2. Business Chapter 7: Problems 1-20, –Master Solutions: Problems 1 and 2, –Master Concepts in action: all, Questions about anything?

5. Bacteria Predominate 10,000+ “Species”, –Mycoplasma genetalium 200 nm – Thiomargarista namibiensis 750  m –soil, water, air, symbionts, –have adapted to aquatic and terrestrial extremes, 100 grams/person, –10 14 bacteria. Metabolism; –Phototrophs, –Chemotrophs, Biochemistry; –‘fix’ or synthesize a huge range of molecules, –break down almost anything, –adapt to just about anything. Molecular Biology; –Clone, –Gene therapy, –Eugenics, –Biotechnology, –Etc. Bacteria Do Almost Everything

8. Bacterial Chromosome...a circular molecule of double helical DNA, – 4 - 5 Mb long in most species studied, –1.6 mm long if broken and stretched out. Inside the cell, the circular chromosome is condensed by super coiling and looping into a densely packed body termed the nucleoid.

9. Extra Chromosomal DNA Plasmids: circular double stranded DNA molecule that replicates independently, –containing one or more (non- essential) genes, smaller than the bacterial chromosome, –may carries genes for pathogenicity, –may carry genes for adaptation to the environment, including drug resistance genes, –1000’s of base pairs long.

10. Bacterial Model Organism Escherichia coli = E. coli Enteric bacteria: inhabits intestinal tracts, –generally non-pathogenic, –grows in liquid, –grows in air, E. coli has all the enzymes it needs for amino-acid and nucleotide biosynthesis, –can grow on minimal media (carbon source and inorganic salts), Divides about every hour on minimal media, –up to 24 generations a day,

11. Growth Equals Cell Division

12. DNA Replication

13. Bacterial mitosis. Why don’t bacteria do meiosis?

14. The (Awesome) Power of Bacterial Genetics... is the potential for studying rare events. Liquid Cultures, 10 9 cells/microliter, Colonies on Agar, 10 7+ cells/colony

15. Counting Bacteria (Serial) Dilution is the Solution 10 -3 10 -5 10 -4

16. Model Model Organism Ease of cultivation,Ease of cultivation, Rapid Reproduction,Rapid Reproduction, Small size,Small size, Fecund (large brood size),Fecund (large brood size), Mutants are available, stable and easy to identify?Mutants are available, stable and easy to identify? Literature?Literature? PubMed Listings: Eubacteria: 612,471, Archaebacteria: 9,420 PubMed Listings: Eubacteria: 612,471, Archaebacteria: 9,420

17. Bacteria Phenotypes colony morphology, –large, small, shiny, dull, round or irregular, –resistance to bactericidal agents, cells unable to synthesize certain raw materials from a minimal media, cells unable to break down complex molecules, essential genes, usually studied as conditional mutants.

18. Prototroph …a cell that is capable of growing on a defined, minimal media (all essentials salts, carbon source), –can synthesize all essential organic compounds, –usually considered the ‘wild-type’ strain. Auxotrophs …a cell that requires a substance for growth that can be produced by a wild-type cell, his -...can’t synthesize histidine (his + = wt) leu -...can’t synthesize leucine (leu + = wt) arg -...can’t synthesize arginine (his + = wt) bio -...can’t synthesize biotin (bio + = wt)

19. Bacterial Nomenclature I genes not specified are considered wild- type, Strain A: met - bio - x Strain B: thr - leu - thi - thr + leu + thi + met + bio +

20. Complete Media… Contains all essential nutrients, plus a carbon source, and supplemented with specific complex molecules, - bacteria uptake molecules that it can not synthesize. Minimal Media… Contains all essential nutrients (usually as salts), plus a carbon source, - bacteria synthesizes the rest.

21. 1 in 10 7 awesome Strain A: met - bio - tri + leu + thi + x Strain B: met + bio + thr - leu - thi - Conjugation Strain C: met + bio + thr + leu + thi + exconjugate

22. Conjugation...temporary fusion of two single-celled organisms for the transfer of genetic material, …the transfer of genetic material is unidirectional. F + Cells (F for Fertility) … F + cells donate genetic material. … F - cells receive genetic material, …there is no reciprocal transfer. F - Cells (F for Fertility)

23. Contact is Required For Mating

24. F Pilus …a filament-like projection from the surface of a bacterium. F+F+ F-F-

25. F Factor …a plasmid whose presence confers F +, or donor ability.

26. F Pilus Attaches to F - Cell

27. Cells are Drawn Together Passageway Forms

28. DNA is Nicked, One Strand is Transferred, Both Strands Replicate Single Strand Moves Across Pilus The single stranded plasmids synthesize complementary strands in their respective cells.

29. Cell Separation Both cells are now F +

30. F Factor Replicates During Binary Fission

31. Properties of the F Factor Can replicate its own DNA, Carries genes required for the synthesis of pili, F + and F - cells can conjugate, –the F factor is copied to the F - cell, resulting in two F + cells, F + cells do not conjugate with F + cells, F Factor sometimes integrates into the bacterial chromosome.

32. Hfr Cells F factor Bacterial Chromosome Inserted F plasmid...F factor integration site,...host (bacteria chromosome) integration site.

34. ...the bacterial chromosome contains many integration sites,...thus, the F factor inserts in different regions of the bacterial chromosome.

35. High Frequency of Recombination (Hfr)...bacteria exhibiting a high frequency of recombination, –an alteration of DNA sequence such that the genotype of subsequent individuals differs from the parent, …HFR cells; strains with a chromosome integrated F factor that is able to mobilize and transfer part of the chromosome to the F - cell.

36. F Pilus Attaches to F - Cell

37. Hfr DNA is Cut

38. F factor and Chromosomal DNA are Transferred

39. Recombination Requires Crossing over Double Crossover

40. DNA not Incorporated into Chromosome are Digested

41. Incomplete Transfer of DNA Interrupted Mating: a break in the pilus during conjugation stops the transfer of DNA, Transfer occurs at a constant rate, –provides a means to map bacterial genes.

42. Hfr to F - Cells Hfr transfer begins in the middle of the F factor, Only 1/10,000 cells transfer the complete chromosome, including the remainder of the F factor, Thus, most recipient cells remain F -.

43. F ’ Cells an F factor from an Hfr cell excises out of the bacterial genome and returns to plasmid form, often carries one or more bacterial genes along, F ’ cells behave like an F + cells, –merizygote: partially diploid for genes copied on the F ’ plasmid, F ’ plasmids can be easily constructed using molecular biology techniques (i.e.vectors).

44. Mutation in Bacteria …the ultimate source of variation in bacteria is spontaneous mutation, –generally errors in DNA replication, …mutations occur in specific genes at a rate of 1 in 10 6 to 1 in 10 7 cells, …adaptive mutations are quickly replicated and adaptive colonies predominate.

45. Spontaneous Mutations DNA replication in E. coli occurs with an error every ~ 10 9 bases. The E. coli genome is 4.6 x 10 6 bases.  An error occurs once per ~ 2000 replications. If a single colony has 10 7 bacteria,  5,000 cells carry a mutation,  or, one mutation every ~ 1,000 bases (across a colony),  or, a mutation in about every gene.

46. Selective Media wild-type bacteria grow on minimal media, media supplemented with selected compounds supports growth of mutant strains, –minimal media + leucine supports leu - cells, –minimal media + leucine + arginine supports leu - arg - –etc. Selective Media: a media in which only the desired strain will grow.

47. Selection...the process that establishes conditions in which only the desired mutant will grow.

48. Problem You want to create a culture of cells that are only methionine auxitrophs?

49. The Wrong Answer Strain 1 x Strain 3 (complete media) How do you get rid of Strain 1? You have a recombinant that is met - only.

50. Correct Answer Strain 2 x Strain 3 (complete media) Grow on Minimal Media Plus Methionine Strain 2 dies because there is no arginine. Strain 3 dies because there is no threonine or thimine. The new exconjugate lives.

51. F factor Review Now F +