1. The Chemical Foundations of Life

3. Element vs. molecule Ionic bond vs. covalent bond Polar vs. nonpolar Hydrogen bond vs. van der Waals force Hydrophilic vs. hydrophobic vs. amphipathic Water – cohesion vs. adhesion solvent vs. solute acid vs. base vs. buffer

4. The Chemical Foundations of Life Here we can see the nucleus with protons and neutrons. 1/10000 質子中子 Electrons can be seen (much larger than they should be) orbiting around the nucleus. 電子

5. —18 electrons

6. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 2.7 Energy levels of an atom’s electrons A ball bouncing down a flight of stairs provides an analogy for energy levels of electrons, because the ball can only rest on each step, not between steps. Third energy level (shell) (a) Second energy level (shell) First energy level (shell) Energy absorbed Energy lost An electron can move from one level to another only if the energy it gains or loses is exactly equal to the difference in energy between the two levels. Arrows indicate some of the step-wise changes in potential energy that are possible. (b) Atomic nucleus

7. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Second shell Helium 2 He First shell Third shell Hydrogen 1 H 2 He 4.00 Atomic mass Atomic number Element symbol Electron-shell diagram Lithium 3 Li Beryllium 4 Be Boron 3 B Carbon 6 C Nitrogen 7 N Oxygen 8 O Fluorine 9 F Neon 10 Ne Sodium 11 Na Magnesium 12 Mg Aluminum 13 Al Silicon 14 Si Phosphorus 15 P Sulfur 16 S Chlorine 17 Cl Argon 18 Ar Figure 2.8 Electron-shell diagrams of the first 18 elements in the periodic table

8. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 2.9 Electron orbitals Electron orbitals. Each orbital holds up to two electrons. 1s orbital2s orbitalThree 2p orbitals1s, 2s, and 2p orbitals (a) First shell (maximum 2 electrons) (b) Second shell (maximum 8 electrons) (c) Neon, with two filled shells (10 electrons) Electron-shell diagrams. Each shell is shown with its maximum number of electrons, grouped in pairs. x Z Y

9. Element vs. molecule Ionic bond vs. covalent bond Polar vs. nonpolar Hydrogen bond vs. van der Waals force Hydrophilic vs. hydrophobic vs. amphipathic Water – cohesion vs. adhesion solvent vs. solute acid vs. base vs. buffer

10. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 2.10 Formation of a covalent bond Hydrogen atoms (2 H) Hydrogen molecule (H 2 ) 1 In each hydrogen atom, the single electron is held in its orbital by its attraction to the proton in the nucleus. When two hydrogen atoms approach each other, the electron of each atom is also attracted to the proton in the other nucleus. 2 The two electrons become shared in a covalent bond, forming an H 2 molecule. 3 + + + + ++

11. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Second shell Helium 2 He First shell Third shell Hydrogen 1 H 2 He 4.00 Atomic mass Atomic number Element symbol Electron-shell diagram Lithium 3 Li Beryllium 4 Be Boron 3 B Carbon 6 C Nitrogen 7 N Oxygen 8 O Fluorine 9 F Neon 10 Ne Sodium 11 Na Magnesium 12 Mg Aluminum 13 Al Silicon 14 Si Phosphorus 15 P Sulfur 16 S Chlorine 17 Cl Argon 18 Ar Figure 2.8 Electron-shell diagrams of the first 18 elements in the periodic table

12. electronegativity

13. Element vs. molecule Ionic bond vs. covalent bond Polar vs. nonpolar Hydrogen bond vs. van der Waals force Hydrophilic vs. hydrophobic vs. amphipathic Water – cohesion vs. adhesion solvent vs. solute acid vs. base vs. buffer

14. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Second shell Helium 2 He First shell Third shell Hydrogen 1 H 2 He 4.00 Atomic mass Atomic number Element symbol Electron-shell diagram Lithium 3 Li Beryllium 4 Be Boron 3 B Carbon 6 C Nitrogen 7 N Oxygen 8 O Fluorine 9 F Neon 10 Ne Sodium 11 Na Magnesium 12 Mg Aluminum 13 Al Silicon 14 Si Phosphorus 15 P Sulfur 16 S Chlorine 17 Cl Argon 18 Ar Figure 2.8 Electron-shell diagrams of the first 18 elements in the periodic table

15. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 2.13 Electron transfer and ionic bonding Cl – Chloride ion (an anion) – The lone valence electron of a sodium atom is transferred to join the 7 valence electrons of a chlorine atom. 1 Each resulting ion has a completed valence shell. An ionic bond can form between the oppositely charged ions. 2 Na Cl + Na Sodium atom (an uncharged atom) Cl Chlorine atom (an uncharged atom) Na + Sodium on (a cation) Sodium chloride (NaCl)

16. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 2.14 A sodium chloride crystal Na + Cl –

17. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Weak Chemical Bonds Hydrogen bonds Van der Waals interactions Ionic interactions Hydrophobic interactions

18. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 2.15 A hydrogen bond Water (H 2 O) Ammonia (NH 3 ) –– ++ O H H ++ –– N H H H A hydrogen bond results from the attraction between the partial positive charge on the hydrogen atom of water and the partial negative charge on the nitrogen atom of ammonia. ++ ++ ++

19. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Unnumbered Figure p. 42

20. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Space-filling model Hybrid-orbital model (with ball-and-stick model superimposed) Unbonded Electron pair 104.5° O H Water (H 2 O) Methane (CH 4 ) H H H H C O H H H C Ball-and-stick model H H H H (b) Molecular shape models. Three models representing molecular shape are shown for two examples; water and methane. The positions of the hybrid orbital determine the shapes of the molecules

21. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 2.17 A molecular mimic Morphine Carbon Hydrogen Nitrogen Sulfur Oxygen Natural endorphin (a) Structures of endorphin and morphine. The boxed portion of the endorphin molecule (left) binds to receptor molecules on target cells in the brain. The boxed portion of the morphine molecule is a close match. (b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell recognize and can bind to both endorphin and morphine. Natural endorphin Endorphin receptors Morphine Brain cell

22. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Unnumbered pg. 44 ReactantsReactionProducts 2 H 2 + + O2O2 2 H 2 O Chemical Equilibrium

23. Element vs. molecule Ionic bond vs. covalent bond Polar vs. nonpolar Hydrogen bond vs. van der Waals force Hydrophilic vs. hydrophobic vs. amphipathic Water – cohesion vs. adhesion solvent vs. solute acid vs. base vs. buffer

25. Element vs. molecule Ionic bond vs. covalent bond Polar vs. nonpolar Hydrogen bond vs. van der Waals force Hydrophilic vs. hydrophobic vs. amphipathic Water – cohesion vs. adhesion solvent vs. solute acid vs. base vs. buffer

27. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 3.3 Water transport in plants Water conducting cells 100 µ m

28. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 3.4 Walking on water

29. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 3.5 Ice: crystalline structure and floating barrier Liquid water Hydrogen bonds constantly break and re-form Ice Hydrogen bonds are stable Hydrogen bond

33. H 2 O + H 2 O  OH – + H 3 O + hydroxide ion H 2 O  H + + OH – hydrogen ion or proton Chemical Equilibrium pH ＝ – log [H + ] acidic pH < 7 basic pH > 7

34. The Chemical Foundations of Life The pH scale is the log 10 of the hydrogen ion concentration in a solution. Water is considered a reference or neutral point with a pH of 7.0. Figure 2-20

35. Buffer CO 2 + H 2 O  H 2 CO 3  H + + HCO 3  Carbon dioxide carbonic acid bicarbonate ion

36. Element vs. molecule Ionic bond vs. covalent bond Polar vs. nonpolar Hydrogen bond vs. van der Waals force Hydrophilic vs. hydrophobic vs. amphipathic Water – cohesion vs. adhesion solvent vs. solute acid vs. base vs. buffer

37. Carbon- the Backbone of Biological Molecules

39. The hydrocarbon skeleton provides a basic framework: Biological Molecules Small and Large Figure 3-3 Saturated vs. unsaturated

40. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 4.5 Variations in carbon skeletons H HH H H C HH HHH H H H H H H H H H H H HHH H H H H H H H H H H H H H H HH HH HH HH HHH H H H HH H H H H H H H C C CCC CCCCCCC CCCCCCCC C C C C C C C C C C C C H H H H H H H (a) Length (b) Branching (c) Double bonds (d) Rings Ethane Propane Butane 2-methylpropane (commonly called isobutane) 1-Butene2-Butene CyclohexaneBenzene

41. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 4.7 Three types of isomers H H H H H H H H H H CO 2 H CH 3 NH 2 C CO 2 H H CH 3 NH 2 XX X X H H HH H H H H HH H C CCCC HH C H H H H H C C C C C C C C C (a) Structural isomers (b) Geometric isomers (c) Enantiomers H L isomerD isomer

42. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 4.8 The pharmacological importance of enantiomers L-Dopa (effective against Parkinson’s disease) D-Dopa (biologically inactive)

43. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 4.9 A comparison of functional groups of female (estradiol) and male (testosterone) sex hormones CH 3 OH HO O CH 3 OH Estradiol Testosterone Female lion Male lion

45. Functional Groups Hydroxyl group R-OH Carbonyl group R-C-H (or R) Carboxyl group R-C Amino group R-N Sulfhydryl group R-SH Phosphate group R-O-P-O – O O OH H H O O–O–