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Viruses and Bacteria
What you need to Know
Plus
Gene Regulation
Phage and Bacteria
Virus
Bacteria
Animal Cell
Structure of Viruses
 Viruses are not cells
 Viruses are very small infectious
particles consisting of nucleic acid
enclosed in a protein coat and, in some
cases, a membranous envelope
Capsids and Envelopes
 A capsid is the protein shell that
encloses the viral genome
 A capsid can have various structures
 Some viruses have structures have
membranous envelopes that help them
infect hosts
 These viral envelopes surround the
capsids of influenza viruses and many
other viruses found in animals
 Viral envelopes, which are derived from
the host cell’s membrane, contain a
combination of viral and host cell
molecules
General Features of Viral
Reproductive Cycles
 Viruses are obligate intracellular
parasites, which means they can
reproduce only within a host cell
 Each virus has a host range, a limited
number of host cells that it can infect
 Viruses use enzymes, ribosomes, and
small host molecules to synthesize
progeny viruses
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Reproductive Cycles of
Phages
 Phages are the best understood of all
viruses
 Phages have two reproductive
mechanisms: the lytic cycle and the
lysogenic cycle
The Lytic Cycle
 The lytic cycle is a phage reproductive cycle
that culminates in the death of the host cell
 The lytic cycle produces new phages and
digests the host’s cell wall, releasing the
progeny viruses
 A phage that reproduces only by the lytic cycle
is called a virulent phage
 Bacteria have defenses against phages,
including restriction enzymes that recognize
and cut up certain phage DNA
LE 18-6
Attachment
Phage assembly
Head
Tails
Release
Entry of phage DNA
and degradation of
host DNA
Tail fibers
Assembly
Synthesis of viral
genomes and proteins
The Lysogenic Cycle
 The lysogenic cycle replicates the phage genome without
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


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destroying the host
The viral DNA molecule is incorporated by genetic
recombination into the host cell’s chromosome
This integrated viral DNA is known as a prophage
Every time the host divides, it copies the phage DNA and
passes the copies to daughter cells
Phages that use both the lytic and lysogenic cycles are
called temperate phages
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LE 18-7
Phage
DNA
The phage attaches to a
host cell and injects its DNA.
Daughter cell
with prophage
Many cell divisions
produce a large
population of
bacteria infected with
the prophage.
Phage DNA
circularizes
Phage
Bacterial
chromosome
Lytic cycle
The cell lyses, releasing phages.
Occasionally, a prophage
exits the bacterial chromosome,
initiating a lytic cycle.
Lysogenic cycle
Certain factors
determine whether
Lytic cycle or Lysogenic cycle
is induced
is entered
New phage DNA and proteins are
synthesized and assembled into phages.
The bacterium reproduces
normally, copying the prophage
and transmitting it to daughter cells.
Prophage
Phage DNA integrates into the
bacterial chromosomes, becoming a
prophage.
Viroids and Prions: The
Simplest Infectious Agents
 Viroids are circular RNA molecules that
infect plants and disrupt their growth
 Prions are slow-acting, virtually
indestructible infectious proteins that
cause brain diseases in mammals
 Prions propagate by converting normal
proteins into the prion version
LE 18-13
Prion
Original
prion
Many prions
Normal
protein
New
prion
The Bacterial Genome and Its
Replication
 The bacterial chromosome is usually a
circular DNA molecule with few
associated proteins
 Many bacteria also have plasmids,
smaller circular DNA molecules that can
replicate independently of the
chromosome
 Bacterial cells divide by binary fission,
which is preceded by replication of the
chromosome
LE 18-14
Replication fork
Origin of
replication
Termination
of replication
Mutation and Genetic
Recombination as Sources of
Genetic Variation
 Since bacteria can reproduce rapidly, new
mutations quickly increase genetic diversity
 More genetic diversity arises by recombination
of DNA from two different bacterial cells
Mechanisms of Gene Transfer and
Genetic Recombination in
Bacteria
 Three processes bring bacterial DNA from
different individuals together:
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Transformation-Transformation is the alteration of a
bacterial cell’s genotype and phenotype by the
uptake of naked, foreign DNA from the surrounding
environment (Griffith)
Transduction -In the process known as
transduction, phages carry bacterial genes from
one host cell to another
Conjugation -Conjugation is the direct transfer of
genetic material between bacterial cells that are
temporarily joined (Pili)
Transposition of Genetic
Elements
 The DNA of a cell can also undergo
recombination due to movement of
transposable elements within the cell’s
genome
 Transposable elements, often called
“jumping genes,” contribute to genetic
shuffling in bacteria
Transposons
 Transposable elements called
transposons are longer and more
complex than insertion sequences
 In addition to DNA required for
transposition, transposons have extra
genes that “go along for the ride,” such
as genes for antibiotic resistance
LE 18-19b
Transposing
Insertion
sequence
Antibiotic
resistance gene
Insertion
sequence
5
3
3
5
Inverted repeat
Transposase gene
Repressible and Inducible
Operons: Two Types of Negative
Gene Regulation
 A repressible operon is one that is usually on; binding of
a repressor to the operator shuts off transcription
 The trp operon is a repressible operon
 An inducible operon is one that is usually off; a molecule
called an inducer inactivates the repressor and turns on
transcription
 The classic example of an inducible operon is the lac
operon, which contains genes coding for enzymes in
hydrolysis and metabolism of lactose
LE 18-22a
Promoter
Regulatory
gene
Operator
lacl
DNA
lacZ
No
RNA
made
3
mRNA
5
Protein
RNA
polymerase
Active
repressor
Lactose absent, repressor active, operon off
LE 18-22b
lac operon
DNA
lacZ
lacl
3
mRNA
5
lacA
Permease
Transacetylase
RNA
polymerase
mRNA 5
-Galactosidase
Protein
Allolactose
(inducer)
lacY
Inactive
repressor
Lactose present, repressor inactive, operon on
 Inducible enzymes usually function in
catabolic pathways
 Repressible enzymes usually function in
anabolic pathways
 Regulation of the trp and lac operons
involves negative control of genes
because operons are switched off by the
active form of the repressor
Positive Gene Regulation
 Some operons are also subject to
positive control through a stimulatory
activator protein, such as catabolite
activator protein (CAP)
 When glucose (a preferred food source
of E. coli ) is scarce, the lac operon is
activated by the binding of CAP
 When glucose levels increase, CAP
detaches from the lac operon, turning it
off
LE 18-23a
Promoter
DNA
lacl
lacZ
CAP-binding site
Active
CAP
cAMP
Inactive
CAP
RNA
Operator
polymerase
can bind
and transcribe
Inactive lac
repressor
Lactose present, glucose scarce (cAMP level high): abundant lac
mRNA synthesized
LE 18-23b
Promoter
DNA
lacl
CAP-binding site
Inactive
CAP
lacZ
Operator
RNA
polymerase
can’t bind
Inactive lac
repressor
Lactose present, glucose present (cAMP level low): little lac
mRNA synthesized
LE 19-2a
2 nm
DNA double helix
Histones
Histone
tails
Histone H1
10 nm
Linker DNA
(“string”)
Nucleosome
(“bead”)
Nucleosomes (10-nm fiber)
LE 19-2b
30 nm
Nucleosome
30-nm fiber
LE 19-2c
Protein scaffold
Loops
300 nm
Looped domains (300-nm fiber)
Scaffold
Concept 19.2: Gene expression
can be regulated at any stage, but
the key step is transcription
 All organisms must regulate which genes
are expressed at any given time
 A multicellular organism’s cells undergo
cell differentiation, specialization in form
and function
Differential Gene Expression
 Differences between cell types result
from differential gene expression, the
expression of different genes by cells
within the same genome
 In each type of differentiated cell, a
unique subset of genes is expressed
 Many key stages of gene expression can
be regulated in eukaryotic cells
Regulation of Chromatin
Structure
 Genes within highly packed
heterochromatin are usually not
expressed
 Chemical modifications to histones and
DNA of chromatin influence both
chromatin structure and gene expression
Histone Modification
 In histone acetylation, acetyl groups are
attached to positively charged lysines in
histone tails
 This process seems to loosen chromatin
structure, thereby promoting the initiation
of transcription
LE 19-4
Histone
tails
DNA
double helix
Amino acids
available
for chemical
modification
Histone tails protrude outward from a nucleosome
Unacetylated histones
Acetylated histones
Acetylation of histone tails promotes loose chromatin
structure that permits transcription
DNA Methylation
 DNA methylation, the addition of methyl groups
to certain bases in DNA, is associated with
reduced transcription in some species
 In some species, DNA methylation causes longterm inactivation of genes in cellular
differentiation
 In genomic imprinting, methylation turns off
either the maternal or paternal alleles of certain
genes at the start of development