2. AP Biology Chapter 18 The Genetics of Viruses and Bacteria 0.25  m Virus Animal cell Bacterium Animal cell nucleus Tobacco mosaic virus Stunts the growth of tobacco plants and gives their leaves a mosaic coloration

3. AP Biology Figure 18.4a, b 18  250 mm 70–90 nm (diameter) 20 nm 50 nm (a) Tobacco mosaic virus (b) Adenoviruses RNA DNA Capsomere Glycoprotein Capsomere of capsid Structure of Viruses Viruses  Are very small infectious particles made of  nucleic acid enclosed in a protein coat Viral genomes may consist of  Double- or single-stranded DNA  Double- or single-stranded RNA A capsid is the protein shell that encloses the viral genome Made from protein subunits called capsomeres

4. AP Biology Viral Reproductive Cycles Viruses are obligate intracellular parasites  They can reproduce only within a host cell Ex: bacteriophages infect E.coli Each virus has a host range  A limited number of host cells that it can infect  Identification of host cell by “lock-and- key” fit Viruses use enzymes, ribosomes, and small molecules of host cells to synthesize a progeny of viruses

5. AP Biology VIRUS Capsid proteins mRNA Viral DNA HOST CELL Viral DNA DNA Capsid Figure 18.5 Entry into cell and uncoating of DNA Replication Transcription Self-assembly of new virus particles and their exit from cell Simplified Viral Reproductive Cycle

6. AP Biology Alternative Reproductive Mechanisms of Phages The lytic cycle  Is a phage reproductive cycle that culminates in the death of the host  Produces new phages, the bacterium lyses and releases the progeny viruses that can then infect healthy cells A phage that reproduces only by the lytic cycle is called a virulent phage  Ex: T4 phage

7. AP Biology The lytic cycle of phage T4, a virulent phagelytic cycle of phage T4 Phage assembly Head Tails Tail fibers Figure 18.6 Attachment. The T4 phage uses its tail fibers to bind to specific receptor sites on the outer surface of an E. coli cell. 1 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. 2 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. 3 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. 4 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. 5

8. AP Biology The Lysogenic Cycle The lysogenic cycle  Replicates the phage genome without destroying the host Phage DNA integrates into bacterial chromosome, becoming a prophage Temperate phages  Are capable of using both the lytic and lysogenic cycles of reproduction Ex: lambda phage

9. AP Biology The lytic and lysogenic cycles of phage, a temperate phagelytic and lysogenic cycles of 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 Lysogenic cycleLytic cycle or Prophage Bacterial chromosome Phage DNA Figure 18.7

10. AP Biology Viral Envelopes Many animal viruses  Have a membranous envelope devirived from the host Viral glycoproteins on the envelope Bind to specific receptor molecules on the surface of a host cell RNA as viral genetic material that infect animals 80–200 nm (diameter) 50 nm (c) Influenza viruses RNA Glycoprotein Membranous envelope Capsid

11. AP Biology Retroviruses, such as HIV, use the enzyme reverse transcriptase  To copy their RNA genome into DNA, which can then be integrated into the host genome as a provirus  2 molecules of ssRNA  2 moelcules of reverse transcriptase Figure 18.9 Reverse transcriptase Viral envelope Capsid Glycoprotein RNA (two identical strands)

12. AP Biology The reproductive cycle of HIV, a retrovirusHIV Figure 18.10 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 Reverse transcriptase catalyzes the synthesis of a DNA strand complementary to the viral RNA. 2 Reverse transcriptase catalyzes the synthesis of a second DNA strand complementary to the first. 3 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 The viral proteins include capsid proteins and reverse transcriptase (made in the cytosol) and envelope glycoproteins (made in the ER). 6 Vesicles transport the glycoproteins from the ER to the cell’s plasma membrane. 7 Capsids are assembled around viral genomes and reverse transcriptase molecules. 8 New viruses bud off from the host cell. 9

13. AP Biology Replication fork Origin of replication Termination of replication Figure 18.14 The Bacterial Genome and Its Replication The bacterial chromosome  Circular DNA molecule with few associated proteins Binary fission Plasmid  smaller circular DNA molecules that can replicate independently of the bacterial chromosome  Replication precedes binary fission

14. AP Biology Three Mechanisms of Gene Transfer & Recombination in Bacteria 1. Transformation  Is the alteration of a bacterial cell’s genotype and phenotype by the uptake of naked, foreign DNA from the surrounding environment Colonies grew Mutant strain arg + trp – Mutant strain arg – trp + No colonies (control) Mixture

15. AP Biology In the process known as transduction  Phages carry bacterial genes from one host cell to another 2. Transduction 1 Figure 18.16 Donor cell Recipient cell A+A+ B+B+ A+A+ A+A+ B–B– A–A– B–B– A+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 – ). 2 3 4 5 Phage DNA A+A+ B+B+

16. AP Biology Conjugation  Is the direct transfer of genetic material between bacterial cells that are temporarily joined 3. Conjugation and Plasmids Figure 18.17 Sex pilus 1  m

17. AP Biology The F Plasmid and Conjugation Cells containing the F plasmid, designated F + cells  Function as DNA donors during conjugation  Transfer plasmid DNA to an F  recipient cell

18. AP Biology Chromosomal genes can be transferred during conjugation  When the donor cell’s F factor is integrated into the chromosome A cell with the F factor built into its chromosome  Is called an Hfr cell The F factor of an Hfr cell  Brings some chromosomal DNA along with it when it is transferred to an F – cell  Results in recombination The F Plasmid and Conjugation

19. AP Biology 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 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 Figure 18.19a Insertion sequence Transposase gene Inverted repeat Inverted repeat 3535 3535 A T C C G G T… T A G G C C A … A C C G G A T… T G G C C T A …

20. AP Biology Transposons Bacterial transposons  Also move about within the bacterial genome  Have additional genes, such as those for antibiotic resistance Figure 18.19b (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. Inverted repeats Transposase gene Insertion sequence Antibiotic resistance gene Transposon 5353 5353

21. AP Biology Different way to Regulate Metabolism Gene regulation  instead of blocking enzyme function, block transcription of genes for all enzymes in tryptophan pathway saves energy by not wasting it on unnecessary protein synthesis = inhibition - - -

22. AP Biology Gene regulation in bacteria Cells vary amount of specific enzymes by regulating gene transcription  turn genes on or turn genes off turn genes OFF example if bacterium has enough tryptophan then it doesn’t need to make enzymes used to build tryptophan turn genes ON example if bacterium encounters new sugar (energy source), like lactose, then it needs to start making enzymes used to digest lactose STOP GO

23. AP Biology Bacteria group genes together Operon  genes grouped together with related functions example: all enzymes in a metabolic pathway  promoter = RNA polymerase binding site single promoter controls transcription of all genes in operon transcribed as one unit & a single mRNA is made  operator = DNA binding site of repressor protein

24. AP Biology operatorpromoter Bacteria group genes together DNATATA RNA polymerase repressor = repressor protein gene1gene2gene3gene4 RNA polymerase ACTIVE repressor protein - binds to DNA at OPERATOR SITE - blocks RNA POLYMERASE - Turning transcription OFF 1234 mRNA enzyme1enzyme2enzyme3enzyme4

25. AP Biology mRNA enzyme1enzyme2enzyme3enzyme4 operatorpromoter Repressible operon: tryptophan DNATATA RNA polymerase tryptophan repressor INACTIVE repressor protein repressor ACTIVE tryptophan – repressor protein complex Synthesis pathway model When excess tryptophan is present, it binds to inactive tryp repressor protein & becomes active which triggers repressor to bind to DNA  blocks (represses) transcription gene1gene2gene3gene4 conformational change in repressor protein! 1234 repressor trp RNA polymerase trp

26. AP Biology mRNA enzyme1enzyme2enzyme3enzyme4 operatorpromoter Inducible operon: lactose DNATATA RNA polymerase repressor ACTIVE repressor protein repressor INACTIVE lactose – repressor protein complex lactose lac repressor gene1gene2gene3gene4 Digestive pathway model When lactose is present, binds to active lac repressor protein & becomes inactive, triggering repressor to release DNA  induces transcription RNA polymerase 1234 lac conformational change in repressor protein! lac

27. AP Biology Operon summary Repressible operon  usually functions in anabolic pathways synthesizing end products (tryptophan)  when end product is present in excess, cell allocates resources to other uses Inducible operon  usually functions in catabolic pathways, digesting nutrients to simpler molecules (lactose)  produce enzymes only when nutrient is available cell avoids making proteins that have nothing to do, cell allocates resources to other uses

28. AP Biology In E. coli, when glucose, a preferred food source, is scarce  The lac operon is activated by the binding of a regulatory protein, catabolite activator protein (CAP) Promoter Lactose present, glucose scarce (cAMP level high): abundant lac mRNA synthesized. If glucose is scarce, the high level of cAMP activates CAP, and the lac operon produces large amounts of mRNA for the lactose pathway. (a) CAP-binding site Operator RNA polymerase can bind and transcribe Inactive CAP Active CAP cAMP DNA Inactive lac repressor lacl lacZ Figure 18.23a Positive Gene Regulation

29. AP Biology When glucose levels in an E. coli cell increase  CAP detaches from the lac operon, turning it off Figure 18.23b (b) Lactose present, glucose present (cAMP level low): little lac mRNA synthesized. When glucose is present, cAMP is scarce, and CAP is unable to stimulate transcription. Inactive lac repressor Inactive CAP DNA RNA polymerase can’t bind Operator lacl lacZ CAP-binding site Promoter