The Chemical Foundations of Life

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. Electrones Electrons can be seen (much larger than they should be) orbiting around the nucleus. The Chemical Foundations of Life Here we can see the nucleus with protons and neutrons. Neutrones Protones 1/10000

5. —18 electrons

6. (a) 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) Energy absorbed Second energy level (shell) First energy level (shell) Energy lost Atomic nucleus (b) 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. Figure 2.7 Energy levels of an atom’s electrons

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

8. Electron orbitals. Each orbital holds up to two electrons. x Y Z 1s orbital 2s orbital Three 2p orbitals 1s, 2s, and 2p orbitals Electron-shell diagrams. Each shell is shown with its maximum number of electrons, grouped in pairs. (b) Second shell (maximum 8 electrons) (a) First shell (maximum 2 electrons) (c) Neon, with two filled shells (10 electrons) Figure 2.9 Electron orbitals

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. Hydrogen atoms (2 H) In each hydrogen atom, the single electron is held in its orbital by its attraction to the proton in the nucleus. + + 1 2 3 When two hydrogen atoms approach each other, the electron of each atom is also attracted to the proton in the other nucleus. + + The two electrons become shared in a covalent bond, forming an H2 molecule. + + Hydrogen molecule (H2) Figure 2.10 Formation of a covalent bond

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

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

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

16. Figure 2.14 A sodium chloride crystal Na+ Cl–

17. Hydrogen bonds Van der Waals interactions Ionic interactions Hydrophobic interactions Weak Chemical Bonds

18. – + H Water (H2O) O 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. H + – Ammonia (NH3) N H H d+ + H + Figure 2.15 A hydrogen bond

19. Unnumbered Figure p. 42

20. Hybrid-orbital model (with ball-and-stick model superimposed) Ball-and-stick model Space-filling model Unbonded Electron pair O O H H H H 104.5° Water (H2O) H H C C 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 H H Methane (CH4)

21. Figure 2.17 A molecular mimic Nitrogen Carbon Hydrogen Sulfur Oxygen Natural endorphin Morphine (a) Structures of endorphin and morphine. The boxed portion of the endorphin molecule (left) binds toreceptor molecules on target cells in the brain. The boxed portion of the morphine molecule is a close match. Natural endorphin Morphine Endorphin receptors Brain cell (b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell recognize and can bind to both endorphin and morphine.

22. Unnumbered pg. 44 + 2 H2 + O2 2 H2O Reactants Reaction Products 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. Figure 3.3 Water transport in plants Water conducting cells 100 µm

28. Figure 3.4 Walking on water

29. Hydrogen bond Ice Hydrogen bonds are stable Liquid water Hydrogen bonds constantly break and re-form Figure 3.5 Ice: crystalline structure and floating barrier

33. H2O + H2O  OH– + H3O+ • hydroxide • ion • H2O  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 log10 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 CO2 + H2O  H2CO3  H+ + HCO3 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. Biological Molecules Small and Large The hydrocarbon skeleton provides a basic framework: Figure 3-3 Saturated vs. unsaturated

40. H H H H H (a) Length H H H C C C C H C H H H H H Ethane Propane H C H H H H H H H H (b) Branching H H H H C C C C C C C H H H H H H H 2-methylpropane (commonly called isobutane) Butane H H H H H H H H (c) Double bonds H H H H C C C C C C C C H H H H 1-Butene 2-Butene H H H H C H H C H C C H H C (d) Rings C H H C C H H C C C H H C H H H Cyclohexane Benzene Figure 4.5 Variations in carbon skeletons

41. H C H H C H H H H H H H H H (a) Structural isomers C C C C C C H H C H C H H H H H H H H H X X H X (b) Geometric isomers C C C C X H H H CO2H CO2H C C (c) Enantiomers H H NH2 NH2 CH3 CH3 L isomer D isomer Figure 4.7 Three types of isomers

42. Figure 4.8 The pharmacological importance of enantiomers L-Dopa (effective against Parkinson’s disease) D-Dopa (biologically inactive)

43. OH CH3 Estradiol HO Female lion OH CH3 CH3 O Testosterone Male lion Figure 4.9 A comparison of functional groups of female (estradiol) and male (testosterone) sex hormones

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 O H O–