Transcript Viruses

Figure 19.1
0.5 mm
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
Capsomere
RNA
DNA
Membranous
RNA
envelope
Capsid
Head
DNA
Tail
sheath
Capsomere
of capsid
Tail
fiber
Glycoprotein
18  250 nm
20 nm
(a) Tobacco
mosaic virus
Glycoproteins
70–90 nm (diameter) 80–200 nm (diameter)
50 nm
(b) Adenoviruses
80  225 nm
50 nm
50 nm
(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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Figure 19.4
1 Entry and
uncoating
DNA
VIRUS
3 Transcription
and manufacture of
capsid proteins
Capsid
2 Replication
HOST
CELL
Viral DNA
mRNA
Viral
DNA
Capsid
proteins
4 Self-assembly of
new virus particles
and their exit from
the cell
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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Animation: Phage T4 Lytic Cycle
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Figure 19.5-1
1 Attachment
Figure 19.5-2
1 Attachment
2 Entry of phage
DNA and
degradation
of host DNA
Figure 19.5-3
1 Attachment
2 Entry of phage
DNA and
degradation
of host DNA
3 Synthesis of
viral genomes
and proteins
Figure 19.5-4
1 Attachment
2 Entry of phage
DNA and
degradation
of host DNA
Phage assembly
4 Assembly
Head
Tail
Tail
fibers
3 Synthesis of
viral genomes
and proteins
Figure 19.5-5
1 Attachment
2 Entry of phage
DNA and
degradation
of host DNA
5 Release
Phage assembly
4 Assembly
Head
Tail
Tail
fibers
3 Synthesis of
viral genomes
and proteins
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
Phage
DNA
Daughter cell
with prophage
The phage
injects its DNA.
Cell divisions
produce a
population of
bacteria infected
with the prophage.
Phage DNA
circularizes.
Phage
Bacterial
chromosome
Occasionally, a prophage
exits the bacterial chromosome,
initiating a lytic cycle.
Lytic cycle
The cell lyses, releasing phages.
Lysogenic cycle
Certain factors
determine whether
lytic cycle
is induced
New phage DNA and proteins
are synthesized and assembled
into phages.
or
lysogenic cycle
is entered
Prophage
The bacterium reproduces,
copying the prophage and
transmitting it to daughter
cells.
Phage DNA integrates into
the bacterial chromosome,
becoming a prophage.
Figure 19.6a
Phage
DNA
The phage
injects its DNA.
Phage DNA
circularizes.
Phage
Bacterial
chromosome
Lytic cycle
The cell lyses, releasing phages.
Certain factors
determine whether
lytic cycle or lysogenic cycle
is entered
is induced
New phage DNA and proteins
are synthesized and assembled
into phages.
Figure 19.6b
Daughter cell
with prophage
Cell divisions
produce a
population of
bacteria infected
with the prophage.
Phage DNA
circularizes.
Occasionally, a prophage
exits the bacterial chromosome,
initiating a lytic cycle.
Lysogenic cycle
Certain factors
determine whether
lytic cycle or lysogenic cycle
Prophage
is entered
is induced
The bacterium reproduces,
copying the prophage and
transmitting it to daughter
cells.
Phage DNA integrates into
the bacterial chromosome,
becoming a prophage.
Replicative Cycles of Animal Viruses
• There are two key variables used to classify
viruses that infect animals
– DNA or RNA?
– Single-stranded or double-stranded?
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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
Capsid and viral genome
enter the cell
RNA
Envelope (with
glycoproteins)
HOST CELL
Template
Viral genome
(RNA)
mRNA
ER
Capsid
proteins
Copy of
genome
(RNA)
Glycoproteins
New virus
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 high
Animal immune systems often can’t keep up.
Two strains of viral genomes can recombine to form
another virus. SIV to HIV
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
 Archaea and Bacteria are prokaryotes
 Single circular DNA with no proteins
 Reproduce using binary fission
 DNA replicates then divides
 Bacteria contain plasmids which are circular pieces
of DNA outside the chromosome
 R plasmids code for antibiotic resistance
 Most plasmids replicate outside the bacterial genome
 Episomes – plasmids that become incorporated into
the host cell’s genome
Binary Fission
Plasmids
 Transcription in prokaryotes is different – no introns
 Transcription and translation are coupled
 Operons – gene clusters that result in metabolic
enzyme production
Gene transfer
 Horizontal gene transfer introduces genetic variation
 Conjugation – donating DNA through pili
 Transduction – introduction of new DNA by a virus
 Transformation – bacteria absorb DNA from
surroundings (our lab)
Conjugation
Transduction
Transformation
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)
Proximal
control
elements
Transcription
start site
Exon
DNA
Upstream
Intron
Exon
Intron
Downstream
Poly-A
signal
Intron Exon
Exon
Cleaved
3 end of
primary
RNA processing
transcript
Promoter
Transcription
Exon
Primary RNA
transcript
5
(pre-mRNA)
Poly-A
signal Transcription
sequence termination
region
Intron Exon
Intron RNA
Coding segment
mRNA
G
P
AAA AAA
P P
5 Cap
5 UTR
Start
Stop
codon codon
3 UTR Poly-A
tail
3
 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
Regulatory
gene
DNA
Promoter
Operator
lacI
lacZ
No
RNA
made
3
mRNA
RNA
polymerase
5
Active
repressor
Protein
(a) Lactose absent, repressor active, operon off
lac operon
DNA
lacI
lacZ
lacY
lacA
RNA polymerase
3
mRNA
5
mRNA 5
-Galactosidase
Protein
Allolactose
(inducer)
Inactive
repressor
(b) Lactose present, repressor inactive, operon on
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
lacI
lacZ
CAP-binding site
cAMP
Operator
RNA
polymerase
Active binds and
transcribes
CAP
Inactive
CAP
Allolactose
Inactive lac
repressor
(a) Lactose present, glucose scarce (cAMP level high):
abundant lac mRNA synthesized
Promoter
DNA
lacI
CAP-binding site
lacZ
Operator
RNA
polymerase less
likely to bind
Inactive
CAP
Inactive lac
repressor
(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
trp operon
Promoter
Promoter
Genes of operon
DNA
trpE
trpR
trpD
trpC
trpB
trpA
C
B
A
Operator
Regulatory
gene
3
RNA
polymerase
Start codon
Stop codon
mRNA 5
mRNA
5
E
Protein
Inactive
repressor
D
Polypeptide subunits that make up
enzymes for tryptophan synthesis
(a) Tryptophan absent, repressor inactive, operon on
DNA
No RNA
made
mRNA
Protein
Active
repressor
Tryptophan
(corepressor)
(b) Tryptophan present, repressor active, operon off
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

Promoter
Activators
DNA
Enhancer
Distal control
element
Gene
TATA box
General
transcription
factors
DNAbending
protein
Group of mediator proteins
RNA
polymerase II
RNA
polymerase II
Transcription
initiation complex
RNA synthesis
1.
2.
3.
Multicellularity
Chromosome complexity
Uncoupling of transcription and translation
Enhancer
Control
elements
Promoter
Albumin gene
Crystallin
gene
LENS CELL
NUCLEUS
LIVER CELL
NUCLEUS
Available
activators
Available
activators
Albumin gene
not expressed
Albumin gene
expressed
Crystallin gene
not expressed
(a) Liver cell
Crystallin gene
expressed
(b) Lens cell
1.
2.
3.
DNA methylation – when CH3 groups attach,
represses transcription
Histone acetylation – activates transcrition
by attaching acetyl groups
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
differently
6. RNA interference (RNAi)
• Short RNA molecules that bind to mRNA and
prevent their translation
• microRNA (miRNA) and short interfering RNA (siRNA)
Animation: RNA Processing
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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 U
8. Protein degradation
• 3-D stage of protein changes shape as protein
ages, marked by ubiquitin for destruction
Animation: mRNA
Degradation
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Animation: Protein Processing
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Animation: Protein Degradation
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Figure 18.14
Ubiquitin
Proteasome
Protein to
be degraded
Ubiquitinated
protein
Proteasome
and ubiquitin
to be recycled
Protein entering
a proteasome
Protein
fragments
(peptides)
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