1. Ch. 18 Warm-up 1. Why do many scientists classify viruses as non-living? 2. Draw the basic structure of a virus. Label and define capsid, viral envelope and nucleic acid.

2. Ch. 18 Warm-up 1. Draw the lytic/lysogenic cycle. 2. What stage of the lytic-lysogenic cycle is a virus virulent? Temperate? 3. What determines a host range?

3. Ch. 18 Warm-Up 1. What was Frederick Griffith’s contribution to our understanding of DNA? (Refer back to Ch. 16) 2. How do bacteria replicate?

4. 1. What is the Central Dogma? 2. How does prokaryotic DNA compare to eukaryotic DNA? 3. How is DNA organized in eukaryotic cells? Review Warm-Up

5. 1. Draw and label the 3 parts of an operon. 2. Contrast inducible vs. repressible operons. 3. How does DNA methylation and histone acetylation affect gene expression? Ch. 18 Warm-Up

6. Lab 6A Warm-Up 1. What are plasmids? 2. What gene(s) are on the plasmid being used in this lab? 1. How can we know if cells have been successfully transformed in this lab?

7. Viruses Chapter 18.1-18.2

8. What you must know: The components of a virus. The differences between lytic and lysogenic cycles.

9. Bacteria vs. Viruses BacteriaVirus Prokaryotic cell Most are free-living (some parasitic) Relatively large size Antibiotics used to kill bacteria Not a living cell (genes packaged in protein shell) Intracellular parasite 1/1000 size of bacteria Vaccines used to prevent viral infection Antiviral treatment

10. Viruses Very small (<ribosomes) Components = nucleic acid + capsid ◦ Nucleic acid: DNA or RNA (double or single-stranded) ◦ Capsid: protein shell ◦ Some viruses also have viral envelopes that surround capsid Limited host range (eg. human cold virus infects upper respiratory tract) Reproduce within host cells

14. Simplified viral replicative cycle

15. Bacteriophage Virus that infects bacterial cells

16. VIDEO: T4 PHAGE INFECTION T4 PHAGE INFECTIONT4 PHAGE INFECTION

17. Lytic Cycle of T4 Phage

18. Bacteriophage Reproduction Lytic Cycle: Lytic Cycle: ◦ Use host machinery to make copies of virus lysis ◦ Death of host cell by rupturing it (lysis) ◦ Virulent phages replicate by this method Lysogenic Cycle: Lysogenic Cycle: ◦ Phage DNA incorporated into host DNA and replicated along with it prophage ◦ Phage DNA = prophage Temperate Phage: uses both methods of replication

19. Lytic Cycle vs. Lysogenic Cycle

20. Animal viruses have a membranous envelope Host membrane forms around exiting virus Difficult for host immune system to detect virus

21. VIDEO: HOW DENGUE VIRUS ENTERS A CELL HOW DENGUE VIRUS ENTERS A CELLHOW DENGUE VIRUS ENTERS A CELL

22. VIDEO: HIV LIFE CYCLE HIV LIFE CYCLEHIV LIFE CYCLE

23. Retrovirus reverse transcriptase RNA virus that uses reverse transcriptase (RNA  DNA) Newly made viral DNA inserted into chromosome of host provirus Host transcribes viral DNA (= provirus) to make new virus parts Example: HIV (Human Immunodeficiency Virus) Example: HIV (Human Immunodeficiency Virus)

24. HIV = Retrovirus

25. HIV ◦ Infects white blood cells ◦ HIV+: provirus (DNA inserted) ◦ AIDS: active viral reproduction

26. Other Human Viruses Herpes virus Smallpox Herpes Simplex Virus 1 (HSV-1) Herpes Simplex Virus 2 (HSV-2) Eradicated in 1979 due to worldwide vaccination campaigns

27. Emerging Viruses Emerging Viruses = mutation of existing viruses Pandemic: global epidemic

28. Current Outbreaks Zika Virus ◦ Spread by Aedes mosquitoes (Aedes aegypti) ◦ Major outbreak in Brazil and Latin America ◦ Linked to birth defects (microcephaly) Dengue Fever Chikungunya

29. Zika Virus (as of Dec. 2015)

30. Drugs for Prevention/Treatment Vaccine: weakened virus or part of pathogen that triggers immune system response to prevent infection ◦ Ex. HPV, MMR, HepA, Flu shot Antiviral Drugs: block viral replication after infection ◦ Ex. Tamiflu (influenza), AZT (HIV)

32. Viroids Small, circular RNA molecules that infect plants Cause errors in regulatory systems that control plant growth Eg. coconut palms in Philippines

33. Prions Misfolded, infectious proteins that cause misfolding of normal proteins Eg. scrapie (sheep), mad cow disease (BSE), Creutzfeldt-Jakob disease (humans), kuru (humans – New Guinea)

34. Diseases caused by prions Prions act slowly – incubation period of at least 10 years before symptoms develop Prions are virtually indestructible (cannot be denatured by heating) No known cure for prion diseases Kuru in New Guinea

35. Prion Neurodegenerative Diseases Alzheimer’s Disease Parkinson’s Disease

36. AMOEBA SISTERS: VIRUSES: VIRUS REPLICATION AND THE MYSTERIOUS COMMON COLD VIRUSES: VIRUS REPLICATION AND THE MYSTERIOUS COMMON COLDVIRUSES: VIRUS REPLICATION AND THE MYSTERIOUS COMMON COLD

37. Bacteria Chapter 18.3

38. What you need to know: Mechanisms that contribute to genetic diversity in prokaryotes, including transformation, conjugation, transduction, and mutation.

39. Genetic Diversity in Prokaryotes Factors: 1. Rapid reproduction (binary fission) 2. Mutations – errors in replication 3. Genetic recombination

40. Genetic Recombination in Bacteria 1. Transformation : uptake of foreign DNA from surroundings 2. Transduction : viruses transfer genes between prokaryotes 3. Conjugation : DNA transferred from one to another

41. Transformation Uptake of foreign DNA from surroundings Observed by Griffith (bacteria & mice)

42. Plasmids  Small ring of DNA that carries a few genes  Replicates separately from bacterial chromosome  Can carry genes for antibiotic resistance gene cloning  Used frequently in genetic engineering for gene cloning

43. AP Bio Lab 6A - Transformation

44. Using plasmids and bacteria in genetic engineering

45. Gene Cloning

46. Transduction Viruses (bacteriophages) carry bacterial genes from one host cell to another Recombine DNA of donor and recipient cell

47. Conjugation One cell donates DNA to another Donors cell extends a sex pilus (“mating bridge”) through which DNA is transferred Requires the presence of a piece of DNA called the F factor to produce the pilus

48. TED-ED: HOW WE CONQUERED THE DEADLY SMALLPOX VIRUS HOW WE CONQUERED THE DEADLY SMALLPOX VIRUSHOW WE CONQUERED THE DEADLY SMALLPOX VIRUS

49. Regulation of Gene Expression by Bacteria 18.4 Transcription

50. What you need to know: The functions of the three parts of an operon. The role of repressor genes in operons..

51. Regulation of metabolic pathways

52. Operon Operon: cluster of related genes with on/off switch Three Parts: 1.Promoter – where RNA polymerase attaches 2.Operator – “on/off”, controls access of RNA poly 3.Genes – code for related enzymes in a pathway Bacterial control of gene expression

53. Regulatory generepressor Regulatory gene: produces repressor protein that binds to operator to block RNA polymerase

54. Repressible Operon (ON  OFF)

55. Repressible Operon  Normally ON  Anabolic (build organic molecules)  Organic molecule product acts as corepressor  binds to repressor to activate it  Operon is turned OFF trp operon  Eg. trp operon

56. trp operon

57. Inducible Operon  Normally OFF  Catabolic (break down food for energy) inducer  Repressor is active  inducer binds to and inactivates repressor  Operon is turned ON lac operon  Eg. lac operon

58. lac operon