MAIN POINTS FROM THE TEXTBOOK     for Monday

• review
  • pp. 25-8:  Chemical reactions and Energy
  • p. 30:  Redox Reactions (Activity 2.1 Redox Reactions may help)
  • pp. 32-35:  Water and pH
  • Box 2.2 (p. 36):  Bonds
  • pp. 44-6:  Amino Acids (study details!)
  • pp. 51-3 + fig. 3.11 and Table 3.2:  Proteins (study details!)
  • p. 94:  ATP
• Catalysis:  pp. 52b-55a, Box 3.3 (pp. 56-7), &  Activity 3.1 Activation Energy and Enzymes
• CHECKLIST:  ATP, molecule, covalent bond, hydrogen bond, ionic bond, chemical reaction, chemical equilibrium, reduction/oxidation reactions (redox reactions), reduce, oxidize, energy, potential energy, kinetic energy, thermal energy, chemical energy, entropy, Gibbs free energy, ions, polarity, solvent, specific heat, acids, bases, acid-base reaction, pH, monomer, polymer, polymerization, condensation, hydrolysis, amino acid, amino functional group, carboxyl functional group, R-group, peptide bond, polypeptide, protein, N-terminus, C-terminus, primary structure, hemoglobin, sickle-cell anemia, secondary structure, alpha-helix, beta-pleated sheet, tertiary structure, quaternary structure, catalyst, enzyme, transition state, activation energy (Ea), hydrophobic, hydrophilic
• MONDAY'S QUIZ PREVIEW:
  •  http://wps.prenhall.com/esm_freeman_biosci_1/0,6452,498255-,00.html 
    • summary review #7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 19 
    •  fig. review #1,2, 6,7,8,
    • Content review #1-9; conceptual review #2 & 5; applying #2 
  • http://wps.prenhall.com/esm_freeman_biosci_1/0,6452,498325-,00.html 
    • summary review #2, 3, 7, 8, 9, 10 
    • figure review #2, 3, 4, 5, 6, 7, 8
    • pp. 67-8 Content review #6; conceptual #1, 2, 4
  • and these:  Do exergonic reactions require activation energy?  What molecule most often supplies the energy needed for cellular endergonic reactions?  Can it be recycled?  Is hydrolysis endergonic or exergonic?  Is synthesis of a polymer from monomers endergonic or exergonic?  Is the synthesis of ATP endergonic or exergonic? 
    

WEDNESDAY's assignment

• RNA ribozymes p. 57, pp. 61d-66
• Enzyme regulation example:  pp. 117-8
• other examples shown in class
  • How DO enzymes and ribozymes work?  how are they affected by temperature and pH, and how does this affect critters?
  • Why don't all your enzymes do their thing all the time?  what REALLY happens at the sub-molecular level???
  • You will be expected to explain and give examples of how enzymes are regulated.  Notice that the point is that all the regulators affect the active site in some way, usually by changing its tertiary shape somehow. 
• CHECKLIST: catalyst, enzyme, transition state, activation energy, nucleotide, ribonucleic acid (RNA), hairpin loop, stem-loop structure, RNA world hypothesis, oligonucleotide ("oligo"), ribozyme, RNA replicase, ligation, in-vitro selection
• QUIZ PREVIEW:
  • http://wps.prenhall.com/esm_freeman_biosci_1/0,6452,498325-,00.html 
    • p. 68 Conceptual review #1 (yes, again), 5; Applying ideas #2
    • summary review #12, 17, 18, 19, 20
  • and also see if you can make logical connections of "active site" to each of these: protein primary structure, point mutation,  inhibitor, pH effect, pH optimum, entropy, activation energy, substrate, reactant, product.  
  •  And for the final exam: Show how a mutation of DNA may result in a major defect of a protein; show how minor mutations may actually help the enzyme "adapt" to specialized environmental conditions.

   

ENERGY and ENZYME INTERNET LINKS

• protease http://cti.itc.Virginia.EDU/~cmg/Demo/pdb/ap/ap.htm 
• restriction enzyme http://www.clunet.edu/BioDev/omm/bamh1/molmast.htm 
• symbiosis a trois (including redox chemistry) http://www.nytimes.com/2001/05/22/science/22OBSER-1.html 
• energy conversions (light to molecular "diving board" motion) http://www.washingtonpost.com/wp-dyn/articles/A62712-2002May9.html 
• more LINKS

NOTE:  many of the animations require a CHIME plug-in.  If this plug-in software has not already been installed on your computer, any web site which requires it will link to the download site.  After you download CHIME, you have to re-boot and then click on it in the "MY COMPUTER" window to install it.  The whole process usually takes about 10 minutes.