TER 26

1. Bacteria and Archaea: The Prokaryotic Domains TER 26 Nitrogen cycle Mycobacterium tuberculosis Color-enhanced images shows rod-shaped bacterium responsible for tuberculosis (Raven et al 2002) Endosymbiotic Theory

2. Structure of a Eukaryotic Animal Cell Structure of a Prokaryotic Cell • Prokaryotic cells have a simple interior organization compared to Eukaryotes. • Membrane-enclosed nucleus lacking • Membrane-enclosed cytoplasmic organelles lacking • Cytoskeleton lacking-support from rigid cell wall Structure of a Eukaryotic Plant Cell

3. Lecture Themes • origins, evolution and diversity • structure and function • ecological function and relationships

4. 1. Prokaryote Phylogeny

5. Genome of the Archaeon Methanococcus jannaschii was sequenced in 1996. Sequencing of M. jannashcii confirmed Carl Woese’s long-standing hypothesis that life traces back to three main lineages, one of which (Archaea) includes prokaryotes that share a more recent common ancestry with eukaryotes than with the prokaryotic “true bacteria”

6. Prokaryotic Structure and Function

7. (Keaton 1993) Cyanobacteria 10 um dia. E. coli 1X2 um Mycoplasma 0.3-0.8 um dia. Bacteriophage 0.07X 0.2 um Viroid 0.01 X 0.3 um Lymphocycte 10 um dia. Largest known prokaryote is the marine bacterium Thiomargarita namibiensis; bright white cell in upper left, about .75 mm dia., attached to two dead ones. Fruitfly in picture for size comparison. Paramecium 30X 75 um Sizes of viruses, bacteria and eukaryotes compared Most bacteria are 1-5 um diameter (most Eukaryotic cells are 10-100 um) Bacillus on the head of a pin

8. Raven et al 2002 Spherical coccus(Enterococcus) Pseudomonas aeruginosa Streptococcus Spirillum volutans Rod-shaped bacillus(E. coli) Bacterial FormThree shapes are especially common among bacteria – spheres, rods and spiralsMost are unicellular, some aggregate transiently, some form permanent aggregations of identical cells;some show division of labor between two or more specialized cell times Helical spirilla(|Aquaspirillum spirosa)

9. Scanning electron micrograph of a colony of streptomyces, one of the actinomycetes. The actinomycetes have a much more complicated morphology than most other bacteria. (Keaton and Gould 1993)

10. Most bacterial cell walls contain peptidoglycan (lacking in Archaea) • Gram staining is an important technique for identifying bacterial; cells stain differentially based on structure and composition of walls • Pathogenesis is related to cell wall structure and composition • Many antibiotics act by preventing formation of cell walls, by inhibiting synthesis of cross-links in peptidoglycan • Many prokaryotes produce capsules that function in adherance and protection • Many prokaryotes have surface appendages called pili that are function in adherance Penicillium chrysogenum Neisseria gonorrhoeae E. coli The exterior surfaces of Prokaryotes. Almost all prokaryotes have a cell wall, and in most that wall contains peptidoglycan – polymers of modified sugars that are cross-linked by short polypeptides

11. Aquaspirillum sinosum • Mechanisms of Motility Many bacteria are motile. Fllagellar action is the most common,but not the only mechanism, for generating movement. • Prokaryotic flagella • Flagella-like helical filaments • Growing gelatinous threads • Motility Behavior • Kinesis • Taxis Spirillum volutans Borrelia burgdorferi Lyme disease symptoms, and the disease vector – a tick

12. 0.05 um 1 um Electron micrograph of E. coli shoing long helical flagella.

13. Vibrio cholerae (pathogen responsbible for cholera); the unsheathed core visible at top of photo is composed of a single crystal of the protein flagellin. In intact flagella, core is surrounded by a flexible sheath. Rotary motion of the motor creates a kind of rotary motion when organism swims. Bacteria swim by rotating their flagella.

14. mesosome • various specialized membranes, but lacking extensive compartmentalization by internal membranes • ribosomes present but differ from eukaryotic ones in size and composition • genomes are smaller and simpler than in eukaryotes; one major chromosome and, in some species, plasmids • Processes of DNA replicatin and protein translation are generally similar to eukaryotes plasma membrane DNA Exensive folded photosynthetic membranes are visisble in Prochloron cell. The single, circular DNA molecule is located in the clear area in the central region of the cell. The mesosome is an infolding of the plasma membrane serves as a point of attachment for DNA in some bacterial cells Infoldings of plasma membrane, similar in ways to cristae of mitochondria, function in cellular respiration in aerobic bacteria Thylakoid membranes of photosynthetic cyanobacteria Cellular and Genomic Organization The organization of cellular components, including the genome, differs substantially between prokaryotes and eukaryotes

15. Cell divisionAsexual reproduction by cell division via binary fission Mechanisms of gene transfer-transformation; genes from environment-conjugation; genes from another prokaryote-transduction genes via a virus Adaptationshort generation time allows favorable mutations and novel genomes arising from gene transfer to spread quickly in rapidly reprducing Growth virtual geometric growth while in environments with unlimited resources Prokaryote Reproduction and Population Growth Prokaryote populations grow and adapt rapidly, through asexual reproduction as well as mechanisms involving gene transfer

16. Dormancy and Endosporulation Some bacteria form highly resistant spores under harsh environmental conditions Antibiotic synthesisSome prokaryotes (and protists and fungi) synthesize and release antibiotic chemicals that inhibit growth of other microbes Sporulating Bacillus cell Bacillus anthracus Adaptations to Harsh Environmental Conditions: Some bacteria are capable of dormancy, endosporulation and antibiotic synthesis

17. Nutritional and Metabolic Diversity

18. Sources: Campbell et al (2002), Freeman (2002), Purves et al (2001) • Nutrition; how an organism obtains two resources from the environment; • -energy • -carbon source to build the organic molecules of cells • Phototrophs; use light energy • Chemotrophs; obtain energy from chemicals taken from the environment • Autotroph; needs only the inorganic compound CO2 as a carbon source • Hetertroph: requires at least one organic nutrient for making other organic compounds

19. Sources: Freeman 2002, Campbell 2002 • The basic themes of metabolism, among all domains are • -extracting usable energy from reduced compounds -using light to produce high-energy electrons-fixing carbon. • All organisms have mechanisms for trapping usable energy in ATP; ATP allows cells to do work; there is no life without ATP • At one point or another, you have studied these metabolic themes as they occur Eukaryotes and perhaps Prokaryotes; photosynthesis(eg,in green plants and respiration (eg in all Eukaryotes) • Prokaryotes show tremendous diversity in metabolic process.in that they have evolved dozens of variations on these most basic themes of metabolism • This Prokarotic metabolic diversity is important for two reasons: • It explains their ecological diversity; they are found almost everywhere because they exploit such a tremendous variety of molecules as food • Global nutrient cycling of (eg nitrogen, phosphorous, sulfur, carbon) is mediated by, exists because, prokaryotes can use them in almost any molecular form Overview of photosynthesis and respiration

20. Sources: Freeman 2002, Campbell 2002 Overview of cellular respiration One (very important!!) example of metabolic pathways by which many species obtain energy for generating ATP by oxidizing reduced organic compounds Highly reduced molecule, glucose, serves as original electron donor (ie, molecule is oxidized) and highly oxidized molecule, oxygen, serves as final electron acceptor Overview of Photosynthesis Many prokaryotes generate ATP by employing electron donors and acceptors other than sugars and oxygen, and produce by-products other than water

21. Source: Freeman (2002), Purves et al (2001) Some Electron Donors and Acceptors Used by Bacteria and Archaea Electron Donor Electron Acceptor Product Metabolic Strategy * H2 or organic compounds SO42- H2S sulfate-reducers H2 CO2 CH4 methanogens CH4 O2 CO2 methanotrophs S or H2S O2 SO42- sulfur bacteria organic compounds Fe3+ Fe2+ iron-reducers NH3 O2 NO2- nitrifiers organic compounds NO3- N2O, NO or N2 denitrifiers (or nitrate reducers) NO2- O2 NO3- nitrosifiers * This column gives the name biologists use to identify species that use a particular metabolic strategy nitrification: oxidation of ammonia to nitrite and nitrate ions denitrification: reduction of nitrogen-containing ions to form nitrogen gas and other products

22. Source: Freeman (2002) • lateral gene transfer has taken place repeatedly through transformation and viral infection • in transfers among bactera and archaea the primary mechanism probably involves loops of mobile DNA (plasmids) • swapped genes tend to be those involved in energy and carbon metabolism (not information processing , eg DNA replication, transcription, protein synthesis) – interesting…as metabolic diversity is a hallmark of the Bacteria and Archaea!! Lateral Gene Transfer. Gray branches show diversification of the three domains. Red branches show movement of genes from species in one part of the tree to species in other parts

23. Nutritional Diversity among Chemoheterotrophs (most known Prokaryotes) • Saprobes; decomposers that absorb nutrients from dead organic matter • Parasites; absorb nutrients from body fluids of living hosts • Relevance of Oxygen to Metabolism among Bacteria and Archaea • Obligate aerobes • Facultative anaerobes • Obligate anaerobes

40. Chapter 26: Bacteria and Archaea: the Prokaryotic Domains Why Three Domains? General Biology of the Prokaryotes Prokaryotes in Their Environments

41. Chapter 26: Bacteria and Archaea: the Prokaryotic Domains Prokaryote Phylogeny and Diversity The Bacteria The Archaea

42. Why Three Domains? • Living organisms can be divided into three domains: Bacteria, Archaea, and Eukarya. The prokaryotic Archaea and Bacteria differ from each other more radically than the Archaea from the Eukarya.

43. Why Three Domains? • Evolutionary relationships of the domains were revealed by rRNA sequences. Their common ancestor lived more than 3 billion years ago, that of the Archaea and Eukarya at least 2 billion years ago. Review Figure 26.2 and Table 26.1

44. figure 26-02.jpg Figure 26.2 Figure 26.2

45. table 26-01.jpg Table 26.1 Table 26.1

46. General Biology of the Prokaryotes • The prokaryotes are the most numerous organisms on Earth,occupying an enormous variety of habitats.

47. General Biology of the Prokaryotes • Most prokaryotes are cocci, bacilli, or spiral forms. Some link together to form associations, but very few are truly multicellular.

48. General Biology of the Prokaryotes • Prokaryotes lack nuclei, membrane-enclosed organelles, and cytoskeletons. Their chromosomes are circular. They often contain plasmids. Some contain internal membrane systems.

49. General Biology of the Prokaryotes • Many prokaryotes move by means of flagella, gas vesicles, or gliding mechanisms. Prokaryotic flagella rotate.

50. General Biology of the Prokaryotes • Prokaryotic cell walls differ from those of eukaryotes. Bacterial cell walls generally contain peptidoglycan. Differences in peptidoglycan content result in different reactions to the Gram stain. Review Figure 26.7