Introduction
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Prokaryotes usually reproduce asexually by cell division.
They may acquire new genes by simple recombination in a sexual process.
They may use infective viruses as carriers for prokaryotic genes.
Viruses are not prokaryotes, but rather intracellular parasites that can reproduce only within living cells.
Probing the Nature of Genes
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Prokaryotes and viruses have advantages for the study of genetics.
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It is relatively easy to work with the small amounts of DNA exhibited by these groups. Bacteria have a
thousandth of the DNA of human cells; a virus typically has a hundredth of the DNA of a bacterium.
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They quickly produce large numbers of individuals. Prokaryotes grow rapidly (E. coli doubles every 20
minutes) and viruses can replicate far more quickly than bacteria.
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Prokaryotes and viruses are usually haploid, making genetic analyses easier.
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The ease of using bacteria and viruses in genetic research has propelled the science of genetics and molecular
biology during the last 50 years.
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Prokaryotes continue to play a central role as tools for biotechnology and for research on eukaryotes.
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Prokaryotes play important ecological roles, including cycling elements in the atmosphere and water.
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Both prokaryotes and viruses present disease challenges to humans.
Viruses: Reproduction and Recombination
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Most viruses are composed of a nucleic acid and a few proteins.
Some infect cells but postpone reproduction until certain cellular conditions are met.
Some reproduce shortly after infecting the cell.
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.
Scientists studied viruses before they could see them
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The tobacco mosaic virus was the first virus to be discovered.
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The Russian botanist Dmitri Ivanovsky, trying to find the cause of tobacco mosaic disease, provided evidence
for the existence of this virus in 1892.
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After passing diseased plant extract through a filter fine enough to contain bacteria, he found that the liquid
filtrate still caused the disease.
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Instead of concluding that the agent was smaller than a bacterium, he assumed the filter was faulty.
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Martinus Beijerinck repeated the experiment in 1898 and showed the agent could pass through agar gel. He
called the infectious agent contagium vivum fluidum, which was later shortened to virus.
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In the late 1930s, the infective agent was crystallized by Wendell Stanley, who won the Nobel prize for his
success. The crystallized virus became infectious again when it was dissolved.
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In the 1950s, direct observation by electron microscopes showed how much viruses differ from bacteria. (See
Table 13.1.)
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The simplest infective agents are viroids, which are made up only of genetic material.
Viruses reproduce only with the help of living cells
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Whole viruses never arise directly from preexisting viruses. They are obligate intracellular parasites that
develop and reproduce only within living cells of specific hosts (the cells of animals, plants, fungi, protists, and
prokaryotes).
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Viruses reproduce using the host’s synthetic machinery and usually destroy the host cell in the process.
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The host cell releases progeny viruses, which then infect new hosts.
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Outside the cell, the individual viral particles are called virions.
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Virion genetic material is either DNA or RNA and is generally surrounded by a capsid, or protein coat.
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Characteristic shapes are determined by the protein coat. (See Figure 13.1.)
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Viruses are unaffected by antibiotics because they lack the cell wall structure and ribosomal biochemistry of
bacteria.
There are many kinds of viruses
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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.
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Whether or not the virion is surrounded by a membrane.
See Figure 13.1 to examine some of these variations.
Bacteriophage reproduce by a lytic cycle or a lysogenic cycle
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Viruses that infect bacteria are called bacteriophage.
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Bacteriophage recognize their host by means of specific binding between proteins in the capsid and receptor
proteins on the host’s cell.
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The virions must get their genetic material into the host cell, and many are equipped with tail assemblies that
inject the phage’s nucleic acid into the host cell.
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The lytic cycle occurs when the virus infects the cell, takes over the cellular machinery, and then lyses
(bursts) the cell, releasing its phage progeny. (See Figure 13.2.)
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In a lysogenic cycle, the host cell does not lyse. Instead, it harbors a quiescent virus for many generations.
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Some viruses reproduce using only the lytic cycle; some use both types of reproductive cycle.
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Phage that only have lytic cycles are called virulent viruses. (See Figure 13.3.)
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The viral genome contains a promoter sequence that attracts host RNA polymerase.
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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.
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In the late stage, viral late genes code for the protein coat and an enzyme that causes host cell lysis, resulting
in viral release.
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The whole process takes around 30 minutes.
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On rare occasions, two viruses infect the same cell at the same time, providing the opportunity for
recombination of genes and the creation of new viral strains.
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Temperate viruses infect bacterial hosts (called lysogenic bacteria) without killing them.
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Lysogenic bacteria have a molecule of noninfective phage DNA called a prophage inserted into their
chromosome.
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Under some conditions, the prophage replicates during the bacterium’s normal reproductive cycle without
otherwise harming the bacterium.
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Certain conditions will activate the prophage, initiating a lytic cycle that results in the release of a large
number of free phage. These phage can then infect other bacteria.
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The lysogenic strategy helps assure long-term survival of a virus by allowing relatively slow, nonlethal
replication under some conditions.
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The lytic strategy permits faster but lethal replication under other conditions.
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(See Video 13.1.)
Lytic bacteriophage could be useful in treating bacterial infections
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Lytic bacteriophage destroy their bacterial hosts, and thus might be useful in treating diseases caused by
bacteria.
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In 1917, the French-Canadian microbiologist Felix D’Herelle noted that when some patients with bacterial
dysentery were recovering from the disease, the quantity of phage near the bacteria was much higher than it was when
the disease was at its peak.
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D’Herelle devised an experiment to test the effectiveness of using phage to control infections of chickens by
the bacterium Salmonella gallinarum.
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Chickens were divided into two groups, one that was given phage and another that was not.
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Both groups were then exposed to the bacterium.
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The phage-protected group did not get the bacterial disease.
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Interest in phage therapy has increased as bacterial resistance to antibiotics becomes more common.
Animal viruses have diverse reproductive cycles
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Almost all vertebrates are susceptible to viral infections.
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Among invertebrates, only arthropods commonly get viral infections.
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Arboviruses infect both insects and vertebrates.
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The vertebrate gets infected through transmission via an arthropod (often an insect) bite.
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The arthropod is called a vector (carrier) for the disease transmission.
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Animal viruses include those that are just particles of protein surrounding a nucleic acid core as well as those
that have a membrane derived from that of the host.
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Some animal viruses have DNA, and some have RNA, but all have small genomes of limited codes.
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Animal viruses enter cells in three different ways:
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Endocytosis of a naked virion.
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Endocytosis of a membrane-encased virus.
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Fusion of a membrane-encased virus with the cell’s membrane.
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Figure 13.4 shows the reproductive cycle of the influenza (RNA type) virus.
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Retroviruses such as HIV (also RNA type) have a more complex reproductive cycle and enter the cell via
membrane fusion. (See Figure 13.5.)
Many plant viruses spread with the help of vectors
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Plant viruses spread horizontally or vertically.
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Horizontal transmission is the spread of viruses from one plant to another.
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Vertical transmission is the transfer of viruses from parent plant to offspring.
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A plant virus has to get through the cell wall and plasma membrane of the host.
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Insects are possible vectors. A virion-laden insect feeding on a plant can penetrate the cell wall and insert the
virus.
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Another means of infection is contact between damaged tissue of an infected and a noninfected plant.
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Vertical transmission can occur through vegetative or sexual reproduction.
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Once inside a plant cell, viruses can spread by moving through plasmodesmata, the cytoplasmic connections
between cells.
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The viruses bind with special proteins that assist their travel through the otherwise too narrow
plasmodesmata pores.
Prokaryotes: Reproduction and Recombination
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Unlike viruses, bacteria and archaea are living cells that carry out basic cellular functions.
Although they reproduce asexually, prokaryotes do have ways of recombining their genes.
The reproduction of prokaryotes gives rise to clones
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The division of single cells into two identical offspring produces clones, or genetically identical individuals.
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If a number of cells are spread on a semisolid medium containing agar, individual cells give rise to clearly
visible colonies. (See Figure 13.6.)
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If a large number of cells are spread, a confluent lawn (one continuous colony) develops after cell division.
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Bacteria also can be grown in a liquid nutrient medium.
In recombination, bacteria conjugate
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In 1946, Joshua Lederberg and Edward Tatum demonstrated the exchange of DNA between two living
bacteria. (See Figure 13.7.)
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Two auxotrophic strains of E. coli, each requiring different amino acid supplements for growth, were grown
together and then plated on minimal medium.
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Prototrophic bacteria (a strain not requiring supplements) were recovered from these mixtures, demonstrating
that genetic recombination had taken place.
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Later experiments showed that the exchange of hereditary information was by direct contact; this form of
genetic exchange is called conjugation.
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One bacterial cell (the recipient) had received DNA from another cell (the donor).
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The physical contact required for conjugation is initiated by a pilus, which is a fine projection produced by
the donor cell. (See Figure 13.8.)
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The DNA transfers through a thin cytoplasmic bridge called a conjugation tube.
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Only a linear (broken) portion of the genome is transferred.
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Once the DNA fragment is inside the recipient cell, it recombines with homologous genes.
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Enzymes cut the DNA in two places and insert the donor region into the recipient’s circular chromosome.
(See Figure 13.9.)
In transformation, cells pick up genes from their environment
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Transformation of bacteria occurs when bacteria take up extracellular DNA and incorporate it. (See Figure
13.10.)
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More than 75 years ago, Frederick Griffith obtained the first evidence for transfer of genes between bacteria.
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This was demonstrated by genetically changing nonvirulent pneumococci bacteria to the virulent form with
transforming substance from killed virulent bacteria. (See Figure 11.1.)
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The transforming substance was later found to be DNA.
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Incorporation of the virulent DNA inside the host cell is very similar to recombination.
In transduction, viruses carry genes from one cell to another
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During the lytic cycle, some bacteriophage package a host bacterium’s DNA in capsids, or viral protein coats.
(See Figure 13.10.)
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Cells infected by such viruses get a segment of another bacterium’s DNA, not the viral DNA.
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In transduction, this bacterial DNA recombines with the chromosomal DNA of the host and alters its genetic
composition.
Plasmids are extra chromosomes in bacteria
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Plasmids are small, circular chromosomes found in many bacteria.
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Each plasmid has an origin of replication and replicates separately from the primary chromosome.
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Plasmids are not viruses, but they move between bacterial cells during conjugation.
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There are different types of plasmids, which are classified according to the kinds of genes they carry.
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Some plasmids (called metabolic factors) carry genes for unusual metabolic functions, such as degrading oils
from oil spills.
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Fertility factors (F factors) are plasmids that carry genes for conjugation.
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Around 25 genes, including the ones responsible for the pilus, are on the F factor plasmid.
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Bacteria with this plasmid are called F+.
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On occasion, this F plasmid inserts into the main chromosome.
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When this occurs, chromosomal genes can be transferred during conjugation. (See Figure 13.11.)
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Some plasmids are resistance factors.
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Resistance factors, or R factors, carry genes that code for proteins that protect the bacteria.
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Antibiotic resistance genes break down or modify antibiotics, or produce components that interfere with
antibiotic activity or prevent their transport.
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These plasmids were discovered in 1957 in Shigella bacteria, which were resistant to several antibiotics.
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Research found that resistance to an entire spectrum of antibiotics could be transferred by conjugation.
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This finding raised the warning that inappropriate use of antibiotics may lead to their becoming ineffective.
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Antibiotic resistance in pathogenic bacteria provides an example of evolution in action.
Transposable elements move genes among plasmids and chromosomes
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Gene transport also can occur within an individual cell. (See Figure 13.12.)
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Such movement involves a segment of chromosome or plasmid DNA that can insert at new locations.
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The movement of these transposable elements into other genes disrupts normal function.
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Long transposable elements (about 5000 base pairs), which include one or more genes, are called
transposons.
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Transposons have contributed to the evolution of plasmids, and there is some evidence that R plasmids
developed antibiotic resistance through transposons.
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Recombination by means of conjugation, transformation, and transduction, or the acquisition of new genes
by means of plasmids and transposable elements, all introduce genetic diversity into bacterial populations, allowing at
least some cells to survive under changing conditions.
Regulation of Gene Expression in Prokaryotes
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Prokaryotes can conserve energy and resources by making proteins only when they are needed.
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Cells can control synthesis or activity of an unneeded protein by regulating or controlling the production of
enzymes.
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Cells can block transcription of the gene that codes for a protein. This method, transcription regulation, is
more efficient than the others, and one used most extensively.
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Cells can hydrolyze the mRNA after it is made.
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Cells can prevent translation of mRNA at the ribosome.
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Cells can hydrolyze the protein after it is made.
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Cells can inhibit the function of the protein.
Regulation of transcription conserves energy
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E. coli prefers glucose as an energy source, but when glucose availability is low and lactose is available, it
can use lactose.
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Lactose is a disaccharide containing galactose -linked to glucose. To be metabolized by E. coli, it is acted
on by three proteins.
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Lactose is transported into the cell by a carrier protein (enzyme) called -galactoside permease.
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Lactose is hydrolyzed to glucose and galactose by the enzyme -galactosidase.
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A third enzyme, -galactosidase transacetylase, is also required for lactose metabolism, although its role in
the process is not yet clear.
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When no lactose is present, levels of all three enzymes are low. When glucose is low and lactose is high,
synthesis of all three enzymes occurs rapidly. If glucose levels rise again, or lactose levels drop, synthesis stops.
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Compounds (such as lactose) that stimulate synthesis of an enzyme are called inducers. (See Figure 13.13.)
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The enzymes produced are inducible enzymes.
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Enzymes made all the time at a constant rate are constitutive enzymes.
A single promoter controls the transcription of adjacent genes
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Structural genes are blueprints that specify the primary structures (amino acid sequence) of a protein
molecule. In other words, structural genes are those that can be transcribed into mRNA.
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The three of these that are involved in lactose metabolism are adjacent to each other on the E. coli
chromosome.
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All are transcribed together when a single promoter binds RNA polymerase.
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Therefore, their synthesis is coordinated.
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Because there is just a single promoter, all genes are transcribed efficiently into a single mRNA.
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When these enzymes are not needed, the mRNA synthesis must be shut down.
Operons are units of transcription in prokaryotes
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Prokaryotes shut down transcription by placing an obstacle between the promoter and its structural genes.
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Just downstream from the promoter, between the promoter and structural genes, is a DNA site called the
operator.
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If a specific protein, the repressor, binds to the operator, it creates an obstacle, and RNA polymerase is
blocked from transcribing the structural genes. (See Figure 13.15.)
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When the repressor is not attached to the operator, mRNA synthesis proceeds.
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The whole unit of genes and their DNA controls is called an operon.
Operator–repressor control that induces transcription: The lac operon
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The operon for the three lactose-metabolizing enzymes is called the lac operon.
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The repressor protein has two binding sites: one for the operator and the other for inducers.
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Binding of the repressor by the inducer molecules (e.g., an analog of lactose) changes the shape of the
repressor by allosteric modification.
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The change in shape prevents the repressor from binding to the operator. (See Figure 13.17.)
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Thus, RNA polymerase can bind to the promoter and start gene transcription of the lac operon.
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If the concentration of the inducer (lactose) drops, the functioning repressor binds the operator, and the
enzymes for lactose metabolism are not synthesized.
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If the concentration of lactose rises, the repressor itself is bound and does not bind the operator. The enzymes
for lactose metabolism are synthesized.
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The repressor protein is coded for by the regulatory gene.
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The regulatory gene that codes for the lac repressor is the i (inducibility) gene.
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The i gene just happens to be located near the lac structural genes. However, not all regulatory genes are near
the operons they control.
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Regulatory genes like i have their own promoter, called pi.
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The i gene is expressed constitutively (i.e., expression is constant).
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Figure 13.16 shows the lac operon for E. coli.
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Summary of the lac operon control: (See Figure 13.17 and Animated Tutorial 13.1.)
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When no inducer (lactose) is present, lac is off.
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The regulator protein (repressor) turns the operon off.
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The i gene produces the repressor.
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The operator and promoter are DNA sequences that are binding sites for regulatory proteins.
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Adding inducer (lactose) turns the operon on.
Operator–repressor control that represses transcription: The trp operon
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The ability to switch off synthesis of an enzyme can be just as important as the ability to switch it on.
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If synthesis of an enzyme can be turned off, it is said to be repressible.
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The trp operon in E. coli is repressible. (See Figure 13.18.)
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In the absence of tryptophan, RNA polymerase transcribes the trp operon, leading to production of enzymes
that synthesize tryptophan.
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When tryptophan is present, it binds to a repressor.
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The repressor is made, whether tryptophan is present or not, by a regulatory gene at another locus.
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The unbound repressor is inactive. When tryptophan binds the repressor, the repressor changes shape and
becomes active. (See Animated Tutorial 13.2.)
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The repressor in turn binds to the operator of the trp operon, blocking production of the enzymes that
synthesize tryptophan.
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As tryptophan concentration rises, production of tryptophan drops off.
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The molecule that binds and activates a repressor is called a corepressor.
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The corepressor may be the end product of the operon (as in the case of tryptophan), or it may be an analog.
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The difference between inducible and repressible systems is small, but significant.
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In inducible systems, an inducer from the cell’s environment prevents a repressor from blocking
transcription.
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In repressible systems, a corepressor produced by the cell activates a repressor, enabling it to block
transcription.
Protein synthesis can be controlled by increasing promoter efficiency
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Another way to regulate transcription is to make the promoter sequence of the operon work more efficiently.
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When glucose is high, even when lactose is available, the lac operon fails to transcribe frequently.
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When glucose is low, and lactose is available, lac structural genes are transcribed.
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Low glucose levels cause elevated levels of cyclic AMP (cAMP).
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The molecule AMP is the monophosphate form of the familiar ATP. Cyclic AMP has a phosphodiester
linkage between its own 5 and 3 carbons.
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When glucose is low and cAMP is high, cAMP binds to a protein called CRP (cAMP receptor protein). (See
Figure 13.19.)
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The CRP–cAMP complex binds the DNA just upstream of the promoter.
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Binding of this site makes it easier for RNA polymerase to bind the promoter and thus increases rates of
transcription.
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When glucose is abundant, cAMP levels drop.
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The CRP–cAMP complex does not form.
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Without the CRP–cAMP complex, RNA polymerase cannot bind to the promoter efficiently.
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The lac structural genes are not transcribed.
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This is called catabolite repression.
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Table 13.2 summarizes positive and negative control in the lac operon.
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cAMP is used widely by both eukaryotes and prokaryotes as a signaling molecule.
Control of Transcription in Viruses
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Viruses also have gene regulation mechanisms.
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Even such “simple” biological agents must activate genes in the right order.
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Early genes must be transcribed before later ones.
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Bacteriophage  is a temperate phage, meaning that it can undergo either a lytic or a lysogenic cycle.
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Temperate viruses need to regulate when to undertake a lytic cycle.
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When host bacteria are growing in rich medium, the prophage remains lysogenic; when the host is less
healthy, the prophage becomes lytic.
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A “genetic switch” determines the prophage behavior. (See Figure 13.20.)
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Two regulatory proteins compete for two operator/promoter sites on the phage DNA.
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One operator controls the lytic gene activities; the other, lysogenic cycles.
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The two regulatory proteins have opposite effects on the two operators.
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cI represses the lytic operator/promoter and activates the lysogenic operator/promoter.
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Cro activates the lytic operator/promoter and represses the lysogenic operator/promoter.
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The relative concentrations of cI and Cro determine the outcome.
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When the host is healthy, the level of Cro is low (and the levels of cI accumulate), lytic behavior is blocked,
and lysogeny ensues.
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When Cro synthesis is high in an unhealthy host, the phage enters a lytic cycle.
Prokaryotic Genomes
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Viral genomes were the first to be sequenced.
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In 1995, Haemophilus influenzae (a bacterium) was the first free-living organism to be completely
sequenced. (See Figure 13.21.)
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Prokaryotic sequencing has revealed details of how bacteria allocate and organize their genes.
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Three types of information can be obtained from a genomic sequence.
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Open reading frames (coding regions of genes) can be recognized by promoter regions and start and stop
codons.
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Amino acid sequences can be deduced from the DNA sequence.
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Gene control sequences of promoters and terminators can be identified.
Functional genomics relates gene sequences to functions
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Functional genomics is the assignment of roles to the products of genes described by genomic sequencing.
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Haemophilus influenzae, which infects humans, has a circular chromosome of 1,830,137 base pairs and
1,743 protein-coding regions.
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When the sequencing of H. influenzae was finished, 42 percent of the genes coded for proteins with unknown
functions.
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Roles for most of the unknown proteins have now been identified by a process known as annotation.
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Comparative genomics involves the comparison of genome sequences of different organisms in order to
relate genes that are either present or missing to the organism’s physiology.
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In addition to the sequences for H. influenzae, those for Mycoplasma genitalium (580,070 base pairs) and E.
coli (4,639,211 base pairs) have been completed.
The sequencing of prokaryotic genomes has medical applications
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Scientists are discovering genes for proteins in prokaryotes that cause infectious diseases. These are potential
targets for new drugs.
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New vaccines may be possible as cell surface antigen coding genes are discovered.
What genes are required for cellular life?
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There are some universal genes needed by all organisms. (See Figure 13.22.)
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There are some universal gene segments, like those coding for an ATP binding site.
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M. genitalium has just 470 genes, the smallest known genome.
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Some genes are dispensable under certain conditions. For example, those for lactose utilization are not
needed by E. coli when it is grown on glucose.
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Using mutagens to knock out genes, scientists have determined that M. genitalium can survive in the
laboratory with just 337 genes!
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This number is termed the “minimal essential genome.”