study guide over labs 1-4

1. BIOL 1108 Review Materials for Lab Practical #1

2. Lab 1: Dichotomous Keys and Microbes are Everywhere

3. Taxonomic keys are used to help identify unknown organisms. They are designed to arrange facts and features into mutually exclusive couplets (organism has a tail; organism does not have a tail). Keys designed with two (and only two) choices are said to be " dichotomous ". These dichotomous couplets require you to choose one path or the other. For the virus key , you are required to decide whether each virus does or does not have: an envelope, DNA or RNA, single-stranded or double-stranded nucleic acid, whether the host is a vertebrate or invertebrate, and whether the virus has a tailpiece or not. Dichotomous keys

4. Rules for writing good dichotomous keys: 1. Questions are written as dichotomous couplets that are mutually exclusive. 2. The first words of each couplet are identical (Tail piece is ., Tail piece is not .) 3. The key should have an indented format , so that each successive question is indented from the previous question. 4. Couplets should be specific (<15 cm or > 15 cm; not &quot;large&quot; or &quot;small&quot;). 5. Couplets should be based on features that are observable or measurable. 6. Couplets should be lettered (A or AA, B or BB) or numbered (1 or 1', 2 or 2') 7. In species names, the genus is always capitalized and the species is always trivialized ( Homo sapiens , Escherichia coli ). 8. Species names are italicized or underlined ( Homo sapiens or Homo sapiens )

5. Viruses

7. (= capsid) (= envelope) Nucleic acid RNA or DNA Parts of a virus : each virus is unique, but all have a nucleic acid (RNA or DNA) surrounded by a protein coat (capsid or capsomere). Some (flu virus) also have an envelope.

8. Viruses (from the Latin word for poison) cause a variety of diseases in Humans

9. Microbes Prokaryotes : – no true nucleus; no organelles. - divided into the Bacteria and Archaea Bacteria : - can be divided into 2 groups: gram-positive & gram-negative - based on whether the peptidoglycan in cell wall is exposed (gram positive) or covered by capsule (gram negative) - capsule protects bacterium from hosts' enzymes, so gram negative bacteria are usually more pathogenic (disease- causing) and virulent.

10. Bacteria: gram staining Staphylococcus aureus Gram positive bacterium Coccus = round shape Escherichia coli gram negative bacterium bacilli = rod shaped

11. Size of bacteria bacteria are much smaller (~1  m) than Eukaryotic cells (~100  m) Eukaryotic cell

12. Shapes of bacterial cells 3 basic shapes: coccus, bacillus, spirillus 1. COCCUS: A spherical or oval-shaped bacterium; plural=cocci. Streptococcus pyogenes

13. 2. BACILLUS: A cylindrical-shaped bacterium; plural=bacilli. gram negative bacilli gram positive bacilli

14. 3. SPIRAL or SPIRILLUS: A corkscrew-shaped bacterium; pl. spirilli . Spirilli bacteria occur in 3 forms: vibrio spirillum spirochete bacteria RBC = red blood cell; WBC = white blood cell

15. Cyanobacteria (= blue-green bacteria) used to be incorrectly called blue-green &quot;algae&quot; &quot;Pond scum&quot; on a Georgia pond – blue-green bacteria are probably the earliest organisms to photosynthesize; some also fix nitrogen Nostoc Oscillatoria

18. 1. Monotrichous 2. Amphitrichous 3. Lophotrichous 4. Petritrichous

19. 2. BACTERIAL CAPSULES Bacterial cell walls are normally composed of protein and lipid (fat) substances, but some bacteria also have a slime capsule , composed of a complex carbohydrate. Capsules often make the bacterium more pathogenic and difficult for your body to attack. Slime capsules on the surface of Pneumonia bacteria capsules

20. 3. Endospores - a dormant, tough structure that forms when a bacterium produces a thick internal wall that encloses its DNA and part of its cytoplasm. The function of an endospores is to ensure the survival of a bacterium through periods of environmental stress. Bacillus subtilis showing endospores as green and the vegetative cell as red Clostridium botulinum , the bacteria that causes botulism, showing endospores in green.

21. Antibiotic Sensitivity: a term used to describe the susceptibility of bacteria to antibiotics. Tests are conducted to see which antibiotic will be most successful in treating a bacterial infection. Testing is done using the Kirby-Bauer method (K-B). Small disks containing different antibiotics are placed onto a plate upon which bacteria are growing (=bacterial lawn). If the bacteria are sensitive to the antibiotic, a clear ring, is seen around the wafer indicating poor growth. Bacterial lawn Disk with anitbiotic Petri dish Compare these two disks. The bottom one is more effective, it kills more bacteria, than the top one. Notice that the clear ring is larger on the bottom one.

22. Protista: Their form and methods of locomotion 1. Protozoans: unicellular heterotrophs 2. Algae: unicellular, colonial, and multicellular autotrophs 3. Slime molds: fungus-like protistans

23. 1. Protozoans: unicellular heterotrophs Pelomyxa (Chaos) carolinensis Pelomyxa (Chaos) carolinensis The giant amoeba is common in freshwater habitats. It moves by pushing a pseudopodium (&quot;false foot&quot;) forward, then streaming the cytoplasm in that direction. Amoebas feed by surrounding, engulfing, and digesting food.

24. Plasmodium vivax Plasmodium vivax is a protozoan parasite that causes malaria in humans. They attack and infect red blood cells causing them to burst. The host often dies from anemia (lack of oxygen delivery to the cells). sporozooites – free-living form mature bacteria in red blood cells

25. Trypanosoma gambiensis stained purple below among red blood cells Trypansoma gambiensis is a flagellated protozoan parasite that causes African (Gambian) sleeping sickness in humans.

26. Paramecium caudatum a ciliate conjugation in Paramecium Paramecium are covered with cilia (look hard) and have many organelles including an oral groove, anal pore, macronucleus and micronucleus.

27. 2. Algae – are Protists that can be unicellular, multicellular, or colonial (forming colonies). All photosynthesize.

28. Ceratium species Ceratium is a genus of single-celled aquatic algae common in fresh water and salt water from the Arctic to the tropics. They are armored dinoflagellates with two unlike flagella. They have characteristics that are both &quot;plant-like&quot; and &quot;animal-like&quot;.

29. Aerial photo of a &quot;red tide&quot; caused by dinoflagellates

31. Diatom showing the glass-like silica walls and two halves

32. Green Algae – Phylum Chlorophyta There are about 8,000 species of green algae. Most are aquatic, but a few species live on land. They all photosynthesize. The green algae are thought to have given rise to the plants. Many species of green algae are multicellular (one individual made up of many cells)

33. But, Spyrogyra, Volvox and other Chlorophytes are colonial (one-celled individuals make up a colony). Spyrogyra Volvox

34. Chlamydomonis Golenkinia Other Chlorophytes are unicellular

35. Brown algae – Phylum Phaeophyta The Phaeophyta are almost entirely marine , frequently dominating rocky shores in cold and temperate waters throughout the world. The giant kelp , Macrocystis pyrifera , forms expansive kelp forests off the west coast of North America and provides habitat and shelter for many other organisms.

36. Red Algae – Phylum Rhodophyta The Rhodophyta are a distinct clade characterized by the accessory reddish photosynthetic pigments and the absence of flagella and centrioles. There are ~6000 species. They are found along the coasts in tropical, temperate and cold-water regions. Red algae are ecologically significant as primary producers, providers of habitat for other marine organisms, and their important role in the establishment of coral reefs.

37. Golden algae – Phylum Chrysophyta Chrysophyta are Protists. About 10,000 species exist. Most are single-celled freshwater and marine algae. The chrysophytes are characterized by their yellowish xanthophyll pigments , which mask the green of the chlorophyll that is also present. Most have cell walls containing silica or calcium.

38. Slime molds slime mold on petri dish Acellular slime molds are diploid, multinucleate masses that creep along the ground and feed on dead organic material. The mass is one large cell referred to as a plasmodium . (Note- Don't confuse this with the genus Plasmodium shown earlier). Slime molds play an ecological role similar to that of fungi. They are decomposers, feeding on dead organic material. They differ in that slime molds ingest their food. The plasmodium has produced dark &quot;fruiting bodies&quot; that contain spores. Note the traces of the former plasmodium in the background

39. Could you write a dichotomous key to separate these Protists? Amoeba Plasmodium Trypanosoma Paramecium Volvox Physarum

40. Fungal Diversity

41. Zygomycota Rhizopus stolonifer – black bread mold

42. Rhizopus conjugation Hyphae: can you see septa? Sporangiospores Zygosporangium

43. Pilobus – &quot; hat-thrower&quot; fungus a close relative of black bread mold

44. Ascomycota – sac fungi Yeasts, truffles, morels, Chestnut blight Sordaria perithecia

45. Aspergillus conidiophores

46. Ergot – a fungus that infects grains

47. Chestnut blight fungus

48. Peziza Close-up of apathocecium with asci and ascospores ascus with 8 ascospores

49. Baker's yeast Saccharomyces cervesisiae

50. Basidiomycota – club fungi Coprinus basidiocarp x-section gills basidiocarp &quot;mushroom&quot;

51. Apple rust Black stem rust of wheat Basidiomycota fungi cause several important crop diseases

52. Deuteromycetes Penicillium chrysogenum magnified Penicillium chrysogenum on petri dish

53. Types of lichens lichens are composed of an algae and fungus hyphae 1. Crustose - encrusting 2. Foliose – leaf-like, no branching 3. Fruticose – bush-like with branching

55. Bryophyta – mosses

56. Moss gametophytes and sporophytes

57. Hepatophytes – liver worts

58. Anthocerophytes – horn worts

59. Vascular Seedless Plants 1. Lycophytes – club mosses 2. Ferns

60. Club mosses

61. Whisk &quot;fern&quot;

62. Ferns

63. Sori on fern stained sori

64. Fern prothallus = gametophyte

65. Christmas fern

66. Cinnamon fern

67. Interrupted fern

68. Rattlesnake Fern

69. Maidenhair Fern

71. 1. Phylum Cycadophyta (cycads)

72. 2. Phylum Ginkgophyta:

73. 3. Phylum Gnetophyta

74. Phylum Gnetophyta Genus: Ephedra

75. Phylum Gnetophyta Genus: Welwitschia

77. Anatomy of an Angiosperm Flower Fig. 30.7 Petal Sepal Anther Stigma Ovule Ovary Receptacle Style Filament ( ♀ ) ( ♂ ) Carpel Stamen

78. Types of Simple Fruits

79. Aggregated fruit (one flower with multiple pistils)

80. Multiple fruits come from multiple flowers

81. Plant leaf x-section

82. Gymnosperm cones – x-section

84. Monocots: multiples of 3 Dicots: multiples of 4 or 5

85. Dicot root: xylem and phloem clustered in middle Monocot root: pith in middle surrounded by xylem and phloem

86. Monocot stem Dicot root Dicot stem Monocot root