA from the surrounding environment


Transduction

• In the process known as transduction

– Phages carry bacterial genes from one host cell to another

1

Figure 18.16

Donorcell

Recipientcell

A+ B+

A+

A+ B–

A– B–

A+

Recombinant cell

Crossingover

Phage infects bacterial cell that has alleles A+ and B+

Host DNA (brown) is fragmented, and phage DNA and proteins are made. This is the donor cell.

A bacterial DNA fragment (in this case a fragment withthe A+ allele) may be packaged in a phage capsid.

Phage with the A+ allele from the donor cell infects a recipient A–B– cell, and crossing over (recombination)between donor DNA (brown) and recipient DNA(green) occurs at two places (dotted lines).

The genotype of the resulting recombinant cell (A+B–) differs from the genotypes of both the donor (A+B+) and the recipient (A–B–).

2

3

4

5

Phage DNA

A+ B+


Conjugation and Plasmids

• Conjugation

– Is the direct transfer of genetic material between bacterial cells that are temporarily joined

Figure 18.17 Sex pilus 1 m


The F Plasmid and Conjugation

• Cells containing the F plasmid, designated F+ cells

– Function as DNA donors during conjugation

– Transfer plasmid DNA to an F recipient cell

Figure 18.18a

A cell carrying an F plasmid(an F+ cell) can form amating bridge with an F– celland transfer its F plasmid.

A single strand of the F plasmid breaks at a specific point (tip of blue arrowhead) and begins tomove into the recipient cell. As transfer continues, the donor plasmid rotates(red arrow).

2 DNA replication occurs inboth donor and recipientcells, using the single parental strands of the F plasmid as templates to synthesize complementary strands.

3 The plasmid in the recipient cell circularizes. Transfer and replication result in a compete F plasmid in each cell. Thus, both cells are now F+.

4

F Plasmid Bacterial chromosome

Bacterial chromosome

F+ cell

F+ cell

F+ cell

Mating bridge

1

Conjugation and transfer of an F plasmid from an F+ donor to an F– recipient

(a)

F– cell


• Chromosomal genes can be transferred during conjugation

– When the donor cell’s F factor is integrated into the chromosome

• A cell with the F factor built into its chromosome

– Is called an Hfr cell

• The F factor of an Hfr cell

– Brings some chromosomal DNA along with it when it is transferred to an F– cell


• Conjugation and transfer of part of the bacterial chromosome from an Hfr donor to an F– recipient, resulting in recombination

F+ cell Hfr cell

F factorThe circular F plasmid in an F+ cellcan be integrated into the circularchromosome by a single crossoverevent (dotted line).

1The resulting cell is called an Hfr cell (for High frequency of recombination).

2

Since an Hfr cell has all the F-factor genes, it can form a mating bridge with an F– cell and transfer DNA.

3 A single strand of the F factorbreaks and begins to move through the bridge. DNA replication occurs in both donor and recipient cells, resulting in double-stranded DNA

4 The location and orientation of the F factor in the donor chromosome determine the sequence of gene transfer during conjugation. In this example, the transfer sequence for four genes is A-B-C-D.

5 The mating bridgeusually breaks well before the entire chromosome andthe rest of the F factor are transferred.

6

Two crossovers can result in the exchange of similar (homologous) genes between the transferred chromosome fragment (brown) and the recipient cell’s chromosome (green).

7 The piece of DNA ending up outside thebacterial chromosome will eventually be degraded by the cell’s enzymes. The recipient cell now contains a new combination of genes but no F factor; it is a recombinant F– cell.

8

Temporarypartialdiploid

Recombinant F–

bacterium

A+B+ C+

D+

F– cell A–B–

C–

D–

A–B–

C–

D– D–

A–

C–B–

A+

B+C+D+A+B+

D+C+

A+

A+

B+

A–B–

C–

D–

A–B+

C–

D–

A+

B+ B–

A+

Hfr cell

D–

A–

C–

B–

A+

B+C+D+

A+

B+

Conjugation and transfer of part of the bacterial chromosome from an Hfr donor to an F– recipient, resulting in recombination

(b)

Figure 18.18b


R plasmids and Antibiotic Resistance

• R plasmids

– Confer resistance to various antibiotics

• Transposable elements

– Can move around within a cell’s genome

– Are often called “jumping genes”

– Contribute to genetic shuffling in bacteria


Figure 18.19a

(a) Insertion sequences, the simplest transposable elements in bacteria, contain a single gene that encodes transposase, which catalyzes movement within the genome. The inverted repeats are backward, upside-down versions of each other; only a portion is shown. The inverted repeat sequence varies from one type of insertion sequence to another.

Insertion sequence

Transposase geneInvertedrepeat

Invertedrepeat

3

5

3

5

A T C C G G T…

T A G G C C A …

A C C G G A T…

T G G C C T A …

Insertion Sequences

• An insertion sequence contains a single gene for transposase

– An enzyme that catalyzes movement of the insertion sequence from one site to another within the genome


Transposons

• Bacterial transposons

– Also move about within the bacterial genome

– Have additional genes, such as those for antibiotic resistance

Figure 18.19b

(b) Transposons contain one or more genes in addition to the transposase gene. In the transposon shown here, a gene for resistance to an antibiotic is located between twin insertion sequences. The gene for antibiotic resistance is carried along as part of the transposon when the transposon is inserted at a new site in the genome.

Inverted repeats Transposase gene

Insertion sequence

Insertion sequence

Antibioticresistance gene

Transposon

5

3

5

3


• Individual bacteria respond to environmental change by regulating their gene expression

• E. coli, a type of bacteria that lives in the human colon

– Can tune its metabolism to the changing environment and food sources


• This metabolic control occurs on two levels

– Adjusting the activity of metabolic enzymes already present

– Regulating the genes encoding the metabolic enzymes

Figure 18.20a, b

(a) Regulation of enzyme activity

Enzyme 1

Enzyme 2

Enzyme 3

Enzyme 4

Enzyme 5

Regulationof geneexpression

Feedbackinhibition

Tryptophan

Precursor

(b) Regulation of enzyme production

Gene 2

Gene 1

Gene 3

Gene 4

Gene 5

–

–


Operons: The Basic Concept

• In bacteria, genes are often clustered into operons, composed of

– An operator, an “on-off” switch

– A promoter

– Genes for metabolic enzymes


• An operon

– Is usually turned “on”

– Can be switched off by a protein called a repressor


Video Clip – trp operon

• The trp operon: regulated synthesis of repressible enzymes

Figure 18.21a

(a) Tryptophan absent, repressor inactive, operon on. RNA polymerase attaches to the DNA at the promoter and transcribes the operon’s genes.

Genes of operon

Inactiverepressor

Protein

Operator

Polypeptides that make upenzymes for tryptophan synthesis

Promoter

Regulatorygene

RNA polymerase

Start codon Stop codon

Promoter

trp operon

5

3mRNA 5

trpDtrpE trpC trpB trpAtrpRDNA

mRNA

E D C B A


DNA

mRNA

Protein

Tryptophan(corepressor)

Active repressor

No RNA made

Tryptophan present, repressor active, operon off. As tryptophanaccumulates, it inhibits its own production by activating the repressor protein.

(b)

Figure 18.21b


Repressible and Inducible Operons: Two Types of Negative Gene Regulation

• In a repressible operon

– Binding of a specific repressor protein to the operator shuts off transcription

• In an inducible operon

– Binding of an inducer to an innately inactive repressor inactivates the repressor and turns on transcription


Video Clip – Lac Operon

• The lac operon: regulated synthesis of inducible enzymes

Figure 18.22a

DNA

mRNA

ProteinActiverepressor

RNApolymerase

NoRNAmade

lacZlacl

Regulatorygene

Operator

Promoter

Lactose absent, repressor active, operon off. The lac repressor is innately active, and inthe absence of lactose it switches off the operon by binding to the operator.

(a)

5

3


mRNA 5'

DNA

mRNA

Protein

Allolactose(inducer)

Inactiverepressor

lacl lacz lacY lacA

RNApolymerase

Permease Transacetylase-Galactosidase

5

3

(b) Lactose present, repressor inactive, operon on. Allolactose, an isomer of lactose, derepresses the operon by inactivating the repressor. In this way, the enzymes for lactose utilization are induced.

mRNA 5

lac operon

Figure 18.22b


• Inducible enzymes

– Usually function in catabolic pathways (break down)

• Repressible enzymes

– Usually function in anabolic pathways (build up)


• Regulation of both the trp and lac operons

– Involves the negative control of genes, because the operons are switched off by the active form of the repressor protein

Figure 18.22a

DNA

mRNA

ProteinActiverepressor

RNApolymerase

NoRNAmade

lacZlacl

Regulatorygene Operator

Promoter

Lactose absent, repressor active, operon off. (a)

5

3

DNA

mRNA

Protein

Tryptophan(corepressor)

Active repressor

No RNA made

Tryptophan present, repressor active, operon off

(b)

Figure 18.21b


Positive Gene Regulation

• Some operons are also subject to positive control

– Via a stimulatory activator protein, such as catabolite activator protein (CAP)


Promoter

Lactose present, glucose scarce (cAMP level high): abundant lac mRNA synthesized.If glucose is scarce, the high level of cAMP activates CAP, and the lac operon produces large amounts of mRNA for the lactose pathway.

(a)

CAP-binding site OperatorRNApolymerasecan bindand transcribe

InactiveCAP

ActiveCAPcAMP

DNA

Inactive lacrepressor

lacl lacZ

Figure 18.23a

• In E. coli, when glucose, a preferred food source, is scarce

– The lac operon is activated by the binding of a regulatory protein, catabolite activator protein (CAP)


Video Clip

• When glucose levels in an E. coli cell increase

– CAP detaches from the lac operon, turning it off

Figure 18.23b(b)Lactose present, glucose present (cAMP level low): little lac mRNA synthesized.

When glucose is present, cAMP is scarce, and CAP is unable to stimulate transcription.

Inactive lacrepressor

InactiveCAP

DNA

RNApolymerasecan’t bind

Operator

lacl lacZ

CAP-binding site

Promoter


Eukaryotic Genomes

• In eukaryotes, the DNA-protein complex, called chromatin

– Is ordered into higher structural levels than the DNA-protein complex in prokaryotes

Figure 19.1


• Chromatin structure is based on successive levels of DNA packing

• Eukaryotic DNA

– Is precisely combined with a large amount of protein

• Eukaryotic chromosomes

– Contain an enormous amount of DNA relative to their condensed length


Nucleosomes, or “Beads on a String”

• Proteins called histones

– Are responsible for the first level of DNA packing in chromatin

– Bind tightly to DNA

• The association of DNA and histones

– Seems to remain intact throughout the cell cycle


• In electron micrographs

– Unfolded chromatin has the appearance of beads on a string

• Each “bead” is a nucleosome

– The basic unit of DNA packing

Figure 19.2 a

2 nm

10 nm

DNA double helix

Histonetails

His-tones

Linker DNA(“string”)

Nucleosome(“bad”)

Histone H1

(a) Nucleosomes (10-nm fiber)


Nucleosome

30 nm

(b) 30-nm fiber

Higher Levels of DNA Packing

• The next level of packing

– Forms the 30-nm chromatin fiber

Figure 19.2 b


• The 30-nm fiber, in turn

– Forms looped domains, making up a 300-nm fiber

Figure 19.2 c

Protein scaffold

300 nm

(c) Looped domains (300-nm fiber)

Loops

Scaffold


• In a mitotic chromosome

– The looped domains themselves coil and fold forming the characteristic metaphase chromosome

Figure 19.2 d

700 nm

1,400 nm

(d) Metaphase chromosome


• In interphase cells

– Most chromatin is in the highly extended form called euchromatin


• Gene expression can be regulated at any stage, but the key step is transcription

• All organisms

– Must regulate which genes are expressed at any given time

• During development of a multicellular organism

– Its cells undergo a process of specialization in form and function called cell differentiation


Differential Gene Expression

• Each cell of a multicellular eukaryote

– Expresses only a fraction of its genes

• In each type of differentiated cell

– A unique subset of genes is expressed

Figure 19.3

Signal

NUCLEUSChromatin

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 cytoplasmDegradation

of mRNA

Translation

Polypetide

CleavageChemical modificationTransport to cellular

destination

Active protein

Degradation of protein

Degraded protein


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 acidsavailablefor chemicalmodification

Histonetails


• Histone acetylation

– Seems to loosen chromatin structure and thereby enhance transcription

Figure 19.4 b(b) Acetylation of histone tails promotes loose chromatin structure that permits transcription

Unacetylated histones Acetylated histones


Organization of a Typical Eukaryotic Gene

• Associated with most eukaryotic genes are multiple control elements

– Segments of noncoding DNA that help regulate transcription by binding certain proteins

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 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(untranslated

region)

Poly-Atail

Chromatin changes

Transcription

RNA processing

mRNAdegradation

Translation


Cleared 3 endof primarytransport


Enhancers and Specific Transcription Factors

• Proximal control elements

– Are located close to the promoter

• Distal control elements, groups of which are called enhancers

– May be far away from a gene or even in an intron


Distal controlelement

Activators

Enhancer

PromoterGene

TATAbox General

transcriptionfactors

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

Video Clip

• An activator

– Is a protein that binds to an enhancer and stimulates transcription of a gene

Figure 19.6


• Some specific transcription factors function as repressors

– To inhibit expression of a particular gene

• Some activators and repressors

– Act indirectly by influencing chromatin structure


• Cancer results from genetic changes that affect cell cycle control

• The gene regulation systems that go wrong during cancer

– Turn out to be the very same systems that play important roles in embryonic development


Types of Genes Associated with Cancer

• The genes that normally regulate cell growth and division during the cell cycle

– Include genes for growth factors, their receptors, and the intracellular molecules of signaling pathways


Oncogenes and Proto-Oncogenes

• Oncogenes

– Are cancer-causing genes

• Proto-oncogenes

– Are normal cellular genes that code for proteins that stimulate normal cell growth and division


• A DNA change that makes a proto-oncogene excessively active

– Converts it to an oncogene, which may promote excessive cell division and cancer

Figure 19.11

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


• The p53 gene encodes a tumor-suppressor protein

– That is a specific transcription factor that promotes the synthesis of cell cycle–inhibiting proteins

Figure 19.12b

UVlight

DNA

Defective ormissingtranscriptionfactor, such asp53, cannotactivatetranscription

MUTATION

Protein thatinhibitsthe cell cycle

pathway, 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.

(b) Cell cycle–inhibiting pathway. In this1

3

2

Protein kinases2

3 Activeformof p53

DNA damagein genome

1


• Mutations that knock out the p53 gene

– Can lead to excessive cell growth and cancer

Figure 19.12c

EFFECTS OF MUTATIONS

Proteinoverexpressed

Cell cycleoverstimulated

Increased celldivision

Cell cycle notinhibited

Protein absent

Effects of mutations. Increased cell division, possibly leading to cancer, can result if the cell cycle is overstimulated, as in (a), or not inhibited when it normally would be, as in (b).

(c)


The Multistep Model of Cancer Development

• Normal cells are converted to cancer cells

– By the accumulation of multiple mutations affecting proto-oncogenes and tumor-suppressor genes


• A multistep model for the development of colorectal cancer

Figure 19.13

Colon

Colon wall

Normal colonepithelial cells

Small benigngrowth (polyp)

Larger benigngrowth (adenoma)

Malignant tumor(carcinoma)

2 Activation ofras oncogene

3 Loss oftumor-suppressorgene DCC

4 Loss oftumor-suppressorgene p53

5 Additionalmutations

1 Loss of tumor-suppressorgene APC (orother)


• Certain viruses

– Promote cancer by integration of viral DNA into a cell’s genome

• Individuals who inherit a mutant oncogene or tumor-suppressor allele

– Have an increased risk of developing certain types of cancer


• Eukaryotic genomes can have many noncoding DNA sequences in addition to genes

• The bulk of most eukaryotic genomes

– Consists of noncoding DNA sequences, often described in the past as “junk DNA”

• However, much evidence is accumulating

– That noncoding DNA plays important roles in the cell (Probably is no such thing as ‘junk DNA’)


The Relationship Between Genomic Composition and Organismal Complexity

• Compared with prokaryotic genomes, the genomes of eukaryotes

– Generally are larger

– Have longer genes

– Contain a much greater amount of noncoding DNA both associated with genes and between genes


Transposable Elements and Related Sequences

• The first evidence for wandering DNA segments

– Came from geneticist Barbara McClintock’s breeding experiments with Indian corn

Figure 19.15


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

Movement of Transposons and Retrotransposons

• Eukaryotic transposable elements are of two types

– Transposons, which move within a genome by means of a DNA intermediate

– Retrotransposons, which move by means of an RNA intermediate

Figure 19.16a, b


Sequences Related to Transposable Elements

• Multiple copies of transposable elements and sequences related to them

– Are scattered throughout the eukaryotic genome

• In humans

– A large portion of transposable element–related DNA consists of a family of similar sequences called Alu elements


Other Repetitive DNA, Including Simple Sequence DNA

• Simple sequence DNA

– Contains many copies of tandemly repeated short sequences

– Is common in centromeres and telomeres, where it probably plays structural roles in the chromosome


Genes and Multigene Families

• Most eukaryotic genes

– Are present in one copy per haploid set of chromosomes

• The rest of the genome

– Occurs in multigene families, collections of identical or very similar genes


DNA RNA transcripts

Non-transcribedspacer Transcription unit

DNA18S 5.8S 28S

rRNA

5.8S28S

18S

• Some multigene families

– Consist of identical DNA sequences, usually clustered tandemly, such as those that code for RNA products

Figure 19.17a Part of the ribosomal RNA gene family


• The classic examples of multigene families of nonidentical genes

– Are two related families of genes that encode globins

Figure 19.17b The human -globin and -globin gene families

-GlobinHeme

Hemoglobin

-Globin

-Globin gene family -Globin gene family

Chromosome 16 Chromosome 11

Embryo

Fetusand adult Embryo Fetus Adult

GA

2

1

2 1


• Duplications, rearrangements, and mutations of DNA contribute to genome evolution

• The basis of change at the genomic level is mutation

– Which underlies much of genome evolution

Does the following produce new and novel information?


Duplication of Chromosome Sets

• 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


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

Figure 19.18

Nonsisterchromatids

Transposableelement

Gene

Incorrect pairingof two homologuesduring meiosis

Crossover

and


Rearrangements of Parts of Genes: Exon Duplication and Exon Shuffling

• A particular exon within a gene

– Could be duplicated on one chromosome and deleted from the homologous chromosome


• 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 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“kfingle” exon (blue)

Portions of ancestral genes TPA gene as it exists today


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 (however, no new information was added)

• Some mechanisms

– Can alter the functions of genes or their patterns of expression and regulation

Prokaryotic eukaryoticgenome

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