The Genetics of Viruses and Prokaryotes

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The Genetics of Viruses and Prokaryotes
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13 The Genetics of Viruses and Prokaryotes

• 13.1 How Do Viruses Reproduce and Transmit Genes?
• 13.2 How Is Gene Expression Regulated in Viruses?
• 13.3 How Do Prokaryotes Exchange Genes?
• 13.4 How Is Gene Expression Regulated in
  Prokaryotes?
• 13.5 What Have We Learned from the Sequencing of
  Prokaryotic Genomes?

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13.1 How Do Viruses Reproduce and Transmit Genes?

• Prokaryotes and viruses make good model
  organisms
• Small genomes
• Reproduce quickly
• Usually haploid

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Figure 13.1 Model Organisms
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13.1 How Do Viruses Reproduce and Transmit Genes?

• Viruses are acellular.
• Most are composed only of nucleic acids and some
  proteins.
• Viruses do not
• Regulate transport of materials into and out of
  themselves
• Perform any metabolic functions

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Table 13.1 Relative Sizes of Microorganisms
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13.1 How Do Viruses Reproduce and Transmit Genes?

• The first virus was discovered in the 1890sit
  was an agent that causes tobacco mosaic disease.
• The agent could pass through a filter that
  retained bacteria, and could diffuse through an
  agar gel.
• The agent was crystallized in 1930s.

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13.1 How Do Viruses Reproduce and Transmit Genes?

• Viruses are obligate intracellular parasites.
• They use the host cells DNA replication and
  protein synthesis machinery to reproduce
  themselves.

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13.1 How Do Viruses Reproduce and Transmit Genes?

• Viruses outside the host cell are called virions.
• They consist of a central core of DNA or RNA,
  surrounded by a capsid of proteins.
• Viruses are not affected by antibiotics that
  target bacterial cell walls or ribosomes.

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13.1 How Do Viruses Reproduce and Transmit Genes?

• Classification
• Genome of DNA or RNA
• Nucleic acid is single- or double-stranded
• Simple or complex shape
• Whether virion is surrounded by a membrane or not
• Type of organism it infects
• Manner of the infection

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Figure 13.2 Virions Come in Various Shapes
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13.1 How Do Viruses Reproduce and Transmit Genes?

• Viruses that infect bacteria are bacteriophage or
  phage.
• Phage binds to a receptor on the host cell wall,
  injects the nucleic acid, then one of two things
  happens

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13.1 How Do Viruses Reproduce and Transmit Genes?

• Phage reproduces immediately and kills the host
  celllytic cyclecell bursts and releases progeny
  viruses.
• Postpones reproduction by integrating into the
  host cells genomelysogenic cycle.

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Figure 13.3 The Lytic and Lysogenic Cycles of
Bacteriophage
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13.1 How Do Viruses Reproduce and Transmit Genes?

• A virulent virus reproduces only by the lytic
  cycle.
• Early stage The virus genome has a promoter that
  attracts host RNA polymerase. Viral genes
  adjacent to the promoter are transcribed.
• Products are proteins that shut down host
  transcription, stimulate viral transcription, and
  digest the hosts chromosomes to provide
  nucleotides.

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13.1 How Do Viruses Reproduce and Transmit Genes?

• Late stage The viral genes that code for the
  capsid and proteins to lyse the host cell are
  transcribed.
• Sequence is controlled so that lysis doesnt
  occur prematurely.

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Figure 13.4 The Lytic Cycle A Strategy for Viral
Reproduction
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13.1 How Do Viruses Reproduce and Transmit Genes?

• Two viruses can infect one cell.
• With two different viral genomes in the same
  cell, there is the possibility of genetic
  recombination by crossing overproducing new
  strains.

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13.1 How Do Viruses Reproduce and Transmit Genes?

• Temperate viruses have a lysogenic cycle.
  Bacteria harboring them are called lysogenic
  bacteria.
• The viral genome is a prophage, incorporated into
  the bacterial genome.
• Activation results in phage entering the lytic
  cycle.

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13.1 How Do Viruses Reproduce and Transmit Genes?

• Bacteriophage have been tested as possible
  control agents for bacteria-caused diseases.

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13.1 How Do Viruses Reproduce and Transmit Genes?

• Animal viruses
• In invertebrates, viruses are common only in
  arthropods.
• Arboviruses are transmitted to vertebrates
  through insect bites. The insect is the vector,
  virus does not harm the vector.

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13.1 How Do Viruses Reproduce and Transmit Genes?

• Enveloped viruses have a membrane derived from
  the host cells plasma membrane.

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13.1 How Do Viruses Reproduce and Transmit Genes?

• Animal viruses enter cells in several ways
• A naked virion is taken up by endocytosis.
• The enveloped virus has glycoproteins that bind
  to receptors on host cell also taken in by
  endocytosis (e.g., influenza).
• The membrane of the host cell and enveloped virus
  fuse (e.g., HIV).

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Figure 13.5 The Reproductive Cycle of the
Influenza Virus
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13.1 How Do Viruses Reproduce and Transmit Genes?

• After reproduction, enveloped viruses escape the
  cell by a budding process.
• An envelope is acquired from the host cells
  plasma membrane in the process.

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13.1 How Do Viruses Reproduce and Transmit Genes?

• HIV is a retrovirus, it has reverse
  transcriptase, which facilitates RNA-directed DNA
  synthesis.
• A DNA provirus is produced that is integrated
  permanently into the hosts genome.
• When proviral DNA is activated, new virions are
  produced.

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Figure 13.6 The Reproductive Cycle of HIV
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13.1 How Do Viruses Reproduce and Transmit Genes?

• Plant viruses may be passed horizontally, from
  one plant to another.
• Or vertically, from parent to offspring.
• Virus must pass cell wall and plasma
  membraneusually associated with vectors, often
  insects.
• In the plant, viruses may spread through the
  plasmodesmata.

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13.1 How Do Viruses Reproduce and Transmit Genes?

• Wheat streak mosaic virus
• The vector is a tiny mite.
• Destruction of photosynthetic tissue causes
  yellow streaks in leavesreduces grain production.

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Figure 13.7 Wheat Streak Mosaic Virus
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13.2 How Is Gene Expression Regulated in Viruses?

• For temperate viruses, a crucial point When
  should the provirus leave the host chromosome and
  start lytic cycle?
• Example Bacteriophage ?uses two regulatory
  proteins to determine the state of health of the
  host cell.
• cI and Cro proteins compete for promoters on the
  viral genome.

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Figure 13.8 Control of Phage ? Lysis and Lysogeny
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13.2 How Is Gene Expression Regulated in Viruses?

• Phage infection is a race between the two
  regulatory proteins.
• When host cell is healthy, synthesis of Cro is
  low, cI winslysogenic cycle.
• When host cell is damaged or stressed, more Cro
  is producedlytic cycle occurs.

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13.3 How Do Prokaryotes Exchange Genes?

• Prokaryotes (Bacteria and Archaea) are living
  cells.
• Reproduction is usually asexual. A single cell
  divides into two identical cellsclones.
• Single cells can be isolated and grown into
  clones as pure cultures.

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Figure 13.9 Growing Bacteria in the Laboratory
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13.3 How Do Prokaryotes Exchange Genes?

• Prokaryotes have several ways of recombining
  genes
• Conjugation
• Transformation
• Transduction
• Plasmids
• Transposable elements

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13.3 How Do Prokaryotes Exchange Genes?

• Conjugation
• Shown by Lederberg and Tatum using two
  auxotrophic mutant strains of E. coli with
  different requirements.
• Mixing the two strains produced a few bacteria
  that could grow on minimal medium.

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Figure 13.10 Lederberg and Tatums Experiment
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13.3 How Do Prokaryotes Exchange Genes?

• Physical contact is required for conjugation.
• Initiated by a thin projectionthe sex pilus.
• A conjugation tube forms between the cells.

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Figure 13.11 Bacterial Conjugation
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13.3 How Do Prokaryotes Exchange Genes?

• Contact is brief, the recipient gets only a
  fragment of the donors DNA.
• Donor DNA lines up with homologous genes in
  recipient cell and crossing over can occur.
• Enzyme activity can cut and rejoin DNA, donor
  genes can be incorporated into recipient genome.

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Figure 13.12 Recombination Following Conjugation
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13.3 How Do Prokaryotes Exchange Genes?

• Transformation
• First discovered by Griffiththe transforming
  principleDNA leaked from dead virulent cells
  and was taken up by nonvirulent cells,
  transforming them into the virulent type.

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Figure 13.13 Transformation and Transduction (A)
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13.3 How Do Prokaryotes Exchange Genes?

• Transduction
• Bacterial DNA fragments are sometimes inserted
  into phage capsidsthis DNA can be injected into
  a new host bacteria cell.
• Incoming DNA fragment can combine with host
  genome.

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Figure 13.13 Transformation and Transduction (B)
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13.3 How Do Prokaryotes Exchange Genes?

• Many bacteria have an extra small, circular
  chromosome called a plasmid.
• Plasmids have a few dozen genes, plus an origin
  (ori).
• Often replicate at the same time as main
  chromosome, but not always.

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13.3 How Do Prokaryotes Exchange Genes?

• Plasmids exist independently of the main
  chromosome.
• Can be transferred during conjugation.
• Plasmids dont need to recombine with the main
  chromosome.

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Figure 13.14 Gene Transfer by Plasmids
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13.3 How Do Prokaryotes Exchange Genes?

• Many plasmids have special genes.
• Metabolic factors are plasmids with genes for
  unusual metabolic functions such as breaking down
  hydrocarbons.
• Fertility factors (F factors) have genes needed
  for conjugation. F factor can be transferred
  during conjugation.

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13.3 How Do Prokaryotes Exchange Genes?

• Resistance factors (R factors or R plasmids) code
  for proteins that modify or destroy antibiotics.
• Some provide resistance to heavy metals.

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13.3 How Do Prokaryotes Exchange Genes?

• R factors have become more abundant in modern
  times, possibly because of the heavy use of
  antibiotics.
• Antibiotic resistance is a serious threat to
  human health.

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13.3 How Do Prokaryotes Exchange Genes?

• Transposable elements DNA sequences that are
  inserted into new locations
• Transposon is a longer transposable element
  (5,000 base pairs) that carries one or more
  additional genes.
• Transposable elements have contributed to the
  evolution of plasmids.

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Figure 13.15 Transposable Elements and Transposons
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13.4 How Is Gene Expression Regulated in
Prokaryotes?

• Prokaryotes make proteins only when they are
  needed.
• Regulation of protein synthesis is usually done
  by transcriptional regulation.

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13.4 How Is Gene Expression Regulated in
Prokaryotes?

• Example E. coli in the intestine has a variable
  food source.
• If lactose is present, three enzymes are required
  for uptake and metabolism of the lactose.
• If grown on medium with no lactose, levels of
  these proteins are very low.

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13.4 How Is Gene Expression Regulated in
Prokaryotes?

• Inducers are compounds that stimulate synthesis
  of a protein (e.g., lactose).
• The proteins produced are inducible proteins.
• Proteins made all the time at a constant rate are
  constitutive.

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Figure 13.16 An Inducer Stimulates the Synthesis
of an Enzyme
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13.4 How Is Gene Expression Regulated in
Prokaryotes?

• The rate of a metabolic pathway can be regulated
  by
• Allosteric regulation of enzyme activity
• Regulation of protein synthesisslower, but
  produces greater energy savings

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Figure 13.17 Two Ways to Regulate a Metabolic
Pathway
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13.4 How Is Gene Expression Regulated in
Prokaryotes?

• Structural genes specify primary protein
  structurethe amino acid sequence.
• The three structural genes for lactose enzymes
  are adjacent on the chromosome, share a promoter,
  and are transcribed together.

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13.4 How Is Gene Expression Regulated in
Prokaryotes?

• Prokaryotes shut down transcription by placing an
  obstaclethe operator between the promoter and
  the structural gene.
• The operator binds to a protein called a
  repressorblocks transcription of mRNA.

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13.4 How Is Gene Expression Regulated in
Prokaryotes?

• Operon the whole unitpromoter, operator, and
  one or more structural genes.
• Operon containing genes for lactose metabolism
  lac operon.

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Figure 13.18 The lac Operon of E. coli
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13.4 How Is Gene Expression Regulated in
Prokaryotes?

• Repressor protein has two binding sites one for
  the operator, one for inducer (lactose).
• Binding to inducer changes the shape of
  repressor, allows promoter to bind RNA
  polymerase.
• When lactose concentration drops, inducers
  separate from repressorsrepressor again binds
  operator, transcriptions stops.

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Figure 13.19 The lac Operon An Inducible System
(Part 1)
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Figure 13.19 The lac Operon An Inducible System
(Part 2)
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13.4 How Is Gene Expression Regulated in
Prokaryotes?

• Repressor proteins are encoded by regulatory
  genes.
• Gene for repressor in lac operoni gene. It also
  has a promoter pi, but no operator.
• The repressor is constitutive.

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13.4 How Is Gene Expression Regulated in
Prokaryotes?

• A protein is repressible if synthesis can be
  turned off by a biochemical cue (e.g., ample
  supply of that protein).
• The trp operon controls synthesis of
  tryptophanit is a repressible system.
• The repressor must first bind with a corepressor,
  in this case tryptophan.

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Figure 13.20 The trp Operon A Repressible System
(Part 1)
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Figure 13.20 The trp Operon A Repressible System
(Part 2)
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13.4 How Is Gene Expression Regulated in
Prokaryotes?

• Inducible systems Substrate of a metabolic
  pathway (inducer) interacts with a regulatory
  protein (repressor)repressor cannot bind to
  operatorallowing transcription.
• Repressible system Product of a metabolic
  pathway (corepressor) interacts with a regulatory
  protein (repressor) allowing it to bind to
  operator, blocking transcription.

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13.4 How Is Gene Expression Regulated in
Prokaryotes?

• Inducible systems control catabolic pathways
  (turned on when substrate is present).
• Repressible systems control anabolic pathways
  (turned on when product is not present).

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13.4 How Is Gene Expression Regulated in
Prokaryotes?

• lac operon can increase efficiency of the
  promoter.
• A regulatory protein CRP binds cAMPthis complex
  binds to DNA just upstream of promoter. Allows
  more efficient binding of RNA polymerase to the
  promoter.

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Figure 13.21 Catabolite Repression Regulates the
lac Operon (Part 1)
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Figure 13.21 Catabolite Repression Regulates the
lac Operon (Part 2)
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13.4 How Is Gene Expression Regulated in
Prokaryotes?

• Catabolite repression The presence of glucose
  lowers the cell concentration of cAMP, thus less
  CRP binding to promoter, resulting in less
  efficient transcription.

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13.4 How Is Gene Expression Regulated in
Prokaryotes?

• The lac and trp systems are negative control of
  transcriptionthe regulatory protein prevents
  transcription.
• Catabolite repression is positive controlthe
  regulatory CRP-cAMP complex activates
  transcription.

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Table 13.2
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13.5 What Have We Learned from the Sequencing of
Prokaryotic Genomes?

• Automated techniques have allowed the sequencing
  of prokaryote and eukaryote genomes.

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13.5 What Have We Learned from the Sequencing of
Prokaryotic Genomes?

• Genomic sequences provide three types of
  information
• Open reading frames are recognized by start and
  stop codons.
• The amino acid sequence of proteins is deduced
  from DNA sequence in reading frame.
• Regulatory sequencespromoters and terminators

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13.5 What Have We Learned from the Sequencing of
Prokaryotic Genomes?

• Functional genomics determining the functions of
  the products of genes.
• Annotation process by which unknown proteins are
  identified.
• Comparative genomics compare genomes of
  different organismscan relate genes to
  physiology.

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Figure 13.22 Functional Organization of the
Genome of H. influenzae
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13.5 What Have We Learned from the Sequencing of
Prokaryotic Genomes?

• Practical applications of genome sequencing
• Chlamydia trachomatis
• Rickettsia prowazekii
• The unique ecosystem of the Sargasso Sea
• Mycobacterium tuberculosis
• Streptomyces coelicolor
• Methanogens
• E. coli strain O157H7

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13.5 What Have We Learned from the Sequencing of
Prokaryotic Genomes?

• Some genes and gene segments are present in all
  organismsuniversal genes.
• Suggests an ancient, minimal set of DNA sequences
  common to all cells.
• Mycoplasma genitalium has the smallest known
  genome482 genes. Transposons are used to
  determine its minimal genome.

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Figure 13.23 Using Transposon Mutagenesis to
Determine the Minimal Genome
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13.5 What Have We Learned from the Sequencing of
Prokaryotic Genomes?

• A group of researchers is attempting to build the
  minimal genome and insert it into an empty
  bacterial cellthis would be human-created life.
• New microbes could be made for many applications.
• But the technology could also be used to cause
  harm(e.g., in biological warfare and terrorism).