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Bacteria & Viruses

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  • 1. Bacteria & Viruses Prokaryotes and Beyond
  • 2. The Prokaryotes
    • Prokaryotes = Monerans
    • The earliest organisms
      • lived & evolved alone on earth for 2 x 10 9 years
    • The smallest independently living things
      • Much smaller than single celled eukaryotes
      • Typical bacteria = 2 µ
      • Average eukaryotic cell = 50-200 µ
    • Outnumber all eukaryotes combined
      • more inhabit your mouth than the total # of people who ever lived!
  • 3. Diversity & Classification
    • 2 branches
    • Archebacteria
      • Confined to extreme environments
      • Similar to early earth
      • More closely related to eukaryotes than to modern bacteria
    • Only a few genera:
      • Methanogens - reduce CO 2 to CH 4
      • Extreme halophiles - salt loving
      • Thermoacidophiles
    • Eubacteria
      • most modern bacteria
      • very diverse
  • 4. Bacterial Classification
  • 5. Prokaryotes vs. Eukaryotes
    • No mitochondria, chloroplasts, or other membrane bound organelles
    • Most are unicellular and much smaller
    • Smaller, simpler genomes
      • DNA not arranged in chromosomes
    • Cell wall is different from plants, fungi, protists
      • contains murein / peptidoglcan (a nitrogen containing polysaccharide)
    • Differ in mechanisms of genetic replication, expression, and recombination
  • 6. Prokaryotic & Eukaryotic Cells
  • 7. Function & Interactions
    • Only a minority cause disease
    • Many are essential to life on earth
    • Decomposers
      • essential to chemical cycles
    • Often live in symbiotic relationships with other organisms
  • 8. Form & Function
    • Single celled
      • some aggregate in 2-celled or several celled groups
      • some form colonies
    • Diversity of shapes
    • 3 most common:
      • spheres = cocci
      • rods = bacilli
      • spirals = spirilla
  • 9. Bacterial Shapes
  • 10. The Bacterial Cell Wall
    • Instead of cellulose, contain peptidoglycan
      • A polymer of modified sugars cross-linked with amino acids
    • The gram stain distinguishes many disease causing bacteria based on the type of cell wall
    • Many antibiotics work by attacking the bacterial cell wall
  • 11. The Gram Stain
    • A valuable tool for distinguishing types of bacteria based on the cell wall
    • Gram (+)
      • accept gram stain
      • have simpler cell walls with large amounts of peptidoglycan
    • Gram (-)
      • do not stain
      • have more complex cell walls with less peptidoglycan
      • cell walls contain lipopolysaccharides
      • are more likely to be pathogenic (cause disease)
      • more resistant to antibiotics
  • 12. The Cell Wall & Gram Stain
  • 13. Gram (+) and (-) Bacteria
  • 14. Antibiotics
    • Many antibiotics work on the cell wall
    • Common antibiotics (e.g. penicillin) work by preventing cross-linking of peptidoglycan
    • Therefore bacteria can’t form new cell walls
    • Therefore no new bacteria are formed
    • Doesn’t effect the host, because only monerans have peptidoglycan
    • Explains added resistance of gram (-) bacteria to these antibiotics
  • 15. Secretion of Antibiotics
    • Most micro-organisms (including protists, monerans & fungi) release antibiotics
    • An evolutionary advantage
    • Helps the organism compete for food and space
  • 16. The Capsule
    • Many bacteria secrete a sticky substance that forms another protective layer, the capsule
    • Outside the cell wall
    • Helps them stick to things
    • Provides protection
  • 17. Motility
    • About half of all monerans are capable of directional movement.
    • 3 mechanisms:
      • flagella - different from eukaryotes
      • spiral shaped bacteria ( spirochetes ) have a filament that spirals around the cell under the outer sheath
        • causes the cell to move like a corkscrew
      • some bacteria secrete slimy chemicals & glide
    • Taxis
      • movement toward or away from a stimulus
      • many bacteria exhibit this form of movement
  • 18. Structure of Prokaryotic Flagella
  • 19. Structures of Movement
  • 20. Prokaryotic Ribosomes
    • Slightly different from eukaryotic ribosomes
    • The basis of some antibiotics
      • tetracycline & chloramphenicol
      • block protein synthesis in prokaryotes only
  • 21. Metabolic Diversity
    • A varied group, similar to eukaryotes
    • Three major groups:
    • Phototrophs
      • use light energy to synthesize organic compounds from CO 2
      • includes cyanobacteria (blue-green algae)
      • have chlorophyll but not chloroplasts
    • Photoheterotrophs
      • can use light to generate ATP
      • must obtain carbon in organic form
    • Chemoheterotrophs
      • Must consume organic molecules for both energy & carbon
      • Most bacteria are chemoheterotrophs
  • 22. Chemoheterotrophs
    • Most bacteria are chemoheterotrophs
    • Consume organic molecules for both energy and carbon
    • Secrete an enzyme that breaks down large molecules of food to smaller molecules that can be absorbed through the cell membrane
    • Many bacteria are saprobes
      • feed on dead plants or animals
      • also called decomposers because they break down decaying material
    • Other bacteria live in or on the bodies of other living organisms
      • some are beneficial ( symbiosis )
      • some are harmful = parasites
  • 23. Oxygen
    • The effects of oxygen on growth are varied
    • Obligate aerobes
      • cannot grow without O 2 for cellular respiration
    • Facultative aerobes
      • use O 2 if available but can also use fermentation
    • Obligate anaerobes
      • cannot use O 2 and are poisoned by it. 
    • Facultative anaerobes
      • don't use O 2 , but aren't harmed
    • Many heterotrophic bacteria are anaerobes
      • classified by their metabolic wastes (acetic acid, lactic acid, etc.)
  • 24. Nitrogen Metabolism
    • Also diverse
    • Monerans are able to metabolize most nitrogen compounds
    • Key to cycling nitrogen through the ecosystem
    • Nitrogen fixation
      • Some monerans can capture N 2 in the atmosphere
      • They have an enzyme that converts N 2 gas to nitrates (NO 3 ) - a form other organisms can use
      • This is the only mechanism that makes atmospheric nitrogen available to other organisms
      • Some plants (clover, beans, etc.) have nitrogen fixing bacteria growing in their roots
  • 25. The Bacterial Genome
    • Bacteria have ~ 1/1000 as much DNA as eukaryotes
    • DNA is one double stranded molecule in the form of a ring
    • No nucleus, so DNA is in the cytoplasm
  • 26. Plasmids
    • Bacteria may also have smaller rings of DNA called plasmids
    • Each plasmid is only a few genes
    • Plasmids carry non-essential genes such as antibiotic resistance, metabolism of special nutrients, etc.
    • Plasmids can carry a sex factor
      • bacteria with the sex factor can conjugate with cells that do not carry the factor.
    • Plasmids replicate independently
    • Can be transferred when bacteria conjugate
  • 27. Growth & Reproduction
    • Neither mitosis nor meiosis occurs in prokaryotes
    • Prokaryotes reproduce asexually by binary fission
    • Genetic recombination does occur in bacteria
  • 28. Genetic Exchange
    • 3 mechanisms of exchange of genetic material:
    • transformation -
      • genes taken up by bacteria from the surrounding environment
    • conjugation -
      • genes are transferred directly from one bacteria to another
    • transduction -
      • genes are transferred between bacteria by means of viruses
    • All are unilateral passage of variable amounts of DNA
    • Mutation is the major source of genetic variation in prokaryotes
  • 29. Bacterial Conjugation
  • 30. Endospores
    • Some bacteria form resistant cells called endospores
    • Can live in stasis indefinitely
      • found 11,000 y.o. bacteria
    • Resist extremes of temperature, pH, etc.
  • 31. Classes of Bacteria
    • The Eubacteria include:
      • Proteobacteria
      • Chlamydia
      • Spirochetes
      • Gram-positive bacteria
      • Cyanobacteria
    • The Archebacteria include:
      • Euryarchaeota
      • Crenarchaeota
  • 32. Prokaryotic Phylogeny
  • 33.
    • There are 5 major clades (divisions) of eubacteria
  • 34. The Proteobacteria
    • A diverse group of gram-negative bacteria
    • Includes photoautotrophs, chemoautotrophs & heterotrophs
    • Includes both anaerobic & aerobic species
    • 5 subgroups:
      • Alpha proteobacteria
      • Beta proteobacteria
      • Gamma proteobacteria
      • Delta proteobacteria – myxobacteria
      • Epsilon proteobacteria - helicobacter
  • 35. Subgroups of Proteobacteria
    • Alpha proteobacteria
      • Most are symbionts or parasites
      • Includes rhizobium, nitrogen fixing bacteria found in the roots of legumes
    • Beta proteobacteria
      • Includes nitosomonas – oxidize NH 4 producing nitrite
    • Gamma proteobacteria
      • Includes photosynthetic bacteria and many enterics such as E. coli , Legionella , Vibrio cholera , salmonella
    • Delta proteobacteria
      • Includes Myxobacteria which form elaborate colonies
      • Bdellovibrios – predators that attack other bacteria
    • Epsilon proteobacteria
      • Closely related to deltas
      • Includes helicobacter which causes stomach ulcers
  • 36. Chlamydia
    • Parasites that can survive only within the cells of animals
    • Gram negative walls are unusual because they lack peptidoglycan
    • One species is the most common cause of blindness in the world
    • Another species causes the most common STD in the U.S.
  • 37. Spirochaetes
    • Helical heterotrophs
    • Have axial filaments = fibers between cell wall and cell membrane
      • Filaments allow a corkscrew motion
    • Many are free living
    • Includes anaerobes that live in mud or H 2 O
    • A few are parasites
    • Includes the organisms that cause syphilis and Lyme disease
  • 38. Gram Positive Bacteria
    • Includes all gram positive bacteria and also a few related gram negative bacteria
    • Colonial actinomycetes were once mistaken for fungus
      • includes Streptomyces , the source of many antibiotics
      • Also includes species that cause tuberculosis & leprosy
    • Includes spore formers such as such as Bacillus & Clostridium
      • Bacillus anthracis
      • Clostridium botulinum
      • Also all Staphylococcus & Streptococcus
    • Mycoplasmas
      • The only bacteria lacking a cell wall
      • Smallest known cells
      • Most live in soil
  • 39. Cyanobacteria
    • Only about 1,500 species
    • Sometimes called blue-green algae
    • Are photosynthetic
      • Don't contain chlorophyll
      • Have 2 photosynthetic pigments not found in plants:
      • phycocyanin - a blue-green pigment
      • phycoerythrin - a red pigment
    • Many are multicellular - form long filaments
      • To reproduce, chains of cells break, and cells at ends of chains divide, increasing length of the filament
    • Some contain heterocysts - thick walled cells that contain enzymes for nitrogen fixation
      • supply other cells with nitrogen
      • other cells supply them with food from photosynthesis
  • 40. Viruses
    • Much smaller than bacteria: .03 - .30
    • Can't be seen with a light microscope
    • Consist of a single molecule of nucleic acid surrounded by a protein coat
    • The nucleic acid molecule can be single or double stranded DNA, or RNA
    • The amount of nucleic acid is much less than bacteria
      • bacteria have enough DNA for 2000 genes
      • many viruses have only 10 genes; the largest is about 100 genes
  • 41. Viral Strategy
    • Viral genes carry instructions for the production of new virus particles
    • Viruses have no ribosomes or other cytoplasmic structures to carry out their genetic instructions
    • Viruses can't live independently; are all parasites of living cells
    • They use the energy and the protein producing machinery of the host cells to make new virus particles
  • 42. Viral Protection
    • The protein coat is made of several hundred protein molecules packed in a geometric pattern
    • Some have a complex capsule surrounding the protein coat
  • 43. Viral Structure
  • 44. Specificity
    • Each type of virus infects a particular type of cell
    • Viruses that infect bacteria = bacteriophage
      • have a ‘tail’ that attaches to bacteria
  • 45. A Bacteriophage
  • 46. Elements of a Bacteriophage
  • 47. Reproduction of Viruses
    • Two primary life cycles
      • Lytic cycle
      • Lysogenic cycle
    • Some have one life cycle or the other
    • Some can shift life cycle type depending on environmental pressures
  • 48. The Lytic Cycle
    • Example E.coli phage:
    • The tail fibers match molecules in host cell membrane - so bind specifically
    • Once the phage is attached, it acts like a syringe - injects its DNA into the host
    • Inside the cell, the phage DNA takes over the cytoplasmic machinery of the host cell
    • The host cell makes copies of the phage DNA
  • 49. The Lytic Cycle (Continued)
    • Host cell ribosomes make proteins according to phage gene instructions.
    • New phage proteins and nucleic acids come together in the cell and form several hundred new phage particles
    • The phage DNA instructs the host cell to self-destruct
    • The host cell makes an enzyme that lyses or digests the bacterial cell wall
    • When the host cell lyses, it releases new phage particles
  • 50. Lytic Cycle of the T4 Phage
  • 51. Modified Lytic Cycle
    • Some viruses have a modified lytic cycle
    • They don't lyse the host cell
    • The virus exits by pushing out through the cell membrane
    • These viruses have capsules that consist partly of host cell membrane & partly viral protein
    • Example: human influenza virus
  • 52. Viral Latency
    • Some viruses can take both active and latent forms.
    • During the active phase, the virus interferes with normal cell metabolism, causing disease symptoms
    • During the latent phase, it's as if the virus has gone to sleep.
      • Although the host cells remain infected, the host is a symptom-free carrier of the disease.
    • The difference between the active and latent manifestations of viral infection results from a switch in viral replication patterns.
      • Some viruses can only replicate by the lytic pathway.
      • Other viruses can inject their DNA into the host cell, but the injected DNA can be inactive until the appropriate cellular event triggers its awakening.
  • 53. The Lysogenic Cycle
    • The latter pathway is called the temperate or lysogenic pathway.
    • After entering the host cell, the viral DNA inserts into host DNA by recombination
      • viral DNA becomes part of host DNA
    • Viral DNA does not take over the host cell
    • When the host cell reproduces, viral genes are also duplicated
    • There may be no active viral particles produced for generations
    • Sporadically, viral DNA will become active and trigger reproduction
  • 54. The Lysogenic Cycle (Continued)
    • When lysogenic viral DNA becomes active, it breaks out of the host DNA  lytic
    • As it breaks out, the viral DNA may take several bacterial genes with it
    • The virus can carry bacterial genes from the previous host to a new host during the infection cycle
      • this process = transduction
      • used in recombinant DNA research
    • It is possible to artificially induce all the cells in a lysogenic culture to enter the lytic pathway by exposing them to UV light, or X-rays.
    • Example: Herpes virus (causes cold sores; may cause cancers
  • 55. Discovery of the Lysogenic Cycle
    • The lysogenic pathway was first discovered in bacteriophages in the early 1920s
    • It was not really understood until the 1950s
    • First explored at the cellular level by Andre' Lwoff, a French scientist.
    • Lwoff knew that some bacterial cultures that grew normally and otherwise seemed perfectly healthy were infected by phage.
    • Although the phage didn't interfere with the host bacteria, such cultures had the ability to cause the lysis or rupture of other bacteria.
    • Thus, the culture was described as "lysogenic."
  • 56. Unraveling the Lysogenic Cycle
    • It was known why such cultures were lethal to other bacteria.
    • The lysogenic effect didn't stem from phage particles floating in the culture
      • The cultures remained lethal even after removal of any free floating phage.
    • The effect was not due to a reserve of phage stored within the host cells
      • No phage were released when the cells of a lysogenic culture were artificially burst open.
  • 57. Lwoff’s Discovery
    • Lwoff observed the growth of single bacterial cells of Bacillus megaterium in tiny droplets of medium.
      • Found that free phage particles were never found floating in droplets that contained only single cells
      • They were found in the colonies derived from single cells.
      • Occasionally, a single cell in a droplet being watched would spontaneously burst, releasing about 100 phage.
    • Concluded that host cells weren’t entirely immune to the phage.
      • When a phage became active, it forced the host to make more phage, eventually killing the host, and releasing new phage when the cell burst.
      • But, the switch from the lysogenic to the lytic pathway was the exception rather than the rule; most of the time the phage was in an inactive form.
  • 58. Phage Lytic & Lysogenic Cycles
  • 59. Are Viruses Alive?
    • Viruses contain nucleic acids & proteins
    • Viruses, by themselves, cannot make or use food, grow or reproduce
    • Some scientists believe viruses were never independently living organisms
    • Others believe viruses evolved from simple bacteria like mycoplasmas & rickettsiae
    • Another hypothesis: viruses are genes that have escaped from the genomes of living cells
    • Not much evidence to support any one of these
  • 60. Beyond Viruses
    • Viroids
      • even smaller & simpler than viruses
      • cause some plant diseases
      • short pieces of RNA with no protein coat
    • Prions
      • Infectious agents that lack nucleic acids
      • “ protein only”
      • BSE
  • 61. Prion Action