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Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsSection A: The Genetics of Viruses1.Researchers discovered viruses by studying a plant disease2. A virus is a genome enclosed in a protective coat3. Viruses can only reproduce within a host cell: an overview4. Phages reproduce using lytic or lysogenic cycles5. Animal viruses are diverse in their modes of infection and replication6. Plant viruses are serious agricultural pests7. Viroids and prions are infectious agents even simpler than viruses.8. Viruses may have evolved from other mobile genetic elements

CHAPTER 18 MICROBIAL MODELS: THE GENETICS OF VIRUSES AND BACTERIAViruses and bacteria are the simplest biological systems - microbial models where scientists find lifes fundamental molecular mechanisms in their most basic, accessible forms.Microbiologists provided most of the evidence that genes are made of DNA, and they worked out most of the major steps in DNA replication, transcription, and translation.Viruses and bacteria also have interesting, unique genetic features with implications for understanding diseases that they cause.IntroductionCopyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsBacteria are prokaryotic organisms.Their cells are much smaller and more simply organized that those of eukaryotes, such as plants and animals.Viruses are smaller and simpler still, lacking the structure and most meta-bolic machinery in cells.Most viruses are little more than aggregates of nucleic acids and protein - genes in a protein coat.Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 18.1The genome of viruses includes other options than the double-stranded DNA that we have studied.Viral genomes may consist of double-stranded DNA, single-stranded DNA, double-stranded RNA, or single-stranded RNA, depending on the specific type of virus.The viral genome is usually organized as a single linear or circular molecule of nucleic acid.The smallest viruses have only four genes, while the largest have several hundred.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsThe capsid is a protein shell enclosing the viral genome.Capsids are build of a large number of protein subunits called capsomeres, but with limited diversity.The capsid of the tobacco mosaic virus has over 1,000 copies of the same protein.Adenoviruses have 252 identical proteins arranged into a polyhedral capsid - as an icosahedron. Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 18.2a & bSome viruses have viral envelopes, membranes cloaking their capsids.These envelopes are derived from the membrane of the host cell.They also have some viral proteins and glycoproteins. Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 18.2cThe most complex capsids are found in viruses that infect bacteria, called bacteriophages or phages.The T-even phages that infect Escherichia coli have a 20-sided capsid head that encloses their DNA and protein tail piece that attaches the phage to the host and injects the phage DNA inside. Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsFig. 18.2d

Viruses are obligate intracellular parasites.They can reproduce only within a host cell.An isolated virus is unable to reproduce - or do anything else, except infect an appropriate host.Viruses lack the enzymes for metabolism or ribosomes for protein synthesis.An isolated virus is merely a packaged set of genes in transit from one host cell to another.3. Viruses can reproduce only within a host cell: an overviewCopyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsEach type of virus can infect and parasitize only a limited range of host cells, called its host range.Viruses identify host cells by a lock-and-key fit between proteins on the outside of virus and specific receptor molecules on the hosts surface.Some viruses (like the rabies virus) have a broad enough host range to infect several species, while others infect only a single species.Most viruses of eukaryotes attack specific tissues.Human cold viruses infect only the cells lining the upper respiratory tract.The AIDS virus binds only to certain white blood cells.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsEach type of virus can infect and parasitize only a limited range of host cells, called its host range.Viruses identify host cells by a lock-and-key fit between proteins on the outside of virus and specific receptor molecules on the hosts surface.Some viruses (like the rabies virus) have a broad enough host range to infect several species, while others infect only a single species.Most viruses of eukaryotes attack specific tissues.Human cold viruses infect only the cells lining the upper respiratory tract.The AIDS virus binds only to certain white blood cells.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsWhile phages are the best understood of all viruses, some of them are also among the most complex.Research on phages led to the discovery that some double-stranded DNA viruses can reproduce by two alternative mechanisms: the lytic cycle and the lysogenic cycle.4. Phages reproduce using lytic or lysogenic cyclesCopyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsIn the lytic cycle, the phage reproductive cycle culminates in the death of the host.In the last stage, the bacterium lyses (breaks open) and releases the phages produced within the cell to infect others.Virulent phages reproduce only by a lytic cycle.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsCopyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 18.4While phages have the potential to wipe out a bacterial colony in just hours, bacteria have defenses against phages.Natural selection favors bacterial mutants with receptors sites that are no longer recognized by a particular type of phage.Bacteria produce restriction nucleases that recognize and cut up foreign DNA, including certain phage DNA.Modifications to the bacterias own DNA prevent its destruction by restriction nucleases.But, natural selection favors resistant phage mutants.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsIn the lysogenic cycle, the phage genome replicates without destroying the host cell.Temperate phages, like phage lambda, use both lytic and lysogenic cycles.Within the host, the virus circular DNA engages in either the lytic or lysogenic cycle.During a lytic cycle, the viral genes immediately turn the host cell into a virus-producing factory, and the cell soon lyses and releases its viral products.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsThe viral DNA molecule, during the lysogenic cycle, is incorporated by genetic recombination into a specific site on the host cells chromosome.In this prophage stage, one of its genes codes for a protein that represses most other prophage genes.Every time the host divides, it also copies the viral DNA and passes the copies to daughter cells.Occasionally, the viral genome exits the bacterial chromosome and initiates a lytic cycle.This switch from lysogenic to lytic may be initiated by an environmental trigger.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsThe lambda phage which infects E. coli demonstrates the cycles of a temperate phage.Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 18.5Many variations on the basic scheme of viral infection and reproductions are represented among animal viruses.One key variable is the type of nucleic acid that serves as a virus genetic material.Another variable is the presence or absence of a membranous envelope.5. Animal viruses are diverse in their modes of infection and replicationCopyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsCopyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Viruses equipped with an outer envelope use the envelope to enter the host cell.Glycoproteins on the envelope bind to specific receptors on the hosts membrane.The envelope fuses with the hosts membrane, transporting the capsid and viral genome inside.The viral genome duplicates and directs the hosts protein synthesis machinery to synthesize capsomeres with free ribosomes and glycoproteins with bound ribosomes.After the capsid and viral genome self-assemble, they bud from the host cell covered with an envelope derived from the hosts plasma membrane, including viral glycoproteins.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsThese enveloped viruses do not necessarily kill the host cell.Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 18.6Some viruses have envelopes that are not derived from plasma membrane.The envelope of the herpesvirus is derived from the nuclear envelope of the host.These double-stranded DNA viruses reproduce within the cell nucleus using viral and cellular enzymes to replicate and transcribe their DNA.Herpesvirus DNA may become integrated into the cells genome as a provirus.The provirus remains latent within the nucleus until triggered by physical or emotional stress to leave the genome and initiate active viral production.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsRetroviruses (class VI) have the most complicated life cycles.These carry an enzyme, reverse transcriptase, which transcribes DNA from an RNA template.The newly made DNA is inserted as a provirus into a chromosome in the animal cell.The hosts RNA polymerase transcribes the viral DNA into more RNA molecules.These can function both as mRNA for the synthesis of viral proteins and as genomes for new virus particles released from the cell.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsHuman immunodeficiency virus (HIV), the virus that causes AIDS (acquired immunodeficiency syndrome) is a retrovirus.The viral particle includes an envelope with glyco-proteins for binding to specific types of red blood cells, a capsid containingtwo identical RNA strandsas its genome and twocopies of reversetranscriptase.Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 18.7aThe reproductive cycle of HIV illustrates the pattern of infection and replication in a retrovirus.After HIV enters the host cell, reverse transcriptase synthesizes double stranded DNA from the viral RNA.Transcription produces more copies of the viral RNA that are translated into viral proteins, which self-assemble into a virus particle and leave the host.Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 18.7bThe link between viral infection and the symptoms it produces is often obscure.Some viruses damage or kill cells by triggering the release of hydrolytic enzymes from lysosomes.Some viruses cause the infected cell to produce toxins that lead to disease symptoms.Other have molecular components, such as envelope proteins, that are toxic.In some cases, viral damage is easily repaired (respiratory epithelium after a cold), but in others, infection causes permanent damage (nerve cells after polio).Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsMany of the temporary symptoms associated with a viral infection results from the bodys own efforts at defending itself against infection.The immune system is a complex and critical part of the bodys natural defense mechanism against viral and other infections.Modern medicine has developed vaccines, harmless variants or derivatives of pathogenic microbes, that stimulate the immune system to mount defenses against the actual pathogen.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsThe first vaccine was developed in the late 1700s by Edward Jenner to fight smallpox.Jenner learned from his patients that milkmaids who had contracted cowpox, a milder disease that usually infects cows, were resistant to smallpox.In his famous experiment in 1796, Jenner infected a farmboy with cowpox, acquired from the sore of a milkmaid with the disease.When exposed to smallpox, the boy resisted the disease.Because of their similarities, vaccination with the cowpox virus sensitizes the immune system to react vigorously if exposed to actual smallpox virus.Effective vaccines against many other viruses exist.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsVaccines can help prevent viral infections, but they can do little to cure most viral infection once they occur.Antibiotics which can kill bacteria by inhibiting enzyme or processes specific to bacteria are powerless again viruses, which have few or no enzymes of their own.Some recently-developed drugs do combat some viruses, mostly by interfering with viral nucleic acid synthesis.AZT interferes with reverse transcriptase of HIV.Acyclovir inhibits herpes virus DNA synthesis.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsIn recent years, several very dangerous emergent viruses have risen to prominence.HIV, the AIDS virus, seemed to appear suddenly in the early 1980s.Each year new strains of influenza virus cause millions to miss work or class, and deaths are not uncommon.The deadly Ebola virus has caused hemorrhagic fevers in central Africa periodically since 1976.Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 18.8aThe emergence of these new viral diseases is due to three processes: mutation, spread of existing viruses from one species to another, and dissemination of a viral disease from a small, isolated population.Mutation of existing viruses is a major source of new viral diseases.RNA viruses tend to have high mutation rates because replication of their nucleic acid lacks proofreading.Some mutations create new viral strains with sufficient genetic differences from earlier strains that they can infect individuals who had acquired immunity to these earlier strains.This is the case in flu epidemics.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsAnother source of new viral diseases is the spread of existing viruses from one host species to another.It is estimated that about three-quarters of new human diseases have originated in other animals.For example, hantavirus, which killed dozens of people in 1993, normally infects rodents, especially deer mice.That year unusually wet weather in the southwestern U.S. increased the mices food, exploding its populations.Humans acquired hantavirus when they inhaled dust containing traces of urine and feces from infected mice. Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 18.8bFinally, a viral disease can spread from a small, isolated population to a widespread epidemic.For example, AIDS went unnamed and virtually unnoticed for decades before spreading around the world. Technological and social factors, including affordable international travel, blood transfusion technology, sexual promiscuity, and the abuse of intravenous drugs, allowed a previously rare disease to become a global scourge.These emerging viruses are generally not new but are existing viruses that expand their host territory.Environmental change can increase the viral traffic responsible for emerging disease.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsPlant viruses can stunt plant growth and diminish crop yields.Most are RNA viruses with rod-shaped capsids produced by a spiral of capsomeres.6. Plant viruses are serious agricultural pestsCopyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 18.9aPlant viral diseases spread by two major routes.In horizontal transmission, a plant is infected with the virus by an external source.Plants are more susceptible if their protective epidermis is damaged, perhaps by wind, chilling, injury, or insects.Insects are often carriers of viruses, transmitting disease from plant to plant.In vertical transmission, a plant inherits a viral infection from a parent.This may occurs by asexual propagation or in sexual reproduction via infected seeds.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsViroids, smaller and simpler than even viruses, consist of tiny molecules of naked circular RNA that infect plants.Their several hundred nucleotides do not encode for proteins but can be replicated by the hosts cellular enzymes.These RNA molecules can disrupt plant metabolism and stunt plant growth, perhaps by causing errors in the regulatory systems that control plant growth.7. Viroids and prions are infectious agents even simpler than virusesCopyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsPrions are infectious proteins that spread a disease.They appear to cause several degenerative brain diseases including scrapie in sheep, mad cow disease, and Creutzfeldt-Jacob disease in humans.According to the leading hypothesis, a prion is a misfolded form of a normal brain protein.It can then convert a normal protein into the prion version, creating a chain reaction that increases their numbers.Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 18.10Candidates for the original sources of viral genomes include plasmids and transposons.Plasmids are small, circular DNA molecules that are separate from chromosomes.Plasmids, found in bacteria and in the eukaryote yeast, can replicate independently of the rest of the cell and are occasionally be transferred between cells.Transposons are DNA segments that can move from one location to another within a cells genome.Both plasmids and transposons are mobile genetic elements.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsCHAPTER 18 MICROBIAL MODELS: THE GENETICS OF VIRUSES AND BACTERIACopyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsSection B: The Genetics of Bacteria1.The short generation span of bacteria helps them adapt to changing environments2. Genetic recombination produces new bacterial strains3. The control of gene expression enables individual bacteria to adjust their metabolism to environmental change

The major component of the bacterial genome is one double-stranded, circular DNA molecule.For E. coli, the chromosomal DNA consists of about 4.6 million nucleotide pairs with about 4,300 genes.This is 100 times more DNA than in a typical virus and 1,000 times less than in a typical eukaryote cell.Tight coiling of the DNA results in a dense region of DNA, called the nucleoid, not bounded by a membrane.In addition, many bacteria have plasmids, much smaller circles of DNA.Each plasmid has only a small number of genes, from just a few to several dozen.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsBacterial cells divide by binary fission.This is preceded by replication of the bacterial chromosome from a single origin of replication. Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 18.11Bacteria proliferate very rapidly in a favorable natural or laboratory environment.Under optimal laboratory conditions E. coli can divide every 20 minutes, producing a colony of 107 to 108 bacteria in as little as 12 hours.In the human colon, E. coli reproduces rapidly enough to replace the 2 x 1010 bacteria lost each day in feces. Through binary fission, most of the bacteria in a colony are genetically identical to the parent cell.However, the spontaneous mutation rate of E. coliis 1 x 10-7 mutations per gene per cell division.This will produce about 2,000 bacteria in the human colon that have a mutation in that gene per day.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsNew mutations, though individually rare, can have a significant impact on genetic diversity when reproductive rates are very high because of short generation spans.Individual bacteria that are genetically well equipped for the local environment clone themselves more prolifically than do less fit individuals.In contrast, organisms with slower reproduction rates (like humans) create most genetic variation not by novel alleles produced through mutation, but by sexual recombination of existing alleles.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsIn addition to mutations, genetic recombination generates diversity within bacterial populations.Here, recombination is defined as the combining of DNA from two individuals into a single genome.Recombination occurs through three processes: transformation transduction conjugation2. Genetic recombination produces new bacterial strainsCopyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsTransformation is the alteration of a bacterial cells genotype by the uptake of naked, foreign DNA from the surrounding environment.For example, harmless Streptococcus pneumoniae bacteria can be transformed to pneumonia-causing cells.This occurs when a live nonpathogenic cell takes up a piece of DNA that happened to include the allele for pathogenicity from dead, broken-open pathogenic cells.The foreign allele replaces the native allele in the bacterial chromosome by genetic recombination.The resulting cell is now recombinant with DNA derived from two different cells.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsMany bacterial species have surface proteins that are specialized for the uptake of naked DNA.These proteins recognize and transport only DNA from closely related bacterial species.While E. coli lacks this specialized mechanism, it can be induced to take up small pieces of DNA if cultured in a medium with a relatively high concentration of calcium ions.In biotechnology, this technique has been used to introduce foreign DNA into E. coli.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsTransduction occurs when a phage carries bacterial genes from one host cell to another.In generalized transduction, a small piece of the host cells degraded DNA is packaged within a capsid, rather than the phage genome.When this pages attaches to another bacterium, it will inject this foreign DNA into its new host.Some of this DNA can subsequently replace the homologous region of the second cell.This type of transduction transfers bacterial genes at random.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsSpecialized transduction occurs via a temperate phage.When the prophage viral genome is excised from the chromosome, it sometimes takes with it a small region of adjacent bacterial DNA.These bacterial genes are injected along with the phages genome into the next host cell.Specialized transduction only transfers those genes near the prophage site on the bacterial chromosome.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsBoth generalized and specialized transduction use phage as a vector to transfer genes between bacteria.Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 18.13Conjugation transfers genetic material between two bacterial cells that are temporarily joined.One cell (male) donates DNA and its mate (female) receives the genes.A sex pilus from the male initially joins the two cells and creates a cytoplasmic bridge between cells.Maleness, the ability to form a sex pilus and donate DNA, results from an F factor as a section of the bacterial chromosome or as a plasmid.Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 18.14Plasmids, including the F plasmid, are small, circular, self-replicating DNA molecules.Episomes, like the F plasmid, can undergo reversible incorporation into the cells chromosome.Temperate viruses also qualify as episomes.Plasmids, generally, benefit the bacterial cell.They usually have only a few genes that are not required for normal survival and reproduction.Plasmid genes are advantageous in stressful conditions.The F plasmid facilitates genetic recombination when environmental conditions no longer favor existing strains.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsThe F factor or its F plasmid consists of about 25 genes, most required for the production of sex pili.Cells with either the F factor or the F plasmid are called F+ and they pass this condition to their offspring.Cells lacking either form of the F factor, are called F-, and they function as DNA recipients.When an F+ and F- cell meet, the F+ cell passes a copy of the F plasmid to the F- cell, converting it.Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 18.15aThe plasmid form of the F factor can become integrated into the bacterial chromosome.The resulting Hfr cell (high frequency of recombination) functions as a male during conjugation.Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 18.15bIn the 1950s, Japanese physicians began to notice that some bacterial strains had evolved antibiotic resistance.The genes conferring resistance are carried by plasmids, specifically the R plasmid (R for resistance).Some of these genes code for enzymes that specifically destroy certain antibiotics, like tetracycline or ampicillin.When a bacterial population is exposed to an antibiotic, individuals with the R plasmid will survive and increase in the overall population.Because R plasmids also have genes that encode for sex pili, they can be transferred from one cell to another by conjugation.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsA transposon is a piece of DNA that can move from one location to another in a cells genome.Transposon movement occurs as a type of recombination between the transposon and another DNA site, a target site.In bacteria, the target site may be within the chromosome, from a plasmid to chromosome (or vice versa), or between plasmids.Transposons can bring multiple copies for antibiotic resistance into a single R plasmid by moving genes to that location from different plasmids.This explains why some R plasmids convey resistance to many antibiotics.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsSome transposons (so called jumping genes) do jump from one location to another (cut-and-paste translocation).However, in replicative transposition, the transposon replicates at its original site, and a copy inserts elsewhere.Most transposons can move to many alternative locations in the DNA, potentially moving genes to a site where genes of that sort have never before existed. Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsThe simplest bacterial transposon, an insertion sequence, consists only of the DNA necessary forthe act of transposition.The insertion sequence consists of the transposase gene, flanked by a pair of inverted repeat sequences.The 20 to 40 nucleotides of the inverted repeat on one side are repeated in reverse along the opposite DNA strand at the other end of the transposon. Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 18.16The transposase enzyme recognizes the inverted repeats as the edges of the transposon.Transposase cuts the transposon from its initial site and inserts it into the target site.Gaps in the DNA strands are filled in by DNA polymerase, creating direct repeats, and then DNA ligase seals the old and new material. Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 18.17An individual bacterium, locked into the genome that it has inherited, can cope with environmental fluctuations by exerting metabolic control.First, cells vary the number of specific enzyme molecules by regulating gene expression.Second, cells adjust the activity of enzymes already present (for example, by feedback inhibition).3. The control of gene expression enables individual bacteria to adjust their metabolism to environmental changeCopyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsFor example, the tryptophan biosynthesis pathway demonstrates both levels of control.If tryptophan levels are high, some of the tryptophan molecules can inhibit the first enzyme in the pathway.If the abundance of tryptophan continues, the cell can stop synthesizing additional enzymes in this pathway by blocking transcription of the genes for these enzymes. Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 18.19In 1961, Francois Jacob and Jacques Monod proposed the operon model for the control of gene expression in bacteria.An operon consists of three elements:the genes that it controls,In bacteria, the genes coding for the enzymes of a particular pathway are clustered together and transcribed (or not) as one long mRNA molecule.a promotor region where RNA polymerase first binds,an operator region between the promotor and the first gene which acts as an on-off switch. Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsBy itself, an operon is on and RNA polymerase can bind to the promotor and transcribe the genes. Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 18.20aHowever, if a repressor protein, a product of a regulatory gene, binds to the operator, it can prevent transcription of the operons genes.Each repressor protein recognizes and binds only to the operator of a certain operon.Regulatory genes are transcribed at low rates continuously. Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsFig. 18.20b

Binding by the repressor to the operator is reversible.The number of active repressor molecules available determines the on and off mode of the operator.Many repressors contain allosteric sites that change shape depending on the binding of other molecules.In the case of the trp operon, when concentrations of tryptophan in the cell are high, some tryptophan molecules bind as a corepressor to the repressor protein.This activates the repressor and turns the operon off.At low levels of tryptophan, most of the repressors are inactive and the operon is transcribed. Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsThe trp operon is an example of a repressible operon, one that is inhibited when a specific small molecule binds allosterically to a regulatory protein.In contrast, an inducible operon is stimulated when a specific small molecule interacts with a regulatory protein. In inducible operons, the regulatory protein is active (inhibitory) as synthesized, and the operon is off.Allosteric binding by an inducer molecule makes the regulatory protein inactive, and the operon is on. Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsThe lac operon, containing a series of genes that code for enzymes, which play a major role in the hydrolysis and metabolism for lactose.In the absence of lactose, this operon is off as an active repressor binds to the operator and prevents transcription.Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 18.21aCopyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsFig. 18.21b When lactose is present in the cell, allolactase, an isomer of lactose, binds to the repressor.

This inactivates the repressor, and the lac operon can be transcribed.

Repressible enzymes generally function in anabolic pathways, synthesizing end products.When the end product is present in sufficient quantities, the cell can allocate its resources to other uses. Inducible enzymes usually function in catabolic pathways, digesting nutrients to simpler molecules.By producing the appropriate enzymes only when the nutrient is available, the cell avoids making proteins that have nothing to do.Both repressible and inducible operons demonstrate negative control because active repressors can only have negative effects on transcription. Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsPositive gene control occurs when an activator molecule interacts directly with the genome to switch transcription on.Even if the lac operon is turned on by the presence of allolactose, the degree of transcription depends on the concentrations of other substrates.If glucose levels are low (along with overall energy levels), then cyclic AMP (cAMP) binds to cAMP receptor protein (CRP) which activates transcription.Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 18.22aThe cellular metabolism is biased toward the utilization of glucose.If glucose levels are sufficient and cAMP levels are low (lots of ATP), then the CRP protein has an inactive shape and cannot bind upstream of the lac promotor.The lac operon will be transcribed but at a low level.Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 18.22bFor the lac operon, the presence / absence of lactose (allolactose) determines if the operon is on or off.Overall energy levels in the cell determine the level of transcription, a volume control, through CRP.CRP works on several operons that encode enzymes used in catabolic pathways.If glucose is present and CRP is inactive, then the synthesis of enzymes that catabolize other compounds is slowed.If glucose levels are low and CRP is active, then the genes which produce enzymes that catabolize whichever other fuel is present will be transcribed at high levels. Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsCopyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsSection A: The World of Prokaryotes1.Theyre (almost) everywhere! An overview of prokaryotic life2.Bacteria and archaea are the two main branches of prokaryote evolution

CHAPTER 27 PROKARYOTES AND THE ORIGINS OF METABOLIC DIVERSITYProkaryotes were the earliest organisms on Earth and evolved alone for 1.5 billion years.Today, prokaryotes still dominate the biosphere.Their collective biomass outweighs all eukaryotes combined by at least tenfold.More prokaryotes inhabit a handful of fertile soil or the mouth or skin of a human than the total number of people who have ever lived.1. Theyre (almost) everywhere! An overview of prokaryotic lifeCopyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsProkarytes are wherever there is life and they thrive in habitats that are too cold, too hot, too salty, too acidic, or too alkaline for any eukaryote.The vivid reds,oranges, andyellows thatpaint theserocks arecolonies ofprokaryotes.Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 27.1We hear most about the minority of prokaryote species that cause serious illness.During the 14th century, a bacterial disease known as bubonic plague, spread across Europe and killed about 25% of the human population.Other types of diseases caused by bacteria include tuberculosis, cholera, many sexually transmissible diseases, and certain types of food poisoning.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsHowever, more bacteria are benign or beneficial.Bacteria in our intestines produce important vitamins.Prokaryotes recycle carbon and other chemical elements between organic matter and the soil and atmosphere.Prokaryotes often live in close association among themselves and with eukaryotes in symbiotic relationships.Mitochondria and chloroplasts evolved from prokaryotes that became residents in larger host cells.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsMolecular evidence accumulated over the last two decades has lead to the conclusion that there are two major branches of prokaryote evolution, not a single kingdom as in the five-kingdom system.These two branches are the bacteria and the archaea.The archaea inhabit extreme environments and differ from bacteria in many key structural, biochemical, and physiological characteristics.2. Bacteria and archaea are the two main branches of prokaryote evolutionCopyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsCurrent taxonomy recognizes two prokaryotic domains: domain Bacteria and domain Archaea.A domain is a taxonomic level above kingdom.The rationale for this decision is that bacteria and archaea diverged so early in life and are so fundamentally different.At the same time, theyboth are structurallyorganized at theprokaryotic level.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsFig. 27.2

In nearly all prokaryotes, a cell wall maintains the shape of the cell, affords physical protection, and prevents the cell from bursting in a hypotonic environment.Most bacterial cell walls contain peptidoglycan, a polymer of modified sugars cross-linked by short polypeptides.The walls of archaea lack peptidoglycan.1. Nearly all prokaryotes have a cell wall external to the plasma membraneCopyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsThe Gram stain is a valuable tool for identifying specific bacteria, based on differences in their cell walls.Gram-positive bacteria have simpler cell walls, with large amounts of peptidoglycans.Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 27.5aGram-negative bacteria have more complex cell walls and less peptidoglycan.An outer membrane on the cell wall contains lipopolysaccharides, carbohydrates bonded to lipids.Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 27.5bAmong pathogenic bacteria, gram-negative species are generally more threatening than gram-positive species.The lipopolysaccharides on the walls are often toxic and the outer membrane protects the pathogens from the defenses of their hosts.Gram-negative bacteria are commonly more resistant than gram-positive species to antibiotics because the outer membrane impedes entry of antibiotics.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsMany antibiotics, including penicillins, inhibit the synthesis of cross-links in peptidoglycans, preventing the formation of a functional wall, particularly in gram-positive species.These drugs are a very selective treatment because they cripple many species of bacteria without affecting humans and other eukaryotes, which do not synthesize peptidoglycans.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsMany prokaryotes secrete another sticky protective layer, the capsule, outside the cell wall.Capsules adhere the cells to their substratum.They may increase resistance to host defenses.They glue together the cells of those prokaryotes that live as colonies.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsAnother way for prokaryotes to adhere to one another or to the substratum is by surface appendages called pili.Pili can fasten pathogenic bacteria to the mucous membranes of its host.Some pili are specialized for holding two prokaryote cells together long enough to transfer DNA during conjugation.Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 27.6CHAPTER 27 PROKARYOTES AND THE ORIGINS OF METABOLIC DIVERSITYCopyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsSection B2: The Structure, Function, and Reproduction of Prokaryotes (continued)3. The cellular and genomic organization of prokaryotes is fundamentally different from that of eukaryotes4. Populations of eukaryotes grow and adapt rapidly

Prokaryotic cells lack a nucleus enclosed by membranes.The cells of prokaryotes also lack the other internal compartments bounded by membranes that are characteristic of eukaryotes.3. The cellular and genomic organization of prokaryotes is fundamentally different from that of eukaryotesCopyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsInstead, prokaryotes used infolded regions of the plasma membrane to perform many metabolic functions, including cellular respiration and photosynthesis.Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 27.8Prokaryotes have smaller, simpler genomes than eukaryotes.On average, a prokaryote has only about one-thousandth as much DNA as a eukaryote.Typically, the DNA is concentrated as a snarl of fibers in the nucleoid region.The mass of fibers is actually the single prokaryotic chromosome, a double-stranded DNA molecule in the form of a ring.There is very little protein associated with the DNA.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsProkaryotes may also have smaller rings of DNA, plasmids, that consist of only a few genes.Prokaryotes can survive in most environments without their plasmids because essential functions are programmed by the chromosomes.However, plasmids provide the cell genes for resistance to antibiotics, for metabolism of unusual nutrients, and other special contingencies.Plasmids replicate independently of the chromosome and can be transferred between partners during conjugation.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsProkaryotes reproduce only asexually via binary fission, synthesizing DNA almost continuously.A single cell in favorable conditions will produce a colony of offspring.4. Populations of prokaryotes grow and adapt rapidlyCopyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 27.9While lacking meiosis and sex as seen in eukarotes, prokaryotes have several mechanisms to combine genes between individuals.In transformation, a cell can absorb and integrate fragments of DNA from their environment.This allows considerable genetic transfer between prokaryotes, even across species lines.In conjugation, one cell directly transfers genes to another cell.In transduction, viruses transfer genes between prokaryotes.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsLacking meiotic sex, mutation is the major source of genetic variation in prokaryotes.With generation times in minutes or hours, prokaryotic populations can adapt very rapidly to environmental changes, as natural selection screens new mutations and novel genomes from gene transfer.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsProkaryote can also withstand harsh conditions.Some bacteria form resistant cells, endospores.In an endospore, a cell replicates its chromosome and surrounds one chromosome with a durable wall.While the outercell may disinte-grate, an endospore,such as this anthraxendospore, dehy-drates, does notmetabolize, andstays protectedby a thick, protective wall.Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 27.10In most environments, prokaryotes compete with other prokaryotes (and other microorganisms) for space and nutrients.Many microorganisms release antibiotics, chemicals that inhibit the growth of other microorganisms (including certain prokaryotes, protists, and fungi).Humans have learned to use some of these compounds to combat pathogenic bacteria.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsCopyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsSection C: Nutrition and Metabolic Diversity1.Prokaryotes can be grouped into four categories according to how they obtain energy and carbon2.Photosynthesis evolved early in prokaryotic life

CHAPTER 27 PROKARYOTES AND THE ORIGINS OF METABOLIC DIVERSITYNutrition here refers to how an organism obtains energy and a carbon source from the environment to build the organic molecules of cells.1. Prokaryotes can be grouped into four categories according to how they obtain energy and carbonCopyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsSpecies that use light energy are phototrophs.Species that obtain energy from chemicals in their environment are chemotrophs.Organisms that need only CO2 as a carbon source are autotrophs.Organisms that require at least one organic nutrient as a carbon source are heterotrophs.These categories of energy source and carbon source can be combined to group prokaryotes according to four major modes of nutrition.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsPhotoautotrophs are photosynthetic organisms that harness light energy to drive the synthesis of organic compounds from carbon dioxide.Among the photoautotrophic prokaryotes are the cyanobacteria.Among the photosynthetic eukaryotes are plants and algae.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsChemoautotrophs need only CO2 as a carbon source, but they obtain energy by oxidizing inorganic substances, rather than light.These substances include hydrogen sulfide (H2S), ammonia (NH3), and ferrous ions (Fe2+) among others.This nutritional mode is unique to prokaryotes.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsPhotoheterotrophs use light to generate ATP but obtain their carbon in organic form.This mode is restricted to prokaryotes.Chemoheterotrophs must consume organic molecules for both energy and carbon.This nutritional mode is found widely in prokaryotes, protists, fungi, animals, and even some parasitic plants.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsCopyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

The majority of known prokaryotes are chemoheterotrophs.These include saprobes, decomposers that absorb nutrients from dead organisms, and parasites, which absorb nutrients from the body fluids of living hosts.Some of these organisms (such as Lactobacillus) have very exacting nutritional requirements, while others (E. coli) are less specific in their requirements.With such a diversity of chemoheterotrophs, almost any organic molecule, including petroleum, can serve as food for at least some species.Those few classes or syntheticorganic compounds that cannot be broken down by bacteria are said to be nonbiodegradable.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsCopyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsSection D: A Survey of Prokaryotic Diversity1.Molecular systematics is leading to a phylogenetic classification of prokaryotes2.Researchers are identifying a great diversity of archaea in extreme environments and in the oceans3. Most known prokaryotes are bacteria

CHAPTER 27 PROKARYOTES AND THE ORIGINS OF METABOLIC DIVERSITYThe limited fossil record and structural simplicity of prokaryotes created great difficulties in developing a classification of prokaryotes.A breakthrough came when Carl Woese and his colleagues began to cluster prokarotes into taxonomic groups based on comparisons of nucleic acid sequences.Especially useful was the small-subunit ribosomal RNA (SSU-rRNA) because all organisms have ribosomes.1. Molecular systematics is leading to phylogenetic classification of prokaryotesCopyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsWoese used signature sequences, regions of SSU-rRNA that are unique, to establish a phylogeny of prokarotes.Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 27.13Early on prokaryotes diverged into two lineages, the domains Archaea and Bacteria.A comparison of the three domains demonstrates that Archaea have at least as much in common with eukaryotes as with bacteria.The archaea also have many unique characteristics.2. Researchers are identifying a great diversity of archaea in extreme environments and in the oceansCopyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsCopyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Most species of archaea have been sorted into the kingdom Euryarchaeota or the kingdom Crenarchaeota.However, much of the research on archaea has focused not on phylogeny, but on their ecology - their ability to live where no other life can.Archaea are extremophiles, lovers of extreme environments.Based on environmental criteria, archaea can be classified into methanogens, extreme halophiles, and extreme thermophilies.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsMethanogens obtain energy by using CO2 to oxidize H2 replacing methane as a waste.Methanogens are among the strictest anaerobes.They live in swamps and marshes where other microbes have consumed all the oxygen.Methanogens are important decomposers in sewage treatment.Other methanogens live in the anaerobic guts of herbivorous animals, playing an important role in their nutrition.They may contribute to the greenhouse effect, through the production of methane.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsExtreme halophiles live in such saline places as the Great Salt Lake and the Dead Sea.Some species merely tolerate elevated salinity; others require an extremely salty environment to grow.Colonies of halophiles form a purple-red scum from bacteriorhodopsin, a photosynthetic pigment very similar to the visual pigment in the human retina. Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 27.14Extreme thermophiles thrive in hot environments.The optimum temperatures for most thermophiles are 60oC-80oC. Sulfolobus oxidizes sulfur in hot sulfur springs in Yellowstone National Park.Another sulfur-metabolizing thermophile lives at 105oC water near deep-sea hydrothermal vents.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsCopyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsSection E: The Ecological Impact of Prokaryotes1.Prokaryotes are indispensable links in the recycling of chemical elements in ecosystems2.Many prokaryotes are symbiotic3. Pathogenic prokaryotes cause many human diseases4.Humans use prokaryotes in research and technology

CHAPTER 27 PROKARYOTES AND THE ORIGINS OF METABOLIC DIVERSITYOngoing life depends on the recycling of chemical elements between the biological and chemical components of ecosystems.If it were not for decomposers, especially prokaryotes, carbon, nitrogen, and other elements essential for life would become locked in the organic molecules of corpses and waste products.Prokaryotes also mediate the return of elements from the nonliving components of the environment to the pool of organic compounds.1. Prokaryotes are indispensable links in the recycling of chemical elements in ecosystemsCopyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsProkaryotes often interact with other species of prokaryotes or eukaryotes with complementary metabolisms.Organisms involved in an ecological relationship with direct contact (symbiosis) are known as symbionts.If one symbiont is larger than the other, it is also termed the host.2. Many prokaryotes are symbioticCopyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsIn commensalism, one symbiont receives benefits while the other is not harmed or helped by the relationship.In parasitism, one symbiont, the parasite, benefits at the expense of the host.In mutualism, both symbionts benefit.For example, while the fishprovides bioluminescentbacteria under its eye withorganic materials, the fishuses its living flashlightto lure prey and to signalpotential mates.Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 27.15Prokaryotes are involved in all three categories of symbiosis with eukaryotes.Legumes (peas, beans, alfalfa, and others) have lumps in their roots which are the homes of mutualistic prokaryotes (Rhizobium) that fix nitrogen that is used by the host.The plant provides sugars and other organic nutrients to the prokaryote.Fermenting bacteria in the human vagina produce acids that maintain a pH between 4.0 and 4.5, suppressing the growth of yeast and other potentially harmful microorganisms.Other bacteria are pathogens.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsExposure to pathogenic prokaryotes is a certainty.Most of the time our defenses check the growth of these pathogens.Occasionally, the parasite invades the host, resists internal defenses long enough to begin growing, and then harms the host.Pathogenic prokaryotes cause about half of all human disease, including pneumonia caused byHaemophilus influenzae bacteria.Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 27.163. Pathogenic prokaryotes cause many human diseasesSome pathogens are opportunistic.These are normal residents of the host, but only cause illness when the hosts defenses are weakened.Louis Pasteur, Joseph Lister, and other scientists began linking disease to pathogenic microbes in the late 1800s.Robert Koch was the first to connect certain diseases to specific bacteria.He identified the bacteria responsible for anthrax and the bacteria that cause tuberculosis.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsKochs methods established four criteria, Kochs postulates, that still guide medical microbiology.(1) The researcher must find the same pathogen in each diseased individual investigated,(2) Isolate the pathogen form the diseased subject and grow the microbe in pure culture,(3) Induce the disease in experimental animals by transferring the pathogen from culture, and(4) Isolate the same pathogen from experimental animals after the disease develops.These postulates work for most pathogens, but exceptions do occur.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsSome pathogens produce symptoms of disease by invading the tissues of the host.The actinomycete that causes tuberculosis is an example of this source of symptoms.More commonly, pathogens cause illness by producing poisons, called exotoxins and endotoxins.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsExotoxins are proteins secreted by prokaryotes.Exotoxins can produce disease symptoms even if the prokaryote is not present.Clostridium botulinum, which grows anaerobically in improperly canned foods, produces an exotoxin that causes botulism.An exotoxin produced by Vibrio cholerae causes cholera, a serious disease characterized by severe diarrhea.Even strains of E. coli can be a source of exotoxins, causing travelers diarrhea.Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsThe decline (but not removal) of bacteria as threats to health may be due more to public-health policies and education than to wonder-drugs.For example, Lyme disease, caused by a spirochete spread by ticks that live on deer, field mice, and occasionally humans, can be cured if antibiotics are administered within a month after exposure.If untreated, Lyme disease causes arthritis, heart disease, and nervous disorders.The best defense is avoiding tick bites and seeking treatment if bit and a character-istic rash develops.Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 27.17Humans have learned to exploit the diverse metabolic capabilities of prokaryotes, for scientific research and for practical purposes.Much of what we know about metabolism and molecular biology has been learned using prokaryotes, especially E. coli, as simple model systems.Increasing, prokaryotes are used to solve environmental problems.3. Humans use prokaryotes in research and technologyCopyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsSoil bacteria, called pseudomonads, have been developed to decompose petroleum products at the site of oil spills or to decompose pesticides.Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 27.19Humans also use bacteria as metabolic factories for commercial products.The chemical industry produces acetone, butanol, and other products from bacteria.The pharmaceutical industry cultures bacteria to produce vitamins and antibiotics.The food industry used bacteria to convert milk to yogurt and various kinds of cheese.The development of DNA technology has allowed genetic engineers to modify prokaryotes to achieve specific research and commercial outcomes.Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings