MAIN POINTS FROM THE TEXTBOOK

  Waiting for a textbook? 
Ask at the main desk of our library for the Biology 103 folder;
it contains photocopies of the first two and a half chapters.

• For Wednesday (Chapter 2a): chemical bonds
  • Freeman, the textbook author, has a hypothesis he emphasizes throughout the chapter. What is that hypothesis? Be able to explain at least one experiment which could test his hypothesis. Then imagine writing a experiment summary. Overall, do you think his hypothesis should be promoted to a theory?  How does his hypothesis differ from the hypothesis of spontaneous generation?
  • The most important parts for understanding the next few chapters are a review of the basics from high school chemistry;  Freeman (the textbook author) makes the review more interesting by putting the basic facts in the context of the hypothesis he emphasizes throughout the chapter.  It's important to make sure you understand these concepts:  
    • How are electrons involved in biological energy, molecule formation, polarity?
    • What are the parts of an atom, and how are they connected to isotopes and to radiometric dating?
    • Bonds:  compare and contrast three types.  How are bonds connected to polarity and solubility?
    • chemical reactions and energy:  how are they related?  (hint:  electrons...)
    • You need to  understand this information well enough to apply it in upcoming chapters and to answer the kinds of questions a certain nerd will put on the tests. 
    • checklist of terms to know:  electron, proton, neutron, molecule, covalent bond, hydrogen bond, ionic bond, ions, cation, anion, electronegativity, polarity, chemical reaction, reactant, product, reduction/oxidation reactions (redox reactions), reduce, oxidize, energy, potential energy, chemical energy,  isotope, radioactive isotope, radiometric dating, chemical equilibrium, endothermic, exothermic, thermal energy, orbital, electron shell, valence, radioactive decay, half-life,  mass, matter, fossil record, molecular weight, kinetic energy, sound energy, mechanical energy, inorganic compounds, organic molecules,  
  • Preview of Test & Quiz Questions from the textbook and its webpage
    •  content review questions (p. 38) #1*, 9*

    • conceptual review #4, 5

    • applying ideas #2, 3

    • figure review #1

   
• For Friday (Chapter 2b): water and pH
  • It's not enough just to know the stuff on pages 32-37 and the answers to all  the questions in the book. You also need to be able to explain how all of this connects to the beginning of the chapter and to Freeman's hypothesis throughout this chapter.. Then, later, you will have to show how everything you know about electrons and bonds and water and pH explains some of the properties of the molecules in chapter 3, 4, 5, etc.
  • Details which are important:
    • What are the properties (characteristics) of water which make it critical for life (on your planet, at least)? 
    • How does the structure of a water molecule explain its properties?  Activity 2.2 on the CD should help with this part.
    • What happens (on a sub-atomic level) to make molecules acidic or basic?  How does the pH scale work?
    • Checklist (especially try to explain how these concepts are connected to water and pH):  electron, proton, neutron, molecule, covalent bond, hydrogen bond, ionic bond, ions, cation, anion, electronegativity, polarity, solvent, specific heat, acids, bases, acid-base reaction, chemical evolution, molecular formula, structural formula, ball-and-stick model, space-filling model, thermal energy, temperature, heat, Kelvin scale, Celsius scale, Fahrenheit scale 
  • Preview of Test & Quiz Questions:  
    • Review the questions (above) about Freeman's hypothesis.  
    • Also review the other quiz questions assigned for Wednesday, because Friday's quiz will cover all assigned parts of chapter 2.
    • these questions from the textbook and its webpage
      • content review questions (p. 38) #1*,2, 7, 8, 9*

      • conceptual review #2, 4, 5, 6

• textbook webpage
• Links to the computer models used in class can be found at
  http://campus.queens.edu/faculty/jannr/molecular  (click on atoms)
• Try the chemistry/biochemistry sections of these links:
  • on-line biology textbook for another explanation of the same information
  • on-line biology tutorial and review yet another way to see it:  http://www.biology.arizona.edu/biochemistry/tutorials/chemistry/main.html 
• Review:   http://web.jjay.cuny.edu/~acarpi/NSC/index.htm [click on "matter and energy," then keep on clicking (and studying, of course) through "acids and bases."] (this review does not include the details required to make an A; it’s just for making sure you understand the basics).  The "visionlearning" updates sometimes have more information. 
• check out the "solid-liquid-gas" animation near the bottom of this site:  http://www.visionlearning.com/library/science/chemistry-1/CHE1.1-matter.htm 
• If you don't need help, you may want to play with the periodic table:
  •  http://www.webelements.com/webelements/index.html
  • http://www.chemdex.org/index.php?sid=283976226&t=sub_pages&cat=220  
  • or http://www.uky.edu/Projects/Chemcomics/html/silver.html
• Or maybe you would like to learn extra stuff about fossils:  http://campus.queens.edu/faculty/jannr/evolution.htm#FOSSILS 
• More about the Miller Experiment
  • History of the Miller experiment http://www.sciencemag.org/cgi/content/full/300/5620/745
  • New (2003) experiment’s results support the theory of a chemoautotrophic origin of life with a CO-driven, (Fe,Ni)S-dependent primordial metabolism. http://www.sciencemag.org/cgi/content/full/301/5635/938
• If you really understand chapter 2, you will be able to write some electron laws or rules.  When you think you've finished chapter 2, try finishing the unfinished laws on this supplement.

1. What we don't know about water:   "Currently available experimental data cannot account for the atmospheric absorption of sunlight."  " The intensities of the absorption lines are determined by the electric dipole moment surface, which describes the charge distribution in the water molecule as a function of the two O-H bond lengths and the bond angle." http://www.sciencemag.org/cgi/content/full/297/5583/943 
   
2. "The Secret Nature of Hydrogen Bonds," http://www.aip.org/physnews/preview/1999/h-bond/h-bond.htm, is a very technical article on new insights into hydrogen bonds.  The implications are that hydrogen bonds are partly covalent and partly electrostatic.
   "How do hydrogen bonds obtain their double identity? The answer lies with the electrons in the hydrogen bonds.
   Electrons, like all other objects in nature, naturally seek their lowest-energy state. To do this, they minimize their total energy, which includes their energy of motion (kinetic energy). Lowering an electron's kinetic energy means reducing its velocity. A reduced velocity also means a reduced momentum. And whenever an object reduces its momentum, it must spread out in space, according to a quantum mechanical phenomenon known as the Heisenberg Uncertainty Principle. In fact, this "delocalization" effect occurs for electrons in many other situations, not just in hydrogen bonds."
   "Implicit in this quantum mechanical picture is that all objects--even the most solid particles--can act like rippling waves under the right circumstances. These circumstances exist in the water molecule, and the electron waves on the sigma [part of the covalent] and hydrogen bonding sites overlap somewhat. Therefore, these electrons become somewhat indistinguishable and the hydrogen bonds cannot be completely be described as electrostatic bonds. Instead, they take on some of the properties of the highly covalent sigma bonds--and vice versa. However, the extent to which hydrogen bonds were being affected by the sigma bonds has remained controversial and has never been directly tested by experiment--until now."
   
3. Excerpted from the New York Times, 6 Sept 2000
   ("Swiss Physicists Face Decision in Race for Atomic Particle" By JAMES GLANZ; http://www.nytimes.com/2000/09/06/science/06PART.html)
   "... physicists... have been searching for a particle called the Higgs boson,
   which theoretical physicists believe may be the source of all mass in the
   universe — in effect, the reason matter has weight. "
   "For decades, particle physicists have worked out a complex theory, the
   Standard Model, which accounts for the masses of all the known
   particles. It also seems to explain three of the four known forces by
   which particles in the universe interact, or exert forces, on one another.
   Those three are the strong nuclear force, which holds together atomic
   nuclei; the weak nuclear force, which causes radioactive decay; and the
   electromagnetic force, whose effects are familiar from magnets and
   electrically charged rods but which also operates at the subatomic level.
   The force of gravity, described by Einstein's theory of relativity, has not
   been successfully incorporated into the Standard Model.
   For the model to predict the particle masses, it requires the existence of
   one particle unlike any other — the Higgs boson. By filling space with a
   molasseslike field of energy, the Higgs serves as a sort of wellspring of
   mass for other particles. But when those particles are smashed together
   violently enough in particle accelerators, the Higgs should appear as a
   particle itself.
   The precise mass of the Higgs is uncertain. The heavier it is, the more
   powerful the accelerator that will be required to create it in those
   collisions. Most of the excitement at CERN has flowed from signals
   indicating that three Higgs bosons may have been captured in one of the
   big particle detectors at an energy of 115 billion electron volts. The mass
   of a hydrogen atom, expressed in those units, is 1 billion electron volts.
   But the signals could simply be statistical flukes, and more data could
   confirm the signal or wipe it out."
   

Anaerobic oxidation of methane as documented (2002) in the Black Sea may have some bearing on Freeman's ideas about chemical evolution (but the article is too technical for most undergraduates):  http://www.sciencemag.org/cgi/content/full/297/5583/1013 (access from library terminals)