Announcements

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Announcements

• Chapter 12 Online Quiz Deadline Midnight
• Todays IA Session w/ Kim Mecir
• 2-3 PM rather than 1-3 PM (today only)

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

• Probing the Nature of Genes
• Viruses Reproduction and Recombination
• Prokaryotes Reproduction and Recombination
• Regulation of Gene Expression in Prokaryotes
• Control of Transcription in Viruses
• Prokaryotic Genomes

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Bacillus anthracis in a human lung - Anthrax
Under proper conditions a Bacillus anthracis
spore becomes a rapidly dividing bacterium that
produces toxins. Spores were distributed in the
U.S. mail in 2001 a serious act of bioterrorism.
Death within 36 hours for nearly all untreated
individuals.
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Borrelia burgdorferi Lyme Disease

• Borrelia burgdorferi (bacterium) pathogen
  associated with Lyme disease

http//www.rzuser.uni-heidelberg.de/ cn6/zecken/i
mages/neuro1.jpg
http//www.wadsworth.org/databank/hirez/hechemy2.g
if
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Lyme Disease

• Some Manifestations of Lyme Disease
• Arthritis
• Encephalitis
• Meningitis
• Loss of concentration
• Loss of memory
• Psychological changes
• Bells palsy (facial paralysis)
• Heart palpitations

Black legged tick
http//bugguide.net/images/
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Polio Virus - Poliomyelitus

• POLIO disease caused by a virus

http//www.med.uc.edu/about/history/images/polio3.
jpg
http//www.book-of-thoth.com/thebook/index.php/Im
agePolyomavirus_SV40_TEM_B82-0338_lores.jpg
http//www.teachspace.org/lauren/polio/images/iron
lung.gif
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Probing the Nature of Genes

• WHY TALK ABOUT BACTERIA VIRUSES? Because the
  study of these has contributed significantly to
  our understanding of genetics (e.g., ID of
  genetic material DNA replication gene
  expression .
• Advantages associated with working with bacteria
  and viruses include
• They have small genomes.
• bacteria (1/1000 DNA) viruses (1/100,000 DNA)
• They quickly produce large numbers of
  individuals.
• Bacteria (double in 20 min) viruses (100X in 2
  hr), highly variable)
• They are usually haploid, making genetic analyses
  easier.

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Viruses Reproduction and Recombination

• Most viruses are composed of a nucleic acid (DNA
  or RNA) and a few proteins. Some with a lipid
  envelope.
• Viruses are acellular (noncellular) and do not
  metabolize energy.
• Viruses do not produce ATP or conduct
  fermentation, cell respiration, or
  photosynthesis.
• Viruses can reproduce only in systems that do
  perform these functions living cells.

Influenza Virus
http//www.virology.net/Big_Virology/EM/virus.gif
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Influenza Virus
http//www.omedon.co.uk/influenza/beans/influenza
20virus.jpg
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Viruses Reproduction and Recombination

• Viruses are obligate intracellular parasites that
  develop and reproduce only within living cells of
  specific hosts.
• Viruses reproduce using the hosts synthetic
  machinery and usually destroy the host cell in
  the process.
• The host cell releases progeny viruses, which
  then infect new hosts.
• Outside the cell, the individual viral particles
  are called virions.
• Viruses are unaffected by antibiotics because
  they lack the cell wall structure and ribosomal
  biochemistry of bacteria.

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Figure 13.1 Virions Come in Various Shapes
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Viruses Reproduction and Recombination

• Viruses are described according to four different
  criteria
• Whether the genome is DNA or RNA
• Whether the nucleic acid is single-stranded or
  double-stranded
• Whether the shape of the virion is a simple or
  complex crystal
• Whether or not the virion is surrounded by a
  membrane

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Viruses Reproduction and Recombination

• A special category of viruses those that infect
  bacteria are called bacteriophage (phage).
• Bacteriophage recognize their host by means of
  specific binding between proteins in the capsid
  and receptor proteins on the hosts cell.
• The virions are equipped with tail assemblies
  that inject the phages nucleic acid into the
  host cell.

http//student.ccbcmd.edu/courses/bio141/ labmanua
/lab11/images/u2fig17a.jpg
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Viruses Reproduction and Recombination

• The viral genome contains a promoter sequence
  that attracts host RNA polymerase.
• In the early stage, viral genes adjacent to the
  promoter are transcribed. Early gene products
  often include proteins that shut down host
  transcription and stimulate viral genome
  replication.
• In the late stage, viral late genes code for the
  protein coat and an enzyme that causes host cell
  lysis, resulting in viral release.

http//www.lbl.gov/Science-Articles/Archive/assets
/images/2004/Dec-20/MeCP2_regulation.jpg
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Viruses Reproduction and Recombination

• The virus may reproduce immediately and kill the
  host, or postpone reproduction by integrating its
  nucleic acid into the hosts genome.
• There are two types of phage reproductive cycles
  the lytic cycle and the lysogenic cycle..
• In the lytic cycle, the infected bacterium lyses,
  releasing the progeny phage. Called virulent
  phage.
• In the lysogenic cycle, the host cell does not
  lyse, but harbors the viral nucleic acid for many
  generations.
• Bacteria harboring phage that are not lytic are
  called lysogenic bacteria. The viruses are called
  temperate phage.

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Viruses Reproduction and Recombination

• Lysogenic bacteria have a molecule of
  noninfective phage DNA called a prophage inserted
  into their chromosome.
• Under some conditions, the prophage replicates
  during the bacteriums normal reproductive cycle
  without otherwise harming the bacterium.
• Certain conditions will activate the prophage,
  initiating a lytic cycle that results in the
  release of a large number of free phage.

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Layered Figure 13.2

• The Lytic and Lysogenic Cycles of Bacteriophage
  (Bacterial Viruses). Layered Figure 13.2

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Figure 13.2 The Lytic and Lysogenic Cycles of
Bacteriophage
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Viruses Reproduction and Recombination

• PHAGE THERAPY
• Lytic bacteriophage destroy their bacterial
  hosts, and thus might be useful in treating
  diseases caused by bacteria

• Early work by DHerelle showed that phage could
  be used to control some bacterial diseases.
• Rise of antibiotics reduced interest in phage
  therapy, but it may become useful again, as
  bacteria become resistant to antibiotics.

http//www.surrey.ac.uk/SBMS/MicrobialSciences/res
earch/
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Next Slide

• GRAPHIC SLIDE!
• The next slide has a photo of a woman who has an
  advanced stage of Kaposis sarcoma, a condition
  associated with AIDS.
• The photo is a bit graphic. If you find human
  disease-associated photos unsettling, look the
  other way while the slide is being discussed.

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Viruses Reproduction and Recombination

• WHAT ABOUT ANIMAL VIRUSES?
• An example HIV (cause of AIDS) This virus
  attacks our immune system. With a weakened
  immune system, pathogens (fungi, bacteria, etc.)
  take over.
• Image Advanced Kaposis sarcoma, a condition
  associated with AIDS. These lesions occur on the
  surface of the body and within the body.

http//www.aidsinfo.ch/bilder/schule_aids/jpg_bild
er/koch18_4.jpg
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Figure 13.5 The Reproductive Cycle of HIV (Part
1)
Human Immunodeficiency Virus
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Layered Figure 13.5

• The Reproductive Cycle of HIV (Human
  Immunodeficiency Virus), the virus that causes
  AIDS. Layered Figure 13.5
• Over 25 million people have died from AIDS thus
  far.

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Figure 13.5 The Reproductive Cycle of HIV (Part
2)
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Prokaryotes Reproduction and Recombination

• Unlike viruses, bacteria and archaea are living
  cells that carry out basic cellular functions.
• The division of single cells into two identical
  offspring produces clones, or genetically
  identical individuals.
• If a number of cells are spread on a semisolid
  medium containing agar, individual cells give
  rise to clearly visible colonies.

http//diverge.hunter.cuny.edu/weiga ng/Images/06
-11_binaryfission_1.jpg
http//www2.cedarcrest.edu/academic/bio/hale/MERC.
html
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Figure 13.6 Growing Bacteria in the Laboratory
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Genetic Recombination

• WHAT ABOUT GENETIC RECOMBINATION IN BACTERIA
  AND ARCHAEA?
• Prokaryotes usually reproduce asexually, but
  nonetheless have several ways of recombining
  their genes. Whereas in eukaryotes, genetic
  recombination occurs between the genomes of two
  parents, recombination in prokaryotes results
  from the interaction of the genome of one cell
  with a much smaller sample of genes a DNA
  fragment -- from another cell.
• Purves et al. (text)

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Genetic Recombination

• Conjugation
• Bacterial conjugation is the transfer of genetic
  material between bacteria through cell-to-cell
  contact. - Wikipedia
• Transformation
• Mechanism for transfer of genetic information in
  bacteria in which pure DNA extracted from
  bacteria of one genotype is taken in through the
  cell surface of bacteria of a different genotoype
  and incorporated into the chromosome of the
  recipient cell. Purves et al.
• Transduction
• Transfer of genes from one bacterium to another,
  with a bacterial virus acting as the carrier of
  the genes. Purves et al.

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Prokaryotes Reproduction and Recombination

• In 1946, Lederberg and Tatum demonstrated the
  exchange of DNA between two living bacteria.
• This exchange is called conjugation.
• The physical contact required for conjugation is
  initiated by a pilus, which is a fine projection
  produced by the donor cell.
• The DNA transfers through a thin cytoplasmic
  bridge called a conjugation tube.
• Once the DNA fragment is inside the recipient
  cell, it recombines with homologous genes.

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Conjugation
http//bio1151.nicerweb.com/doc/class/bio1151/Lock
ed/media/ch18/18_17Conjugation_LP.jpg
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Figure 13.9 Recombination Following Conjugation
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Prokaryotes Reproduction and Recombination

• Transformation of bacteria occurs when bacteria
  take up extracellular DNA and incorporate it.
• More than 75 years ago, Frederick Griffith
  obtained the first evidence for transfer of genes
  between bacteria.
• In transduction, viruses carry genes from one
  cell to another
• During the lytic cycle, some bacteriophage
  package a host bacteriums DNA in capsids, or
  viral protein coats.
• Cells infected by such viruses get a segment of
  another bacteriums DNA, not the viral DNA.
• In transduction, this bacterial DNA recombines
  with the chromosomal DNA of the host and alters
  its genetic composition.

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Figure 13.10 Transformation and Transduction
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Figure 13.11 Gene Transfer by Plastids
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Prokaryotes Reproduction and Recombination

• Plasmids are small, circular chromosomes found in
  many bacteria.
• Each plasmid replicates separately from the
  primary chromosome.
• Plasmids move between bacterial cells during
  conjugation.
• Different types of plasmids are classified
  according to the kinds of genes they carry.
• Some plasmids (metabolic factors) carry genes for
  unusual metabolic functions, such as degrading
  oils from oil spills.

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Prokaryotes Reproduction and Recombination

• Fertility factors (F factors) are plasmids that
  carry genes for conjugation.
• Around 25 genes, including the ones responsible
  for the pilus, are on the F factor plasmid.
• Bacteria with this plasmid are called F.
• On occasion, this F plasmid inserts into the main
  chromosome.
• When this occurs, chromosomal genes can be
  transferred during conjugation.

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Prokaryotes Reproduction and Recombination

• Some plasmids are resistance factors (R factors)
  and carry genes that code for proteins that
  protect the bacteria.
• Antibiotic resistance genes interfere with
  antibiotic activity or transport.
• Research found that resistance to an entire
  spectrum of antibiotics could be transferred by
  conjugation.
• This finding raised the warning that
  inappropriate use of antibiotics may lead to
  their becoming ineffective.

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Prokaryotes Reproduction and Recombination

• Segments of chromosomes or plastids that can move
  into other genes within a cell are called
  transposable elements.
• The movement of these transposable elements into
  other genes disrupts normal function.
• Long transposable elements (about 5000 base
  pairs), which include one or more genes, are
  called transposons.
• Transposons have contributed to the evolution of
  plasmids, and there is some evidence that R
  factors developed antibiotic resistance through
  transposons.

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Figure 13.12 Transposable Elements and
Transposons
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Figure 13.7 Lederberg and Tatums Experiment
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Till next time
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Announcements

• Grading Curve Students with averages above 80
  receive the same number of points as students
  with averages below or at 80.

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E. coli Conservation of Energy and Resources
If there is no lactose around, why make enzymes
that are designed to break it down?
http//www3.niaid.nih.gov/NR/rdonlyres/49477C30-05
13-47BE-88FC-17974CB1F952/0/e_coli.jpg
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Choices
If you were E. coli and you wanted to cut the
production of an enzyme, at what point along the
production line would you do it?
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Regulation of Gene Expression in Prokaryotes

• Prokaryotes can conserve energy and resources by
  making proteins only when they are needed.
• Cells can regulate protein synthesis by several
  methods
• Block transcription of the gene that codes for a
  protein
• Hydrolyze the mRNA after it is made
• Prevent translation of mRNA at the ribosome
• Hydrolyze the protein after it is made
• Inhibit the function of the protein
• In most cases, bacteria choose to block
  transcription.

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Recall Transcription How is this Blocked?
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An Example

• An Example of How Transcription is Stopped
• in the World of Escherichia coli
• LACTOSE METABOLISM

http//biology.clc.uc.edu/graphics/bio104/lactose
201.jpg
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An Example E. coli and Lactose

• E. coli prefers glucose as an energy source, but
  can use lactose if glucose is low.
• Three enzymes are required for lactose
  metabolism.
• ß-galactoside permease (carrier protein in the
  cell membrane that moves sugars into the cell.)
• ß-galactosidase (an enzyme that catalyzes the
  hydrolysis of lactose into glucose and
  galactose.)
• ß-galactoside transacetylase (involved in lactose
  metabolism, but role in the process is not
  clear.)
• The three structural genes involved in lactose
  metabolism are adjacent to each other on the E.
  coli chromosome.
• All are transcribed together into a single mRNA
  when a single promoter binds RNA polymerase.

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Structural Genes Associated with Lactose
Metabolism
http//www.emc.maricopa.edu/faculty/farabee/biobk/
operon.gif
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lac operon

• The whole unit of genes and their DNA controls is
  called an operon.
• The operon for the three lactose-metabolizing
  enzymes is called the lac operon.

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Repressors and Operators and Promoters, Oh My!

• Prokaryotes shut down transcription by placing an
  obstacle between the promoter (where RNA
  polymerase attaches) and its structural genes,
  called the operator.
• If a specific protein, the repressor, binds to
  the operator, it creates an obstacle, and RNA
  polymerase is blocked from transcribing the
  structural genes. When the repressor is not
  attached to the operator, mRNA synthesis
  proceeds.

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Regulation of Gene Expression in Prokaryotes

• Okay, lets give E. coli some lactose.
• Presence of lactose stimulates production of
  enzymes associated with lactose metabolism.
  Therefore, lactose is considered an inducer.
• The repressor protein has two binding sites one
  for the operator and the other for inducers
  (lactose and some other ß-galactosides).
• Binding of the repressor by the inducer molecules
  (lactose) changes the shape of the repressor by
  allosteric modification.

Images cut from text images (Purves et al.)
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Figure 13.17 The lac Operon An Inducible System
(Part 1)
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Figure 13.17 The lac Operon An Inducible System
(Part 2)
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Source of Repressor
Where did the repressor come from?
Enzymes (proteins) that are produced because of
the presence of an inducer are called inducible
enzymes (proteins) (e.g., the three above).
Enzymes that are made all of the time are called
constitutive enzymes (proteins). The repressor
is a constitutive protein.
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Regulation of Gene Expression in Prokaryotes

• The repressor protein is coded for by the
  regulatory gene.
• The regulatory gene that codes for the lac
  repressor is the i (inducibility) gene.
• The i gene is located near the lac structural
  genes. However, not all regulatory genes are near
  the operons they control.
• Regulatory genes like i have their own promoter,
  called pi.
• The i gene is expressed constitutively
  (expression is constant).

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Regulation of Gene Expression in Prokaryotes

• Summary of the lac operon control
• When no inducer (lactose) is present, lac is off.
• The regulator protein (repressor) turns the
  operon off.
• The i gene produces the repressor.
• The operator and promoter are DNA sequences that
  are binding sites for regulatory proteins.
• Adding inducer (lactose) turns the operon on.

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Another Example trp Operon

• What if E. coli normally makes a substance
  (e.g., tryptophan), but then finds itself in an
  environment loaded with tryptophan. Does it make
  sense to expend the energy to make it?

amino acid
http//www3.niaid.nih.gov/NR/rdonlyres/49477C3 0-0
513-47BE-88FC-17974CB1F952/0/e_coli.jpg
http//www.biochem.northwestern.edu/holmgren/ Glos
sary/Images/pics/amino_acids/Tryptophan.gif
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Regulation of Gene Expression in Prokaryotes

• If synthesis of an enzyme can be turned off, it
  is said to be repressible.
• The trp operon in E. coli is repressible.
• In the absence of tryptophan, RNA polymerase
  transcribes the trp operon, leading to production
  of enzymes that synthesize tryptophan.
• When tryptophan is present, it binds to a
  repressor, which becomes active.
• The repressor binds to the operator of the trp
  operon, blocking production of enzymes for
  tryptophan synthesis.

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Figure 13.18 The trp Operon A Repressible
System (Part 1)
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Metabolic Pathway
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Figure 13.18 The trp Operon A Repressible
System (Part 2)
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A Review of trp Operon

• Layered Figure 13.18 The trp Operon A
  Repressible System

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Regulation of Gene Expression in Prokaryotes

• The molecule that binds and activates a repressor
  is called a corepressor.
• The corepressor may be the end product of the
  operon (as in the case of tryptophan), or an
  analog.
• In inducible systems, an inducer from the cells
  environment prevents a repressor from blocking
  transcription.
• In repressible systems, a corepressor produced by
  the cell activates a repressor, enabling it to
  block transcription.

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Figure 13.21 Functional Organization of the
Genome of H. influenzae