Prokaryotes: Bacteria & Archaea

1. Prokaryotes:Bacteria & Archaea A Troubled Taxonomy! Chapter 28 & pages 419 - 421 Lecture outlines on Black Board as pdf and ppt files

2. Why study these organisms? • Biomass & number of species! • Disease • Gene cloning • Bioremediation • Global change • Oxygen • Nitrogen cycle & pollution • Model organisms for research • Extremophiles

3. What do I think you should take away from our discussion of prokaryotes? • Tremendous diversity that allows prokaryotes to inhabit virtually all environments • Thus they posses great variations in genes and gene products that provide life essential functions in these environments

4. Where do we find bacteria & archaea?

5. Define Prokaryote • Characteristics: see Table 28.1 • Figures 7.1 through 7.5

6. Table 28.1

7. Fig 7.1 Draw the picture and tell the story

8. Prokaryotic Features: • Supercoiled DNA • One or more circular chromosomes • Few associated proteins • Nucleoid region (vs. nucleus)

9. Fig 7.3

10. Prokaryotic Genome (pages 419 - 421) • Size of genome proportional to metabolic capabilities • Tremendous diversity of genes • Redundancy is common • Multiple chromosomes • Many small, extra-chromosomal DNAs called plasmids

11. Genome size & metabolic capabilities • Mycoplasma - parasite that causes pneumonia • Acquires most nutrients from the host • Few enzymes, ergo few genes! • E. coli & Psuedomonas • Inhabits soils and humans! • Synthesizes almost all organic molecules

12. Prokaryotic Genome (pages 419-21) • Size of genome proportional to metabolic capabilities • Tremendous diversity of genes • Many are unique to a species • Redundancy within a genome is common • Multiple chromosomes are not uncommon • Many small, extra-chromosomal DNAs called plasmids

13. Plasmids • Small number of genes • Copied independently of chromosomal DNA • May or may not be necessary for growth • Site of antibiotic resistance • Allows for lateral transfer of genes • Even among different species!

14. Fig 20.4: Lateral Gene Transfer

15. Evidence for Lateral Gene Transfer between species • Stretches of DNA are more similar to those in genes of distantly related species than those more closely related. • The proportion of G-C base pairs to A-T base pairs in a gene is remarkably different from the base composition in the rest of the DNA

16. Thermotoga maritima • Same habitats - deep sea hydrothermal vents • 25% of genome of this bacterium is closely related to genomes found in resident archaea • Occur in distinctive clusters in DNA

17. Also…. • Evidence for prokaryotic parasites picking up genes from eukaryotic hosts! • Intracellular parasitic bacteriumChlamydia trachomatis • Contains ~ 35 eukaryotic genes • Mechanism? ?????

18. What we are doing: • Table 28.1 - Differences among organisms of the three Kingdoms • Bacteria and Archaea: • Why we study them • Structure • Genetic diversity, how it is generated, and what are the consequences • See especially lateral gene transfer

19. Summary: • Characterized Prokaryotes & Eukarotes & Archaea (Table 28.1) • Note: mechanisms of generating diversity in prokaryotes • Moving into Prokaryotic Diversity • Morphological • Metabolic

20. Fig 5.5

21. Other Prokaryotic Characteristics • Lack of compartmentalization or Organelles • Little cytoskeleton • Recent discovery of any cytoskeletal elements • Protein FtsZ

22. Fig 11.8 (page 230): FstZ Filaments

24. Protein FtsZ http://www.umass.edu/microbio/chime/pipe/ftsz/present/ftszinvivo.htm

25. Organization and function of FstZ filaments in eubacteria McIntosh, J. R. et al. J Cell Sci 2010;123:3425-3434

26. Phylogeny? Archaea? Prokaryotes but phylogenetically closer to Eukaryotes than to Bacteria

27. Table 28.1

28. Fig 28.12

29. Fig 1.9 You are here

30. What the heck are the Archaea? http://www.ucmp.berkeley.edu/archaea/archaea.html

31. Archaea • No nuclear envelope • Cell wall made of unique polysaccharides • Unique plasma membrane lipids • Ribosomes and RNA polymerase similar to those found in Eukaryotes

32. Looking for Archeae

33. Some Archaea

34. Fig 1.9 You are here

35. Dr. Carl Woese: utilized rRNA sequences

36. Fig 7.4: Bacterial Ribosome

37. A word about rRNA…. http://www.biochem.uwo.ca/meds/medna/rRNA.html

38. Human vs. E. coli 5S rRNA http://www.biochemj.org/bj/371/0641/3710641.pdf

39. Table 28.1

40. Fig 7.3

41. Fig 5.3: Review of Sugar Structure

42. Fig 5.4a:  linkage

43. Table 5.1a: Starch

44. Table 5.1c: Cellulose

45. Table 5.1e: Peptidoglycan

46. Function of cell wall: rigidity H2O High [solute] Bacterial cell Result = hydrostatic pressure for structure

47. Table 5.1e: Peptidoglycan:Bacterial Cell Walls

48. Table 5.1c: Cellulose:Eukaryotic & some Archaeacell walls

49. Things to know to this point… • Table - differences among 3 major groups of organisms • Mechanisms for generating genetic diversity in Archaea and Prokaryotes • Types and structures of carbohydrates in extracellular cell walls • rRNA & FtsZ (I am pulling this stuff right out of your textbook!)