Marks Reading Quizzes and Assignments

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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

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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

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Summary of Last Class

• Chemical building blocks of life polymers, long
  chains of similar elements (monomers)
• Amino acids -gt components of protein
• Nucleotides -gt 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

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Feedback

• Most unclear item from last week's readings?

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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

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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)

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Exponential Growth

• Generation 2 (2 cells)

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Exponential Growth

• Generation 3 (4 cells)

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Exponential Growth

• Generation 4 (8 cells)

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Exponential Growth

• Generation 5 (16 cells)

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Exponential Growth

• Generation 6 (32 cells)

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Exponential Growth

• Generation 7 (64 cells)

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Exponential Growth

• Generation 8 (128 cells)

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Exponential Growth

• Generation 9 (256 cells)

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Exponential Growth

• Generation 10 (512 cells)

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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

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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

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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?

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Exponential Growth

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

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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)

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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
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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)

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Virus

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

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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

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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

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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

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Virus

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

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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)

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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)

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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!

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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.

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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
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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

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Photosynthesis

• 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

6 H2O 6 CO2 -gt C6H12O6 6 O2
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Photosynthesis

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

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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

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Photosynthesis
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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

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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

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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

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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.

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Cambrian Explosion

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

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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)

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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

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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'

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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