VIRUSES

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VIRUSES

• Chapter 19

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Size Comparisons
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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.

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Viral Structures Figure 19.3
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Viral Genomes

• The genome of a virus may be single-or- double
  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.

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Viral Reproduction

• Viruses can reproduce ONLY within a HOST cell
• Lack enzymes for metabolism or ribosomes for
  protein synthesis
• Sothey use enzymes, ribosomes, and small
  molecules of host cells to synthesize progeny
  viruses.
• Each type of virus can infect and parasitize only
  a limited range of host cells (called a host
  range).
• 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.

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Overview of Viral Reproduction - Figure
19.4http//www.sumanasinc.com/webcontent/animatio
ns/content/herpessimplex.html

• 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.

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5 Steps of Virus Replication

• 1. Attachment
• 2. Penetration
• 3. Replication and Synthesis
• 4. Assembly
• 5. Release
• Virus uses hosts 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 cells surface area limitations, the cell
  bursts open and new viruses are released to
  infect other cells exponential increase .

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Bacteriophages (Phage Virus)

• Phages are viruses that infect bacterial cells.
• Phages are the most complex viruses
• They are the best understood viruses
• Phages reproduce using lytic or lysogenic cycles

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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
• Ex. Cold virus
• 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 cells 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. E. coli infection
• Viruses that reproduce by both lytic and
  lysogenic cycles are called temperate viruses

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Lytic Lysogenic Cycles Figure
19.6http//highered.mcgraw-hill.com/sites/0072556
781/student_view0/chapter17/animation_quiz_2.html
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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.
• BUTnatural selection also favors resistant phage
  mutants!

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Animal Viruses Table 18.1

• 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 cells
  plasma membrane, so host cell may not be killed.
• Lets look at figure 18.6 on page 334 in the
  textbook.

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Retroviruses

• Retroviruses are viruses that contain RNA instead
  of DNA and replicate in an unusual way.
• Have most complicated reproductive cycles
• 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).
• 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.

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Reproductive Cycle of HIV - Figure
19.8http//www.sumanasinc.com/webcontent/animatio
ns/content/lifecyclehiv.swf
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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.

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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.

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Antibodies Vaccines Interferons

• Antibodies are made by hosts immune system after
  infection occurs (if host survives the infection)
• 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
• 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

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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)

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Emerging Viruses

• Emerging viruses that cause new outbreaks of
  disease are usually existing viruses that manage
  to expand their host territory.
• AIDS
• Hantavirus
• Ebola (hemorrhagic fever)
• Nipah virus
• Influenza
• What contributes to spread of emerging viruses?
• 1. Mutation
• 2. Spread from one species to another
• 3. Dissemination from small, isolated population

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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.

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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

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Evolution of Viruses

• Viruses exist somewhere between life and
  non-life
• They display many (but not all) characteristics
  of lifeincluding the ability to EVOLVE!
• Viruses probably evolved AFTER the first cells
  appeared
• They are naked bits of nucleic acid that perhaps
  evolved from plasmids or transposons MOBILE
  GENETIC ELEMENTS!

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Bacteria
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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.
• 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.

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Replication of the Bacterial Chromosome Figure
18.11

• 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.

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Producing New Bacterial Strains

• 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
• http//highered.mcgraw-hill.com/sites/0072556781/s
  tudent_view0/chapter13/animation_quiz_1.html
• Transduction
• http//highered.mcgraw-hill.com/sites/0072556781/s
  tudent_view0/chapter13/animation_quiz_2.html
• Conjugation
• http//highered.mcgraw-hill.com/sites/0072556781/s
  tudent_view0/chapter13/animation_quiz_3.html

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Figure 18.12 Detecting genetic recombination in
bacteria
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Important Definitionshttp//highered.mcgraw-hill.
com/sites/0072556781/student_view0/chapter13/anima
tion_quiz_1.html

• Transformation alteration of bacterial cells
  genotype by the uptake of naked, foreign DNA from
  the surrounding environment.

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Important Definitionshttp//highered.mcgraw-hill.
com/sites/0072556781/student_view0/chapter13/anima
tion_quiz_2.html

• Transduction process where phages carry
  bacterial genes from one host cell to another (2
  types generalized and specialized)
• Generalized phage transfers bacterial genes
  randomly
• http//highered.mcgraw-hill.com/classware/ala.do?i
  sbn0072464631alaidala_661332
• Specialized - Only certain genes are transferred
  the ones near the prophage site on the
  bacterial chromosome
• http//highered.mcgraw-hill.com/sites/0072556781/s
  tudent_view0/chapter17/animation_quiz_3.html?isbn
  0072556781firstNameMIlastNamemyEmailmySty
  leprofEmailprofStyletaEmailtaStyleotherE
  mailotherStyle

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Figure 18.13 Transduction (Layer 1)
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Figure 18.13 Transduction (Layer 2)
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Figure 18.13 Transduction (Layer 3)
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Figure 18.13 Transduction (Layer 4)
37
Important Definitionshttp//highered.mcgraw-hill.
com/sites/0072556781/student_view0/chapter13/anima
tion_quiz_3.html

• Conjugation direct transfer of genetic material
  between 2 bacterial cells that are temporarily
  joined
• 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

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Conjugation Figure 18.14

• 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.

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Plasmids

• Plasmids are small, circular, self-replicating
  DNA molecules 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.

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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.

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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.
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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.
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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- cells chromosome. A recombinant F- cell will
result. Pieces of DNA ending up outside the
bacterial chromosome will eventually be degraded
by the cells 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.
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Transposonshttp//highered.mcgraw-hill.com/sites/
0072556781/student_view0/chapter13/animation_quiz_
5.html

• 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

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Types of Transposonshttp//highered.mcgraw-hill.c
om/olc/dl/120082/bio36.swf

• Insertion Sequences consist of only one gene,
  which codes for transposase the enzyme
  responsible for moving the sequence from one
  place to another.
• 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

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Barbara McClintock

• American geneticist
• Worked with Indian corn (maize) in 1940s and
  50s
• 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

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Insertion Sequence Transposons

• Insertion Sequences simplest of the bacterial
  transposons
• 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

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Figure 18.16 Insertion sequences, the simplest
transposons

1. The one gene of an insertion sequence codes for
   transposase, which catalyzes the transposons
   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.

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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.

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Composite Transposons

• Composite Transposon include extra genes in
  addition to the transposition DNA
• benefit bacteria by helping them to adapt to new
  environments

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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.