viruses – ch. 9 in cliffs, pg. 135. the discovery of viruses tobacco mosaic disease stunts growth...

Viruses – Ch. 9 in Cliffs, pg. 135

The Discovery of Viruses

• Tobacco mosaic disease stunts growth of tobacco plants and gives their leaves a mosaic coloration

• In the late 1800s, researchers hypothesized that a particle smaller than bacteria caused the disease

• In 1935, Wendell Stanley confirmed this hypothesis by crystallizing the infectious particle, now known as tobacco mosaic virus (TMV)

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Structure of Viruses

• Viruses are not cells• A virus is a very small infectious particle

consisting of nucleic acid enclosed in a protein coat and, in some cases, a membranous envelope

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Viral Genomes

• Viral genomes may consist of either– Double- or single-stranded DNA, or

– Double- or single-stranded RNA

• Depending on its type of nucleic acid, a virus is called a DNA virus or an RNA virus

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Capsids and Envelopes

• A capsid is the protein shell that encloses the viral genome

• Capsids are built from protein subunits called capsomeres

• A capsid can have various structures• An envelope can incorporate phospholipids and

proteins from host cell of animals

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Figure 19.3

Capsomereof capsid

RNA CapsomereDNA

Glycoprotein Glycoproteins

Membranousenvelope RNA

CapsidHead

DNA

Tailsheath

Tailfiber

18 250 nm 80 225 nm70–90 nm (diameter) 80–200 nm (diameter)

20 nm 50 nm 50 nm 50 nm(a)Tobacco

mosaic virus(b) Adenoviruses (c) Influenza viruses (d) Bacteriophage T4

• Bacteriophages, also called phages, are viruses that infect bacteria

• They have the most complex capsids found among viruses

• Phages have an elongated capsid head that encloses their DNA

• A protein tail piece attaches the phage to the host and injects the phage DNA inside

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Host cells

• Viruses are intracellular parasites, which means they can replicate only within a host cell

• Each virus has a host range, a limited number of host cells that it can infect

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Replication

• Once a viral genome has entered a cell, the cell begins to make viral proteins

• The virus makes use of host enzymes, ribosomes, tRNAs, amino acids, ATP, and other molecules

• Viral nucleic acid molecules and capsomeres spontaneously self-assemble into new viruses

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Animation: Simplified Viral Reproductive Cycle

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VIRUS

2

1

3

4

Entry anduncoating

Replication

Transcriptionand manufacture ofcapsid proteins

Self-assembly ofnew virus particlesand their exit fromthe cell

DNA

Capsid

HOSTCELL

Viral DNA

ViralDNA

mRNA

Capsidproteins

Figure 19.4

Replication of Phages

• Phages are the best understood of all viruses• Phages have two reproductive mechanisms: the

lytic cycle and the lysogenic cycle

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The Lytic Cycle

• The lytic cycle - lyses• The lytic cycle produces new phages and lyses

(breaks open) the host’s cell wall, releasing the new viruses

• A phage that reproduces only by the lytic cycle is called a virulent phage

• Bacteria have defenses against phages, including restriction enzymes that recognize and cut up certain phage DNA

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© 2011 Pearson Education, Inc.

Animation: Phage T4 Lytic Cycle

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Figure 19.5-5

Attachment

2

1

5

43

Entry of phageDNA anddegradation of host DNA

Release

Synthesis ofviral genomesand proteins

Assembly

Phage assembly

Head Tail Tailfibers

The Lysogenic Cycle

• The lysogenic cycle replicates the phage genome without destroying the host

• The viral DNA molecule is incorporated into the host cell’s chromosome

• This integrated viral DNA is known as a prophage• Every time the host divides, it copies the phage

DNA and passes the copies to daughter cells

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Animation: Phage Lambda Lysogenic and Lytic Cycles

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• An environmental signal can trigger the virus genome to exit the bacterial chromosome and switch to the lytic mode

• Phages that use both the lytic and lysogenic cycles are called temperate phages

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Figure 19.6

New phage DNA and proteinsare synthesized and assembledinto phages.

The cell lyses, releasing phages.

Phage

PhageDNA

The phageinjects its DNA.

Bacterialchromosome

Lytic cycle

lytic cycleis induced

or

Phage DNAcircularizes.

Certain factorsdetermine whether

lysogenic cycleis entered

Lysogenic cycle

Prophage

Daughter cellwith prophage

Occasionally, a prophageexits the bacterial chromosome,initiating a lytic cycle.

Cell divisionsproduce apopulation ofbacteria infectedwith the prophage.

The bacterium reproduces,copying the prophage andtransmitting it to daughtercells.

Phage DNA integrates intothe bacterial chromosome,becoming a prophage.

New phage DNA and proteinsare synthesized and assembledinto phages.

The cell lyses, releasing phages.

Phage

PhageDNA

The phageinjects its DNA.

Bacterialchromosome

Lytic cycle

lytic cycleis induced

or

Phage DNAcircularizes.

Certain factorsdetermine whether

lysogenic cycleis entered

Figure 19.6a

lytic cycleis induced

or

Phage DNAcircularizes.

Certain factorsdetermine whether

lysogenic cycleis entered

Lysogenic cycle

Prophage

Daughter cellwith prophage

Occasionally, a prophageexits the bacterial chromosome,initiating a lytic cycle.

Cell divisionsproduce apopulation ofbacteria infectedwith the prophage.

The bacterium reproduces,copying the prophage andtransmitting it to daughtercells.

Phage DNA integrates intothe bacterial chromosome,becoming a prophage.

Figure 19.6b

Viral Envelopes

• Many viruses that infect animals have a membranous envelope

• Viral glycoproteins on the envelope bind to specific receptor molecules on the surface of a host cell

• Some viral envelopes are formed from the host cell’s plasma membrane as the viral capsids exit

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Figure 19.7

Capsid

RNA

Envelope (withglycoproteins)

Capsid and viral genomeenter the cell

HOST CELL

Viral genome(RNA)Template

mRNA

ERCapsidproteins

Copy ofgenome(RNA)

New virus

Glyco-proteins

DNA or RNA viruses

• DNA serves as a template for mRNA and viral protein production

• RNA viruses serve as a template for mRNA then viral protein production

Retroviruses

ssRNA that use reverse transcriptase (enzyme) to make DNA

That DNA is then transcribed to mRNA using the cell’s machinery.

RNA errors are great – mutation level is highAnimal immune systems often can’t keep up.Two strains of viral genomes can recombine

to form another virus. SIV to HIV

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Animation: HIV Reproductive Cycle

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Evolution of Viruses

• Viruses do not fit our definition of living organisms• Since viruses can replicate only within cells, they

probably evolved as bits of cellular nucleic acid• Candidates for the source of viral genomes are

plasmids, circular DNA in bacteria and yeasts, and transposons, small mobile DNA segments

• Plasmids, transposons, and viruses are all mobile genetic elements

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Prokaryotes (Bacteria)

Archaea and Bacteria are prokaryotesSingle circular DNA with no proteinsReproduce using binary fissionDNA replicates then dividesBacteria contain plasmids which are circular pieces

of DNA outside the chromosomeR plasmids code for antibiotic resistanceMost plasmids replicate outside the bacterial genomeEpisomes – plasmids that become incorporated into

the host cell’s genomeMetabolism controlled by operons

Binary Fission

Plasmids

Transcription in prokaryotes is different – no introns

Transcription and translation are coupled

Gene transfer

Horizontal gene transfer introduces genetic variation

Conjugation – donating DNA through piliTransduction – introduction of new DNA by a

virusTransformation – bacteria absorb DNA from

surroundings (our lab)

Conjugation

Transduction

Transformation

STEM CELLS

• Beginning embryological cells• Will be determined at a “later date”• As genes are turned on or off (due to the work of

repressors, activators, methylation, acetylation) the cell is determined.

• Morphogenesis is the change of an organism’s phenotype throughout its development of

REPRODUCTIVE CLONING

• Making an animal with same DNA as a donor• Unfertilized egg cell is replaced by somatic

nucleus of an udder• Transcription factors in stem cells are not present

in egg cell stage, so fixed determination is un-fixed

DOLLY

Gene Expression

• Gene expression is the act of going from genotype to phenotype

• DNA to mRNA to Protein• Genes are regulated by turning on and off

transcription

The lac operon in E.coli is the method by which E. coli make enzymes that metabolize lactose

Regulatory gene – produces the repressor

Repressor binds to the operator when lactose is absent

No Transcription – RNA polymerase cannot bind to the promoter

Figure 18.8-3

Enhancer(distal control

elements)

DNA

UpstreamPromoter

Proximalcontrol

elementsTranscription

start site

Exon Intron Exon ExonIntron

Poly-Asignal

sequenceTranscriptiontermination

region

DownstreamPoly-Asignal

Exon Intron Exon ExonIntron

Transcription

Cleaved3 end ofprimarytranscript

5Primary RNAtranscript(pre-mRNA)

Intron RNA

RNA processing

mRNA

Coding segment

5 Cap 5 UTRStart

codonStop

codon 3 UTR

3

Poly-Atail

PPPG AAA AAA

When lactose is present, it binds to the repressor pulling it off the operator

RNA polymerase binds the promoter – transcription begins

Lactose-digesting enzymes are made

(a) Lactose absent, repressor active, operon off

(b) Lactose present, repressor inactive, operon on

Regulatorygene

Promoter

Operator

DNA lacZlacI

lacI

DNA

mRNA5

3

NoRNAmade

RNApolymerase

ActiverepressorProtein

lac operon

lacZ lacY lacADNA

mRNA

5

3

Protein

mRNA 5

Inactiverepressor

RNA polymerase

Allolactose(inducer)

-Galactosidase Permease Transacetylase

Another example – positive feedback Activator regulatory protein – CAP is

activated by cAMP When glucose is up, cAMP levels are

down, CAP is inactive When glucose is absent, cAMP is up, CAP

is active and activates the lac operon to produce enzymes that break down lactose

Traditional lac operon is negative regulation

Know table on pg. 138

Figure 18.5 Promoter

DNA

CAP-binding site

lacZlacI

RNApolymerasebinds andtranscribes

Operator

cAMPActiveCAP

InactiveCAP

Allolactose

Inactive lacrepressor

(a) Lactose present, glucose scarce (cAMP level high):abundant lac mRNA synthesized

Promoter

DNA

CAP-binding site

lacZlacI

OperatorRNApolymerase lesslikely to bind

Inactive lacrepressor

InactiveCAP

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

Trp operon. E.coli will make tryptophan from scratch, but if it is in the surroundings, the E.coli will absorb it.

Different from the lac operon

Promoter

DNA

Regulatory gene

mRNA

trpR

5

3

Protein Inactive repressor

RNApolymerase

Promoter

trp operon

Genes of operon

Operator

mRNA 5

Start codon Stop codon

trpE trpD trpC trpB trpA

E D C B A

Polypeptide subunits that make upenzymes for tryptophan synthesis

(a) Tryptophan absent, repressor inactive, operon on

(b) Tryptophan present, repressor active, operon off

DNA

mRNA

Protein

Tryptophan (corepressor)

Activerepressor

No RNAmade

Proximal control elements are located close to the promoter

Distal control elements, groupings of which are called enhancers, may be far away from a gene or even located in an intron

Some transcription factors function as repressors, inhibiting expression of a particular gene by a variety of methods

A particular combination of control elements can activate transcription only when the appropriate activator proteins are present

ActivatorsDNA

EnhancerDistal controlelement

PromoterGene

TATA box

Generaltranscriptionfactors

DNA-bendingprotein

Group of mediator proteins

RNApolymerase II

RNApolymerase II

RNA synthesisTranscriptioninitiation complex

1. Multicellularity2. Chromosome complexity3. Uncoupling of transcription and

translation

Controlelements

Enhancer Promoter

Albumin gene

Crystallingene

LIVER CELLNUCLEUS

Availableactivators

Albumin geneexpressed

Crystallin genenot expressed

(a) Liver cell

LENS CELLNUCLEUS

Availableactivators

Albumin genenot expressed

Crystallin geneexpressed

(b) Lens cell

1. DNA methylation – when CH3 groups attach, represses transcription

2. Histone acetylation – activates transcrition by attaching acetyl groups

3. Histone methylation – represses at the histone.

4. Transcription initiation• General transcription factors – present in all

transcription events• Attaches RNA polymerase to the promoter

region• Target the TATA box• Specific Trans. Factors – activators and

repressors specific to each cell type (ex. Liver and eye cells), bind to enhancer region on gene.

5. RNA processing• Each cell splices the primary mRNA transcript

differently6. RNA interference (RNAi)• Short RNA molecules that bind to mRNA and

prevent their translation• microRNA (miRNA) and short interfering RNA

(siRNA)

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Animation: RNA ProcessingRight-click slide / select “Play”

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Animation: Blocking Translation

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7. mRNA degradation• Degradation of the polyA tail and 5’ cap• Degradation of areas rich in A and U8. Protein degradation• 3-D stage of protein changes shape as protein

ages, marked by ubiquitin for destruction

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Animation: mRNA Degradation

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Animation: Protein Processing

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Animation: Protein Degradation

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Figure 18.14

Protein tobe degraded

Ubiquitin

Ubiquitinatedprotein

Proteasome

Protein enteringa proteasome

Proteasomeand ubiquitinto be recycled

Proteinfragments(peptides)