Test 2 - Learning Objectives Systematics and Phylogeny (Chapter 23) 1. define cladistics, and monophyletic, paraphyletic, polyphyletic clades.(Fig.

26:10) Cladistics: approach to systematics where species are placed into groups called clades Monophyletic: clade containing an ancestor and all of its descendents Paraphyletic: clade containing an ancestor and only some of its descendents Polyphyletic: clade descendents of more than one ancestor

2. define phylogeny, taxonomy, systematics, taxon, sister taxa, branch point, ingroup outgroup. Phylogeny: study of similarities and differences in organisms Taxonomy: the ordered division and naming of organisms Systematics: the study of evolutionary history of organisms using fossils, morphologies, and molecular/genetic data Taxon: a taxonomic unit at any level of hierarchy Sister Taxa: groups that share an immediate common ancestor Branch Point: (node) point of divergence for two species Ingroup: the various species being studied Outgroup: a species that is closely related to the ingroup 3. list in order the Linnean classification hierarchy. Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species 4. know how to read a phylogenetic tree. 5. differentiate homology from analogy. Both deal with similarity between species, but homology results from a common ancestor and analogy results from convergent evolution. 6. define shared ancestral and shared derived character. Shared Ancestral Character: originates in an ancestor of the taxon Shared Derived Character: evolutionary novelty unique to a particular clade

7. name and describe the 3 domains. Eukarya: eukaryotes, nuclear membrane Archea: prokaryotic, no nuclear membrane, possess unique ancient evolutionary history, considered some of the oldest species of organisms on Earth; extreme environments Bacteria: prokaryotic, no nuclear membrane, contain most known pathogenic prokaryotic organisms

9. understand how to draw a cladogram from a character table. 10. discuss how phylogenetic analysis can help identify patterns of disease transmission. Can trace back the source of diseases; allows for more accurate/possibly less study to find a cure; factors that cause epidemics can be assessed using phylogenetic patterns

The Tree of Life - Evolution of First Organisms (Chapter 26.1 and 26.2 and Powerpoint) 1. explain spontaneous generation and tell how Francesco Redi, Spallazanni, and Pasteur disproved this idea. Spontaneous generation says that life spontaneously arose from non-living material Francesco Redi: meat in open jar = maggots, meat in closed jar = no maggots Spallazanni: heat, leave open = microbes; heat, cork = no microbes Pasteur: heat, secluded = no microbes; break top = microbes Each experiment showed that the life was coming from outside sources

2. explain why Precambrian fossils are so rare. Because technology has only recently allowed scientists to discern the fossils in the rocks

3. describe and date the oldest and most primitive fossils found on Earth Prokaryotic Cells - 3.5 BYA Eukaryotic Cells - 1.5 BYA Diverse algae and soft bodied invertebrates - 635 MYA

4. define prebiotic evolution and explain how prebiotic evolution is different than spontaneous generation. Prebiotic Evolution: development of organisms from non-living matter Different from spontaneous generation in that it has four main stages: abiotic synthesis of small organic molecules, joining these small pieces into macromolecules, packaging these molecules into protocells that have different internal environment, and origin of self replicating molecules needed for inheritance.

5. briefly describe Haldane and Oparins hypothesis and the Urey - Miller experiment. Haldane and Oparin proposed that the building blocks of life were formed in the primitive Earth Urey and Miller recreated this in the lab by sending electricity through many of the early Earths gases and the resulting cooled liquid contained organic molecules

6. define proteinoid microspheres. Proteinoid Microspheres: amino acids placed in heated water, cooled, assembled into tiny, stable selectively permeable spheres

7. describe the endosymbiotic theory. In a nutshell, the mitochondrion and chloroplast originated from an aerobic heterotrophic prokaryote and photosynthetic prokaryote, repectively.

8. state the relationship between the geologic timeline and life on earth. The geologic timeline comes from the study of fossils which reflect biological events and environmental changes

9. name the three eons included in the time frame that was classically referred to as the Precambrian. List their time spans and the general characteristics of each eon. Hadean Eon: 4.5 3.8 BYA; rockless; hot; no oxygen Archean Eon: 3.8 2.5 BYA; water vapor cooled; rock record begins; mostly nitrogen Proterozoic Eon: 2.5 - .5 BYA; 2 large continents; oxygen accumulating; earliest eukaryotic cells; soft bodied invertebrates

10. discuss how stromatolites were/are formed. Stromatolites were formed as huge mounded colonies of cyanobacteria and other microorganisms trap fine sediment; alternating layers of organisms and sediment

11. state the eon (and approximate date) in which the first prokaryotes and eukaryotes arose. Prokaryotic Archean, 3.5 BYA Eukaryotic Proterozoic, 1.5 BYA

12. briefly discuss the theory of plate tectonics and continental drift, and this could have affected biological evolution. Basically, plate tectonics describe the movement of the continents, aka continental drift. Contributed to the Ordovician extinction and possibly Devonian

13. list and discuss the general characteristics of the three eras in the Phanerozoic Eon. Paleozoic: most land in two continents; huge glaciers; ice age; air much like present; hard parts developed Mesozoic: nonflowering seed plants dominate; reptiles (dinosaurs) diversified; first mammals (Megazostrodon); modern insects Cenozoic: mammals diversified; human evolution; primates

14. compare the time occupied by the Precambrian (Hadeon, Archaeon, Proterozoic) to the time occupied by the Phanerozoic. Animals as we know them today were actually evolving in the Phanerozoic Eon, whereas only cells and invertebrates are found in the Precambrian Atmosphere was unlivable for humans in the Precambrian, but became more like the present in the Phanerozoic

15. name the Rockless eon, the Age of Fish, the Age of Amphibians, the Age of Reptiles, the Age of Human Civilization, Age of Gymnosperm Radiation, Angiosperm Radiation. Rockless Eon Hadean Age of Fish Devonian Age of Amphibians Carboniferous Age of Reptiles Permian Age of Human Civilization Neogene Age of Gymnosperm Radiation Triassic Age of Angiosperm Radiation - Cretaceous

16. state when there was a mass extinction of dinosaurs and most other reptiles. End of the Cretaceous Period

17. state when the first mammals appeared. Mesozoic

18. list the three periods in the Mesozoic Era. Triassic Jurassic Cretaceous

19. state the era and period in which modern humans appeared. Cenozoic Era, Neogene Period

20. discuss the theorized causes of mass extinctions in Earths history. Boldies: asteroid that hits Earth and the sun is blocked out, which causes huge climate change; layers of element rarely found on Earth but prominently found on asteroids (iridium) is found in massive quantities in the layers associated with extinctions Continental Drift: plates moving causes extreme climate change Global Warming: no polar ice caps; Permian Extinction

Viruses (Chapter 27) 1. describe the basic structure of animal and plant virus, including the type of nucleic acids found, capsid, nucleocapsid, capsomeres, envelope. Nucleic acid (DNA or RNA, and single or double stranded) surrounded by the capsid, a protein shell that is made up of capsomeres. The combination of the nucleic acid inside the capsid is called the nucleocapsid, which may also by surrounded by a lipid envelope acquired from exiting the host cells.

2. discuss why viruses are not considered to be living entities. They are not made of cells They cannot replicate w/o a host cell Metabolically inactive unless inside host cell

3. list the types of cells that may be infected by viruses. Animal, Plant, Fungi, Protists, and Bacteria

4. list the properties normally used to classify viruses. Structure Size Range Envelope? Type of Nucleic Acid Type of Host Cell

5. list the average size range of viruses. 20 400 nm

6. describe the structure of bacteriophages. Capsid for a head, Tail Sheath neck, and Tail Fibers for legs

7. describe and differentiate between the lytic and lysogenic cycles in viruses. Lytic Cycle: results in the lysing of the cell Lysogenic Cycle: viral DNA is incorporated into the host cell and the host cell replicates, taking with it the viral DNA; later will transition to the lytic cycle

8. name the cause of human genital warts and cervical cancer. HPV Human Papillomavirus

9. discuss the role of reverse transcriptase in Retroviruses. Give an example of a Retrovirus. Allows the retrovirus to turn RNA into DNA, and then integrate that DNA into the host cell HIV and other cancers

10. discuss why cold season starts in late August early September. School Starts: allows for viruses to spread more Lower Humidity: makes the mucus membrane more susceptible to viruses

11. briefly discuss different drugs used to fight viral infections. Basically try to stop viral replication at some stage Possibly through inhibiting reverse transcriptase or protease, preventing viral uncoating, preventing penetration, or preventing DNA replication (Acyclovir)

12. define viroid and prion and give an example of a disease caused by each. Viroid: naked strand of RNA not covered by a capsid; plant diseases Prion: protein molecules with a misshapen structure that somehow causes similar proteins to be misshapen; Mad Cow Disease

13. discuss the MMR immunization. Provides immunity to measles, mumps, and rubella; Maurice Hilleman; 1960s Prokaryotes (Chapter 28) 1. list the two domains containing prokaryotes. Bacteria and Archea

2. state the average size of prokaryotes. 0.2 10 micrometers

3. state the method of reproduction. Binary Fission

4. describe the basic structure of prokaryotes, as well as specialized features. Surrounded by a cell wall, plasma membrane, and a capsule. Fimbrae: small fibers; attached all over Flagella: longer fibers; used for movement Pilus: enable conjugation (passing on of traits)

5. state the major components of bacterial cell walls. Peptidoglycan (chains of sugars linked w/ amino acids)

6. state the function of flagella, cilia, endospores, plasmids, and capsules. Flagella: movement Cilia: movement/sensory Endospores: survival in extreme environments Plasmids: trait transfer (conjugation) Capsules: fools host cell

7. describe the basic shapes of prokaryotes. Spirilla: long, spiral shaped Bacilli: short, almost pill shaped Cocci: small round, bean shaped