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Chapter1

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Chapter1

  1. 1. Life, Chemistry, and Water Chapter 2
  2. 2. Why It Matters <ul><li>Bioremediation of selenium </li></ul>Fig. 2-1, p. 22
  3. 3. 2.1 The Organization of Matter: Elements and Atoms <ul><li>Living organisms are composed of about 25 key elements </li></ul><ul><li>Elements are composed of atoms, which combine to form molecules </li></ul>
  4. 4. Matter <ul><li>Matter occupies space, has mass, is composed of elements </li></ul><ul><li>Elements cannot be broken down into simpler substances </li></ul><ul><ul><li>92 naturally-occurring elements </li></ul></ul><ul><ul><li>15+ artificially-synthesized elements </li></ul></ul>
  5. 5. 25 Key Elements in Living Organisms <ul><li>96% of the weight of living organisms = carbon, hydrogen, oxygen, and nitrogen </li></ul><ul><li>4% = calcium, phosphorus, potassium, sulfur, sodium, chlorine, and magnesium </li></ul><ul><li>0.01% = nine trace elements vital to biological functions </li></ul>
  6. 6. Proportions of Elements Fig. 2-2, p. 23
  7. 7. Atoms and Molecules <ul><li>Atoms </li></ul><ul><ul><li>Smallest units of elements </li></ul></ul><ul><li>Molecules </li></ul><ul><ul><li>Formed from atoms </li></ul></ul><ul><ul><li>Combined in fixed numbers and ratios </li></ul></ul><ul><li>Compounds </li></ul><ul><ul><li>Molecules with different component atoms </li></ul></ul>
  8. 8. 2.2 Atomic Structure <ul><li>The atomic nucleus contains protons and neutrons </li></ul><ul><li>The nuclei of some atoms are unstable and tend to break down to form simpler atoms </li></ul><ul><li>The electrons of an atom occupy orbitals around the nucleus </li></ul>
  9. 9. 2.2 (cont.) <ul><li>Orbitals occur in discrete layers around an atomic nucleus </li></ul><ul><li>The number of electrons in the outermost energy level of an atom determines its chemical activity </li></ul>
  10. 10. Atomic Structure <ul><li>Atomic nucleus contains protons and neutrons </li></ul><ul><li>Electrons travel around nucleus in orbitals </li></ul>Fig. 2-3, p. 24
  11. 11. Animation: Electron arrangements in atoms
  12. 12. Atomic Nucleus <ul><li>Protons </li></ul><ul><ul><li>Positively charged </li></ul></ul><ul><li>Atomic number </li></ul><ul><ul><li>Number of protons in an element </li></ul></ul><ul><li>Neutrons </li></ul><ul><ul><li>Uncharged </li></ul></ul>
  13. 13. Atomic Mass <ul><li>Atomic mass = mass of protons + neutrons (electrons have insignificant mass) </li></ul><ul><ul><li>Proton = 1 dalton = 1.66 X 10 -24 grams </li></ul></ul><ul><ul><li>Neutron = 1 dalton </li></ul></ul>
  14. 14. Isotopes <ul><li>Atoms of an element with differing numbers of neutrons </li></ul><ul><li>Differ in physical but not chemical properties </li></ul>Fig. 2-4, p. 24
  15. 15. Fig. 2-4a, p. 24 3 H (tritium) 1 proton 2 neutrons atomic number = 1 mass number = 3 Isotopes of hydrogen 1 H 1 proton atomic number = 1 mass number = 1 2 H (deuterium) 1 proton 1 neutron atomic number = 1 mass number = 2
  16. 16. Fig. 2-4b, p. 24 Isotopes of carbon 12 C 6 protons 6 neutrons atomic number = 6 mass number = 12 13 C 6 protons 7 neutrons atomic number = 6 mass number = 13 14 C 6 protons 8 neutrons atomic number = 6 mass number = 14
  17. 17. Animation: Isotopes of hydrogen
  18. 18. Radioisotopes <ul><li>Some isotope nuclei are unstable and break down (decay) </li></ul><ul><ul><li>Release particles of matter and energy ( radioactivity ) </li></ul></ul><ul><li>Radioisotopes decay at a steady rate </li></ul><ul><ul><li>Used to estimate the age of organic material, rocks, fossils </li></ul></ul><ul><ul><li>Used as tracers to label molecules in chemical reactions </li></ul></ul>
  19. 19. Electrons <ul><li>Electron are negatively charged </li></ul><ul><li>Number of electrons = number of protons </li></ul><ul><li>Electron mass = 1/1800 dalton </li></ul>
  20. 20. Electron Orbitals <ul><li>Electrons are found in regions of space called energy levels ( shells ) </li></ul><ul><li>Within each energy level, electrons are grouped into electron orbitals </li></ul>
  21. 21. Electron Orbitals <ul><li>1 s = lowest energy level </li></ul><ul><ul><li>1 = closest to the nucleus </li></ul></ul><ul><ul><li>s = spherical shape </li></ul></ul><ul><ul><li>Holds up to 2 electrons </li></ul></ul>
  22. 22. Electron Orbitals <ul><li>Second energy level </li></ul><ul><ul><li>One 2 s orbital (spherical shape, up to 2 electrons) </li></ul></ul><ul><ul><li>Three 2 p orbitals (dumbbell shape, up to 2 electrons in each) </li></ul></ul>
  23. 23. Electrons Orbitals <ul><li>Neon atom = 10 electron </li></ul>
  24. 24. Animation: The shell model of electron distribution
  25. 25. Electron Orbitals <ul><li>Third energy level </li></ul><ul><ul><li>Up to 18 electrons in 9 orbitals </li></ul></ul><ul><li>Fourth energy level </li></ul><ul><ul><li>Up to 32 electrons in 16 orbitals </li></ul></ul><ul><li>Outermost orbital typically has 1 to 8 electrons in 4 orbitals ( valence electrons ) </li></ul>
  26. 26. Electron Orbitals Fig. 2-6, p. 27
  27. 27. Fig. 2-6, p. 27 Hydrogen (H) First energy level Neon (Ne) Lithium (Li) Beryllium (Be) Boron (B) Carbon (C) Nitrogen (N) Oxygen (O) Fluorine (F) Second energy level Third energy level Argon (Ar) Sodium (Na) Magnesium (Mg) Aluminum (Al) Silicon (Si) Phosphorus (P) Sulfur (S) Chlorine (Cl) Helium (He) Energy level 1 Energy level 2 Energy level 3 Elements not found Amount in living organisms Common elements Trace elements Number of electrons in energy levels Atomic number Number of electrons ( e – ) Number of protons ( p + )
  28. 28. Animation: Predicting the number of bonds of elements
  29. 29. Valence Electrons <ul><li>If outermost energy level filled, atoms are stable and unreactive </li></ul><ul><li>Atoms tend to lose, gain, or share electrons to fill the outermost energy level </li></ul><ul><li>Leads to chemical bonds and forces that hold atoms together in a molecule </li></ul>
  30. 30. 2.3 Chemical Bonds <ul><li>Ionic bonds are multidirectional and vary in strength </li></ul><ul><li>Covalent bonds are formed by electrons in shared orbitals </li></ul><ul><li>Unequal electron sharing results in polarity </li></ul><ul><li>Polar molecules tend to associate with each other and exclude nonpolar molecules </li></ul>
  31. 31. 2.3 (cont.) <ul><li>Hydrogen bonds also involve unequal electron sharing </li></ul><ul><li>Van der Waals forces are weak attractions over very short distances </li></ul><ul><li>Bonds form and break in chemical reactions </li></ul>
  32. 32. Ions (1) <ul><li>Charged atoms </li></ul><ul><ul><li>Cation: Positively charged ion </li></ul></ul><ul><ul><li>Anion: Negatively charged ion </li></ul></ul><ul><li>Ionic Bond </li></ul><ul><ul><li>Forms between atoms that gain or lose valence electrons completely </li></ul></ul>
  33. 33. Ions (2) <ul><li>One atom loses an electron and becomes positively charged </li></ul><ul><ul><li>Na + :11 protons + 10 electrons </li></ul></ul><ul><li>One atom gains an electron and becomes negatively charged </li></ul><ul><ul><li>Cl – :17 protons + 18 electrons </li></ul></ul>
  34. 34. Ionic Bond Fig. 2-7, p. 28
  35. 35. Fig. 2-7a, p. 28 a. Ionic bond formation between sodium and chlorine Cl – Electron loss Electron gain Sodium atom 11 e – 11 p + Na Sodium ion 10 e – 11 p + Na + Chlorine atom 17 e – 17 p + Chlorine ion 18 e – 17 p + Cl
  36. 36. Fig. 2-7a, p. 28 Stepped Art Cl – Sodium ion 10 e – 11 p + Na + Chlorine ion 18 e – 17 p + Electron loss Electron gain Sodium atom 11 e – 11 p + Na Chlorine atom 17 e – 17 p + Cl
  37. 37. Fig. 2-7b, p. 28 b. Crystals of sodium chloride (NaCl) Cl – Na +
  38. 38. Ionic Bond <ul><li>Exerts attractive force over greater distance than other bonds </li></ul><ul><li>Attractive force extends in all directions </li></ul><ul><li>Varies in strength depending on presence of other charged substances </li></ul>
  39. 39. Covalent Bond <ul><li>Two atoms share a pair of electrons </li></ul><ul><li>Shared orbitals occur at discrete angles and directions </li></ul>
  40. 40. Covalent Bonds Fig. 2-8, p. 30
  41. 41. Fig. 2-8a, p. 30 a. Shared orbitals of methane (CH 4 )
  42. 42. Fig. 2-8b, p. 30 b. Space-filling model of methane
  43. 43. Fig. 2-8c, p. 30 c. A carbon “building block” used to make molecular models
  44. 44. Fig. 2-8d, p. 30 d. Cholesterol Hydrogen Carbon Oxygen
  45. 45. Animation: How atoms bond
  46. 46. Unequal Electron Sharing <ul><li>Electronegativity </li></ul><ul><ul><li>Measure of atom’s attractions for electrons shared in a chemical bond </li></ul></ul><ul><li>Nonpolar covalent bond </li></ul><ul><ul><li>Electrons shared equally </li></ul></ul><ul><li>Polar covalent bond </li></ul><ul><ul><li>Electrons shared unequally </li></ul></ul>
  47. 47. Unequal Electron Sharing <ul><li>Water is a polar molecule </li></ul>Fig. 2-9, p. 30
  48. 48. Polar Molecules <ul><li>Tend to associate with other polar molecules and to exclude nonpolar molecules </li></ul><ul><li>Polar molecules that associate readily with water are hydrophilic (“water preferring”) </li></ul><ul><li>Nonpolar molecules excluded by water are hydrophobic (“water avoiding”) </li></ul>
  49. 49. Hydrogen Bond <ul><li>Unequal electron sharing between a hydrogen atom and another atom (oxygen, nitrogen, sulfur) </li></ul><ul><ul><li>Hydrogen gets partial positive charge, other atom gets partial negative charge </li></ul></ul><ul><ul><li>Charges attract to form hydrogen bond </li></ul></ul>
  50. 50. Hydrogen Bond <ul><li>Weak bond, useful in stabilizing large biological molecules such as proteins </li></ul>
  51. 51. Van der Waals Forces <ul><li>Natural changes in electron density of molecules </li></ul><ul><li>Regions of positive and negative charge </li></ul><ul><ul><li>Cause molecules to stick together briefly </li></ul></ul><ul><li>Weaker than hydrogen bonds </li></ul><ul><ul><li>Help stabilize large biological molecules such as proteins </li></ul></ul>
  52. 52. Van der Waals Forces <ul><li>Gecko toes: </li></ul>Fig. 2-11, p. 32
  53. 53. Fig. 2-11, p. 32 d. Pads on a seta a. Gecko inverted on glass b. Gecko toe c. Setae on toe
  54. 54. Chemical Reactions <ul><li>When molecules form or break chemical bonds </li></ul><ul><li>Reactants enter into a chemical reaction </li></ul><ul><li>Products leave a reaction </li></ul><ul><li>6 CO 2 + 6 H 2 O -> C 6 H 12 O 6 + 6 O 2 </li></ul>carbon dioxide water a sugar molecular oxygen reactants products
  55. 55. 2.4 Hydrogen Bonds and the Properties of Water <ul><li>Lattice of hydrogen bonds gives water unusual properties </li></ul><ul><li>Hydrogen-bond lattice of water forms polar and nonpolar environments in and around cells </li></ul><ul><li>The small size and polarity of its molecules makes water a good solvent </li></ul><ul><li>The hydrogen-bond lattice gives water other life-sustaining properties as well </li></ul>
  56. 56. Hydrogen-Bond Lattice of Water <ul><li>Water lattice </li></ul><ul><ul><li>Neighboring water molecules form hydrogen bonds temporarily </li></ul></ul><ul><ul><li>Difficult for nonpolar substances to penetrate the lattice </li></ul></ul><ul><ul><li>Polar or charged substances penetrate easily </li></ul></ul>
  57. 57. Ice Lattice <ul><li>Ice lattice </li></ul><ul><ul><li>A rigid, crystalline structure </li></ul></ul><ul><ul><li>Water molecules in the ice lattice are spread farther apart than in liquid water </li></ul></ul><ul><ul><li>Ice is less dense than water and floats </li></ul></ul>
  58. 58. Hydrogen-Bond Lattice of Water Fig. 2-12, p. 33
  59. 59. Fig. 2-12, p. 33 b. Hydrogen-bond lattice of ice a. Hydrogen-bond lattice of liquid water
  60. 60. Animation: Structure of water
  61. 61. <ul><li>Membrane molecules have one polar end and one nonpolar (lipid) end </li></ul><ul><li>In water, lipid molecules are forced into a double layer (bilayer) that forms the membrane </li></ul><ul><ul><li>Hydrophilic ends face water </li></ul></ul><ul><ul><li>Hydrophobic ends associate inside </li></ul></ul>Water, Lipids, and Membranes
  62. 62. Membranes: The Lipid Bilayer Fig. 2-13, p. 34
  63. 63. Fig. 2-13, p. 34 Membrane covering cell surface Water molecule Polar end of membrane molecule Nonpolar end of membrane molecule Polar water solution outside cell Nonpolar region inside membrane Polar water solution inside cell
  64. 64. Hydration Layer <ul><li>Water forms hydration layer over surfaces of polar and charged biological molecules, particularly proteins </li></ul><ul><li>Separates ions and molecules from each other so they can enter a solution </li></ul><ul><ul><li>Water = solvent </li></ul></ul><ul><ul><li>Dissolved substance = solute </li></ul></ul>
  65. 65. Hydration Layer <ul><li>Hydration layers around Na + and Cl – ions keep salt in solution </li></ul>Fig. 2-14, p. 34
  66. 66. Animation: Spheres of hydration
  67. 67. Solutions <ul><li>Concentration </li></ul><ul><ul><li>Number of ions or molecules per unit volume </li></ul></ul><ul><li>Mole </li></ul><ul><ul><li>6.022 X 10 23 molecules ( Avogadro’s number ) </li></ul></ul><ul><ul><li>1 mole of substance = molecular weight in grams </li></ul></ul><ul><ul><li>1 mole NaCl = 23 + 35 = 58g </li></ul></ul><ul><li>Molarity (moles per liter) </li></ul><ul><ul><li>1 molar solution = 1 mole/liter = 1 M </li></ul></ul><ul><ul><li>1 M NaCl = 58 g/L </li></ul></ul>
  68. 68. High Specific Heat <ul><li>Water temperature increases slowly as heat is added </li></ul><ul><ul><li>Must break hydrogen bonds to allow water molecules to move faster </li></ul></ul><ul><ul><li>Helps moderate and stabilize temperature of organisms and environment </li></ul></ul><ul><ul><li>c (calorie) = heat to raise 1g of water 1°C </li></ul></ul><ul><ul><li>C (Calorie) = 1,000 calories = 1 kilocalorie (kcal) </li></ul></ul>
  69. 69. High Heat of Vaporization <ul><li>Water absorbs a large amount of heat to break loose from liquid water and form a gas </li></ul><ul><ul><li>Some animals sweat (water evaporation cools skin and underlying blood vessels) </li></ul></ul><ul><ul><li>Plants evaporate water from leaves (cools heat absorbed from sunlight) </li></ul></ul>
  70. 70. Water Molecules Resist Separation <ul><li>Cohesion </li></ul><ul><ul><li>Attraction between water molecules </li></ul></ul><ul><li>Adhesion </li></ul><ul><ul><li>Attraction of water molecules to surfaces with charged or polar molecules </li></ul></ul>
  71. 71. Surface Tension <ul><li>Forms at surface of water in contact with air </li></ul><ul><li>Hydrogen bonds resist stretching, giving surface strength </li></ul>Fig. 2-15, p. 36
  72. 72. Fig. 2-15a, p. 36 H 2 O a. Air Water surface
  73. 73. Fig. 2-15b, p. 36
  74. 74. 2.5 Water Ionization and Acids, Bases, and Buffers <ul><li>Substances act as acids or bases by altering the concentrations of H + and OH − ions in water </li></ul><ul><li>Buffers help keep pH under control </li></ul>
  75. 75. Water Ionization <ul><li>Water dissociates to form ions: </li></ul><ul><li>H 2 O ↔ H + + OH – </li></ul><ul><li>H + (protons) = hydrogen ions </li></ul><ul><li>OH – = hydroxide ions </li></ul><ul><li>In pure water, concentration of H + = OH – </li></ul>
  76. 76. Acids and Bases <ul><li>Acids release H + as they dissolve in water </li></ul><ul><ul><li>Solution becomes acidic </li></ul></ul><ul><li>HCl ↔ H + + Cl – </li></ul><ul><li>Bases gather H + or release OH − in solution </li></ul><ul><ul><li>Solution becomes basic </li></ul></ul><ul><li>NaOH ↔ Na + + OH – </li></ul>
  77. 77. pH Scale <ul><li>Measures relative concentrations of H + and OH − ( acidity ) in a water solution on a scale of 0 to 14 </li></ul><ul><li>pH = –log 10 [H + ] </li></ul><ul><li>Pure water: [H + ] = [OH − ] = 1 X 10 -7 M </li></ul><ul><ul><li>pH 7 (neutral) = – log 10 [ 1 X 10 -7 ] </li></ul></ul><ul><ul><li>pH < 7 is acidic, pH > 7 is basic </li></ul></ul>
  78. 78. pH Scale Fig. 2-16, p. 37
  79. 79. Fig. 2-16, p. 37 Hydrochloric acid (HCl) Gastric fluid (1.0–3.0) Lemon juice, cola drinks, some acid rain Vinegar, wine, beer, oranges Tomatoes Bananas Black coffee Sodium hydroxide (NaOH) Bread Typical rainwater Urine (5.0–7.0) Milk (6.6) Pure water [H+] = [OH–] Blood (7.3–7.5) Egg white (8.0) Seawater (7.8–8.3) Baking soda Phosphate detergents, bleach, antacids Soapy solutions, milk of magnesia Household ammonia (10.5–11.9) Hair remover Oven cleaner
  80. 80. Animation: The pH scale
  81. 81. Acid Rain Fig. 2-17, p. 38
  82. 82. Buffers (1) <ul><li>Regulate pH of living cells </li></ul><ul><li>Absorb or release H + to compensate for changes in H + concentration </li></ul><ul><li>H 2 CO 3 ↔ HCO 3 – + H + </li></ul>
  83. 83. Buffers (2) <ul><li>If cell is too acidic </li></ul><ul><ul><li>Push reaction to the left </li></ul></ul><ul><ul><li>Remove some H + ions </li></ul></ul><ul><li>If cell is too basic </li></ul><ul><ul><li>Push reaction to the right </li></ul></ul><ul><ul><li>Add more H + ions </li></ul></ul><ul><li>Help keep cells close to neutral pH </li></ul>
  84. 84. Hyperventilation <ul><li>Breathing too fast removes buffering capacity from the blood </li></ul>Fig. 2-18, p. 39
  85. 85. Fig. 2-18, p. 39 Adverse physiological effects, such as dizziness, visual impairment, fainting, seizures, or death Rapid breathing Blood CO 2 concentration decreases Blood carbonic acid level decreases Blood pH changes from normal levels
  86. 86. Fig. 2-18, p. 39 Stepped Art Adverse physiological effects, such as dizziness, visual impairment, fainting, seizures, or death Rapid breathing Blood CO 2 concentration decreases Blood carbonic acid level decreases Blood pH changes from normal levels
  87. 87. Video: Covalent bonds
  88. 88. Video: The wine of life
  89. 89. Video: Isotopes

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