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The Genetics of Viruses and Bacteria Microbial Models Viruses come in many shapes and sizes Compare the size of a Eukaoryotic cell, Bacterial Cell and a Virus Discovery of the Virus Adolph Meyer a German Scientist studied the Tobacco Mosaic Virus. Thought it was caused by a very small bacteria because it could not be viewed through the microscope. Dimitri Ivanosky a Russian Scientist Filtered the sap to get rid of the bacteria. The plants still received the infection when sprayed with the filtered sap. Still thought the pathogen were very small bacteria. Martinus Beijerink a Dutch Botanist Discovered that this infectious particle could reproduce. Sprayed plants with filtered sap and their sap infected other plants. Infection was not diluted on subsequent infections. Could not grow outside the host in culture medium. Could not be inactivated with alcohol like bacteria Wendell Stanley an American Scientist Finally crystallized this infectious particle and viewed it under the electron microscope. Viral Composition Capsid – protein coat Sometimes an envelope – glycoproteins acid – DNA or RNA. Never both. Can be single or double stranded. Nucleic Some have tail fibers – Bacteriophage T4 Viruses Are Obligate Intracellular Parasites They lack their own enzymes to perform metabolism and reproduction. They utilize the host’s enzymatic machinery to accomplish these tasks. Viruses have a host range or are host specific. Rabies infects more than one host Eukaryotic viruses are usually tissue specific. • Rhinoviruses, Adenoviruses, Herpes, HIV Bacteriophage (phage virus) Reproductive Cycles of Virus Lytic Cycle – destroys the host cell The range of organisms that a virus can attack is called the host range Viral proteins are translated by host enzymes and new viral particles are produced. Viral particles are assembled and the host cell is lysed. Host cell death occurs. Bacterial cells possess restriction endonucleases that destroy foreign DNA. The bacterial DNA is methylated to protect from destruction. Lytic Cycle Lysogenic Cycle Can Be Used For Cloning Viruses can infect without destroying the host cell. They integrate their DNA into the host cell and turn off their own genes. These types of viruses are called temperate viruses. Bacterial cells that possess these viral genes are celled prophages. Viral DNA can be replicated along with the host cell’s DNA. Lysogenic Cycle Lysogenic Viruses can be Triggered to Become Lytic Viruses Radiation, chemicals or any host cell stress can cause the virus to enter the lytic cycle and destroy the host cell. Some prophages (bacterial cells that possess viral gene) express prophage genes that alter the phenotype of the host cell. Bacteria produce endotoxins that originate from viral genes.(Diptheria, Scarlet Fever and Botulism) Genes can be inserted into bacterial cells using viruses in a process called Transduction. RNA as Viral Genetic Material Recall: mRNA serves as the template for new genetic material. Reverse transcriptase produces DNA from mRNA. transcribes RNA into DNA, retroactively “backward”, integrating the viral DNA (provirus) into the hosts genome, never to leave Newly made DNA integrates into the host chromosome. Viruses that do this are called retroviruses. HIV; human immunodeficiency virus CAUSES AIDS; acquired immunodeficiency syndrome HIV Infection HIV Infection The host’s RNA polymerase transcribes viral RNA from the DNA. RNA serves as both a template and mRNA. RNA viruses mutate more rapidly because replication of RNA does not have to undergo the same proofreading steps as replicating DNA. Transduction When phage viruses acquire bits of bacterial DNA as they infect cells, resulting in genetic recombination Generalized-movement of a random piece of bacterial DNA as the phage lyses the donor to the recipient in the lytic cycle Restricted/temperate/specialized- transfer of a specific piece of DNA next to the prophage site (bacterial cells that possess viral gene) Prophage When viral DNA is integrated into the bacterial chromosome (Plasmid) Transduction Viral Diseases in Animals 1- Viruses may damage or kill cells by causing the release of hydrolytic enzymes from lysosomes •Amount of damage depends on the ability of infected tissue to regenerate by mitosis - Respiratory tract epithelium repairs quickly from adenovirus infection - Nerve tracts affected by polio virus is permanent •Find host cells using “lock & key” fit with proteins on virus & host cell receptors 2- Some viruses cause infected cells that produce toxins that lead to disease symptoms Prions and Viroids The simplest Infectious Agents Prions • Prions are infectious proteins. They contain no RNA or DNA and have a long incubation period (~10 years) - cause degenerative brain diseases like scrapes and Creutzfeldt-Jakob disease. - abnormal shaped brain proteins induce normal proteins to assume an abnormal shape propagating itself. Prions –slow-acting, virtually indestructible infectious –cause brain diseases in mammals –Propagate by converting normal proteins into the prion version Viroids Viroids are tiny molecules of naked circular RNA that infect plants. - only several hundred nucleotides long. - a molecule can be an infectious agent. - disrupt metabolism by interfering with the host genome. Viral Diseases in Plants •More than 2,000 types of viral diseases of plants are known •Common symptoms of viral infection include –Spots on leaves and fruits, stunted growth, and damaged flowers or roots Viral Diseases in Plants •Plant viruses spread disease in two major modes –Horizontal transmission, entering through damaged cell walls –Vertical transmission, inheriting the virus from a parent Emerging Viruses •Appear suddenly or suddenly come to the attention of medical scientists 3 processes contribute to emerging viruses 1. Mutation of existing viruses as RNA is not corrected by proofreading e.g. SARS 2. Spread from one host species to another e.g. Hanta Virus 3. Dissemination from a small isolated population e.g. HIV SARS – Severe Acute Respiratory Syndrome (b) The SARS-causing agent is a coronavirus (a) Young ballet students in Hong Kong like this one (colorized TEM), so named for the wear face masks to protect themselves “corona” of glycoprotein spikes protruding from from the virus causing SARS. the envelope. Figure 18.11 A, B Small Pox Polio Polio Herpes Simplex Hepatitis Varicella Zoster Mumps Measles - Rubeola Other Viruses that affect humans •Influenza Virus •Rubella •Parvo-virus •Epstein Barr Virus •Hanta Virus •(HPV) Human Papilloma Virus •(RSV) Respiratory Syncytial Virus •Rabies •Rhinovirus •Rotavirus •West Nile Virus BACTERIA 18.3 Bacteria •Rapid reproduction, mutation, and genetic recombination contribute to the genetic diversity of bacteria The Bacterial Genome and Its Replication •The bacterial chromosome –Is usually a circular DNA molecule with few associated proteins •In addition to the chromosome –Many bacteria have plasmids, smaller circular DNA molecules that can replicate independently of the bacterial chromosome The Bacterial Genome and Its Replication •Bacterial cells divide by binary fission –Which is preceded by replication of the bacterial chromosome in both directions from a single point of origin Replication fork Origin of replication Termination of replication Binary Fission Mutation and Genetic Recombination as Sources of Genetic Variation •Since bacteria can reproduce rapidly –New mutations can quickly increase a population’s genetic diversity •Genetic diversity –Can also arise by recombination of the DNA from two different bacterial cells Remember that prokaryotes don’t undergo meiosis or fertilization Recombination in Bacteria •Three processes bring bacterial DNA from different individuals together, since meiosis and fertilization do nor occur in bacteria –Transformation –Transduction –Conjugation Transformation Is the alteration of a bacterial cell’s genotype and phenotype by the uptake of naked, foreign DNA from the surrounding environment Transduction Phages carry bacterial genes from one host cell to another Conjugation and Plasmids •Conjugation –Is the direct transfer of genetic material between bacterial cells that are temporarily joined DNA transfer is one way Figure 18.17 Sex pilus 1 m The F Plasmid and Conjugation •Cells containing the F (fertility) plasmid, designated F+ cells –Function as DNA donors during conjugation –F plasmid contains genes for the production of pili (cytoplasmic bridges that serve as connection sites) –Transfer plasmid DNA to an F recipient cell F Plasmid Bacterial chromosome F+ cell F+ cell Mating bridge F– cell 2 1 A cell carrying an F plasmid (an F+ cell) can form a mating bridge with an F– cell and transfer its F plasmid. Figure 18.18a F+ cell Bacterial chromosome 3 A single strand of the F plasmid breaks at a specific point (tip of blue arrowhead) and begins to move into the recipient cell. As transfer continues, the donor plasmid rotates (red arrow). 4 DNA replication occurs in both donor and recipient cells, using the single parental strands of the F plasmid as templates to synthesize complementary strands. The plasmid in the recipient cell circularizes. Transfer and replication result in a compete F plasmid in each cell. Thus, both cells are now F+. F Plasmid recombination Chromosomal genes can be transferred during conjugation when the donor cell’s F factor is integrated into the chromosome Hfr (high frequency of recombination) cell A cell with the F factor built into its chromosome The F factor of an Hfr cell Brings some chromosomal DNA along with it when it is transferred to an F– cell R plasmids and Antibiotic Resistance -R plasmids make cells in which it is present resistant to specific antibiotics -ampicillin, tetracycline -R plasmid can be transferred via conjugation -Increase in resistant bacteria over time, evolutionary advantage (concerning?!) Other forms of genetic variability: Transposition of Genetic Elements •Transposable elements –Can move around within a cell’s genome –Are often called “jumping genes” –Contribute to genetic shuffling in bacteria by folding the DNA Transposons •Bacterial transposons –Also move about within the bacterial genome –Have additional genes, such as those for antibiotic resistance Transposon Insertion sequence Antibiotic resistance gene Insertion sequence 5 5 3 3 Inverted repeats Transposase gene (b) Transposons contain one or more genes in addition to the transposase gene. In the transposon shown here, a gene for resistance to an antibiotic is located between twin insertion sequences. The gene for antibiotic resistance is carried along as part of the transposon when the transposon is inserted at a new site in the genome. Figure 18.19b Other forms of genetic variability: Insertion Sequences •An insertion sequence contains a single gene for transposase –An enzyme that catalyzes movement of the insertion sequence from one site to another within the genome Insertion sequence 3 A T C C G G T… A C C G G A T… 3 5 TAG G C CA… TG G C CTA… 5 Transposase gene Inverted Inverted repeat repeat (a) Insertion sequences, the simplest transposable elements in bacteria, contain a single gene that encodes transposase, which catalyzes movement within the genome. The inverted repeats are backward, upside-down versions of each other; only a portion is shown. The inverted repeat sequence varies from one type of insertion sequence to another. Figure 18.19a Prokaryotic Gene Expression •Individual bacteria respond to environmental change by regulating their gene expression •E. coli, a type of bacteria that lives in the human colon –Can tune its metabolism to the changing environment and food sources Response to the environment •This metabolic control occurs on two levels –Adjusting the activity of metabolic enzymes already present –Regulating the genes encoding the metabolic enzymes (a) Regulation of enzyme activity Precursor Feedback inhibition Enzyme 1 Feedback Inhibition: (b) Regulation of enzyme production Gene 1 Operons: Adjusting the activity of metabolic enzymes already present Enzyme 2 Gene 2 Enzyme 3 Gene 3 Regulation of gene expression – Enzyme 4 Gene 4 – Enzyme 5 Tryptophan Figure 18.20a, b Gene 5 Regulating the genes encoding the metabolic enzymes Operons: The Basic Concept •In bacteria, genes are often clustered into operons, composed of –An operator, an “on-off” switch –A promoter –Genes for metabolic enzymes •An operon –Is usually turned “on” –Can be switched off by a protein called a repressor Operon Parts •The regulatory gene codes for the repressor protein. •The promoter site is the attachment site for RNA polymerates. •The operator site is the attachment site for the repressor protein. •The structural genes code for the proteins. •The repressor protein is different for each operon and is custom fit to the regulatory metabolite. Whether or not the repressor protein can bind to the operator site is determined by the type of operon. Operon Parts •The regulatory metabolite is either the product of the reaction or the reactant depending on the type of operon. •The repressor protein is different for each operon and is custom fit to the regulatory metabolite. Whether or not the repressor protein can bind to the operator site is determined by the type of operon. •The regulatory metabolite is either the product of the reaction or the reactant depending on the type of operon. The trp operon: regulated synthesis of repressible enzymes trp operon Promoter DNA Promoter Genes of operon trpD trpC trpE trpR Regulatory gene mRNA 5 3 Operator Start codon RNA polymerasemRNA 5 Inactive repressor trpA Stop codon E Protein trpB D C B A Polypeptides that make up enzymes for tryptophan synthesis (a) Tryptophan absent, repressor inactive, operon on. RNA polymerase attaches to the DNA at the promoter and transcribes the operon’s genes. Figure 18.21a DNA No RNA made mRNA Protein Active repressor Tryptophan (corepressor) (b) Tryptophan present, repressor active, operon off. As tryptophan accumulates, it inhibits its own production by activating the repressor protein. Figure 18.21b Trp Operon Repressible and Inducible Operons: Two Types of Negative Gene Regulation •In a repressible operon –Binding of a specific repressor protein to the operator shuts off transcription (Found in anabolic pathways) •In an inducible operon –Binding of an inducer to an innately inactive repressor inactivates the repressor and turns on transcription (Found in catabolic pathways) Lac Operon The lac operon: regulated synthesis of inducible enzymes Promoter Regulatory gene DNA Operator lacl lacZ 3 mRNA Protein No RNA made RNA polymerase 5 Active repressor (a) Lactose absent, repressor active, operon off. The lac repressor is innately active, and in the absence of lactose it switches off the operon by binding to the operator. Figure 18.22a Lac Operon “off” lac operon DNA lacz lacl 3 mRNA 5 lacA RNA polymerase mRNA 5' 5 mRNA -Galactosidase Protein Allolactose (inducer) lacY Permease Transacetylase Inactive repressor (b) Lactose present, repressor inactive, operon on. Allolactose, an isomer of lactose, derepresses the operon by inactivating the repressor. In this way, the enzymes for lactose utilization are induced. Figure 18.22b Lac Operon “on” Types of Operons Inducible enzymes Usually function in catabolic pathways Repressible enzymes Usually function in anabolic pathways