Chapter 21

1. Chapter 21 Viruses, Bacteria & Archaea

2. Viruses • Probably evolved after first cells, existing originally as fragments of cellular nucleic acid that could move from cell to cell. • Viruses are acellular, aggregates of nucleic acids (either DNA or RNA) and protein. • Tiny, infectious particles • The tobacco mosaic virus was the first identified by Iwanowsky (Russian) in 1892 when he found that they could pass through the smallest filters designed for bacteria. • Virus from Latin meaning poison

3. Viral Diseases in Humans (Mader, 9th ed.)

4. Viral Structure- threadlike to polyhedral shapes • 1. genome – inner core consisting of either double or single-stranded RNA or DNA • 2. capsid - protein coat that encompasses the viral genome • 3. envelopes - membranous structures associated with the capsids of certain viruses (influenza), derived partly from the host cell’s plasma membrane

5. Virus structure

6. Viruses • Require a host cell to replicate which may be plant, animal, or bacterium. • obligate intracellular parasites • host specific • capable of mutation - e.g. flu viruses • Bacteriophage viruses attack bacterial cells. • The "T-phages" were bacteriophages that attack E. coli and were among the first studied.

7. T-even bacteriophage

8. Viral Life Cycle - Bacteriophages • lytic cycle - viral DNA or RNA is injected into the host cell where it directs the synthesis of more of the viral genome and more viral capsids which are then assembled inside the host cell. The name refers to the fact that the virus then causes the host cell to rupture (lyse) releasing the newly produced viruses. • lysogenic cycle - viral DNA is integrated into the host cell DNA and may be carried for years or may switch to the lytic cycle. While latent, the viral DNA is called a prophage.

9. Reproduction of bacteriophage

10. Viral Life Cycle • Bacteria defend themselves through the manufacture of restriction enzymes which break the viral DNA that enters the cell. • In this way they restrict the growth of viruses.

11. Reproduction of Animal Viruses • similar to bacteriophages, but there are modifications • capsid and envelope (derived from host cell plasma membrane) attach/fuse w host cell • virus genome covered by the capsid penetrates the host cell • inside the virus is uncoated; viral genome (DNA or RNA) proceeds with biosynthesis • newly assembled viral particles are released by budding • during release by budding, viral particles acquire a membranous envelope (from lipids, proteins & carbs) of host plasma membrane

12. Retroviruses • RNA animal viruses that have a DNA stage • a. Retroviruses contain the enzyme reverse transcriptase that uses RNA as a template to produce cDNA; cDNA is a copy of the viral genome. • b. Viral cDNA is integrated into host DNA and is replicated as host DNA replicates. • c. Viral DNA is transcribed; new viruses are produced by biosynthesis and maturation; release is by budding.

13. Examples of Human Viruses • Viruses cause infectious diseases in plants and animals, including humans: • papillomavirus - warts, cervical cancer • herpes virus -herpes simplex I (cold sores); herpes simplex II (genital herpes); varicella zoster (chicken pox, shingles); Epstein-Barr virus (mono, Burkitt's lymphoma) • hepatitis virus • Adenoviruses - which can cause specific cancers • poxvirus - smallpox, cowpox • parvovirus - parvo

14. Human viruses (continued) • picomavirus - poliovirus, rhinovirus (cold) • togaviruses - rubella, yellow fever, encephalitis • rhabdovirus - rabies • paramyxoviruses - measles, mumps • orthomyxoviruses - infleunza • retroviruses – HIV (AIDS), RNA tumor viruses.

15. Emerging viruses HIV • an emergingvirus: the causative agent of a disease that has only recently arisen and infected people • HIV (human immunodeficiency virus) - AIDs • Retrovirus that mutated from virus which formerly only infected monkeys – “jumped species” • West Nile encephalitis virus • Severe acute respiratory syndrome (SARS)

16. Viroids and Prions • Viroids are naked strands of RNA, a dozen of which cause crop diseases • Prions (infectious proteinaceous particles) are newly discovered disease agents that differ from viruses and bacteria. • rogue proteins with a wrongly-shaped tertiary structure that cause other proteins to distort • Creutzfeldt-Jakob disease in humans, and scrapie and mad cow disease (BSE) in cattle are due to prions.

17. Vaccines against viruses • Antigens prepared to promote active immunity without causing disease • Vaccines were first developed by the English physician Edward Jenner in 1796 when he found the connection between cowpox and smallpox. Since that time smallpox has been entirely eliminated as a human disease.

18. Domain Bacteria and Domain Archaea The Prokaryotes • Archaea previously w/ bacteria – Carl Woese discovered their rRNA had different sequence of base pairs than the bacteria. • Bacteria and Archaea likely from common ancestor • Eukarya branched from Archael line

19. Survey of Life Forms Bacteria and Archaea – Prokaryotes • Origin of Life on Earth – fossil record • Important Dates in Geological Time: • 4.5 billion years ago - Earth forms • 4.0 - 3.0 billion years ago - * Origin of Life • 3.5 billion years ago - Oldest prokaryotic organisms • 1.5 billion years ago - Earliest eukaryotic organisms • 0.5 billion years ago - Earliest animals • * How did life originate ?

20. Early work – origin of life • 1862 - Louis Pasteur (France) disproves the belief in "spontaneous generation" • Demonstrated that sterile broth will not grow bacteria unless it is first directly exposed to air (where bacteria are abundant).

21. Early work – origin of life, contd. • 1920 - Alexander Oparin (Russia) theorizes about the early atmosphere on earth during the time when life arose. Oparin believed the early atmosphere consisted of water vapor (H2O), hydrogen (H2), methane (CH4), and ammonia (NH3), but no molecular oxygen (O2). This represented an atmosphere that contained not only the four essential elements in biochemistry (carbon, nitrogen, hydrogen, and oxygen), but was also a "reducing atmosphere" that would favor the formation of more complex molecules (carbohydrates, lipids, proteins, and nucleic acids) necessary to form the first cells.

22. Early work – origin of life, contd. • 1953 - Stanley Miller (United States) performed experiments to test whether the atmospheric conditions that Oparin suggested would allow the formation of the molecules necessary to form cells. Miller discovered that Oparin's reducing atmosphere was conducive to the formation of carbohydrates, proteins, nucleic acids, and lipids

23. Major Events Necessary to the Origin of Life on Earth • 1. Atmosphere must contain sources of carbon, hydrogen, oxygen, and nitrogen. • 2. Large molecules (carbohydrates, lipids, proteins, and nucleic acids) must form from the smaller compounds in the atmosphere and primitive seas. • 3. Cell membranes must form from the large molecules. • 4. Genetic machinery must be installed within a cell to control replication and other cell functions. • 5. Eukaryotic cells must evolve from prokaryotic cells.

24. Proposed Early "Cells" • coacervates (coacervate droplets)- first cells as tiny spherical drops - had lipid-based membranes as proposed by Oparin • microspheres - first cells had protein-based membranes as proposed by Sidney Fox (American biochemist).

25. Origin of the Cell's Genetic Machinery • Short strands of RNA most likely served as the first genes capable of replicating themselves. • Certain proteins may have served as enzymes catalyzing the replication process, and the relationship between nucleic acids and proteins began. • DNA would have formed much later to contain the genetic code, and to complete what we now think of as the "normal" genetic sequence in which DNA is transcribed into RNA, and RNA is then translated into a protein.

26. From Prokaryotic to Eukaryotic Cells • Prokaryotic cells preceded eukaryotic cells. The present structure of the eukaryotic cell was formed by enfolding the cell membrane. The mitochondria and the chloroplasts present in cells evolved from a bacteria-like organism (mitochondrion) and an alga-like organism (chloroplast) that invaded early cells and developed a favorable (mutualistic) association.

27. Bacteria and Cyanobacteria (blue-green bacteria) – Kingdom Monera • The simplest bacteria may represent the types of organisms that were among the first to evolve on earth. • Bacteria and blue-green bacteria are composed of prokaryotic cells that contain no membrane-bound internal organelles and no true nucleus. • Prokaryotic organisms thrive in habitats that are often too hot, cold, acidic, alkaline for eukaryotic organisms.

28. The major bacterial shapes • coccus (spherical) • bacillus (rod-shaped) • spirochete (spiral-shaped)

29. Common Cocci • Staphylococcus - staph infections, food poisoning • Streptococcus - strep infections, scarlet fever • Neisseria gonorrhoeae - causes gonorrhea

30. Common Bacilli • Escherichia coli (E. coli) - intestinal bacteria • Lactobacillus - ferments milk sugar Common Spirochetes • Treponema pallidum - causes syphilis

31. Bacteria - Human diseases- pathogens • Pathogens can – • Produce a toxin and/or • adhere to certain cells surfaces • and sometimes invade organs or cells • Toxins –released when bacteria die • Organic molecules • Protein • Part of bacterial cell wall

32. Antibiotics – why are they effective? • Inhibit protein synthesis by bacterial ribosomes • Erythromycin, tetracyclines • Inhibit cell wall biosynthesis by blocking peptidoglycan formation • Penicillin, ampicillin

33. Bacteria - Human diseases • anthrax • bacterial pneumonia • typhus • typhoid fever • tuberculosis • leprosy • bubonic plague • tetanus • botulism • gangrene • cholera.

34. Bacterial diseases in humans

35. Bacillus anthracis

36. Bacteria - beneficial roles • decomposers in nature • recycling nitrogen within ecosystems (nitrogen-fixing bacteria) • producing any number of important industrial products (vinegar, yogurt, alcohol).

37. Bacteria - characteristics • Bacteria do have cell membranes. Most have cell walls made of a material called peptidoglycan. • Many of the pathogenic bacteria form protective "capsules" outside of the cell membrane. • Many bacteria also form endospores, dormant forms that are capable of withstanding extreme temperature and pH ranges.

38. Bacterial motility • Bacterial cells may move by three different mechanisms: • 1. flagella • 2. spiral filaments (spirochetes) • 3. gliding Taxis - movement oriented toward (attractant) or away from (repellant) a stimulus • 1. chemotaxis • 2. phototaxis

39. Bacterium w/ flagella

40. General Bacteria Diagram nucleoid fimbriae

41. Bacterial genetics • Bacteria do possess a nuclear region (although not membrane-bound), and both DNA and RNA • Bacteria have one major chromosome and several smaller, circular sequences of DNA known as plasmids which endow special properties on the bacterium.

42. Bacterial genetics • Bacteria reproduce asexually by a process known as binary fission, where the chromosome replicates and the two copies separate as the cell enlarges. Newly formed plasma membrane and cell wall will divide the cell into two cells.

43. Genetic recombination in bacteria may actually occur by three mechanisms • 1. conjugation - genes (plasmids) transferred directly from one bacteria to another by way of a sex pilus • 2. transformation - genes from living or dead prokaryotes are taken up from the surrounding environment • 3. transduction - genes are transferred between bacteria by means of viruses (bacteriophages in lysogenic cycle)

44. Bacterial nutrition: • 1. photoautotrophs - light as energy source, carbon dioxide used to synthesize organic molecules (cyanobacteria) • 2. photoheterotrophs - light as energy source, but obtain carbon from complex organic molecules

45. Bacterial nutrition: • 3. chemoautotrophs - energy from oxidation of inorganic substances (H2S, NH3), carbon dioxide as a carbon source (sulfur bacteria) • 4. chemoheterotrophs - organic molecules provide both energy and carbon source –these are the aerobic saprotrophs (decomposers)

46. Bacterial metabolism: • 1. obligate aerobes - use oxygen for cellular respiration • 2. facultative anaerobes - will use oxygen but can also grow by fermentation in anaerobic environments • 3. obligate anaerobes - cannot use oxygen (Clostridium) which causes gangrene, botulism, and tetanus

47. Cyanobacteria/bacteria - Nitrogen metabolism -important in nitrogen cycle • 1. "nitrogen-fixation" - conversion of atmospheric nitrogen N2, into ammonia (NH3); accomplished by a variety of free-living bacteria (Nitrobacter) and mutualistic cyanobacteria – Rhizobium w/ legumes • 2. Nitrosomonas – “nitrifying” bacteria oxidize ammonia (NH3) into nitrite (NO2) • 3. "denitrification" - Pseudomonas - converts nitrite into atmospheric nitrogen

48. Cyanobacteria – blue-green bacteria • They photosynthesize in the same manner as plants, having other pigments that mask chlorophyll • They can be unicellular, colonial, or filamentous • Common in fresh and marine waters, in soil, and in harsh environs such as hot springs • Some species are symbiotic with other organisms (e.g., liverworts, ferns, and corals). • Lichens are a symbiotic relationship where the cyanobacteria provide organic nutrients to the fungus and the fungus protects and supplies inorganic nutrients.

49. The Archaea – Ties to Domain Bacteria and Domain Eukarya • Archaea are prokaryotes with molecular characteristics that distinguish them from bacteria and eukaryotes; their rRNA base sequence is different from that in bacteria • Because archaea and some bacteria are both found in extreme environments (hot springs, thermal vents, salt basins), they may have diverged from a common ancestor.

50. The Archaea – Ties to Domain Bacteria and Domain Eukarya • Later, the eukarya split from the archaea; • archaea and eukarya share some ribosomal proteins not found in bacteria; and archaea initiate transcription in the same manner, and have similar types of tRNAs as the eukarya