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Mrs. Bradbury
AP Biology - Chapter 18
Microbial Models:
The Genetics of
Viruses and Bacteria
Discovery of Viruses
 1883: Mayer was looking for
the cause of Tobacco mosaic
disease which stunts the
growth of tobacco and gives leaves a mosaic coloration.
Mayer proposed that the disease was contagious and that
the infectious agent was a small bacterium.
 1897: Beijerinck discovered that the agent in the sap could
reproduce while inside of the plant by doing serial infections.
Agent must be much smaller and simpler than a bacterium.
 1935: Stanley crystallized the infectious particle now known
as Tobacco Mosaic Virus (TMV) after the discovery of the
electron microscope.
Virus Size & Structure
 Only 20 nm in diameter (smaller than a ribosome)
 Not cells—much simpler
 Made of a nucleic acid enclosed in a protein coat and
in some cases a membranous envelope
Viral Structure
 Viral Genome: organized as a single linear or circular
piece of nucleic acid. Can include anywhere from
4-100s of genes
Double Stranded DNA
Single Stranded DNA
•Double Stranded RNA
•Single Stranded RNA
 Capsids and Envelopes:
Capsids or protein shells come in a variety of shapes: rods,
helical, polyhedral, etc…)
Capsids are built from a large number of protein subunits
Envelopes are membranes which cloak the capsid and are
made from host cell membrane with viral proteins.
Envelopes help viruses infect their host.
Viral Reproduction
Viruses are obligate intracellular parasites
Viruses lack the enzymes for metabolism and have
no ribosomes or other organelle for making proteins,
thus isolated viruses are unable to reproduce.
Each type of virus can infect and parasitize only
a limited range of host cells called its host
range.
Viruses identify hosts by a ―lock-and-key‖ fit between
proteins on the outside of the virus and specific
receptor molecules on the cell.
They can be specific to families (mammals), a single
species, or even a single tissue.
Viral Infection
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Viral genome enters a host
cell—mechanism depends
on the type of virus
Viral genome
commandeers the host and
reprograms the cell to copy
viral nucleic acid and
manufacture viral proteins
New viruses assemble
spontaneously
Viruses copy hundreds to
thousands of times and
emerge from the host to
infect others. Sometimes
destroying the host in the
process
Phage Reproduction
2 possible reproductive cycles
Virulent viruses reproduce using the Lytic Cycle,
where the cycle ends in the death or lysis of the host
Temperate viruses reproduce using the Lysogenic
Cycle, where the host is not destroyed but hides in
the DNA of the host as a prophage and is
reproduced along with the host’s DNA, passing virus
to offspring. (These viruses can produce some
proteins including toxins which may damage cells)
Temperate viruses can enter the lytic cycle usually
due to an environmental trigger.
Lytic Cycle
Lysogenic Cycle
Bacterial Defenses
 Bacteria are not defenseless against viruses.
 Some have mutations in their receptor sites and no
longer allow the virus to enter.
 Cellular enzymes called restriction nucleases cut
up foreign DNA including phage DNA.
 Restriction Enzymes – bacterial enzymes that
naturally protect bacteria against intruding foreign
DNA.
 Bacterial hosts and their viral parasites are
continually coevolving.
Reproduction of Animal Viruses
Animal virus infection can differ from
phages depending on the type of nucleic
acid (ssDNA, dsDNA, RNA, etc…) they
contain and the presence or absence of a
viral envelope.
Viral Envelopes
 Outer membrane or envelopeoutside the capsid - is made of a
lipid bilayer which has
glycoproteins which bind to
receptors and enter the host.
Viruses can replicate inside the
cell and then go through
exocytosis to leave the host.
 These viruses can go through a
lysogenic-type infection where
they incorporate into the DNA as
a provirus (like Herpes).
RNA Viruses
• Viruses with RNA as
their genetic material
can act differently
– The viral RNA can act as a
template to make DNA
– In retroviruses (meaning
backwards) the viral RNA can
produce DNA using an
enzyme called reverse
transcriptase the DNA then
integrates as a provirus into a
chromosome of the host cell.
– Viral RNA and protein
synthesis will then occur.
Followed by Capsid assembly
and release of new virions or
transformation of host cell into
a cancerous state.
– Ex: HIV – virus that causes
AIDS
Common Human Viruses
Smallpox
Polio
Measles
Herpes
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Smallpox
Measles, Mumps
Polio
Common Cold
Influenza (flu)
HIV/AIDS
Hepatitis
Herpes (warts, cold
sores, Chickenpox,
Shingles, EpsteinBarr)
 Rubella
 Rabies
Causes of Viral Diseases in Animals
The link between viral infection and
symptoms produced is often obscure
Some viruses damage or kill cells by releasing
hydrolytic enzymes from lysosomes.
Some viruses can produce toxins including their
envelopes.
The damage caused by a virus is related
to the ability of the infected tissue to
regenerate.
Flu in respiratory tract vs. Polio in nerve cells.
Prevention of Viral Diseases in Animals
 Vaccines are harmless variants or derivatives of pathogenic
microbes that stimulate the immune system to mount
defenses against the actual pathogen and prevent infection.
 1st vaccine was for smallpox created by Edward Jenner and
was derived from cowpox.
 Vaccination sensitizes the immune system to react
vigorously if ever exposed to the actual virus.
 There are very few drugs to fight viruses, one that does work
with HIV is AZT which inhibits the action of reverse
transcriptase.
Emerging Viruses
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Viruses that make an apparent sudden appereance.
HIV/AIDS ―appeared‖ in the early 1980’s
1993 dozens in the SW US died of Hantavirus
Ebola virus causes hemorrhagic fever in Central Africa
1999 Nipah virus killed hundreds in Malaysia and
destroyed the country’s pig industry
 Every year a new flu hospitalizes thousands
 Where do these new viruses come from?
Causes of Emerging Viruses
 Mutation of existing viruses
RNA viruses have a high rate of mutation because there
is no proofreading like with DNA.
Mutations enable viruses to evolve into new genetic
varieties which can infect those which are immune to the
old version ex. flu
 Spread of a virus from one host species to
another ex. Hantavirus came from deer mice.
 Dissemination of a viral disease from a small,
isolated population can lead to an epidemic.
Viruses and Cancer
 Tumor viruses transform cells by inserting viral nucleic
acids into host cell DNA.
 Oncogenes - viral genes that trigger transformation of a
cell to a cancerous state.
 Usually need to activate more then 1 oncogene to completely
transform a cell and often work in combination with a carcinogens.
 Proto-oncogenes are versions of these genes found in
normal cells and code for genes affecting the cell cycle
(Ex: growth factor receptors).
 Cells can also become cancerous if the expression of a
proto-oncogene is affected.
 It is likely that viruses only cause cancer with a
combination of other mutagenic events – carcinogens.
Plant Viruses
 Plant viruses can stunt plant growth and destroy crop yields
 Most are RNA viruses
 Can be spread in 2 routes:
 Horizontal Transmission: a plant is infected from an external source
which must get through the epidermis (outer layer). More susceptible if
damaged by wind, chilling, injury, or insects.
 Vertical Transmission: plant inherits a virus from a parent especially
from asexual propagation or via infected seeds.
 Viruses spread easily through plants because of
plasmodesmata connecting cells and allowing the virus to flow
from one cell to the next.
Viroids
Viroids: tiny molecules of naked circular
RNA that infects plants.
RNA does not encode proteins but can replicate
inside of the host and can disrupt the
metabolism, development, and growth of a plant
cell.
Seem to cause errors in regulatory systems that
control growth.
Prions
Prions: infectious proteins which appear
to cause a variety of degenerative brain
diseases including mad cow disease.
Current theories on prions is that they are a
misfolded form of a protein normally present in
brain cells.
When the prion gets into the cell containing the
normal form of the protein, the prion converts
them all into the prion version and may trigger
chain reactions to produce more of themselves.
What is a Virus?
Viruses: Most complex molecules or the
simplest form of life?
Do not fit our usually definition of life: They
cannot reproduce independently or produce
ATP.
Yet viruses have a genome with the same
genetic code as living organisms and can
mutate and evolve.
Evolution of Viruses
 Because they depend on cells they must have evolved
after cells.
 Hypothesis:
 Viruses originated from fragments of cellular nucleic acids that
could move from one cell to another
 Evidence:
 Viruses have more in common genetically with their host than
other viruses
 Some viral genes are essentially identical to genes of the host
(oncogenes)
 Use host mechanisms for reproduction
 Probably originated as naked nucleic acids like viroids and
have evolved capsids and envelopes.
Bacterial Genome
 Bacterial genome is one
double-stranded, circular
DNA molecule.
 Bacteria contain 4.6 million base pairs which includes
4,300 genes.
 This is larger than a viral genome, but much smaller than a
eukaryotic cell genome.
 Bacterial chromosome is kept in the nucleoid region that
is NOT bound by a membrane.
 Bacteria also have plasmids or small circles of selfreplicating extrachromosomal DNA .
 F plasmids can be reversibly incorporated into the chromosome
and facilitates genetic recombination.
 Episomes are any genetic element that can exist either as a
plasmid or as part of the chromosome.
Bacterial Replication
 Bacteria divide by replicating the
chromosome and binary fission.
Semi-conservative-bidirectional
Single origin of replication
 Bacteria are asexual and each
colony are genetically identical to
the parent cell, except for
mutations.
 Bacteria can proliferate quickly,
under optimal conditions E.coli
can divide every 20 minutes.
Evolution of Bacteria
 New mutations can have an impact on genetic
diversity (Unlike higher organisms in which genetic
recombination from sexual reproduction is
responsible for most genetic diversity within
populations.)
 Individual bacteria that are well suited to their
environment clone more quickly than less fit
individuals.
 Bacteria can also genetically recombine or pass
DNA from one to another in 3 manners
Transformation
Transduction
Conjugation
Genetic Recombination in Bacteria
 Transformation: Process of gene transfer during
which a bacterial cell assimilates foreign DNA from
the surroundings.
 Transduction: phages carry bacterial genes from
one host to another.
Generalized Transduction: when viruses are
packaged within capsids, a random piece of bacterial
DNA ends up inside of the virus. The virus itself will be
defective, but can transfer DNA to a new bacteria
Specialized Transduction: a temperate phage
integrates as a prophage at a specific site. When the
phage genome is excised from the chromosome it
takes a small region of the bacterial DNA that was
adjacent to the prophage and transfers only certain,
specific genes to another bacteria
Transduction
Conjugation
 Conjugation is the direct transfer of
genetic material between two
bacterial cells that are temporarily
joined
 Conjugation is the bacterial version of sex.
 The DNA transfer is one-way, the donor is referred to as
―male‖ and the receiver is referred to as ―female.‖
 The Male (F+) uses appendages called sex pili to attach to
the female (F-) and forms a temporary cytoplasmic bridge for
the DNA to be transferred.
 ―Maleness‖ is determined by having an F (fertility) factor in
the DNA, either in the chromosome or on a plasmid.
 F factors have about 25 genes, most are required for the formation
of sex pili.
R plasmids – antibiotic resistance
 R plasmids contain genes for antibiotic
resistance by containing enzymes that destroy
certain antibiotics.
 R plasmids can be transferred by conjugation.
 Can transfer resistance genes to bacteria of
different species – including pathogenic strains.
 Causes concern because of natural selection,
eventually all bacteria will become resistant to
specific antibiotics.
Transposons
 A transposon is a transposable or movable genetic
element. A ―jumping gene‖
A piece of DNA that can be moved from one location to
another in a cell’s genome.
They can never exist independently like a plasmid or a
prophage.
They can either jump (cut-and-paste: conservative
transposition) to move about or make a copy to be
inserted elsewhere in the genome (replicative
transposition).
 In bacteria, transposons can move within the chromosome,
to a plasmid, or from a plasmid to the chromosome, or from
one plasmid to another.
Insertion Sequences
 Insertion sequences are the simplest type of transposons.
 They are made of only the genes necessary for transposition.
 Nucleotide sequence coding for transposase
 Inverted repeats
 Transposase recognizes these repeats as the boundaries of a
transposon and cuts and reseals
 Insertion sequences cause mutations when then land within
the coding sequence of a gene – significant role in bacterial
evolution.
Transposon Movement
Composite Transposons
 Composite Transposons are more complex than
insertion sequences containing multiple genes
sandwiched between the insertion sequences.
 Generate genetic diversity by moving genes from one
chromosome to another, or another species.
Control of Gene Expression
 Depending on
environmental conditions,
cells need to turn on or turn
off certain pathways within
their metabolism.
 Metabolic control occurs on
two levels:
 Cells can vary the numbers
of enzyme molecules made:
regulation of gene
expression.
 Cells can adjust the activity
of enzymes: regulation of
enzyme activity (allosteric
inhibition)
Operons— The basic concept
 Operons - a regulated cluster of adjacent
structural genes with related functions.
Single promoter region for all adjacent genes.
 Ex: E.coli synthesizes tryptophan (trp) from a
precursor molecule in a series of steps, each
reaction using its own enzyme.
 5 genes coding for the enzymes are clustered
together on the chromosome using one promoter.
Transcription will make one long mRNA coding for all 5
enzymes in the pathway.
 Advantage of grouping genes is that they can all
use the same ―on-off‖ switch.
Operon—Structure
 Made of the operator, the promoter, and the
transcription unit (genes).
 Operator: on/off switch. Found within the
promoter, the operator controls the access of RNA
polymerase to the genes’
By itself the operator is on, RNA polymerase can bind and
transcribe.
The operator can be turned off by a repressor which binds
to the operator and blocks transcription. Repressors bind
specifically and are reversible.
The repressor is the product of a regulatory gene, located
some distance away from the operon it controls and has its
own promoter.
Ex: trp Operon
Ex: trp Operon
 An operator switches between on and off modes
depending on the number of repressors.
 Regulatory proteins are usually allosteric, with two
alternative shapes, active and inactive.
 Ex: Tryptophan binds to the repressor’s allosteric site,
causing the repressor to change its conformation.
 The activated repressor binds to the operator, which
switches the trp operon off.
Tryptophan functions as a corepressor.
Corepressors - small molecules that bind to a
repressor causing the repressor to change into its
active conformation. (Ex: tryptophan)
trp Operon Regulation
Repressible Vs. Inducible Operons
 Their genes are switched
on until a specific
metabolite activates the
repressor.
 They generally function in
anabolic pathways.
 Pathway end product
switches off its own
production by repressing
enzyme synthesis.
 Ex: trp Operon
 Their genes are switched
off until a specific
metabolite inactivates the
repressor.
 They function in catabolic
pathways.
 Enzyme synthesis is
switched on by the
nutrient the pathway
uses.
 Ex: lac Operon
Ex: lac Operon – Inducible operon
 When the disaccharide lactose is available, the bacteria require the enzyme
β-galactosidase to break it down.
 The gene for β-galactosidase is a part of the lac operon which includes other
proteins needed for the metabolism of lactose.
 This operator is usually blocked by a lac repressor, which is coded for by a
regulatory gene lacI.
 Lactose acts as an inducer and inactivates the repressor, turning on the
operon.
Figure 18.21a The lac operon: regulated synthesis of inducible enzymes
Positive Gene Regulation
• Positive control only occurs if an activator molecule interacts
directly with the genome to turn on transcription.
• Ex: cAMP or cyclic AMP is a small molecule that accumulates
when glucose levels are low.
• cAMP Receptor Protein (CRP)
• When cAMP binds to the allosteric site on CRP, the protein becomes
active and can bind to a site on the lac promoter causing the DNA to
bend and makes it easier for RNA polymerase to bind
Growth Curves for bacteria and viruses
Explain the difference between the graphs