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Chapter 18
The Genetics of Viruses and Bacteria PowerPoint Lectures for Biology, Seventh Edition Neil Campbell and Jane Reece
Lectures by Chris Romero Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Overview: Microbial Model Systems • Viruses called bacteriophages – Can infect and set in motion a genetic takeover of bacteria, such as Escherichia coli
Figure 18.1 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
0.5 µm
• E. coli and its viruses – Are called model systems because of their frequent use by researchers in studies that reveal broad biological principles
• Beyond their value as model systems – Viruses and bacteria have unique genetic mechanisms that are interesting in their own right
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Recall that bacteria are prokaryotes – With cells much smaller and more simply organized than those of eukaryotes
• Viruses – Are smaller and simpler still Virus
Bacterium Animal cell
Animal cell nucleus
Figure 18.2
0.25 µm
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• Concept 18.1: A virus has a genome but can reproduce only within a host cell • Scientists were able to detect viruses indirectly – Long before they were actually able to see them
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
The Discovery of Viruses: Scientific Inquiry • Tobacco mosaic disease – Stunts the growth of tobacco plants and gives their leaves a mosaic coloration
Figure 18.3 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• In the late 1800s – Researchers hypothesized that a particle smaller than bacteria caused tobacco mosaic disease
• In 1935, Wendell Stanley – Confirmed this hypothesis when he crystallized the infectious particle, now known as tobacco mosaic virus (TMV)
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Structure of Viruses • Viruses – Are very small infectious particles consisting of nucleic acid enclosed in a protein coat and, in some cases, a membranous envelope
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Viral Genomes • Viral genomes may consist of – Double- or single-stranded DNA – Double- or single-stranded RNA
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Capsids and Envelopes • A capsid – Is the protein shell that encloses the viral genome – Can have various structures Capsomere of capsid
RNA Capsomere
DNA
Glycoprotein 70–90 nm (diameter) 18 × 250 mm
20 nm
50 nm
Figure 18.4a, b (a) Tobacco mosaic virus (b) Adenoviruses Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Some viruses have envelopes – Which are membranous coverings derived from the membrane of the host cell Membranous envelope
Capsid RNA
Glycoprotein 80–200 nm (diameter)
Figure 18.4c
50 nm (c) Influenza viruses
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• Bacteriophages, also called phages – Have the most complex capsids found among viruses Head
Tail sheath
DNA
Tail fiber
80 × 225 nm
Figure 18.4d Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
50 nm (d) Bacteriophage T4
General Features of Viral Reproductive Cycles • Viruses are obligate intracellular parasites – They can reproduce only within a host cell
• Each virus has a host range – A limited number of host cells that it can infect
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• Viruses use enzymes, ribosomes, and small molecules of host cells – To synthesize progeny viruses Entry into cell and uncoating of DNA
DNA Capsid
VIRUS
Transcription Replication
HOST CELL Viral DNA mRNA
Viral DNA
Capsid proteins
Self-assembly of new virus particles and their exit from cell
Figure 18.5 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Reproductive Cycles of Phages • Phages – Are the best understood of all viruses – Go through two alternative reproductive mechanisms: the lytic cycle and the lysogenic cycle
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The Lytic Cycle • The lytic cycle – Is a phage reproductive cycle that culminates in the death of the host – Produces new phages and digests the host’s cell wall, releasing the progeny viruses
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• The lytic cycle of phage T4, a virulent phage 1 Attachment. The T4 phage uses
2 Entry of phage DNA
its tail fibers to bind to specific receptor sites on the outer surface of an E. coli cell.
and degradation of host DNA. The sheath of the tail contracts, injecting the phage DNA into the cell and leaving an empty capsid outside. The cell’s DNA is hydrolyzed.
5 Release. The phage directs production of an enzyme that damages the bacterial cell wall, allowing fluid to enter. The cell swells and finally bursts, releasing 100 to 200 phage particles.
Phage assembly
4 Assembly. Three separate sets of proteins
3 Synthesis of viral genomes
self-assemble to form phage heads, tails, and tail fibers. The phage genome is packaged inside the capsid as the head forms. Figure 18.6
Head
Tails
Tail fibers
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
and proteins. The phage DNA directs production of phage proteins and copies of the phage genome by host enzymes, using components within the cell.
The Lysogenic Cycle • The lysogenic cycle – Replicates the phage genome without destroying the host
• Temperate phages – Are capable of using both the lytic and lysogenic cycles of reproduction
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• The lytic and lysogenic cycles of phage λ, a temperate phage Phage DNA The phage attaches to a host cell and injects its DNA. Phage DNA circularizes Phage Occasionally, a prophage exits the bacterial chromosome, initiating a lytic cycle.
Bacterial chromosome
Lytic cycle The cell lyses, releasing phages.
Lysogenic cycle Certain factors determine whether
Lytic cycle is induced
Figure 18.7
Many cell divisions produce a large population of bacteria infected with the prophage.
or
New phage DNA and proteins are synthesized and assembled into phages.
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Lysogenic cycle is entered
Prophage
The bacterium reproduces normally, copying the prophage and transmitting it to daughter cells.
Phage DNA integrates into the bacterial chromosome, becoming a prophage.
Reproductive Cycles of Animal Viruses • The nature of the genome – Is the basis for the common classification of animal viruses
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• Classes of animal viruses
Table 18.1 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Viral Envelopes • Many animal viruses – Have a membranous envelope
• Viral glycoproteins on the envelope – Bind to specific receptor molecules on the surface of a host cell
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• The reproductive cycle of an enveloped RNA virus 1 Glycoproteins on the viral envelope
Capsid
bind to specific receptor molecules (not shown) on the host cell, promoting viral entry into the cell.
RNA Envelope (with glycoproteins)
2 Capsid and viral genome enter cell
HOST CELL Viral genome (RNA) Template 5 Complementary RNA strands also function as mRNA, which is translated into both capsid proteins (in the cytosol) and glycoproteins for the viral envelope (in the ER).
3 The viral genome (red) functions as a template for synthesis of complementary RNA strands (pink) by a viral enzyme.
mRNA Capsid proteins ER
Glycoproteins
Copy of genome (RNA)
4 New copies of viral genome RNA are made using complementary RNA strands as templates.
6 Vesicles transport envelope glycoproteins to the plasma membrane. 8 New virus 7 A capsid assembles
Figure 18.8
around each viral genome molecule.
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RNA as Viral Genetic Material • The broadest variety of RNA genomes – Is found among the viruses that infect animals
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• Retroviruses, such as HIV, use the enzyme reverse transcriptase – To copy their RNA genome into DNA, which can then be integrated into the host genome as a provirus Glycoprotein
Viral envelope Capsid
Reverse transcriptase
Figure 18.9 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
RNA (two identical strands)
• The reproductive cycle of HIV, a retrovirus HIV
Membrane of white blood cell
1 The virus fuses with the cell’s plasma membrane. The capsid proteins are removed, releasing the viral proteins and RNA.
2 Reverse transcriptase catalyzes the synthesis of a DNA strand complementary to the viral RNA. HOST CELL
3 Reverse transcriptase catalyzes the synthesis of a second DNA strand complementary to the first.
Reverse transcriptase Viral RNA
0.25 µm HIV entering a cell
RNA-DNA hybrid
4 The double-stranded DNA is incorporated as a provirus into the cell’s DNA.
DNA
NUCLEUS Chromosomal DNA RNA genome for the next viral generation
Provirus
mRNA
5 Proviral genes are transcribed into RNA molecules, which serve as genomes for the next viral generation and as mRNAs for translation into viral proteins.
6 The viral proteins include capsid proteins and reverse transcriptase (made in the cytosol) and envelope glycoproteins (made in the ER).
Figure 18.10
New HIV leaving a cell
9 New viruses bud off from the host cell.
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8 Capsids are assembled around viral genomes and reverse transcriptase molecules.
7 Vesicles transport the glycoproteins from the ER to the cell’s plasma membrane.
Evolution of Viruses • Viruses do not really fit our definition of living organisms • Since viruses can reproduce only within cells – They probably evolved after the first cells appeared, perhaps packaged as fragments of cellular nucleic acid
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• Concept 18.2: Viruses, viroids, and prions are formidable pathogens in animals and plants • Diseases caused by viral infections – Affect humans, agricultural crops, and livestock worldwide
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Viral Diseases in Animals • Viruses may damage or kill cells – By causing the release of hydrolytic enzymes from lysosomes
• Some viruses cause infected cells – To produce toxins that lead to disease symptoms
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• Vaccines – Are harmless derivatives of pathogenic microbes that stimulate the immune system to mount defenses against the actual pathogen – Can prevent certain viral illnesses
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Emerging Viruses • Emerging viruses – Are those that appear suddenly or suddenly come to the attention of medical scientists
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• Severe acute respiratory syndrome (SARS) – Recently appeared in China
(a) Young ballet students in Hong Kong (b) The SARS-causing agent is a coronavirus wear face masks to protect themselves like this one (colorized TEM), so named for the “corona” of glycoprotein spikes protruding from from the virus causing SARS. the envelope. Figure 18.11 A, B Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Outbreaks of “new” viral diseases in humans – Are usually caused by existing viruses that expand their host territory
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Viral Diseases in Plants • More than 2,000 types of viral diseases of plants are known • Common symptoms of viral infection include – Spots on leaves and fruits, stunted growth, and damaged flowers or roots
Figure 18.12 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Plant viruses spread disease in two major modes – Horizontal transmission, entering through damaged cell walls – Vertical transmission, inheriting the virus from a parent
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Viroids and Prions: The Simplest Infectious Agents • Viroids – Are circular RNA molecules that infect plants and disrupt their growth
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• Prions – Are slow-acting, virtually indestructible infectious proteins that cause brain diseases in mammals – Propagate by converting normal proteins into the prion version Prion
Original prion
Many prions Normal protein
New prion
Figure 18.13 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Concept 18.3: Rapid reproduction, mutation, and genetic recombination contribute to the genetic diversity of bacteria • Bacteria allow researchers – To investigate molecular genetics in the simplest true organisms
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The Bacterial Genome and Its Replication • The bacterial chromosome – Is usually a circular DNA molecule with few associated proteins
• In addition to the chromosome – Many bacteria have plasmids, smaller circular DNA molecules that can replicate independently of the bacterial chromosome
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• Bacterial cells divide by binary fission – Which is preceded by replication of the bacterial chromosome Replication fork Origin of replication
Termination of replication
Figure 18.14 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Mutation and Genetic Recombination as Sources of Genetic Variation • Since bacteria can reproduce rapidly – New mutations can quickly increase a population’s genetic diversity
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• Further genetic diversity – Can arise by recombination of the DNA from two different bacterial cells EXPERIMENT
Researchers had two mutant strains, one that could make arginine but not tryptophan (arg+ trp–) and one that could make tryptophan but not arginine (arg− trp+). Each mutant strain and a mixture of both strains were grown in a liquid medium containing all the required amino acids. Samples from each liquid culture were spread on plates containing a solution of glucose and inorganic salts (minimal medium), solidified with agar. Mixture
Mutant strain arg+ trp–
Figure 18.15
Mutant strain arg− trp+
RESULTS Only the samples from the mixed culture, contained cells that gave rise to colonies on minimal medium, which lacks amino acids.
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Mixture
Mutant strain arg+ trp–
Mutant strain arg– trp+
No colonies (control)
CONCLUSION
Colonies grew
No colonies (control)
Because only cells that can make both arginine and tryptophan (arg+ trp+ cells) can grow into colonies on minimal medium, the lack of colonies on the two control plates showed that no further mutations had occurred restoring this ability to cells of the mutant strains. Thus, each cell from the mixture that formed a colony on the minimal medium must have acquired one or more genes from a cell of the other strain by genetic recombination.
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Mechanisms of Gene Transfer and Genetic Recombination in Bacteria • Three processes bring bacterial DNA from different individuals together – Transformation – Transduction – Conjugation
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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
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Transduction • In the process known as transduction – Phages carry bacterial genes from one host cell to another Phage DNA
A+ B+
1 Phage infects bacterial cell that has alleles A+ and B+
2 Host DNA (brown) is fragmented, and phage DNA
A+ B+
and proteins are made. This is the donor cell.
Donor cell 3 A bacterial DNA fragment (in this case a fragment with
the A+ allele) may be packaged in a phage capsid. A+ 4 Phage with the A+ allele from the donor cell infects
a recipient A–B– cell, and crossing over (recombination) between donor DNA (brown) and recipient DNA (green) occurs at two places (dotted lines).
Crossing over A+ A– B– Recipient cell
5 The genotype of the resulting recombinant cell (A+B–)
Figure 18.16
differs from the genotypes of both the donor (A+B+) and the recipient (A–B–).
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A+ B– Recombinant cell
Conjugation and Plasmids • Conjugation – Is the direct transfer of genetic material between bacterial cells that are temporarily joined
Figure 18.17 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Sex pilus
1 µm
The F Plasmid and Conjugation • Cells containing the F plasmid, designated F+ cells – Function as DNA donors during conjugation – Transfer plasmid DNA to an F− recipient cell
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• Conjugation and transfer of an F plasmid from an F+ donor to an F− recipient
F Plasmid
Bacterial chromosome
F+ cell
F+ cell
Mating bridge F– cell
Bacterial chromosome
1 A cell carrying an F plasmid (an F+ cell) can form a mating bridge with an F– cell and transfer its F plasmid.
2 A single strand of the F plasmid breaks at a specific point (tip of blue arrowhead) and begins to move into the recipient cell. As transfer continues, the donor plasmid rotates (red arrow).
F+ cell 3 DNA replication occurs in 4 both donor and recipient cells, using the single parental strands of the F plasmid as templates to synthesize complementary strands.
Figure 18.18a
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The plasmid in the recipient cell circularizes. Transfer and replication result in a compete F plasmid in each cell. Thus, both cells are now F+.
(a) Conjugation and transfer of an F plasmid from an F+ donor to an F– recipient
• Chromosomal genes can be transferred during conjugation – When the donor cell’s F factor is integrated into the chromosome • A cell with the F factor built into its chromosome – Is called an Hfr cell • The F factor of an Hfr cell – Brings some chromosomal DNA along with it when it is transferred to an F– cell
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• Conjugation and transfer of part of the bacterial chromosome from an Hfr donor to an F– recipient, resulting in recombination Hfr cell
F+ cell
F factor
1
Hfr cell
A+
The circular F plasmid in an F+ cell can be integrated into the circular chromosome by a single crossover event (dotted line).
B+
C+
The resulting cell is called an Hfr cell (for High frequency of recombination).
D+
C+ B+
D+
2
D+ C+
A+
B+
A+
D+ C+
B+
A+
A+
F– cell 3
B–
C– A–
B+ D–
Since an Hfr cell has all the F-factor genes, it can form a mating bridge with an F– cell and transfer DNA.
B–
A–
B+ A+
B–
C– A–
A+
D–
4 A single strand of the F factor breaks and begins to move through the bridge. DNA replication occurs in both donor and recipient cells, resulting in double-stranded DNA
Temporary partial diploid 7
C–
B–
C– D–
5 The location and orientation of the F factor in the donor chromosome determine the sequence of gene transfer during conjugation. In this example, the transfer sequence for four genes is A-B-C-D.
D–
Two crossovers can result in the exchange of similar (homologous) genes between the transferred chromosome fragment (brown) and the recipient cell’s chromosome (green).
Figure 18.18b Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
B– A+
B+
B+ A+
A–
C– A–
D–
6
B–
C– A–
D–
The mating bridge usually breaks well before the entire chromosome and the rest of the F factor are transferred.
Recombinant F– bacterium
8 The piece of DNA ending up outside the bacterial chromosome will eventually be degraded by the cell’s enzymes. The recipient cell now contains a new combination of genes but no F factor; it is a recombinant F– cell.
(b) Conjugation and transfer of part of the bacterial chromosome from an Hfr donor to an F– recipient, resulting in recombination
R plasmids and Antibiotic Resistance • R plasmids – Confer resistance to various antibiotics
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Transposition of Genetic Elements • Transposable elements – Can move around within a cell’s genome – Are often called “jumping genes” – Contribute to genetic shuffling in bacteria
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Insertion Sequences • An insertion sequence contains a single gene for transposase – An enzyme that catalyzes movement of the insertion sequence from one site to another within the genome Insertion sequence 3′
A T C C G G T…
A C C G G A T…
3′
5′
TAGGCCA…
TGGCCTA…
5′
Transposase gene Inverted Inverted repeat repeat (a) Insertion sequences, the simplest transposable elements in bacteria, contain a single gene that encodes transposase, which catalyzes movement within the genome. The inverted repeats are backward, upside-down versions of each other; only a portion is shown. The inverted repeat sequence varies from one type of insertion sequence to another. Figure 18.19a Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Transposons • Bacterial transposons – Also move about within the bacterial genome – Have additional genes, such as those for antibiotic resistance Transposon
Insertion sequence
Antibiotic resistance gene
Insertion sequence
5′
5′
3′
3′
Inverted repeats Transposase gene (b) Transposons contain one or more genes in addition to the transposase gene. In the transposon shown here, a gene for resistance to an antibiotic is located between twin insertion sequences. The gene for antibiotic resistance is carried along as part of the transposon when the transposon is inserted at a new site in the genome. Figure 18.19b Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Concept 18.4: Individual bacteria respond to environmental change by regulating their gene expression • E. coli, a type of bacteria that lives in the human colon – Can tune its metabolism to the changing environment and food sources
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• This metabolic control occurs on two levels – Adjusting the activity of metabolic enzymes already present – Regulating the genes encoding the metabolic enzymes (a) Regulation of enzyme activity Precursor
Feedback inhibition
(b) Regulation of enzyme production
Enzyme 1 Gene 1
Enzyme 2 Gene 2
Regulation of gene expression
Enzyme 3 Gene 3
– Enzyme 4 Gene 4
– Enzyme 5 Gene 5 Tryptophan
Figure 18.20a, b Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Operons: The Basic Concept • In bacteria, genes are often clustered into operons, composed of – An operator, an “on-off” switch – A promoter – Genes for metabolic enzymes
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• An operon – Is usually turned “on” – Can be switched off by a protein called a repressor
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• The trp operon: regulated synthesis of repressible enzymes trp operon Promoter
DNA
Promoter Genes of operon trpD trpC trpE
trpR
trpB
trpA
Operator Regulatory gene mRNA 5′
3′
RNA polymerase
Start codon
Stop codon
mRNA 5′ E
Protein
Inactive repressor
D
C
B
A
Polypeptides that make up enzymes for tryptophan synthesis
(a) Tryptophan absent, repressor inactive, operon on. RNA polymerase attaches to the DNA at the promoter and transcribes the operon’s genes. Figure 18.21a Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
DNA No RNA made
mRNA
Protein
Active repressor
Tryptophan (corepressor) (b) Tryptophan present, repressor active, operon off. As tryptophan accumulates, it inhibits its own production by activating the repressor protein. Figure 18.21b Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Repressible and Inducible Operons: Two Types of Negative Gene Regulation • In a repressible operon – Binding of a specific repressor protein to the operator shuts off transcription
• In an inducible operon – Binding of an inducer to an innately inactive repressor inactivates the repressor and turns on transcription
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• The lac operon: regulated synthesis of inducible enzymes Promoter Regulatory gene
DNA
Operator
lacl
lacZ
3′ mRNA
Protein
5′
No RNA made RNA polymerase
Active repressor
(a) Lactose absent, repressor active, operon off. The lac repressor is innately active, and in the absence of lactose it switches off the operon by binding to the operator. Figure 18.22a Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
lac operon
DNA
lacl
lacz
3′ mRNA
5′
lacA
RNA polymerase mRNA 5' 5′ mRNA
β-Galactosidase
Protein Allolactose (inducer)
lacY
Permease
Transacetylase
Inactive repressor
(b) Lactose present, repressor inactive, operon on. Allolactose, an isomer of lactose, derepresses the operon by inactivating the repressor. In this way, the enzymes for lactose utilization are induced. Figure 18.22b
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• Inducible enzymes – Usually function in catabolic pathways
• Repressible enzymes – Usually function in anabolic pathways
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• Regulation of both the trp and lac operons – Involves the negative control of genes, because the operons are switched off by the active form of the repressor protein
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Positive Gene Regulation • Some operons are also subject to positive control – Via a stimulatory activator protein, such as catabolite activator protein (CAP)
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• In E. coli, when glucose, a preferred food source, is scarce – The lac operon is activated by the binding of a regulatory protein, catabolite activator protein Promoter (CAP) DNA
lacl
lacZ
CAP-binding site cAMP
Inactive CAP
RNA Operator polymerase can bind Active and transcribe CAP
Inactive lac repressor
(a) Lactose present, glucose scarce (cAMP level high): abundant lac mRNA synthesized. If glucose is scarce, the high level of cAMP activates CAP, and the lac operon produces Figure 18.23a large amounts of mRNA for the lactose pathway. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• When glucose levels in an E. coli cell increase – CAP detaches from the lac operon, turning it off Promoter DNA
lacl
lacZ
CAP-binding site
Operator RNA polymerase can’t bind
Inactive CAP
Inactive lac repressor
(b) Lactose present, glucose present (cAMP level low): little lac mRNA synthesized. When glucose is present, cAMP is scarce, and CAP is unable to stimulate transcription. Figure 18.23b
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The Genetics of Viruses and Bacteria PowerPoint Lectures for Biology, Seventh Edition Neil Campbell and Jane Reece
Lectures by Chris Romero Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Overview: Microbial Model Systems • Viruses called bacteriophages – Can infect and set in motion a genetic takeover of bacteria, such as Escherichia coli
Figure 18.1 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
0.5 µm
• E. coli and its viruses – Are called model systems because of their frequent use by researchers in studies that reveal broad biological principles
• Beyond their value as model systems – Viruses and bacteria have unique genetic mechanisms that are interesting in their own right
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Recall that bacteria are prokaryotes – With cells much smaller and more simply organized than those of eukaryotes
• Viruses – Are smaller and simpler still Virus
Bacterium Animal cell
Animal cell nucleus
Figure 18.2
0.25 µm
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Concept 18.1: A virus has a genome but can reproduce only within a host cell • Scientists were able to detect viruses indirectly – Long before they were actually able to see them
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
The Discovery of Viruses: Scientific Inquiry • Tobacco mosaic disease – Stunts the growth of tobacco plants and gives their leaves a mosaic coloration
Figure 18.3 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• In the late 1800s – Researchers hypothesized that a particle smaller than bacteria caused tobacco mosaic disease
• In 1935, Wendell Stanley – Confirmed this hypothesis when he crystallized the infectious particle, now known as tobacco mosaic virus (TMV)
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Structure of Viruses • Viruses – Are very small infectious particles consisting of nucleic acid enclosed in a protein coat and, in some cases, a membranous envelope
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Viral Genomes • Viral genomes may consist of – Double- or single-stranded DNA – Double- or single-stranded RNA
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Capsids and Envelopes • A capsid – Is the protein shell that encloses the viral genome – Can have various structures Capsomere of capsid
RNA Capsomere
DNA
Glycoprotein 70–90 nm (diameter) 18 × 250 mm
20 nm
50 nm
Figure 18.4a, b (a) Tobacco mosaic virus (b) Adenoviruses Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Some viruses have envelopes – Which are membranous coverings derived from the membrane of the host cell Membranous envelope
Capsid RNA
Glycoprotein 80–200 nm (diameter)
Figure 18.4c
50 nm (c) Influenza viruses
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• Bacteriophages, also called phages – Have the most complex capsids found among viruses Head
Tail sheath
DNA
Tail fiber
80 × 225 nm
Figure 18.4d Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
50 nm (d) Bacteriophage T4
General Features of Viral Reproductive Cycles • Viruses are obligate intracellular parasites – They can reproduce only within a host cell
• Each virus has a host range – A limited number of host cells that it can infect
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Viruses use enzymes, ribosomes, and small molecules of host cells – To synthesize progeny viruses Entry into cell and uncoating of DNA
DNA Capsid
VIRUS
Transcription Replication
HOST CELL Viral DNA mRNA
Viral DNA
Capsid proteins
Self-assembly of new virus particles and their exit from cell
Figure 18.5 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Reproductive Cycles of Phages • Phages – Are the best understood of all viruses – Go through two alternative reproductive mechanisms: the lytic cycle and the lysogenic cycle
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
The Lytic Cycle • The lytic cycle – Is a phage reproductive cycle that culminates in the death of the host – Produces new phages and digests the host’s cell wall, releasing the progeny viruses
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• The lytic cycle of phage T4, a virulent phage 1 Attachment. The T4 phage uses
2 Entry of phage DNA
its tail fibers to bind to specific receptor sites on the outer surface of an E. coli cell.
and degradation of host DNA. The sheath of the tail contracts, injecting the phage DNA into the cell and leaving an empty capsid outside. The cell’s DNA is hydrolyzed.
5 Release. The phage directs production of an enzyme that damages the bacterial cell wall, allowing fluid to enter. The cell swells and finally bursts, releasing 100 to 200 phage particles.
Phage assembly
4 Assembly. Three separate sets of proteins
3 Synthesis of viral genomes
self-assemble to form phage heads, tails, and tail fibers. The phage genome is packaged inside the capsid as the head forms. Figure 18.6
Head
Tails
Tail fibers
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
and proteins. The phage DNA directs production of phage proteins and copies of the phage genome by host enzymes, using components within the cell.
The Lysogenic Cycle • The lysogenic cycle – Replicates the phage genome without destroying the host
• Temperate phages – Are capable of using both the lytic and lysogenic cycles of reproduction
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• The lytic and lysogenic cycles of phage λ, a temperate phage Phage DNA The phage attaches to a host cell and injects its DNA. Phage DNA circularizes Phage Occasionally, a prophage exits the bacterial chromosome, initiating a lytic cycle.
Bacterial chromosome
Lytic cycle The cell lyses, releasing phages.
Lysogenic cycle Certain factors determine whether
Lytic cycle is induced
Figure 18.7
Many cell divisions produce a large population of bacteria infected with the prophage.
or
New phage DNA and proteins are synthesized and assembled into phages.
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Lysogenic cycle is entered
Prophage
The bacterium reproduces normally, copying the prophage and transmitting it to daughter cells.
Phage DNA integrates into the bacterial chromosome, becoming a prophage.
Reproductive Cycles of Animal Viruses • The nature of the genome – Is the basis for the common classification of animal viruses
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• Classes of animal viruses
Table 18.1 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Viral Envelopes • Many animal viruses – Have a membranous envelope
• Viral glycoproteins on the envelope – Bind to specific receptor molecules on the surface of a host cell
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• The reproductive cycle of an enveloped RNA virus 1 Glycoproteins on the viral envelope
Capsid
bind to specific receptor molecules (not shown) on the host cell, promoting viral entry into the cell.
RNA Envelope (with glycoproteins)
2 Capsid and viral genome enter cell
HOST CELL Viral genome (RNA) Template 5 Complementary RNA strands also function as mRNA, which is translated into both capsid proteins (in the cytosol) and glycoproteins for the viral envelope (in the ER).
3 The viral genome (red) functions as a template for synthesis of complementary RNA strands (pink) by a viral enzyme.
mRNA Capsid proteins ER
Glycoproteins
Copy of genome (RNA)
4 New copies of viral genome RNA are made using complementary RNA strands as templates.
6 Vesicles transport envelope glycoproteins to the plasma membrane. 8 New virus 7 A capsid assembles
Figure 18.8
around each viral genome molecule.
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RNA as Viral Genetic Material • The broadest variety of RNA genomes – Is found among the viruses that infect animals
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• Retroviruses, such as HIV, use the enzyme reverse transcriptase – To copy their RNA genome into DNA, which can then be integrated into the host genome as a provirus Glycoprotein
Viral envelope Capsid
Reverse transcriptase
Figure 18.9 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
RNA (two identical strands)
• The reproductive cycle of HIV, a retrovirus HIV
Membrane of white blood cell
1 The virus fuses with the cell’s plasma membrane. The capsid proteins are removed, releasing the viral proteins and RNA.
2 Reverse transcriptase catalyzes the synthesis of a DNA strand complementary to the viral RNA. HOST CELL
3 Reverse transcriptase catalyzes the synthesis of a second DNA strand complementary to the first.
Reverse transcriptase Viral RNA
0.25 µm HIV entering a cell
RNA-DNA hybrid
4 The double-stranded DNA is incorporated as a provirus into the cell’s DNA.
DNA
NUCLEUS Chromosomal DNA RNA genome for the next viral generation
Provirus
mRNA
5 Proviral genes are transcribed into RNA molecules, which serve as genomes for the next viral generation and as mRNAs for translation into viral proteins.
6 The viral proteins include capsid proteins and reverse transcriptase (made in the cytosol) and envelope glycoproteins (made in the ER).
Figure 18.10
New HIV leaving a cell
9 New viruses bud off from the host cell.
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8 Capsids are assembled around viral genomes and reverse transcriptase molecules.
7 Vesicles transport the glycoproteins from the ER to the cell’s plasma membrane.
Evolution of Viruses • Viruses do not really fit our definition of living organisms • Since viruses can reproduce only within cells – They probably evolved after the first cells appeared, perhaps packaged as fragments of cellular nucleic acid
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• Concept 18.2: Viruses, viroids, and prions are formidable pathogens in animals and plants • Diseases caused by viral infections – Affect humans, agricultural crops, and livestock worldwide
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Viral Diseases in Animals • Viruses may damage or kill cells – By causing the release of hydrolytic enzymes from lysosomes
• Some viruses cause infected cells – To produce toxins that lead to disease symptoms
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• Vaccines – Are harmless derivatives of pathogenic microbes that stimulate the immune system to mount defenses against the actual pathogen – Can prevent certain viral illnesses
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Emerging Viruses • Emerging viruses – Are those that appear suddenly or suddenly come to the attention of medical scientists
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• Severe acute respiratory syndrome (SARS) – Recently appeared in China
(a) Young ballet students in Hong Kong (b) The SARS-causing agent is a coronavirus wear face masks to protect themselves like this one (colorized TEM), so named for the “corona” of glycoprotein spikes protruding from from the virus causing SARS. the envelope. Figure 18.11 A, B Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Outbreaks of “new” viral diseases in humans – Are usually caused by existing viruses that expand their host territory
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Viral Diseases in Plants • More than 2,000 types of viral diseases of plants are known • Common symptoms of viral infection include – Spots on leaves and fruits, stunted growth, and damaged flowers or roots
Figure 18.12 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Plant viruses spread disease in two major modes – Horizontal transmission, entering through damaged cell walls – Vertical transmission, inheriting the virus from a parent
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Viroids and Prions: The Simplest Infectious Agents • Viroids – Are circular RNA molecules that infect plants and disrupt their growth
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• Prions – Are slow-acting, virtually indestructible infectious proteins that cause brain diseases in mammals – Propagate by converting normal proteins into the prion version Prion
Original prion
Many prions Normal protein
New prion
Figure 18.13 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Concept 18.3: Rapid reproduction, mutation, and genetic recombination contribute to the genetic diversity of bacteria • Bacteria allow researchers – To investigate molecular genetics in the simplest true organisms
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The Bacterial Genome and Its Replication • The bacterial chromosome – Is usually a circular DNA molecule with few associated proteins
• In addition to the chromosome – Many bacteria have plasmids, smaller circular DNA molecules that can replicate independently of the bacterial chromosome
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• Bacterial cells divide by binary fission – Which is preceded by replication of the bacterial chromosome Replication fork Origin of replication
Termination of replication
Figure 18.14 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Mutation and Genetic Recombination as Sources of Genetic Variation • Since bacteria can reproduce rapidly – New mutations can quickly increase a population’s genetic diversity
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• Further genetic diversity – Can arise by recombination of the DNA from two different bacterial cells EXPERIMENT
Researchers had two mutant strains, one that could make arginine but not tryptophan (arg+ trp–) and one that could make tryptophan but not arginine (arg− trp+). Each mutant strain and a mixture of both strains were grown in a liquid medium containing all the required amino acids. Samples from each liquid culture were spread on plates containing a solution of glucose and inorganic salts (minimal medium), solidified with agar. Mixture
Mutant strain arg+ trp–
Figure 18.15
Mutant strain arg− trp+
RESULTS Only the samples from the mixed culture, contained cells that gave rise to colonies on minimal medium, which lacks amino acids.
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Mixture
Mutant strain arg+ trp–
Mutant strain arg– trp+
No colonies (control)
CONCLUSION
Colonies grew
No colonies (control)
Because only cells that can make both arginine and tryptophan (arg+ trp+ cells) can grow into colonies on minimal medium, the lack of colonies on the two control plates showed that no further mutations had occurred restoring this ability to cells of the mutant strains. Thus, each cell from the mixture that formed a colony on the minimal medium must have acquired one or more genes from a cell of the other strain by genetic recombination.
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Mechanisms of Gene Transfer and Genetic Recombination in Bacteria • Three processes bring bacterial DNA from different individuals together – Transformation – Transduction – Conjugation
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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
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Transduction • In the process known as transduction – Phages carry bacterial genes from one host cell to another Phage DNA
A+ B+
1 Phage infects bacterial cell that has alleles A+ and B+
2 Host DNA (brown) is fragmented, and phage DNA
A+ B+
and proteins are made. This is the donor cell.
Donor cell 3 A bacterial DNA fragment (in this case a fragment with
the A+ allele) may be packaged in a phage capsid. A+ 4 Phage with the A+ allele from the donor cell infects
a recipient A–B– cell, and crossing over (recombination) between donor DNA (brown) and recipient DNA (green) occurs at two places (dotted lines).
Crossing over A+ A– B– Recipient cell
5 The genotype of the resulting recombinant cell (A+B–)
Figure 18.16
differs from the genotypes of both the donor (A+B+) and the recipient (A–B–).
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A+ B– Recombinant cell
Conjugation and Plasmids • Conjugation – Is the direct transfer of genetic material between bacterial cells that are temporarily joined
Figure 18.17 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Sex pilus
1 µm
The F Plasmid and Conjugation • Cells containing the F plasmid, designated F+ cells – Function as DNA donors during conjugation – Transfer plasmid DNA to an F− recipient cell
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• Conjugation and transfer of an F plasmid from an F+ donor to an F− recipient
F Plasmid
Bacterial chromosome
F+ cell
F+ cell
Mating bridge F– cell
Bacterial chromosome
1 A cell carrying an F plasmid (an F+ cell) can form a mating bridge with an F– cell and transfer its F plasmid.
2 A single strand of the F plasmid breaks at a specific point (tip of blue arrowhead) and begins to move into the recipient cell. As transfer continues, the donor plasmid rotates (red arrow).
F+ cell 3 DNA replication occurs in 4 both donor and recipient cells, using the single parental strands of the F plasmid as templates to synthesize complementary strands.
Figure 18.18a
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The plasmid in the recipient cell circularizes. Transfer and replication result in a compete F plasmid in each cell. Thus, both cells are now F+.
(a) Conjugation and transfer of an F plasmid from an F+ donor to an F– recipient
• Chromosomal genes can be transferred during conjugation – When the donor cell’s F factor is integrated into the chromosome • A cell with the F factor built into its chromosome – Is called an Hfr cell • The F factor of an Hfr cell – Brings some chromosomal DNA along with it when it is transferred to an F– cell
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• Conjugation and transfer of part of the bacterial chromosome from an Hfr donor to an F– recipient, resulting in recombination Hfr cell
F+ cell
F factor
1
Hfr cell
A+
The circular F plasmid in an F+ cell can be integrated into the circular chromosome by a single crossover event (dotted line).
B+
C+
The resulting cell is called an Hfr cell (for High frequency of recombination).
D+
C+ B+
D+
2
D+ C+
A+
B+
A+
D+ C+
B+
A+
A+
F– cell 3
B–
C– A–
B+ D–
Since an Hfr cell has all the F-factor genes, it can form a mating bridge with an F– cell and transfer DNA.
B–
A–
B+ A+
B–
C– A–
A+
D–
4 A single strand of the F factor breaks and begins to move through the bridge. DNA replication occurs in both donor and recipient cells, resulting in double-stranded DNA
Temporary partial diploid 7
C–
B–
C– D–
5 The location and orientation of the F factor in the donor chromosome determine the sequence of gene transfer during conjugation. In this example, the transfer sequence for four genes is A-B-C-D.
D–
Two crossovers can result in the exchange of similar (homologous) genes between the transferred chromosome fragment (brown) and the recipient cell’s chromosome (green).
Figure 18.18b Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
B– A+
B+
B+ A+
A–
C– A–
D–
6
B–
C– A–
D–
The mating bridge usually breaks well before the entire chromosome and the rest of the F factor are transferred.
Recombinant F– bacterium
8 The piece of DNA ending up outside the bacterial chromosome will eventually be degraded by the cell’s enzymes. The recipient cell now contains a new combination of genes but no F factor; it is a recombinant F– cell.
(b) Conjugation and transfer of part of the bacterial chromosome from an Hfr donor to an F– recipient, resulting in recombination
R plasmids and Antibiotic Resistance • R plasmids – Confer resistance to various antibiotics
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Transposition of Genetic Elements • Transposable elements – Can move around within a cell’s genome – Are often called “jumping genes” – Contribute to genetic shuffling in bacteria
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Insertion Sequences • An insertion sequence contains a single gene for transposase – An enzyme that catalyzes movement of the insertion sequence from one site to another within the genome Insertion sequence 3′
A T C C G G T…
A C C G G A T…
3′
5′
TAGGCCA…
TGGCCTA…
5′
Transposase gene Inverted Inverted repeat repeat (a) Insertion sequences, the simplest transposable elements in bacteria, contain a single gene that encodes transposase, which catalyzes movement within the genome. The inverted repeats are backward, upside-down versions of each other; only a portion is shown. The inverted repeat sequence varies from one type of insertion sequence to another. Figure 18.19a Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Transposons • Bacterial transposons – Also move about within the bacterial genome – Have additional genes, such as those for antibiotic resistance Transposon
Insertion sequence
Antibiotic resistance gene
Insertion sequence
5′
5′
3′
3′
Inverted repeats Transposase gene (b) Transposons contain one or more genes in addition to the transposase gene. In the transposon shown here, a gene for resistance to an antibiotic is located between twin insertion sequences. The gene for antibiotic resistance is carried along as part of the transposon when the transposon is inserted at a new site in the genome. Figure 18.19b Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Concept 18.4: Individual bacteria respond to environmental change by regulating their gene expression • E. coli, a type of bacteria that lives in the human colon – Can tune its metabolism to the changing environment and food sources
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• This metabolic control occurs on two levels – Adjusting the activity of metabolic enzymes already present – Regulating the genes encoding the metabolic enzymes (a) Regulation of enzyme activity Precursor
Feedback inhibition
(b) Regulation of enzyme production
Enzyme 1 Gene 1
Enzyme 2 Gene 2
Regulation of gene expression
Enzyme 3 Gene 3
– Enzyme 4 Gene 4
– Enzyme 5 Gene 5 Tryptophan
Figure 18.20a, b Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Operons: The Basic Concept • In bacteria, genes are often clustered into operons, composed of – An operator, an “on-off” switch – A promoter – Genes for metabolic enzymes
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• An operon – Is usually turned “on” – Can be switched off by a protein called a repressor
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• The trp operon: regulated synthesis of repressible enzymes trp operon Promoter
DNA
Promoter Genes of operon trpD trpC trpE
trpR
trpB
trpA
Operator Regulatory gene mRNA 5′
3′
RNA polymerase
Start codon
Stop codon
mRNA 5′ E
Protein
Inactive repressor
D
C
B
A
Polypeptides that make up enzymes for tryptophan synthesis
(a) Tryptophan absent, repressor inactive, operon on. RNA polymerase attaches to the DNA at the promoter and transcribes the operon’s genes. Figure 18.21a Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
DNA No RNA made
mRNA
Protein
Active repressor
Tryptophan (corepressor) (b) Tryptophan present, repressor active, operon off. As tryptophan accumulates, it inhibits its own production by activating the repressor protein. Figure 18.21b Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Repressible and Inducible Operons: Two Types of Negative Gene Regulation • In a repressible operon – Binding of a specific repressor protein to the operator shuts off transcription
• In an inducible operon – Binding of an inducer to an innately inactive repressor inactivates the repressor and turns on transcription
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• The lac operon: regulated synthesis of inducible enzymes Promoter Regulatory gene
DNA
Operator
lacl
lacZ
3′ mRNA
Protein
5′
No RNA made RNA polymerase
Active repressor
(a) Lactose absent, repressor active, operon off. The lac repressor is innately active, and in the absence of lactose it switches off the operon by binding to the operator. Figure 18.22a Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
lac operon
DNA
lacl
lacz
3′ mRNA
5′
lacA
RNA polymerase mRNA 5' 5′ mRNA
β-Galactosidase
Protein Allolactose (inducer)
lacY
Permease
Transacetylase
Inactive repressor
(b) Lactose present, repressor inactive, operon on. Allolactose, an isomer of lactose, derepresses the operon by inactivating the repressor. In this way, the enzymes for lactose utilization are induced. Figure 18.22b
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• Inducible enzymes – Usually function in catabolic pathways
• Repressible enzymes – Usually function in anabolic pathways
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• Regulation of both the trp and lac operons – Involves the negative control of genes, because the operons are switched off by the active form of the repressor protein
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Positive Gene Regulation • Some operons are also subject to positive control – Via a stimulatory activator protein, such as catabolite activator protein (CAP)
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• In E. coli, when glucose, a preferred food source, is scarce – The lac operon is activated by the binding of a regulatory protein, catabolite activator protein Promoter (CAP) DNA
lacl
lacZ
CAP-binding site cAMP
Inactive CAP
RNA Operator polymerase can bind Active and transcribe CAP
Inactive lac repressor
(a) Lactose present, glucose scarce (cAMP level high): abundant lac mRNA synthesized. If glucose is scarce, the high level of cAMP activates CAP, and the lac operon produces Figure 18.23a large amounts of mRNA for the lactose pathway. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• When glucose levels in an E. coli cell increase – CAP detaches from the lac operon, turning it off Promoter DNA
lacl
lacZ
CAP-binding site
Operator RNA polymerase can’t bind
Inactive CAP
Inactive lac repressor
(b) Lactose present, glucose present (cAMP level low): little lac mRNA synthesized. When glucose is present, cAMP is scarce, and CAP is unable to stimulate transcription. Figure 18.23b
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