1. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. CHAPTER 28 LECTURE SLIDES To run the animations you must be in Slideshow View. Use the buttons on the animation to play, pause, and turn audio/text on or off. Please note: once you have used any of the animation functions (such as Play or Pause), you must first click in the white background before you advance the next slide.

2. Prokaryotes Chapter 28

3. The First Cells Microfossils are fossilized forms of microscopic life –Oldest are 3.5 billion years old –Seem to resemble present-day prokaryotes 3

4. Stromatolites are mats of cyanobacterial cells that trap mineral deposits –Oldest are 2.7 billion years old –Modern forms are also known 4

5. Living things are selective in the carbon isotopes used –Living things incorporate carbon-12 –Higher level of carbon-12 than nonliving things Isotopic analysis of carbon-12 in fossils suggests that carbon fixation was active as much as 3.8 BYA 5

6. Biomarkers –Organic molecules of biological origin –Proven difficult to find –Hydrocarbons derived from fatty acid tails of lipids were found in ancient rocks Indicates that cyanobacteria are at least 2.7 billion years old –Possible origin of life pushed back beyond 3.5 BYA 6

7. Prokaryotic Diversity Oldest, structurally simplest, and most abundant forms of life Abundant for over a billion years before eukaryotes Less than 10% of species are known Fall into 2 domains –Bacteria (also called Eubacteria) –Archaea (formerly called Archaebacteria) Many archaeans are extremophiles 7

8. Unicellularity –Most are single-celled –Amy stick together to form associations –Some can form complex biofilms Cell size –Size varies tremendously –Most are less than 1  m in diameter Chromosome –Single circular double-stranded DNA –Found in the nucleoid region of cell –Often have plasmids Cell division –Most divide by binary fission 8

9. Genetic recombination –Occurs through horizontal gene transfer –NOT a form of reproduction Internal compartmentalization –No membrane-bounded organelles –No internal compartment –Ribosomes differ from eukaryotic form Flagella –Simple in structure –Different from eukaryotic flagella Metabolic diversity –Oxygenic and anoxygenic photosynthesis –Chemolithotrophic 9

10. Bacteria vs. Archaea Plasma membrane –All prokaryotes have a plasma membrane –Bacterial lipids are unbranched Use ester bonds –Archaean membranes are formed on glycerol skeleton with ether linkages (not ester) Hydrocarbons may be branched or have rings Tetraether polymer allows extremophiles to withstand high temperatures 10

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12. Cell wall –All prokaryotes have cell walls –Bacteria have peptidoglycan –Archaea lack peptidoglycan DNA replication –Both have single replication origin –Archaeal DNA replication is more similar to that of eukaryotes Gene Expression –Archaeal transcription and translation are more similar to those of eukaryotes 12

13. Early Classification Characteristics Relied on staining characteristics and observable phenotypes 1.Photosynthetic or nonphotosynthetic 2.Motile or nonmotile 3.Unicellular, colony-forming, or filamentous 4.Formation of spores or division by transverse binary fission 5.Importance as human pathogens or not 13

14. Molecular Classification 1.Amino acid sequences of key proteins 2.Percent guanine–cytosine content 3.Nucleic acid hybridization –Closely related species will have more base pairing 4.Gene and RNA sequencing –Especially rRNA 5.Whole-genome sequencing 14

15. 15 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Common ancestor Domain Bacteria Domain Archaea Domain Eukarya

16. Based on these molecular data, several prokaryotic groupings have been proposed Bergey’s Manual of Systematic Bacteriology, 2 nd edition –3 of 5 volumes completed Large scale sequencing of random samples indicates vast majority of bacteria have never been cultured or studied in detail 16

17. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. CrenarchaeotaEuryarchaeotaAquificaeThermotogaeChloroflexi Thermophiles Bacteria Archaea BacilliClostridiumActinobacteria Gram-positive bacteria High G/CLow G/C (Firmicutes) EuryarchaeotaAquificaeBacilliActinobacteriaSpirochaetes 25.96 µm Archaea differ greatly from bacteria. Although both are prokaryotes, archaeal cell walls lack peptidoglycan; plasma membranes are made of different kinds of lipids than bacterial plasma membranes; RNA and ribosomal proteins are more like eukaryotes than bacteria. Mostly anaerobic. Examples include Methanococcus, Thermoproteus, Halobacterium. The Aquificae represent the deepest or oldest branch of bacteria. Aquifex pyrophilus is a rod- shaped hyper- thermophile with a temperature optimum at 85°C; a chemo- autotroph, it oxidizes hydrogen or sulfur. Several other related phyla are also thermophiles. Gram-positive bacteria. Largely solitary; many form endospores. Responsible for many significant human diseases, including anthrax (Bacillus anthracis); botulism (Clostridium botulinum); and other common diseases (staphylococcus, streptococcus). Some gram-positive bacteria form branching filaments and some produce spores; often mistaken for fungi. Produce many commonly used antibiotics, including streptomycin and tetracycline. One of the most common types of soil bacteria; also common in dental plaque. Streptomyces, Actinomyces. Long, coil-shaped cells that stain gram- negative. Common in aquatic environments. Rotation of internal filaments produces a corkscrew movement. Some spirochetes such as Treponema pallidum (syphilis) and Borrelia burgdorferi (Lyme disease) are significant human pathogens. 1.37 µm 1 µm 23.80 µm22.15 µm Deinococcus- Thermus a: © SPL/Photo Researchers, Inc.; b; © Dr. R. Rachel and Prof. Dr. K. O. Stetten, University of Regensburg, Lehrstuhl fuer Mikrobiologie, Regensburg, Germany; c: © Andrew Syred/SPL/Photo Researchers, Inc.; d: © Microfi ield Scientifi c Ltd/SPL/Photo Researchers, Inc.; e: © Alfred Paseika/SPL/Photo Researchers, Inc. 17

18. 18 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. f: © Dr. Robert Calentine/Visuals Unlimited; g: © Science VU/S. Watson/Visuals Unlimited; h: © Dennis Kunkel Microscopy, Inc.; i: © Prof. Dr. Hans Reichenbach, Helmholtz Centre for Infection Research, Braunschweig Cyanobacteria Chlorobi BetaGammaDelta ProteobacteriaPhotosynthetic Spirochaetes CyanobacteriaBetaGammaDelta 25.04 µm 10.57 µm 750 µm Cyanobacteria are a form of photosynthetic bacterium common in both marine and freshwater environ- ments. Deeply pigmented; often responsible for “blooms” in polluted waters. Both colonial and solitary forms are common. Some filamentous forms have cells specialized for nitrogen fixation. A nutritionally diverse group that includes soil bacteria like the lithotroph Nitrosomonas that recycle nitrogen within ecosystems by oxidizing the ammonium ion (NH 4 + ). Other members are heterotrophs and photoheterotrophs. Gammas are a diverse group including photosynthetic sulfur bacteria, pathogens, like Legionella, and the enteric bacteria that inhabit animal intestines. Enterics include Escherichia coli, Salmonella (food poisoning), and Vibrio cholerae (cholera). Pseudomonas are a common form of soil bacteria, responsible for many plant diseases, and are important opportunistic pathogens. The cells of myxobacteria exhibit gliding motility by secreting slimy polysaccharides over which masses of cells glide; when the soil dries out, cells aggregate to form upright multicellular colonies called fruiting bodies. Other delta bacteria are solitary predators that attack other bacteria (Bdellovibrio) and bacteria used in bioremediation (Geobacter). Epsilon– Helicobacter Alpha– Rickettsia

19. Prokaryotic Cell Structure 3 basic shapes –Bacillus – Rod-shaped –Coccus – Spherical –Spirillum – Helical-shaped 19

20. Cell wall –Peptidoglycan forms a rigid network Maintains shape Withstands hypotonic environments Archaea have a similar molecule –Gram stain Gram-positive bacteria have a thicker peptidoglycan wall and stain a purple color Gram-negative bacteria contain less peptidoglycan and do not retain the purple-colored dye – retain counterstain and look pink 20

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22. Gram positive bacteria –Thick, complex network of peptidoglycan –Also contains lipoteichoic and teichoic acid Gram negative bacteria –Thin layer of peptidoglycan –Second outer membrane with lipopolysaccharide –Resistant to many antibiotics 22

23. S-layer –Rigid paracrystalline layer found in some bacteria and archaea –Outside of peptidoglycan or outer membrane layers in gram-negative and gram-positive bacteria –Diverse functions – often involves adhesion Capsule –Gelatinous layer found in some bacteria –Aids in attachment –Protects from the immune system 23

24. Flagella –Slender, rigid, helical structures –Composed of the protein flagellin –Involved in locomotion – spins like propeller Pili –Short, hairlike structures –Found in gram-negative bacteria –Aid in attachment and conjugation 24

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26. Endospores –Develop a thick wall around their genome and a small portion of the cytoplasm –When exposed to environmental stress –Highly resistant to environmental stress Especially heat –When conditions improve can germinate and return to normal cell division –Bacteria causing tetanus, botulism, and anthrax 26

27. Internal membrane –Invaginated regions of plasma membrane –Function in respiration or photosynthesis 27 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. a. b. a: © Science VU/S. W. Watson/Visuals Unlimited; b: © Norma J. Lang/Biological Photo Service 0.47µm 0.86µm

28. Nucleoid region –Contains the single, circular chromosome –May also contain plasmids Ribosomes –Smaller than those of eukaryotes –Differ in protein and RNA content –Targeted by some antibiotics 28

29. Prokaryotic Genetics Prokaryotes do not reproduce sexually 3 types of horizontal gene transfer –Conjugation – cell-to-cell contact –Transduction – by bacteriophages –Transformation – from the environment All 3 processes also observed in archaea 29

30. Conjugation Plasmids may encode advantageous info –Are not required for normal function In E. coli, conjugation is based on the presence of the F plasmid (fertility factor) –F + cells contain the plasmid –F - cells do not 30

31. F + cell produces F pilus that connects it to F - cell Transfer of F plasmid occurs through conjugation bridge F plasmid copied through rolling circle replication The end result is two F + cells 31

32. The F plasmid can integrate into the bacterial chromosome –Events similar to crossing over in eukaryotes –Homologous recombination Hfr cell (high frequency of recombination) –F plasmid integrated into chromosome –Replicated every time host divides The F plasmid can also excise itself by reversing the integration process –An inaccurate excision may occur picking up some chromosomal DNA – F ′ plasmid 32

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35. Transduction Generalized transduction –Virtually any gene can be transferred –Occurs via accidents in the lytic cycle –Viruses package bacterial DNA and transfer it in a subsequent infection Specialized transduction –Occurs via accidents in the lysogenic cycle –Imprecise excision of prophage DNA –Only a few host genes can be transferred 35

36. 36 Infection with Phage Phage adheres to cell.Phage DNA is injected in to cell.Phage DNA is replicated and host DNA is degraded. Phage particles are packaged with DNA and are released. Infection with Transducing Phage Cell contains DNA from donor. Transducing phage adheres to cell. Phage injects a piece of chromosomal DNA. DNA is incorporated by homologous recombination. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

37. 37 Please note that due to differing operating systems, some animations will not appear until the presentation is viewed in Presentation Mode (Slide Show view). You may see blank slides in the “Normal” or “Slide Sorter” views. All animations will appear after viewing in Presentation Mode and playing each animation. Most animations will require the latest version of the Flash Player, which is available at http://get.adobe.com/flashplayer.

38. Transformation Natural transformation –Occurs in many bacterial species, including Streptococcus which was studied by Griffith –DNA that is released from a dead cell is picked up by another live cell –Encoded by bacterial chromosome Not an accident of plasmid or phage biology 38

39. Artificial transformation –Some species do not naturally undergo transformation –Accomplished in the lab –Used to transform E. coli for molecular cloning 39

40. 40 Please note that due to differing operating systems, some animations will not appear until the presentation is viewed in Presentation Mode (Slide Show view). You may see blank slides in the “Normal” or “Slide Sorter” views. All animations will appear after viewing in Presentation Mode and playing each animation. Most animations will require the latest version of the Flash Player, which is available at http://get.adobe.com/flashplayer.

41. R (resistance) plasmids –Encode antibiotic resistance genes –Acquire genes through transposable elements –Important factor in appearance of antibiotic resistant strains of Staphylococcus aureus Virulence plasmids or transduction –Encode genes for pathogenic traits –Enterobacteriaceae –E. coli O157:H7 strain 41

42. Mutations can arise spontaneously in bacteria as with any organism –Radiation and chemicals increase likelihood Auxotrophs are nutritional mutants –Studied using replica plating Mutations (and plasmids) can spread rapidly in a population –Methicilin-resistant Staphylococcus aureus (MRSA) –Vancomycin-resistant Staphylococcus aureus (VRSA) 42

43. Prokaryotic Metabolism Acquisition of Carbon –Autotrophs – from inorganic CO 2 Photoautotrophs – energy from Sun Chemolithoautotrophs – energy from oxidizing inorganic substances –Heterotrophs – from organic molecules Photoheterotrophs – light as energy source but obtain organic carbon made by other organisms Chemoheterotroph – both carbon atoms and energy from organic molecules –Humans are also an example 43

44. Type III secretion system –Found in many gram-negative bacteria –Molecular syringe to inject virulence proteins into host cell cytoplasm –Yersinia pestis (bubonic plague), Salmonella, Shigella 44

45. Human Bacterial Disease In the early 20 th century, infectious diseases killed 20% of children before the age of five –Sanitation and antibiotics considerably improved the situation In recent years, however, many bacterial diseases have appeared and reappeared 45

46. Tuberculosis (TB) Scourge for thousands of years Mycobacterium tuberculosis Afflicts the respiratory system Thwarts immune system Easily transferred from person to person through the air Multidrug-resistant (MDR) strains are very alarming 46

47. Dental caries (tooth decay) –Plaque consists of bacterial biofilms –Streptococcus sobrinus ferments sugar to lactic acid –Tooth enamel degenerates Peptic ulcers –Helicobacter pylori is the main cause –Treated with antibiotics 47

48. Sexually transmitted diseases (STDs) Gonorrhea –One of the most prevalent communicable diseases in North America. –Neisseria gonorrhoeae –Transmitted through exchange of body fluids –Can pass from mom to baby via birth canal Chlamydia –Chlamydia trachomatis –“Silent STD” – incidence has skyrocketed –Can cause PID and heart disease 48

49. Syphilis –Treponema pallidum –Transmitted through sex or contact with open chancre –Can pass from mom to baby via birth canal –Four distinct stages Primary – Chancre – highly infectious Secondary – Rash – infectious Tertiary – Latency – no longer infectious but attacking internal organs Quaternary – Damage now evident 49

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51. Beneficial Prokaryotes Decomposers release a dead organism’s atoms to the environment Fixation –Photosynthesizers fix carbon into sugars Ancient cyanobacteria added oxygen to air –Nitrogen fixers reduce N 2 to NH 3 (ammonia) Anabaena in aquatic environments Rhizobium in soil 51

52. Symbiosis refers to the ecological relationship between different species that live in direct contact with each other –Mutualism – both parties benefit Nitrogen-fixing bacteria on plant roots Cellulase-producing bacteria in animals –Commensalism – one organism benefits and the other is unaffected –Parasitism – one organism benefits and the other is harmed 52

53. Bacteria are used in genetic engineering –“Biofactories” that produce various chemicals, including insulin and antibiotics Bacteria are used for bioremediation –Remove pollutants from water, air, and soil –Biostimulation – adds nutrients to encourage growth of naturally occurring microbes Exxon Valdez oil spill 53