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Marks – Reading Quizzes and Assignments

Marks – Reading Quizzes and Assignments. Reading Quiz: 0 NCR, 4 NCR+, 7 CR, 8 CR+, 0 CR++ Assignments: 0 NCR, 0 NCR+, 2 CR, 15 CR+, 0 CR++. Missed Assignments, Quizzes. Put answers up on web page as soon as possible Can't accept late assignments

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Marks – Reading Quizzes and Assignments

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  1. Marks – Reading Quizzes and Assignments • Reading Quiz: • 0 NCR, 4 NCR+, 7 CR, 8 CR+, 0 CR++ • Assignments: • 0 NCR, 0 NCR+, 2 CR, 15 CR+, 0 CR++

  2. Missed Assignments, Quizzes • Put answers up on web page as soon as possible • Can't accept late assignments • Will accept short (~1 page) writeups for 2 points on • Items in the news • Project topics

  3. Summary of Last Class • Chemical building blocks of life: polymers, long chains of similar elements (monomers) • Amino acids -> components of protein • Nucleotides -> components of DNA, RNA • DNA: storehouse of genetic information • RNA: translates DNA to protein • Protein: molecular machines • Amino acids seem to form quite easily in Hydrogen-rich environment: Urey-Miller experiment

  4. Feedback: • Most unclear item from last week's readings?

  5. What we're going to cover today • From Biochemistry to Biology • Exponential Growth • Phylogenic Trees • Viruses • Prokaryotes • Archaebacteria • Bacteria • Photosynthesis • Eukaryotes • Sexual Reproduction • Biological Complexity • Web of Life

  6. Exponential Growth • In processes involving self-replication (like life), exponential growth naturally arises • Effects all facets of growth • Imagine a `cell' that divides every generation (or that has two children, and then then parent dies) • Generation 1 (1 cell)

  7. Exponential Growth • Generation 2 (2 cells)

  8. Exponential Growth • Generation 3 (4 cells)

  9. Exponential Growth • Generation 4 (8 cells)

  10. Exponential Growth • Generation 5 (16 cells)

  11. Exponential Growth • Generation 6 (32 cells)

  12. Exponential Growth • Generation 7 (64 cells)

  13. Exponential Growth • Generation 8 (128 cells)

  14. Exponential Growth • Generation 9 (256 cells)

  15. Exponential Growth • Generation 10 (512 cells)

  16. Exponential Growth • Such growth is said to be exponential, or geometric. • Once the process is exponential, everything is exponential: • Number of children • Number of reproductions • Amount of area/resources needed • Rate of growth • Anything with a fixed `doubling time' is exponential

  17. Exponential Growth • This exponential growth is the source of the intense competition for resources underlying evolutionary adaptation • Very soon, resources begin getting scarce; any species or mutation which has an advantge has a much better chance of thriving

  18. Exponential Growth • Everything starts happening faster as exponential growth proceeds • Mutation rate; in mammals, ~1 per 100,000 reproductions per gene • By generation 10, ~512 individuals. How long before significant number of mutations expected in a given gene?

  19. Exponential Growth • Everything is exponential • By generation 20, already expect ~20 mutations • That too is exponentially increasing • By generation 25, > 600 • By generation 30, > 20000 • Dividing by 100,000 just means it takes a little longer before it takes off

  20. Tree of Life • Phylogenetic tree • `Family Tree' of species • Distance from neighbors, root indicates how genetically different • Three distinct branches: • Archaea (includes `extremophiles) • Bacteria • Eukaryotes (includes all life visible to naked eye)

  21. Building a Phylogenetic Tree • Difficult: Only have genetic information from the present. • Can take genetic informtion from present day species and examine differences • Number of differences in genome: `genetic distance' • Simplest: if constant mutation rate, can work backwards and see how long ago two species must have first differed • Can infer most recent common ancestor Inferred ancestor Inferred ancestor Evolution Time Genetic Distance

  22. Virus • Not Included • Self-replicating DNA or RNA • Not self sufficient • Requires the mechanisms of a living cell to propagate it • As a result, much smaller than bacteria (largest virus ~ smallest bacteria)

  23. Virus • Propagates by latching onto target cell • Virus usually has `spikes' on its outer coating which allow it to target particular sorts of cells

  24. Virus • Propagates by latching onto target cell • Virus usually has `spikes' on its outer coating which allow it to target particular sorts of cells • Inserts its own genetic information (DNA, or RNA) into cell

  25. Virus • Propagates by latching onto target cell • Virus usually has `spikes' on its outer coating which allow it to target particular sorts of cells • Inserts its own genetic information (DNA, or RNA) into cell • Cells machinery begins processing this genetic information as if it was its own • Replicates copies of virus

  26. Virus • Propagates by latching onto target cell • Virus usually has `spikes' on its outer coating which allow it to target particular sorts of cells • Inserts its own genetic information (DNA, or RNA) into cell • Cells machinery begins processing this genetic information as if it was its own • Replicates copies of virus • Eventually cell dies, new copies of virus escape

  27. Virus • Alive? • Inert RNA/DNA/protein until collides with target cell • Incapable of independent action, growth, reproduction • Not generally considered to be living.

  28. Prokaryotes • Simplest form of life • Includes bacteria (like E. Coli) and archaebacteria • No complex internal structure • DNA lies together in a blob • Prokaryotic DNA consists of one ring • Processes occur throughout cell • Many reproduce by cell division (asexual)

  29. Prokaryotes • Among the earliest forms of life • Earliest fossils: ~2.5 BYA • Evidence for life before that: biomarkers • Differences in isotopic abundances in Oxygen, sulfur • Increase in Oxygen • Microbes can leave `compression' fossils, or leave more detailed fossils in very fine silt • Here see fossils of algae, and modern algae (round things)

  30. Stromatalites • `Mat' of cyanobacteria (blue-green algae) • Photosynthesis • Produce oxygen, lime, gel-like secretion • Gel protects them from UV • Gel traps sand • Layers form as new generations `born' • Rare now, but still found in parts of Australia • Species remains nearly unchanged for ~ 3 BY!

  31. Prokaryotes • Consist of Bacteria, and the more ancient Archaebacteria • Archaea: Carle Woese, U. of Illinois • Differences between the two: wall, membrane structures; metabolism • Many of the `extremophiles' are in domain Archaea.

  32. Extremophiles • Unlike more `advanced' forms of life, prokaryotes thrive in startling variety of environments • Can live with, without, or only without oxygen • Can live in very acidic, alkaline, hot, cold, dark, or salty enviroments • Early earth would have been rich with these enviroments M. Jannaschii thrives near underwater volcanic vents in temperatures, pressures, darkness, and lack of oxygen that would kill other life

  33. Need For Oxygen • Existance of life with varying tolerances for oxygen is consistant with our picture of early Earth: • No free oxygen at start (tied up in CO2, water) • Oxygen-intolerant life • Photosynthesis generated more and more oxygen • Oxygen-ambivalent life • Finally enough oxygen that some species could reliably depend on it

  34. Photosynthesis 6 H2O + 6 CO2 -> C6H12O6 + 6 O2 • A process that uses light energy to convert water, carbon dioxide to sugar (a useful fuel) plus oxygen • Clorophyll is the key molecule in this process • Absorbs some light, triggers a chemical reaction

  35. Photosynthesis • Suggestively, Clorophyll absorbs mainly in blue/green region of spectrum • Shorter wavelength -> more energy, but is easily absorbed by water • Photosynthesis powered by green light can happen much deeper underwater

  36. Photosynthesis • Plants have specialized cell units (chloroplasts) which are dedicated to the process of photosynthesis • In prokaryotes, process happens throughout cell • Cholorophyll lives in the thylkoid

  37. Photosynthesis

  38. Xtreme Photosynthesis • Green sulfur bacteria can photosynthesize with very little oxygen or light around • Photosynthesize Sulfur using Hydrogen Sulfide instead of water • Spit out Sulfur instead of Oxygen • Can even occur using infrared, instead of green light • These conditions make it ideal for living near volcanic vents • Lots of sulfur • Not so much light

  39. Eukaryotes • Has a nucleus, and other `organelles’ • DIVISION OF LABOUR • Mitocondrion: energy factory • Chloroplast (plants): photosynthesis • Nucleus: protects DNA; interface between DNA and rest of cell

  40. Eukaryotes • Because of increased complexity, greatly increased genetic information • ~100-1000x DNA of prokaryote • Has to describe all of the increased structure in cell • May reproduce sexually or asexually

  41. Sexual Reproduction • Allows greater mixing of genes • Rather than waiting for single mutation, can have combination of genes randomly generated • Greatly speeds up evolutionary process for complex organisms where genes interact.

  42. Cambrian Explosion • Soon after the arrival of eukaryotes on the scene, there was a huge explosion of species • Cambrian Explosion • Exponential growth -> one expects this, but before sexual reproduction, evolution occurred much more slowly

  43. Multicellular life • Development of cells that already divided labour allowed for the next step • Multi-cellular life • Most mammals -- trillions or tens of trillions of cells, all interdependant • Once cell was used to relying on one organelle for some job, can `learn’ to rely on another cell entirely to do job • Once this occurred, the possible combinations of life forms skyrocketed (Cambrian Explosion)

  44. Multicellular life • So many possibilities that they never appear to repeat • Trilobite, an enormously successful multicellular animal, thrived for tens of millions of years; extinct with dinasaurs • Never to reappear • On the other hand, a successful species can survive indefinately (?) • Blue-Green Algae

  45. Summary • Prokaryotes: Very simple, no nucleus/organelles, wide variety of enviroments • Eukaryotes: `Division of labour' in cell. Possibly originated with early symbiosis. Much more DNA because of increased complexity • Eukaryotic life allowed multi-cellular life • Cambrian Explosion • Mutations • Sexual Reproduction speeds evolution • Species don't repeat • Intelligence...? • `Web of life'

  46. Next Week • Half way mark • No reading quiz • Review of first half of class: Parts 1, 2, 3 of textbook • Large assignment on first half of class

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