BIOB170 EXAM 1

78 flashcards · Other · by jackcummings

1. lineage

   A series of populations, species, or genes descended from a single ancestor over evolutionary time.

2. phylogeny

   The evolutionary history of a particular group of organisms or their genes.

3. phylogenetic tree

   A graphic representation of lines of descent among organisms or their genes.

4. node

   In phylogenetics, a split in a phylogenetic tree when one lineage diverges into two.

5. root

   In reference to phylogenetic trees: the base (oldest) part of the tree

6. taxon

   A biological group (typically a species or a clade) that is given a name.

7. clade

   A monophyletic group made up of an ancestor and all of its descendants.

8. sister species

   Two species that are each other’s closest relatives.

9. sister clades

   Two phylogenetic groups that are each other’s closest relatives.

10. Three Domain Characteristics:

11. Monophyletic clade

    a group of organisms that consists of all the descendants of a common ancestor

12. Polyphyletic clade

    A polyphyletic taxon is defined as one that does not include the common ancestor of all members of the taxon

13. systematics

    The scientific study of the diversity and relationships among organisms.c

14. synapomorphy

    A trait that arose in the ancestor of a phylogenetic group and is present (sometimes in modified form) in all of its members, thus helping to delimit and identify that group. Also called a shared derived trait.

15. convergent evolution

    Independent evolution of similar features from different ancestral traits.

16. evolutionary reversal

    The reappearance of an ancestral trait in a group that had previously acquired a derived trait.

17. homologous

    Any features shared by two or more species that have been inherited from a common ancestor

18. homoplasy

    The presence in multiple groups of a trait that is not inherited from the common ancestor of those groups. Can result from convergent evolution, evolutionary reversal, or parallel evolution.

19. ingroup

    In a phylogenetic study, the group of organisms of primary interest.

20. outgroup

    In phylogenetics, a group of organisms used as a point of reference for comparison with the groups of primary interest (the ingroup).

21. parsimony principle

    Principle that states that the preferred explanation of observed data is the simplest explanation.

22. molecular clock

    The approximately constant rate of divergence of macromolecules from one another over evolutionary time; used to date past events in evolutionary history.

23. Polyphyletic clade

    Pertaining to a group that consists of multiple distantly related organisms, and does not include the common ancestor of the group.

24. Paraphyletic clade

    Pertaining to a group that consists of an ancestor and some, but not all, of its descendants.

25. Photoautotroph

    Photosynthesis

26. Great oxygenation event

27. Proto-earth formed when?

    4.6 billion years ago

28. First prokaryotic cells when? (Cyanobacteria -> Stomatalites)

    3.5 billion years ago

29. Great Oxygenation Event?

    2.3 billion years ago

30. Ediacaran fauna?

    Precambrian - About 541 million years ago. (Large, complex, multicellular organisms)

31. First unicellular Eukaryotic cells?

    2.7 billion years ago

32. Multicellular Eukaryotes?

    600 million years ago

33. Cambrian Explosion?

    541 million years ago, lasted 20-25 million years. (Almost all present animal phyla appeared during this period)

34. First cyanobacteria?

    2.5 - 2.7 billion years ago

35. Burgress Shale?

    505 million years ago - Middle of Cambrian

36. First Insects?

    419 million years ago

37. Gymnosperms (conifers, ginkos)?

    250 million years ago

38. First Dinosaurs?

    243 million years ago

39. Angiosperms (seed plants)?

    145 million years ago

40. Trassic-Jurassic Boundary?

    201 million years ago

41. Dinosaurs go extinct, not birds?

    66 million years ago

42. Mammals

    66 million years ago

43. Primates

    34 million years ago

44. First Homo primates

    2.6 million years

45. Humans first arrive in North America

    25,000 years ago

46. Clovis points

    12,800 - 13,000 years ago

47. Humans first start domesticating plants and animals

    10,000 years ago

48. Group with greatest number of species?

    Insects

49. Group with greatest genetic diversity?

    Bacteria

50. Group with greatest morphological diversity?

    Animals

51. Group with greatest biomass?

    Plants

52. Group with greatest nutritional/metabolic diversity?

    Bacteria

53. Where are we in ToL?

    We are in the Opisthokonts - monophyletic group that includes animals and fungi

54. Our binominal name?

    Homo sapiens

55. Linnean classification system order?

    Species->Genus->Family->Order->Class->Phylum->Kingdom->Domain->Life

56. Linnean location?

57. Why aren't viruses on the Tree of Life?

    Not cellular organisms - rather, they require other cellular organism to complete their lifecycles. Important and abundant (about 103010^{30}1030 viruses in the ocean)

58. First "tree of life"?

    Ernst Haeckel, 1866 Was based heavily on morphology, bacteria have very little. Thus, were grouped in little clade at base of protists.

59. Who started the universal Tree of Life?

    Care Woese in the 1970's.

60. How did Carl Woese use ribosomal RNA sequences to establish the universal tree of life?

    found in all cellular organisms is highly conserved - evolves very slow is the enzymatic moeity of the ribosome can be sequences without having cultured the bacteria.

61. W hat is bigger, total mass of bacteria or total mass of all animals?

    bacteria

62. Most massive animal group?

    Arthropods (includes insects)

63. What is a black smoker?

    a geothermal vent on the seabed which ejects superheated water containing much suspended matter, typically black sulfide minerals. The walls are made of precipitated metals and sulfides, along with thick layers of hyperthermophilic (Hyper-”a lot” Thermo-”temperature” Philic-”liking”) Bacteria and Archaea (yellow and green)

64. Giant tube worms?

    Giant tube worms living on the ocean floor, near “black smokers” exist due to gut bacteria Riftia: has no mouth or anus, lives on the sea floor near black smokers and is one of the fastest growing animals known These chemoautotrophic gut bacteria eat HS, O2, and fix CO2 ... ... into the carbohydrates necessary for the worm (which is a chemoheterotroph, of course) to survive

65. Recent research suggests the Archaea domain are: monophyletic, paraphyletic, or polyphyletic?

    paraphyletic This implies that Eukaryotes are not sister to the Archaea, but rather they are derived from within the Archaea

66. Thermus aquaticus?

    In the Deinococcus–Thermus phylum Tom Brock discovered in 1960's doing research into bacteria that lived in hot spring runoffs at Yellowstone National Park. (Octopus Spring) Pink, filamentous bacteria living at 88ºC A gram negative Bacilli (rod)

67. Where else does Thermus aquaticus live besides hotsprings?

    water heaters

68. How does PCR work?

    Starting with a single double-stranded DNA molecule Step 1: Break (or denature) the hydrogen bonds with heat, usually 95ºC Step 2: Drop the temperature back to down to 50ºC or so, and small DNA primers hydrogen bind to the original DNA strands Step 3: Raise the temperature to about 65ºC, and an enzyme called DNA polymerase makes copies of the original strands. You now have two copies where you originally had one. Step 4: Repeat about 30 times. 2 strands become 4, 4 becomes 8, 8 becomes 16 … 230…

69. Who had the idea for PCR?

    Kary Mullis

70. Why is PCR so slow if you use a DNA polymerase enzyme from E. coli?

    The heat denature step is at 95ºC! This temperature kills most enzymes dead in just a few seconds. If you do not use thermostable DNA polymerases, for example one from Taq, your enzyme will be denatured (killed) every time you heat the DNA to 95ºC and so you need to add it every cycle!

71. What did PCR with Taq polymerase allow?

    1. Getting large amounts of DNA from very small starting material (amplifying DNA). 2. Getting large amounts of new sequence from very small amounts of known starting sequence. 3. It made DNA cloning cheap, easy, even routine. 4. It made genetic testing cheap, easy, and routine (BRCA1, HIV, CF, PFU, etc.) 5. It made the study of ancient DNA possible. 6. It has made genetic testing easy for forensics. It has been used to free innocent people. 7. It has made testing for infectious diseases cheap…

72. How dense is bacteria living in the ocean?

    1 Billion Bacteria in a liter of seawater!

73. What does each drop of water from the ocean contain?

    nearly a complete microscopic food web

74. Total biomass of aquatic ecosystems?

    6 Gt carbon

75. E. coli?

    Escherichia coli. First isolated in 1885 by the German physician Theodor Escherich from stool samples of healthy children. In the Gammaproteobacteria. It’s also in the Enterobacteriaceae, or the enteric bacteria. Very important group! E. coli is a Gram-negative rod. It has flagella, so it’s motile. E. coli K-12 has a 4,600,000 bp genome (4.6 Mb). It has about 4,300 genes.

76. How does LGT happen in bacteria?

    Transformation—bacteria can take up naked DNA, donor can be any organism. Transduction—bacteria can get DNA from viruses, donor tends to be somewhat related to recipient. Conjugation—bacteria can exchange DNA directly w/ structures, donor tends to be closely related to recipient.

77. Coding density of Bacterial and Archaeal genomes?

    About 1 gene/1000bps

78. E. coli core genome size?

    About 2,200 genes, but with an "open" pangenomore - The more genomes sequenced, the more genes added to the potential reservoir for E. coli.