The Genetics of Viruses & Bacteria What do you know about viruses? How big are viruses? - small 0.25 m Virus Animal cell Bacterium Animal cell nucleus

(a) Tobacco mosaic virus The Genetics of Viruses & Bacteria What do you know about viruses? How big are viruses? What are the components of a virus? Nucleic acid genome Protein capsid 18  250 mm 70–90 nm (diameter) 80–200 nm (diameter) 80  225 nm 20 nm 50 nm (a) Tobacco mosaic virus (b) Adenoviruses (c) Influenza viruses (d) Bacteriophage T4 RNA Capsomere of capsid DNA Capsomere Glycoprotein Membranous envelope Capsid Head Tail fiber Tail sheath

Table 18.1 Classes of Animal Viruses

The Genetics of Viruses & Bacteria What do you know about viruses? How big are viruses? What are the components of a virus? How do viruses identify appropriate cells to infect? Viruses bind to specific receptors May cross species or be tissue-specific 5. What is the lytic cycle of a bacteriophage?

Figure 18.6 The lytic cycle of phage T4, a virulent phage Attachment. The T4 phage uses its tail fibers to bind to specific receptor sites on the outer surface of an E. coli cell. Entry of phage DNA and degradation of host DNA. The sheath of the tail contracts, injecting the phage DNA into the cell and leaving an empty capsid outside. The cell’s DNA is hydrolyzed. Synthesis of viral genomes and proteins. The phage DNA directs production of phage proteins and copies of the phage genome by host enzymes, using components within the cell. Assembly. Three separate sets of proteins self-assemble to form phage heads, tails, and tail fibers. The phage genome is packaged inside the capsid as the head forms. Release. The phage directs production of an enzyme that damages the bacterial cell wall, allowing fluid to enter. The cell swells and finally bursts, releasing 100 to 200 phage particles. 1 2 4 3 5 Phage assembly Head Tails Tail fibers

The Genetics of Viruses & Bacteria What do you know about viruses? How big are viruses? What are the components of a virus? How do viruses identify appropriate cells to infect? What is the lytic cycle of a bacteriophage? What is the lysogenic cycle of a bacteriophage?

Figure 18. 7 The lytic and lysogenic cycles of phage , Figure 18.7 The lytic and lysogenic cycles of phage , a temperate phage Many cell divisions produce a large population of bacteria infected with the prophage. The bacterium reproduces normally, copying the prophage and transmitting it to daughter cells. Phage DNA integrates into the bacterial chromosome, becoming a prophage. New phage DNA and proteins are synthesized and assembled into phages. Occasionally, a prophage exits the bacterial chromosome, initiating a lytic cycle. Certain factors determine whether The phage attaches to a host cell and injects its DNA. Phage DNA circularizes The cell lyses, releasing phages. Lytic cycle is induced Lysogenic cycle is entered or Prophage Bacterial chromosome Phage DNA

The Genetics of Viruses & Bacteria What do you know about viruses? How big are viruses? What are the components of a virus? How do viruses identify appropriate cells to infect? What is the lytic cycle of a bacteriophage? What is the lysogenic cycle of a bacteriophage? How do retroviruses (like HIV) reproduce? Reverse transcriptase – RNA back to DNA Helper T cells Reverse transcriptase Viral envelope Capsid Glycoprotein RNA (two identical strands)

Figure 18.10 The reproductive cycle of HIV, a retrovirus Vesicles transport the glycoproteins from the ER to the cell’s plasma membrane. 7 The viral proteins include capsid proteins and reverse transcriptase (made in the cytosol) and envelope glycoproteins (made in the ER). 6 The double-stranded DNA is incorporated as a provirus into the cell’s DNA. 4 Proviral genes are transcribed into RNA molecules, which serve as genomes for the next viral generation and as mRNAs for translation into viral proteins. 5 Reverse transcriptase catalyzes the synthesis of a second DNA strand complementary to the first. 3 catalyzes the synthesis of a DNA strand complementary to the viral RNA. 2 New viruses bud off from the host cell. 9 Capsids are assembled around viral genomes and reverse transcriptase molecules. 8 mRNA RNA genome for the next viral generation Viral RNA RNA-DNA hybrid DNA Chromosomal DNA NUCLEUS Provirus HOST CELL Reverse transcriptase New HIV leaving a cell HIV entering a cell 0.25 µm HIV Membrane of white blood cell The virus fuses with the cell’s plasma membrane. The capsid proteins are removed, releasing the viral proteins and RNA. 1

The Genetics of Viruses & Bacteria What do you know about viruses? How big are viruses? What are the components of a virus? How do viruses identify appropriate cells to infect? What is the lytic cycle of a bacteriophage? What is the lysogenic cycle of a bacteriophage? How do retroviruses (like HIV) reproduce? How do “new” viruses emerge? Mutation of an existing virus since there is no proofreading Spread of an existing virus from 1 host species to another Spread of viral disease from a small isolated population 9. What is the difference between horizontal & vertical transmission? Horizontal – 1 organism spreads to another Vertical – 1 organism inherits disease from parent 10. What are viroids & prions? Viroids – tiny molecules of naked, circular RNA that infect plants, several hundred nucleotides long Prions – infectious proteins (NO genetic material) Slow incubation period – at least 10 yrs Virtually indestructible 1997 Nobel Prize in Medicine – Stanley Prusiner

Figure 18.13 Model for how prions propagate Normal protein Original prion New prion Many prions Mad cow disease Creutzfeldt-Jakob disease

The Genetics of Viruses & Bacteria What do you know about viruses? How big are viruses? What are the components of a virus? How do viruses identify appropriate cells to infect? What is the lytic cycle of a bacteriophage? What is the lysogenic cycle of a bacteriophage? How do retroviruses (like HIV) reproduce? How do “new” viruses emerge? 9. What is the difference between horizontal & vertical transmission? 10. What are viroids & prions? 11. How is bacterial DNA different from eukaryotic DNA? Bacterial Eukaryotic Circular chromosome Linear chromosomes Nucleoid region Nucleus No introns (all exons) Introns & exons Transcription coupled w/ translation Transcription & translation separate How does bacterial DNA replicate its circular chromosome? - Figure 16.16

Figure 16.16 A summary of bacterial DNA replication Overall direction of replication Helicase unwinds the parental double helix. Molecules of single- strand binding protein stabilize the unwound template strands. The leading strand is synthesized continuously in the 5 3 direction by DNA pol III. Leading strand Origin of replication Lagging OVERVIEW Replication fork DNA pol III Primase Primer DNA pol I DNA ligase 1 2 3 Primase begins synthesis of RNA primer for fifth Okazaki fragment. 4 DNA pol III is completing synthesis of the fourth fragment, when it reaches the RNA primer on the third fragment, it will dissociate, move to the replication fork, and add DNA nucleotides to the 3 end of the fifth fragment primer. 5 DNA pol I removes the primer from the 5 end of the second fragment, replacing it with DNA nucleotides that it adds one by one to the 3’ end of the third fragment. The replacement of the last RNA nucleotide with DNA leaves the sugar- phosphate backbone with a free 3 end. 6 DNA ligase bonds the 3 end of the second fragment to the 5 end of the first fragment. 7 Parental DNA 5 3

The Genetics of Viruses & Bacteria What do you know about viruses? How big are viruses? What are the components of a virus? How do viruses identify appropriate cells to infect? What is the lytic cycle of a bacteriophage? What is the lysogenic cycle of a bacteriophage? How do retroviruses (like HIV) reproduce? How do “new” viruses emerge? 9. What is the difference between horizontal & vertical transmission? 10. What are viroids & prions? 11. How is bacterial DNA different from eukaryotic DNA? Bacterial Eukaryotic Circular chromosome Linear chromosomes Nucleoid region Nucleus No introns (all exons) Introns & exons Transcription coupled w/ translation Transcription & translation separate How does bacterial DNA replicate its circular chromosome? Figure 16.16 Problem with circular chromosome?????? Solved – topoisomerase

Table 16.1 Bacterial DNA replication proteins and their functions

Figure 18.14 Replication of a bacterial chromosome Replication fork Origin of replication Termination of replication

The Genetics of Viruses & Bacteria What do you know about viruses? How big are viruses? What are the components of a virus? How do viruses identify appropriate cells to infect? What is the lytic cycle of a bacteriophage? What is the lysogenic cycle of a bacteriophage? How do retroviruses (like HIV) reproduce? How do “new” viruses emerge? 9. What is the difference between horizontal & vertical transmission? 10. What are viroids & prions? 11. How is bacterial DNA different from eukaryotic DNA? How does bacterial DNA replicate its circular chromosome? Can bacterial cells do genetic recombination? 3 (4) ways Transformation – uptake of external DNA by a cell – Griffith Transduction – phage transfers bacterial DNA Conjugation – bacterial sex – direct transfer of genetic material (Transposons)

Figure 18.16 Generalized transduction Phage DNA Donor cell Recipient cell A+ B+ B– A– Recombinant cell Crossing over Phage infects bacterial cell that has alleles A+ and B+ Host DNA (brown) is fragmented, and phage DNA and proteins are made. This is the donor cell. A bacterial DNA fragment (in this case a fragment with the A+ allele) may be packaged in a phage capsid. Phage with the A+ allele from the donor cell infects a recipient A–B– cell, and crossing over (recombination) between donor DNA (brown) and recipient DNA (green) occurs at two places (dotted lines). The genotype of the resulting recombinant cell (A+B–) differs from the genotypes of both the donor (A+B+) and the recipient (A–B–). 1 2 3 4 5

Figure 18.17 Bacterial conjugation Sex pilus 1 m

Figure 18.18 Conjugation and recombination in E. coli A cell carrying an F plasmid (an F+ cell) can form a mating bridge with an F– cell and transfer its F plasmid. 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). 2 DNA replication occurs in both donor and recipient cells, using the single parental strands of the F plasmid as templates to synthesize complementary strands. 3 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+. 4 F Plasmid Bacterial chromosome Bacterial chromosome F– cell F+ cell Hfr cell F factor The circular F plasmid in an F+ cell can be integrated into the circular chromosome by a single crossover event (dotted line). The resulting cell is called an Hfr cell (for High frequency of recombination). Since an Hfr cell has all the F-factor genes, it can form a mating bridge with an F– cell and transfer DNA. A single strand of the F factor breaks and begins to move through the bridge. DNA replication occurs in both donor and recipient cells, resulting in double-stranded DNA The location and orientation of the F factor in the donor chromosome determine the sequence of gene transfer during conjugation. In this example, the transfer sequence for four genes is A-B-C-D. 5 The mating bridge usually breaks well before the entire chromosome and the rest of the F factor are transferred. 6 Two crossovers can result in the exchange of similar (homologous) genes between the transferred chromosome fragment (brown) and the recipient cell’s chromosome (green). 7 The piece of DNA ending up outside the bacterial chromosome will eventually be degraded by the cell’s enzymes. The recipient cell now contains a new combination of genes but no F factor; it is a recombinant F– cell. 8 Temporary partial diploid Recombinant F– bacterium Conjugation and transfer of an F plasmid from an F+ donor to an F– recipient (a) Conjugation and transfer of part of the bacterial chromosome from an Hfr donor to an F– recipient, resulting in recombination (b) A+ B+ C+ D+ F– cell A– B– C– D– Mating bridge Plasmid – extra-chromosomal, small, circular, self-replicating DNA

Figure 18.19 Transposable genetic elements in bacteria Insertion sequence 3 5 3 5 A T C C G G T… A C C G G A T… T A G G C C A … T G G C C T A … Inverted repeat Transposase gene Inverted 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. Transposon Insertion sequence Antibiotic resistance gene Insertion sequence 5 3 5 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.

The Genetics of Viruses & Bacteria What do you know about viruses? How big are viruses? What are the components of a virus? How do viruses identify appropriate cells to infect? What is the lytic cycle of a bacteriophage? What is the lysogenic cycle of a bacteriophage? How do retroviruses (like HIV) reproduce? How do “new” viruses emerge? 9. What is the difference between horizontal & vertical transmission? 10. What are viroids & prions? 11. How is bacterial DNA different from eukaryotic DNA? How does bacterial DNA replicate its circular chromosome? Can bacterial cells do genetic recombination? How are metabolic pathways regulated? Inhibition of enzyme activity – protein level Inhibition of transcription – mRNA level

Figure 18.20 Regulation of a metabolic pathway (a) Regulation of enzyme activity Enzyme 1 Enzyme 2 Enzyme 3 Enzyme 4 Enzyme 5 Regulation of gene expression Feedback inhibition Tryptophan Precursor (b) Regulation of enzyme production Gene 2 Gene 1 Gene 3 Gene 4 Gene 5 –

The Genetics of Viruses & Bacteria What do you know about viruses? How big are viruses? What are the components of a virus? How do viruses identify appropriate cells to infect? What is the lytic cycle of a bacteriophage? What is the lysogenic cycle of a bacteriophage? How do retroviruses (like HIV) reproduce? How do “new” viruses emerge? 9. What is the difference between horizontal & vertical transmission? 10. What are viroids & prions? 11. How is bacterial DNA different from eukaryotic DNA? How does bacterial DNA replicate its circular chromosome? Can bacterial cells do genetic recombination? How are metabolic pathways regulated? Inhibition of enzyme activity – protein level Inhibition of transcription – mRNA level What is an operon? A coordinately regulated cluster of genes whose products function in a common pathway Repressible – usually on – tryptophan – trp operon Inducible – usually off – lactose – lac operon

Figure 18.21 The trp operon: regulated synthesis of repressible enzymes (a) Tryptophan absent, repressor inactive, operon on. RNA polymerase attaches to the DNA at the promoter and transcribes the operon’s genes. Genes of operon Inactive repressor Protein Operator Polypeptides that make up enzymes for tryptophan synthesis Promoter Regulatory gene RNA polymerase Start codon Stop codon trp operon 5 3 mRNA 5 trpD trpE trpC trpB trpA trpR DNA mRNA E D C B A

DNA mRNA Protein Tryptophan (corepressor) Active repressor No RNA made Tryptophan present, repressor active, operon off. As tryptophan accumulates, it inhibits its own production by activating the repressor protein. (b)

Figure 18.22 The lac operon: regulated synthesis of inducible enzymes DNA mRNA Protein Active repressor RNA polymerase No RNA made lacZ lacl Regulatory gene Operator Promoter 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. (a) 5 3

lacl mRNA 5' DNA mRNA Protein Allolactose (inducer) Inactive repressor lacz lacY lacA RNA polymerase Permease Transacetylase -Galactosidase 5 3 (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. mRNA 5 lac operon