1. Chemical Foundations for Cells Chapter 2

2. Chemical Benefits and Costs Understanding of chemistry provides fertilizers, medicines, etc. Understanding of chemistry provides fertilizers, medicines, etc. Chemical pollutants damage ecosystems Chemical pollutants damage ecosystems

3. Bioremediation Use of living organisms to withdraw harmful substances from the environment

4. Elements Fundamental forms of matter Fundamental forms of matter Can’t be broken apart by normal means Can’t be broken apart by normal means 92 occur naturally on Earth 92 occur naturally on Earth

5. Most Common Elements in Living Organisms OxygenHydrogenCarbonNitrogen

6. Fig. 2.2, p. 21

7. What Are Atoms? Smallest particles that retain properties of an element Smallest particles that retain properties of an element Made up of subatomic particles: Made up of subatomic particles: Protons (+) Protons (+) Electrons (-) Electrons (-) Neutrons (no charge) Neutrons (no charge)

8. Fig. 2.3, p. 22 HYDROGEN HELIUM electron proton neutron Hydrogen and Helium Atoms

9. Protons Positively charged Positively charged Found in the nucleus Found in the nucleus Has a mass Has a mass

10. Neutrons No charge No charge Found in the nucleus Found in the nucleus Has a mass Has a mass

11. Electrons Negatively charged Negatively charged Constantly moving around in the electron cloud surrounding the nucleus Constantly moving around in the electron cloud surrounding the nucleus Negligible Mass (1/1840 the mass of a proton) Negligible Mass (1/1840 the mass of a proton)

12. What information does the Periodic Table of Elements contain?

14. Atomic Number Number of protons Number of protons All atoms of an element have the same atomic number All atoms of an element have the same atomic number Atomic number of hydrogen = 1 Atomic number of hydrogen = 1 Atomic number of carbon = 6 Atomic number of carbon = 6

15. Mass Number Number of protons + Number of neutrons Isotopes vary in mass number

16. How can we determine the number of neutrons? Subtract the total number of protons from the atomic mass. Subtract the total number of protons from the atomic mass.

17. Determine the symbol, number of protons, neutrons and electrons of each of the following elements. Hydrogen Hydrogen Sodium Sodium Oxygen Oxygen Iron Iron

18. Isotopes Atoms of an element with different numbers of neutrons (different mass numbers) Atoms of an element with different numbers of neutrons (different mass numbers) Carbon 12 has 6 protons, 6 neutrons Carbon 12 has 6 protons, 6 neutrons Carbon 14 has 6 protons, 8 neutrons Carbon 14 has 6 protons, 8 neutrons

19. Radioisotopes Have an unstable nucleus that emits energy and particles Have an unstable nucleus that emits energy and particles Radioactive decay transforms radioisotope into a different element Radioactive decay transforms radioisotope into a different element Decay occurs at a fixed rate Decay occurs at a fixed rate

20. Radioisotopes as Tracers Tracer is substance with a radioisotope attached to it Tracer is substance with a radioisotope attached to it Emissions from the tracer can be detected with special devices Emissions from the tracer can be detected with special devices Following movement of tracers is useful in many areas of biology Following movement of tracers is useful in many areas of biology

21. Thyroid Scan Thyroid Scan Measures health of thyroid by detecting radioactive iodine taken up by thyroid gland Measures health of thyroid by detecting radioactive iodine taken up by thyroid gland normal thyroidenlargedcancerous

22. Other Uses of Radioisotopes Drive artificial pacemakers Drive artificial pacemakers Radiation therapy Radiation therapy Emissions from some radioisotopes can destroy cells. Some radioisotopes are used to kill small cancers.

23. What Determines Whether Atoms Will Interact? The number and arrangement of their electrons

24. Electrons Carry a negative charge Carry a negative charge Repel one another Repel one another Are attracted to protons in the nucleus Are attracted to protons in the nucleus Move in orbitals - volumes of space that surround the nucleus Move in orbitals - volumes of space that surround the nucleus Z X When all p orbitals are full y

25. Electron Cloud Broken into different energy levels (orbitals) Broken into different energy levels (orbitals) 1st level can hold - 2 electrons 1st level can hold - 2 electrons 2nd level can hold - 8 electrons 2nd level can hold - 8 electrons 3rd level can hold - 18 electrons 3rd level can hold - 18 electrons sub level A holds 8 electrons sub level A holds 8 electrons sub level B holds 10 electrons sub level B holds 10 electrons

26. Every atom wants a complete outer energy level to be as stable as possible. Every atom wants a complete outer energy level to be as stable as possible. In order to do this the atom has three choices In order to do this the atom has three choices donate electrons donate electrons accept electrons accept electrons share electrons share electrons

27. Electron Vacancies Unfilled shells make atoms likely to react Unfilled shells make atoms likely to react Hydrogen, carbon, oxygen, and nitrogen all have vacancies in their outer shells Hydrogen, carbon, oxygen, and nitrogen all have vacancies in their outer shells CARBON 6p+, 6e - NITROGEN 7p+, 7e - HYDROGEN 1p+, 1e -

28. Draw models of the following atoms. Include the number of protons, neutrons and electons. Helium, Carbon, Oxygen

29. Important Bonds in Biological Molecules Ionic Bonds Covalent Bonds Hydrogen Bonds

30. http://www.bozemanscience.com/biology- main-page/ http://www.bozemanscience.com/biology- main-page/

31. Ion Formation Atom has equal number of electrons and protons - no net charge Atom has equal number of electrons and protons - no net charge Atom loses electron(s), becomes positively charged ion Atom loses electron(s), becomes positively charged ion Atom gains electron(s), becomes negatively charged ion Atom gains electron(s), becomes negatively charged ion

32. Ionic Bonding Ionic Bonding One atom loses electrons, becomes positively charged ion One atom loses electrons, becomes positively charged ion Another atom gains these electrons, becomes negatively charged ion Another atom gains these electrons, becomes negatively charged ion Charge difference attracts the two ions to each other Charge difference attracts the two ions to each other

33. Formation of NaCl Sodium atom (Na) Sodium atom (Na) Outer shell has one electron Outer shell has one electron Chlorine atom (Cl) Chlorine atom (Cl) Outer shell has seven electrons Outer shell has seven electrons Na transfers electron to Cl forming Na + and Cl - Na transfers electron to Cl forming Na + and Cl - Ions remain together as NaCl Ions remain together as NaCl

34. 7mm SODIUM ATOM 11 p + 11 e - SODIUM ION 11 p + 10 e - electron transfer CHLORINE ATOM 17 p + 17 e - CHLORINE ION 17 p + 18 e - Fig. 2.10a, p. 26 Formation of NaCl

35. Ionic Bonding Practice Show how the following compounds form as a result of ionic bonding Show how the following compounds form as a result of ionic bonding NaF - Sodium Flouride NaF - Sodium Flouride MgO - Magnesium Oxide MgO - Magnesium Oxide Li 2 S - Lithium Sulfide Li 2 S - Lithium Sulfide

36. Covalent Bonding Atoms share a pair or pairs of electrons to fill outermost shell Single covalent bond Double covalent bond Triple covalent bond

37. Covalent Bonds

38. Covalent Bonding Practice Show how the following compounds form as a result of ionic bonding Show how the following compounds form as a result of ionic bonding H 2 S - Hydrogen Sulfide H 2 S - Hydrogen Sulfide NH 3 - Nitrogen Trihydride (Ammonia) NH 3 - Nitrogen Trihydride (Ammonia) F 2 - Diatomic Fluorine F 2 - Diatomic Fluorine

39. Nonpolar Covalent Bonds Atoms share electrons equally Atoms share electrons equally Nuclei of atoms have same number of protons Nuclei of atoms have same number of protons Example: Hydrogen gas (H-H) Example: Hydrogen gas (H-H)

40. Polar Covalent Bonds Number of protons in nuclei of participating atoms is NOT equal Number of protons in nuclei of participating atoms is NOT equal Electrons spend more time near nucleus with most protons Electrons spend more time near nucleus with most protons Water - Electrons more attracted to O nucleus than to H nuclei Water - Electrons more attracted to O nucleus than to H nuclei

41. Polar Bonding During covalent bonding the sharing of electrons is not always equal. This unequal sharing leads to slightly positive and negative regions.

42. Hydrogen Bonding Molecule held together by polar covalent bonds has no NET charge Molecule held together by polar covalent bonds has no NET charge However, atoms of the molecule carry different charges However, atoms of the molecule carry different charges Atom in one polar covalent molecule can be attracted to oppositely charged atom in another such molecule Atom in one polar covalent molecule can be attracted to oppositely charged atom in another such molecule

43. one large molecule another large molecule a large molecule twisted back on itself Fig. 2.12, p. 27 Examples of Hydrogen Bonds

44. Chemical Bonds, Molecules, & Compounds Bond is union between electron structures of atoms Bond is union between electron structures of atoms Atoms bond to form molecules Atoms bond to form molecules Molecules may contain atoms of only one element - O 2 Molecules may contain atoms of only one element - O 2 Molecules of compounds contain more than one element - H 2 O Molecules of compounds contain more than one element - H 2 O

45. Chemical Bookkeeping Use symbols for elements when writing formulas Use symbols for elements when writing formulas Formula for glucose is C 6 H 12 O 6 Formula for glucose is C 6 H 12 O 6 6 carbons 6 carbons 12 hydrogens 12 hydrogens 6 oxygens 6 oxygens

46. Chemical Bookkeeping Chemical equation shows reaction Chemical equation shows reaction Reactants ---> Products Equation for photosynthesis: Equation for photosynthesis: 6CO 2 + 6H 2 O ---> + C 6 H 12 O 6 + 6H 2 O 6CO 2 + 6H 2 O ---> + C 6 H 12 O 6 + 6H 2 O

47. REACTANTSPRODUCTS 6CO 2 CARBON DIOXIDE 12H 2 O WATER + C 6 H 12 O 6 GLUCOSE 6H 2 O WATER + 6 carbons 12 oxygens 24 hydrogens 12 oxygens 6 carbons 12 hydrogens 6 oxygens 12 hydrogens 6 oxygens Fig. 2.9, p. 25 6O 2 OXYGEN + 12 oxygens sunlight energy

48. Reactants The elements or compounds that enter into a chemical reaction The elements or compounds that enter into a chemical reaction

49. Product The elements or compounds produced by a chemical reaction The elements or compounds produced by a chemical reaction

50. Energy in Reactions

51. What is Energy? Capacity to do work Capacity to do work Forms of energy Forms of energy Potential energy Potential energy Kinetic energy Kinetic energy Chemical energy Chemical energy

52. What Can Cells Do with Energy? Energy inputs become coupled to energy-requiring processes Energy inputs become coupled to energy-requiring processes Cells use energy for: Cells use energy for: Chemical work Chemical work Mechanical work Mechanical work Electrochemical work Electrochemical work

53. First Law of Thermodynamics The total amount of energy in the universe remains constant The total amount of energy in the universe remains constant Energy can undergo conversions from one form to another, but it cannot be created or destroyed Energy can undergo conversions from one form to another, but it cannot be created or destroyed

54. One-Way Flow of Energy The sun is life’s primary energy source The sun is life’s primary energy source Producers trap energy from the sun and convert it into chemical bond energy Producers trap energy from the sun and convert it into chemical bond energy All organisms use the energy stored in the bonds of organic compounds to do work All organisms use the energy stored in the bonds of organic compounds to do work

55. Second Law of Thermodynamics No energy conversion is ever 100 percent efficient No energy conversion is ever 100 percent efficient The total amount of energy is flowing from high-energy forms to forms lower in energy The total amount of energy is flowing from high-energy forms to forms lower in energy

56. Energy Changes & Cellular Work Energy changes in cells tend to run spontaneously in the direction that results in a decrease in usable energy

57. Endergonic Reactions Energy input required Energy input required Product has more energy than starting substances Product has more energy than starting substances product with more energy (plus by-products 60 2 and 6H 2 O) ENERGY IN 612

58. Exergonic Reactions Energy is released Energy is released Products have less energy than starting substance Products have less energy than starting substance ENERGY OUT energy-rich starting substance + 60 2 products with less energy 66

59. Properties of Water PolarityTemperature-StabilizingCohesiveSolvent

60. Water Is a Polar Covalent Molecule Molecule has no net charge Molecule has no net charge Oxygen end has a slight negative charge Oxygen end has a slight negative charge Hydrogen end has a slight positive charge Hydrogen end has a slight positive charge O HH

61. O H H O H H + _ + + + _ + + Liquid Water

62. Surface Tension The cohesive nature of water allows it to overcome the density of objects. The cohesive nature of water allows it to overcome the density of objects. Demonstration Demonstration Allows for water walking insects and lizards. Allows for water walking insects and lizards.

63. EXPLAIN…. Using Scientific principles, terminology, critical thinking, to explain what this photo represents..

64. Hydrophilic & Hydrophobic Substances Hydrophilic substances Hydrophilic substances Polar Polar Hydrogen bond with water Hydrogen bond with water Example: sugar Example: sugar Hydrophobic substances Hydrophobic substances Nonpolar Nonpolar Repelled by water Repelled by water Example: oil Example: oil

65. Temperature-Stabilizing Effects Temperature-Stabilizing Effects Liquid water can absorb much heat before its temperature rises Liquid water can absorb much heat before its temperature rises Why? Why? Much of the added energy disrupts hydrogen bonding rather than increasing the movement of molecules Much of the added energy disrupts hydrogen bonding rather than increasing the movement of molecules

66. Evaporation of Water Large energy input can cause individual molecules of water to break free into air Large energy input can cause individual molecules of water to break free into air As molecules break free, they carry away some energy (lower temperature) As molecules break free, they carry away some energy (lower temperature) Evaporative water loss is used by mammals to lower body temperature Evaporative water loss is used by mammals to lower body temperature

67. Why Ice Floats In ice, hydrogen bonds lock molecules in a lattice In ice, hydrogen bonds lock molecules in a lattice Water molecules in lattice are spaced farther apart then those in liquid water Water molecules in lattice are spaced farther apart then those in liquid water Ice is less dense than water Ice is less dense than water

68. Water Cohesion Hydrogen bonding holds molecules in liquid water together Hydrogen bonding holds molecules in liquid water together Creates surface tension Creates surface tension Allows water to move as continuous column upward through stems of plants Allows water to move as continuous column upward through stems of plants

69. Water Is a Good Solvent Ions and polar molecules dissolve easily in water Ions and polar molecules dissolve easily in water When solute dissolves, water molecules cluster around its ions or molecules and keep them separated When solute dissolves, water molecules cluster around its ions or molecules and keep them separated

70. Fig. 2.16, p. 29 Na + Cl – – – – – – – – – – – – + + + + + + + + + + + + + + + + + + Spheres of Hydration

71. Affects on Weather Releases heat when condensation occurs. Absorbs heat when evaporation occurs. Impact: 1. Weather is cooler on the shore than inland during the summer. 2. Weather is warmer on the shore than inland during the winter.

72. Density Density of water decrease when it moves from the liquid to the solid state. Density of water decrease when it moves from the liquid to the solid state. Impact: Allows for organisms to survive in colder aquatic environments and insulates the water below preventing the seas and lakes from freezing.

73. BACK TO CHEMISTRY!!!! BACK TO CHEMISTRY!!!!

74. Mixtures, Solutions and Suspensions A mixture is composed of 2 or more elements or compounds that are physically mixed but not combined. A mixture is composed of 2 or more elements or compounds that are physically mixed but not combined. Examples: salt and pepper, sand, atmosphere Examples: salt and pepper, sand, atmosphere

75. Solutions Evenly mixed throughout the solution. Evenly mixed throughout the solution.

77. Solute vs. Solvent Solute is dissolved by the solvent. Solute is dissolved by the solvent. Both are either polar or non polar. Both are either polar or non polar.

78. Suspensions Materials do not dissolve but they are so small they do not settle. Materials do not dissolve but they are so small they do not settle. Example: cloudy river water Example: cloudy river water

79. What is Blood? Solution and a suspension Solution and a suspension Solution - dissolved sugars, sodium, potassium, Oxygen, Carbon Dioxide Solution - dissolved sugars, sodium, potassium, Oxygen, Carbon Dioxide Suspension - white blood cells, red blood cells Suspension - white blood cells, red blood cells

81. Acids, Bases and pH

82. Hydrogen Ions: H + Unbound protons Unbound protons Have important biological effects Have important biological effects Form when water ionizes Form when water ionizes

83. The pH Scale Measures H + concentration of fluid Measures H + concentration of fluid Change of 1 on scale means 10X change in H + concentration Change of 1 on scale means 10X change in H + concentration Highest H + Lowest H + 0---------------------7-------------------14 Acidic Neutral Basic

84. Examples of pH Pure water is neutral with pH of 7.0 Pure water is neutral with pH of 7.0 Acidic Acidic Stomach acid: pH 1.0 - 3.0 Stomach acid: pH 1.0 - 3.0 Lemon juice: pH 2.3 Lemon juice: pH 2.3 Basic Basic Seawater: pH 7.8 - 8.3 Seawater: pH 7.8 - 8.3 Baking soda: pH 9.0 Baking soda: pH 9.0

86. Fig. 2.17, p. 30

87. Acids & Bases Acids Acids Donate H + when dissolved in water Donate H + when dissolved in water Acidic solutions have pH < 7 Acidic solutions have pH < 7 Bases Bases Accept H + when dissolved in water Accept H + when dissolved in water Basic solutions have pH > 7 Basic solutions have pH > 7

88. Weak and Strong Acids Weak acids Weak acids Reluctant H + donors Reluctant H + donors Can also accept H after giving it up Can also accept H after giving it up Carbonic acid (H 2 CO 3 ) is example Carbonic acid (H 2 CO 3 ) is example Strong acids Strong acids Completely give up H + when dissolved Completely give up H + when dissolved Hydrochloric acid (HCl) is example Hydrochloric acid (HCl) is example

89. Buffer Systems Minimize shifts in pH Minimize shifts in pH Partnership between weak acid and base it forms when dissolved Partnership between weak acid and base it forms when dissolved Two work as pair to counter shifts in pH Two work as pair to counter shifts in pH

90. Carbonic Acid-Bicarbonate Buffer System When blood pH rises, carbonic acid dissociates to form bicarbonate and H + When blood pH rises, carbonic acid dissociates to form bicarbonate and H + H 2 C0 3 -----> HC0 3 - + H + When blood pH drops, bicarbonate binds H + to form carbonic acid When blood pH drops, bicarbonate binds H + to form carbonic acid HC0 3 - + H + -----> H 2 C0 3

91. Salts Compounds that release ions other than H + and OH - when dissolved in water Compounds that release ions other than H + and OH - when dissolved in water Example: NaCl releases Na + and Cl – Example: NaCl releases Na + and Cl – Many salts dissolve into ions that play important biological roles Many salts dissolve into ions that play important biological roles

92. End of Chapter 2