viruses – ch. 9 in cliffs, pg. 135. the discovery of viruses tobacco mosaic disease stunts growth...
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Viruses – Ch. 9 in Cliffs, pg. 135
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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
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• 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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© 2011 Pearson Education, Inc.
Animation: Simplified Viral Reproductive Cycle
Right-click slide / select “Play”
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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
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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
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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.
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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
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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
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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
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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
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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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© 2011 Pearson Education, Inc.
Animation: HIV Reproductive Cycle
Right-click slide / select “Play”
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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
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Binary Fission
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Plasmids
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Transcription in prokaryotes is different – no introns
Transcription and translation are coupled
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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)
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Conjugation
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Transduction
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Transformation
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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
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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
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DOLLY
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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
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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
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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
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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
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(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
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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
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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
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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
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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
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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
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ActivatorsDNA
EnhancerDistal controlelement
PromoterGene
TATA box
Generaltranscriptionfactors
DNA-bendingprotein
Group of mediator proteins
RNApolymerase II
RNApolymerase II
RNA synthesisTranscriptioninitiation complex
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1. Multicellularity2. Chromosome complexity3. Uncoupling of transcription and
translation
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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
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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.
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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.
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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)