Biophysics 354
Lecture 1

Introduction

• Course Outline and recommended texts
• Grading policy
• Problems sets
• Exams
• Evolution of the biosphere

  Geological time

  (From Introduction to Evolutionary Biology.)

  
                                                          Millions of years ago
          Preambrian Time
                  Archean Era                             4600-2500
                  Proterozoic Era                         2500-570
          Phanerozoic Time
                  Paleozoic Era
                          Cambrian Period                 570-505
                          Ordovician Period               505-438
                          Silurian Period                 438-408
                          Devonian Period                 408-360
                          Carboniferous Period            360-286
                          Permian Period                  286-245
                  Mesozoic Era
                          Triassic Period                 245-208
                          Jurassic Period                 208-144
                          Cretaceous Period               144-66.4
                  Cenozoic Era
                          Tertiary Period
                                  Paleocene Epoch         66.4-57.8
                                  Eocene Epoch            57.8-38.6
                                  Oligocene Epoch         38.6-23.7
                                  Miocene Epoch           23.7-5.3
                                  Pliocene Epoch          5.3-1.6
                          Quarternary Period
                                  Pleistocene Epoch       1.6-0.01
                                  Holocene Epoch          0.01-0
  

  Universal phylogeny

  
                                                    *** green bacteria
                                              *******
                                              *     *** flavobacteria
                      BACTERIA          *******
                                        *     ********* spirochetes
                            *************
                            *           *         ***** gram negative bacteria
                            *           *  ********
                            *           *  *      ***** purple bacteria
                            *           ****      ***
                            *              *        *** eukaryotic mitochondria
                       ******              *
                       *    *              *       ***** gram positive bacteria 
                       *    *              *********
                       *    *                      ***** cyanobacteria
                       *    *                      **** eukaryotic chloroplasts
          **************    *
          *            *    *************************** deinococci
          *            *
          *            ******************************** thermotagales
          *
       ****
          *     ARCHAEA                 *************** halophiles
          *                    **********
          *                    *        *************** methanogens
          *             ********
          *             *      ************************ methanogens
          *    **********
          *    *        *
          *    *        ******************************* thermophiles
          * ****
          * *  *
          * *  **************************************** thermophiles
          * *
          ***                                      **** choanoflagellates
            *                                  *****
            *    EUKARYOTES                    *   **** animals
            *                            *******
            *                            *     ******** fungi
            *                      *******
            *                      *     ************** plants
            *                  *****
            *                  *   ******************** ciliates
            *            *******
            *            *     ************************ cellular slime molds
            *       ******
            *       *    ****************************** flagellates
            *********
                    *********************************** microsporidia
  
  

  A brief history of the biosphere

  Years ago		Event
  
  4.5 billion		Formation of solar system
  3.8 billion		Oldest rocks in geological record
  3.5 billion		Stromatolites - fossil bacteria (cyanobacteria?)
  2.2 billion		Atmosphere became oxidizing (age of rust layer)
  1.5-2 billion		Eukaryote cell evolved
  0.65-1 billion		First metazoans
  650 million		Trilobites and similar fossils
  250 million		First dinosaurs
  150 million		First mammals
  65 million 		Last disosaurs
  4.5 million		Hominids diverge from apes
  1.5 million		Early man
  10 thousand		Early civilization
  

  • Evolution FAQs
    
    • The Origin of Species (Full text)
      
  • The geological record
  • Three domains of life

• The major cycles of the biosphere
  The biosphere is in a steady state in which the elements which make up living things are circulated through cycles of reactions. Of these, the carbon cycle is the most prominent, but nitrogen, phosphorous, and sulfur cycles are also important. In the synthetic phase, photosynthesis in plants is used to build up complex molecules from simple ones, and in the degradative phase, animals break down complex molecules to their simple oxidized forms by respiration, and bacteria and fungi by fermentation and respiration.

  The input of energy through photosynthesis generates biomass with an energy equivalent 10-30 times that involved in all anthropogenic processes. Since photosynthesis operates with a low efficiency (1-10%), the energy flux through photosynthesis is 100-1000 times all that associated with human activity.

  • Chemical cycles of the Biosphere, a few facts and figures
  • Carbon cycle, Diary of Captain Carbon!
  • Global Carbon cycle
  • Nitrogen cycle
• The role of photosynthesis and bioenergetics in evolution.
  Photosynthetic forms are found in almost all branches of the Bacteria, but in none of the Archaea. In contrast, although the early biosphere was anaerobic, electron transfer enzymes are found in both, and clearly have a common origin. The ATP synthase enzyme, which uses the H⁺ gradient generated by electron transfer to make ATP, also shows strong evidence for a common origin before the separation of the two main prokaryotic branches. It therefore seems likely that both these latter processes, and the chemiosmotic mechanism of energy transduction they catalyze, predate photosynthesis, so that the early stages of evolution were driven by the modest free energy gradients available from anaerobic fermentation, and electron transfer to acceptors other than oxygen. It seems likely that photosynthesis evolved early in the Bacteria, and that the exploitation of light as an energy source drove the diversification of species that led to the separation of the two main branches of the prokaryote world.
• The major metabolic pathways
  • Major metabolic pathways
• Mitochondrial and chloroplasts
  Mitochondrial are thought to have originated from a symbiotic association of a respiratory eubacterium with a fermentative archaeal host. The record of this origin is clear in the DNA and protein synthetic apparatus of the mitochondrion, as the remnants of the apparatus needed for a free living cell. Similarly, the sequences of mitochindrial enzymes show a common origin with those of modern non-sulfur photosynthetic bacteria and the respiratory bacteria which developed from them.

  Similarly, the chloroplast originated from a cyanobacterial symbiont, and the DNA, apparatus for protein sysnthesis, and sequence alignments, show similar evidence of its origin.

  For both mitochondria and chloroplasts, the host cell has taken over much of the task of protein sysnthesis, and this has let to a redistribution of DNA to the nucleus, and the evolution of pathways for a traffic in protein across the membranes of the organelles. Possible advantages to this redistribution are:

  • The host cell takes control of the organelle.
  • The activities of the organelle can be fine-tuned by addition of regulatory subunits.
  • The regulation allows for a better coordination of activities between the host and the organelle.
  • The DNA in the host cell nucleus is protected from damage by free radicals generated by oxidative metabolism, because the repair mechanisms in the nucleus are better than in the organelle.
  • The Virtual Cell
• The eukaryote cell as a mirror of evolution.
  The separate origins of the mitochondria (and chloroplast), and the host cell, are reflected not only in their DNA and protein synthetic apparatus, but also in their metabolic activities. Glycolysis in the cytoplasm reflects the fermentative life-style of the archaeal progenitor of the host; the aerobic metabolism and respiratory chain of the mitochondrion reflects its origin as a respiratory bacterium.
  Click here for an overview of the Tree of Life
  • The Tree of Life Home Page
  • Phylogenetic tree
  • The Ribosome Database Project

Useful Links

• Photosynthesis Tutorial by our own John Cheeseman
• Photosynthesis Hypertextbook
  
• Introduction to reactions of Photosynthesis
  

Carbon cycle and Global Change

• Global Change Program at Iowa State and course synopsis, with links to lectures
• Index to Climate Change Fact Sheets.
• The role of the oceans in carbon exchange
• Oceans and the carbon cycle.
• Plants People & The Environment - Plant Biology 102 from UIUC