Transcript Nerve activates contraction

Microbial Models:
The Genetics of Viruses
Chapter 18
Part I
Size Comparisons – Figure 18.1
The Genetics of Viruses

A virus is a genome enclosed in a protective
coat.


Genome is an entire set of genes (DNA or RNA)
Capsid is the protein coat that encloses the viral
genome.


Capsids are built from a large number of protein subunits
called capsomeres.
Viral Envelopes: accessory structures that help
viruses infect their host – these are membranes
cloaking the capsid.

Envelopes are derived from the membrane of the host cell.
Viral Structures – Figure 18.2
Viral Genomes

The genome of a virus may be single-ordouble stranded DNA or single-or-double
stranded RNA.
 Called
a DNA-like or RNA-like virus depending
on the nucleic acid found in the genome.

The genome is usually organized as a single
linear or circular molecule of nucleic acid.
Viral Reproduction


Viruses can reproduce ONLY within a HOST cell
Lack enzymes for metabolism or ribosomes for
protein synthesis


Each type of virus can infect and parasitize only a limited
range of host cells (called a host range).


So…they use enzymes, ribosomes, and small molecules of host
cells to synthesize progeny viruses.
Some viruses (like rabies) have a broad enough host range to
infect several species, while others infect only a single species.
Most viruses of eukaryotes attack specific tissues:


Human cold viruses infect only the cells lining the upper
respiratory tract.
The AIDS virus binds only to certain white blood cells.
Overview of Viral Reproduction - Figure 18.3
•
•
•
After entering the cell, the viral
DNA uses host nucleotides and
enzymes to replicate itself.
The viral DNA uses other host
resources to produce its capsid
proteins by transcription and
translation.
The new viral DNA and capsid
proteins assemble into new virus
particles, which leave the cell.
5 Steps of Virus Replication
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1. Attachment
2. Penetration
3. Replication and Synthesis
4. Assembly
5. Release
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Virus uses host’s nucleotides and enzymes to replicate itself.
At the same time, other host resources are used to make new
capsid proteins by transcription and translation.
The new viral genomes and capsids are assembled into new virus
particles; when the number exceeds the cell’s surface area
limitations, the cell bursts open and new viruses are released to
infect other cells – exponential increase .
Bacteriophages (Phage Virus)

Phages are viruses
that infect bacterial
cells.

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Phages are the most
complex viruses
They are the best
understood viruses
Phages reproduce
using lytic or
lysogenic cycles
Speed of Viral Takeover

Lytic Cycle: A phage reproductive cycle that culminates in the
death of the host cell.

In the lytic cycle, the virus takes over the host cell immediately and
reproduces quickly – the host cell can lyse within a few minutes
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
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Viruses that reproduce by lytic cycles are called virulent viruses
Lysogenic Cycle: A phage reproductive cycle that replicates
the phage genome without destroying the host.

In the lysogenic cycle, the virus “hides” in the original host cell’s DNA until
optimal conditions for viral survival are present (provirus or prophage);
then, because the host cell has reproduced, the virus will reproduce and
emerge from MULTIPLE cells at once, causing much more severe cellular
damage. Once free from the cell, the phage will initiate a lytic cycle.


Ex. Cold virus
Ex. E. coli infection
Viruses that reproduce by both lytic and lysogenic cycles are
called temperate viruses
Lytic & Lysogenic Cycles – Figure 18.4
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Defense System of Bacteria

While phages have the potential to wipe out a
bacterial colony in just hours, bacteria have
defenses against phages.
 Natural
selection favors bacterial mutants with
receptor sites that are no longer recognized by a
particular type of phage.
 Bacteria produce restriction nucleases that
recognize and cut up foreign DNA, including certain
phage DNA.
 BUT…natural selection also favors resistant phage
mutants!
Animal Viruses – Table 18.1
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•
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Many animal viruses have a membranous envelope
present that is used to enter and exit the host cell.
This envelope is a lipid bilayer with glycoproteins
that bind to specific receptors molecules on the
surface of the host cell (for attachment).
Viral envelope is derived from the host cell’s
plasma membrane, so host cell may not be killed.
Let’s look at figure 18.6 on page 334 in the
textbook.
Retroviruses

Retroviruses are viruses that contain RNA instead of DNA
and replicate in an unusual way.


Following infection of the host cell, their RNA serves as a
template for the synthesis of complementary DNA (called
cDNA because it is complementary to the RNA from which it
was copied).


Have most complicated reproductive cycles:
THUS, THESE RETROVIRUSES REVERSE THE USUAL FLOW OF
INFORMATION FROM DNA TO RNA.
This reverse transcription occurs under the direction of an
enzyme called reverse transcriptase.


Retroviruses usually insert themselves into the host genome,
become permanent residents, and are capable of making multiple
copies of the viral genome for years.
Examples of retroviruses are the polio virus and the HIV virus, which
causes AIDS.
Reproductive Cycle of HIV - Figure 18.6
http://www.sumanasinc.com/webcontent/animations/content/lifecyclehiv.swf
Plant Viruses

Plant viruses are serious agricultural pests
because they can stunt plant growth and
diminish crop yields.
 Most
plant viruses are single stranded RNA
viruses.
 They enter plant cells through damaged cell
walls or are inherited from a parent.
Controlling Viruses

Diseases causes by viruses are difficult to
treat:
 Drugs
are only used to treat SYMPTOMS, not
cure the disease (just make patient feel better for
short duration)

The only methods to control viruses are to
PREVENT illness:
 Vaccines
and antibody production, use of
interferon in body.
Antibodies & Vaccines & Interferons

Antibodies are made by host’s immune system after infection
occurs (if host survives the infection)

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Help inactivate viruses and destroy harmful bacteria
Are specific for viruses or bacteria
Once an antibody is produced that recognizes a specific virus or bacteria, then
that strain will be ineffective on that individual organism
Vaccines are harmless variants or derivatives of pathogenic
microbes

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Stimulate the immune system to mount defenses against a specific pathogen
Developed by Edward Jenner – cowpox used to develop smallpox vaccination
Vaccinated or immunized again disease


Ex. MMR, DPT, polio, smallpox, influenze,rabies, hepatitis C
Interferons are chemicals in the body that are activated when cells
are attacked

Cell under seige produces interferon which binds to neighboring cells’ cell
membranes to warn them of the dangerous pathogen
Antibiotics and Viruses

Antibiotics are powerless against viruses!
 Antibiotics kill
bacteria by inhibiting enzymes or processes
specific to the pathogens; since viruses have no metabolism
of their own, the antibiotics do not work.

Only drugs that have any effect on viruses are ones
that interfere with nucleic acid synthesis – AZT (with
HIV), acyclovir (with herpesvirus)…or with protein
production (protease inhibitors with AIDS)
Emerging Viruses

Emerging viruses that cause new outbreaks of disease are
usually existing viruses that manage to expand their host
territory.
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AIDS
Hantavirus
Ebola (hemorrhagic fever)
Nipah virus
Influenza

What contributes?
1. Mutation
2. Spread from one species to another
3. Dissemination from small, isolated population
Viroids

Viroids – tiny molecules of naked circular
DNA that infect plants:

do not encode proteins
 can replicate in host plant cells using
cellular enzymes
 disrupt the metabolism of cell and stunt
growth of whole plant

Point is that MOLECULES can be an
infectious agent.
Prions


Prions are infectious proteins; misfolded form
of a protein normally found in brain cells
Cause degenerative brain diseases


Ex. Scrapie, mad cow disease, Creutzfeldt-Jakob
disease
When prion gets into a cell containing the
normal form of the brain cell protein, prion
converts the normal protein to the prion
version
Microbial Models:
The Genetics of Bacteria
Chapter 18
Part II
The Genetics of Bacteria

The major component of the bacterial genome is one
DOUBLE STRANDED, CIRCULAR DNA molecule which is
smaller and less complex than that of eukaryotes.
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Different from eukaryotic chromosomes which have linear DNA
molecules associated with large amounts of protein.
Within bacterium, the chromosome is so tightly packed that it fills only
part of the cell – dense region called nucleoid – NOT bound by
membrane like the nucleus of eukaryotic cell.
Replication of DNA occurs from single origin of replication on circular
DNA and transcription/translation can be coupled in prokaryotes.
Generally have few or no introns – so majority of genome is
expressed.
Gene regulation is controlled using operons.
In addition, many bacteria have PLASMIDS, much smaller
circles of DNA.

Each plasmid has only a small number of genes, from just a few to
several dozen.
Replication of the Bacterial Chromosome
– Figure 18.11
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Bacterial cells divide via
binary fission.
This is preceded by
replication of the bacterial
chromosome from a
single origin of
replication.
From a single origin of
replication – DNA synthesis
progresses in both
directions around the
circular chromosome.
Because binary fission is
asexual, most bacterial
colonies are genetically
identical to the parent cell.
Producing New Bacterial Strains
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
Bacteria do not undergo meiosis and fertilization as do
eukaryotic organisms – they “reproduce” via means of
genetic recombination:
The genetic recombination in bacteria includes:

Transformation
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Transduction
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
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Conjugation

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Figure 18.12 Detecting genetic recombination in bacteria
Important Definitions
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Transformation – alteration of bacterial cell’s
genotype by the uptake of naked, foreign DNA
from the surrounding environment.
Important Definitions
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Transduction – phages carry bacterial
genes from one host cell to another (2
types – generalized and specialized)
Generalized – phage transfers bacterial
genes randomly
 Specialized - Only certain genes are
transferred – the ones near the prophage site
on the bacterial chromosome

Figure 18.13 Transduction (Layer 1)
Figure 18.13 Transduction (Layer 2)
Figure 18.13 Transduction (Layer 3)
Figure 18.13 Transduction (Layer 4)
Important Definitions
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
Conjugation – direct transfer of genetic material
between 2 bacterial cells that are temporarily
joined:
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DNA transfer is one-way (one cell donating DNA and
its “mate” receiving the genes)
The donor (male) uses pili to attach to the female
“maleness” – the ability to form sex pili and donate
DNA during conjugation results from the presence of
an F factor (F for fertility)
F factors can either be a segment of DNA within
the bacterial chromosome or as a plasmid
Conjugation – Figure 18.14
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The E. coli “male (right) extends sex pili, one of which is
attached to a “female” cell.
The two cells will be drawn close together, allowing a
cytoplasmic bridge to form between them.
Through this tube, the “male” will transfer DNA to the
“female.”
This mechanism of DNA transfer is called conjugation.
Plasmids

Plasmids are small, circular, self-replicating DNA
molecule separate from the bacterial chromosome

If a genetic element can exist as either a plasmid or as
a part of the bacterial chromosome, that genetic
element is called an EPISOME

Plasmids have only a small number of genes, and these
are not necessary for the survival and reproduction of
the bacterium; BUT, they can confer advantages – F
plasmids and R plasmids


F plasmid – fertility – bacteria that contain F plasmids are F+ and
carry genes for production of pili.
R plasmid – resistance to antibodies – such as ampicillin or
tetracycline.
Figure 18.15 Conjugation and recombination in E. coli (Layer 1)
1. Cells that carry an F plasmid are called F+ cells.
They are “male” because they can transfer an F
plasmid to a “female” F- cell.
2. In this way, an F- cell can become F+.
3. The F plasmid replicates as it transfers, so that
the donor cell remains F+.
Figure 18.15 Conjugation and recombination in E. coli (Layer 2)
This process is similar to phage DNA joining the
host chromosome as a prophage. Crossing over
occurs between the two DNA circles at a specific
site on each.
Figure 18.15 Conjugation and recombination in E. coli (Layer 3)
Replication and transfer of the Hfr chromosome begins at a fixed point within the F
factor.
The conjugation bridge usually breaks well before the entire chromosome and most of
the F factor are transferred.
Figure 18.15 Conjugation and recombination in E. coli (Layer 4)
Crossing over can occur between genes on the fragment of bacterial
chromosome transferred from the Hfr cell and the same genes on the
recipient F- cell’s chromosome.
A recombinant F- cell will result. Pieces of DNA ending up outside the
bacterial chromosome will eventually be degraded by the cell’s enzymes
or lost in cell division.
THE DNA REPLICATION THAT ACCOMPANIES TRANSFER OF AN F
PLASMID OR PART OF AN Hfr BACTERIAL CHROMOSOME IS
CALLED ROLLING-CIRCLE REPLICATION.
Transposons
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Transposons are pieces of DNA that can move from one
location to another “jumping genes”
These NEVER exist independently
Movement of transposons occurs as a type of
recombination between the transposon and another DNA
site (target site) that comes in contact with the transposon
Ability to scatter certain genes throughout the genome
makes transposition fundamentally different from other
mechanisms of genetic shuffling – DOES NOT depend on
complementary base sequences
Types of Transposons
1.
Insertion Sequences – consist of only one
gene, which codes for transposase – the
enzyme responsible for moving the sequence
from one place to another.

2.
Can cause mutations when they happen to land within the
coding sequence of a gene or within a DNA region that
regulates gene expression.
Composite Transposon – are longer and
include extra genes, such as a gene for
antibiotic resistance or for seed color.

benefit bacteria by helping them to adapt to new environments
Barbara McClintock
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American geneticist
Worked with Indian corn
(maize) in 1940’s and 50’s
Identified changes in the color
of corn kernels that made
sense only if there were
mobile genetic elements
capable of moving from one
location to another in the
genome
Changes in color of corn
kernels
Awarded Nobel Prize in 1983
Insertion Sequence Transposons
1.
Insertion Sequences – simplest of the
bacterial transposons:
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
consist ONLY of the DNA necessary for
transposition
Sometimes called “jumping genes”
codes for transposase
bracketed by inverted repeats (non coding
sequences of DNA about 20 to 40 nucleotides
long)
See page 345
Figure 18.16 Insertion sequences, the simplest transposons
1. The one gene of an insertion sequence codes for transposase,
which catalyzes the transposon’s movement.
2. The inverted repeats are backward, upside-down versions of
each other.
3. In transposition, transposases bind to the inverted repeats and
catalyze the cutting and resealing of DNA required for insertion
of the transposon at a target site.
Figure 18.17 Insertion of a transposon and creation of direct repeats
1. First, transposase enzyme
makes staggered cuts in the
2 DNA strands at the target
site.
2. The transposon is then
joined to the single-stranded
ends at the target site.
3. Finally, the gaps in the DNA
strands are filled in by DNA
polymerase and sealed by
ligase. This results in direct
repeats, identical segments
of DNA on either side of the
transposon.
Composite Transposons
1.
Composite Transposon – include extra
genes in addition to the transposition
DNA

benefit bacteria by helping them to adapt to
new environments
Figure 18.18 Anatomy of a composite transposon
A composite transposon consists of one or more genes located
between twin insertion sequences.
The transposon here has a gene for resistance to an antibiotic,
which is carried along as part of the transposon when the
transposon is inserted at a new site in the genome.
Microbial Models:
The Control of Gene Expression in
Bacteria
Chapter 18
Part III
Control of Bacterial Gene Expression

2 ways to control:
regulate gene expression (what enzymes
are made)
2. Adjust the activity of enzymes already
present
1.

OPERON MODEL: discovered in 1961
by Francois Jacob and Jacques Monod
Figure 18.19 Regulation of a metabolic pathway
In the pathway for
tryptophan synthesis,
an abundance of
tryptophan can both:
(a) Repress expression
of the genes for all
the enzymes needed
for the pathway;
(b) Inhibit the activity of
the first enzyme in
the pathway
(feedback inhibition).
In this example, the
symbols (-) stands for
“inhibition”.
What is an Operon?


An operon is essentially a set of genes and the
switches that control the expression of those
genes.
Operon consists of:
 operator
 promotor
 and

genes that they control
All together, the operator, the promoter, and the
genes they control – the entire stretch of DNA
required for enzyme production for the pathway
– is called an operon.
Types of Operons

Trp operon – repressible operon is always in
the on position until it is not needed and becomes
repressed or switched off.

Lac operon – inducible operon is always off
until it is induced to turn on.


BOTH OF THESE ARE EXAMPLES OF NEGATIVE GENE
CONTROL BECAUSE OPERONS ARE TURNED OFF BY THE
ACTIVE FORM OF THE REPRESSOR PROTEIN!
See figures 18.20 & 18.21
Figure 18.20a The trp operon: regulated synthesis of repressible enzymes
Tryptophan is an amino acid produced by an anabolic pathway
catalyzed by repressible enzymes.
If tryptophan is absent, the repressor is inactive, the operon is on,
and RNA polymerase attaches to the DNA at the promoter and
transcribes the operon’s genes.
Figure 18.20b The trp operon: regulated synthesis of repressible enzymes (Layer 1)
As tryptophan accumulates, it inhibits its own production by
activating the repressor protein.
Figure 18.20b The trp operon: regulated synthesis of repressible enzymes (Layer 2)
The repressor
switches the
operon off by
binding to the
operator and
blocking
access of RNA
polymerase to
the promoter.
Tryptophan binds to
an allosteric site on
the protein, causing
its conformation to
change to the active
form.
Figure 18.21a The lac operon: regulated synthesis of inducible enzymes
The lac repressor is innately active, and in the absence of
lactose it switches off the operon by binding to the
operator.
Figure 18.21b The lac operon: regulated synthesis of inducible enzymes
Allolactose, an isomer of lactose, depresses the operon by
inactivating the repressor. In this way, the enzymes for
lactose metabolism are induced if lactose is present.
Positive Gene Regulation

PRESENT ONLY WHEN AN ACTIVATOR
MOLECULE INTERACTS DIRECTLY
WITH THE GENOME TO SWITCH
TRANSCRIPTION ON
 EX.
cAMP receptor protein
 Page 350-351
Figure 18.22a Positive control: cAMP receptor protein
Figure 18.22b Positive control: cAMP receptor protein
Factors Affecting Ability of Repressor to Bind
to Operator
• Co-Repressor : Activates a Repressor
o Seen in the TRP Operon
o Co-Repressor is tryptophan
o Turns normally “on” Operon “off”
• Inducer: Inactivates a Repressor, Induces the
Gene to be Transcribed
o Seen in the LAC Operon
o Inducer is allolactose
o Turns normally “off” Operon “on”
Positive Regulation: cAMP Receptor
Protein (CRP)
• Positive control of Operon
– Binds to DNA next to Promoter of
Operon
– Stimulates Transcription of the
genes
• Glucose is preferred over
Lactose
• If Glucose is low, Lactose will
be metabolized
– Lactose binds to Repressor,
deactivates
– Low glucose means high cAMP in
cell
– cAMP binds to CRP, activates it
– CRP + cAMP binds to DNA near
promoter
– Stimulates Transcription
Review: Structure/Function of Prokaryotic Chromosomes
1.
2.
shape (circular/nonlinear/loop)
less complex than eukaryotes (no histones/less
elaborate structure/folding)
size (smaller size/less genetic information/fewer
genes)
replication method (single origin of
replication/theta replication)
transcription/translation may be coupled
generally few or no introns (noncoding segments)
majority of genome expressed
operons are used for gene regulation and control
3.
4.
5.
6.
7.
8.
□
NOTE: plasmids – more common but not unique to
prokaryotes/not part of prokaryote chromosome