20 ch02chemistry2008[1]

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  • Domains of Study Domain of BioMolecules Domain of Cells Domain of Organisms Domain of Populations Domain of Communities
  • Sulfur on the LEFT Magnesium on the RIGHT
  • Oxygen has medium electronegativity so doesn’t pull electrons all the way off hydrogen whereas chlorine would. So oxygen forms a polar covalent bond. Carbon has only a weak electronegativity so forms a nonpolar covalent bond
  • APBio/TOPICS/Biochemistry/MoviesAP/03_02WaterStructure_A.swf
  • APBio/TOPICS/Biochemistry/Movies AP/hydrogenbonds-Thinkwell.swf
  • APBio/TOPICS/04Biochemistry/MoviesAP/03_03WaterTransport_A.swf
  • What dissolves in water easily? polar or non-polar molecules? How about Oxygen? Does that dissolve in H 2 O?
  • What dissolves in water easily? polar or non-polar molecules? How about Oxygen? Does that dissolve in H 2 O?
  • What dissolves in water easily? polar or non-polar molecules? How about Oxygen? Does that dissolve in H 2 O?
  • In pure water only 1 water molecule in every 554 million is dissociated
  • Exercise = acidic in muscles CO 2 = carbonic acid lactic acid body uses buffers to counter act this
  • 20 ch02chemistry2008[1]

    1. 1. The Chemistry of Life
    2. 2. Why are we studying chemistry? <ul><li>Chemistry is the foundation of Biology </li></ul>
    3. 3. Proton Neutron Electron Hydrogen 1 proton 1 electron Oxygen 8 protons 8 neutrons 8 electrons + 0 – <ul><li>Everything is made of matter </li></ul><ul><li>Matter is made of atoms </li></ul>
    4. 4. The World of Elements C Different kinds of atoms = elements H O N P S Na K Mg Ca
    5. 5. Life requires ~25 chemical elements <ul><li>About 25 elements are essential for life </li></ul><ul><ul><li>Four elements make up 96% of living matter: </li></ul></ul><ul><ul><ul><li>• carbon (C) • hydrogen (H) </li></ul></ul></ul><ul><ul><ul><li>• oxygen (O) • nitrogen (N) </li></ul></ul></ul><ul><ul><li>Four elements make up most of remaining 4%: </li></ul></ul><ul><ul><ul><li>• phosphorus (P) • calcium (Ca) </li></ul></ul></ul><ul><ul><ul><li>• sulfur (S) • potassium (K) </li></ul></ul></ul>
    6. 6. <ul><li>Effect of electrons </li></ul><ul><ul><li>electrons determine chemical behavior of atom </li></ul></ul><ul><ul><li>depends on number of electrons in atom’s outermost shell </li></ul></ul><ul><ul><ul><li>valence shell </li></ul></ul></ul>Bonding properties How does this atom behave?
    7. 7. <ul><li>Effect of electrons </li></ul><ul><ul><li>chemical behavior of an atom depends on number of electrons in its valence shell </li></ul></ul>Bonding properties What’s the magic number? How does this atom behave? How does this atom behave?
    8. 8. Elements & their valence shells Elements in the same row have the same number of shells Moving from left to right, each element has a sequential addition of electrons (& protons)
    9. 9. Elements & their valence shells Elements in the same column have the same valence & similar chemical properties Remember some food chains are built on reducing O to H 2 O & some on reducing S to H 2 S
    10. 10. Chemical reactivity <ul><li>Atoms tend to </li></ul><ul><ul><li>complete a partially filled valence shell </li></ul></ul><ul><ul><li>or </li></ul></ul><ul><ul><li>empty a partially filled valence shell </li></ul></ul>This tendency drives chemical reactions… and creates bonds – – –
    11. 11. Bonds in Biology <ul><li>Weak bonds </li></ul><ul><ul><li>hydrogen bonds </li></ul></ul><ul><ul><ul><li>attraction between + and – </li></ul></ul></ul><ul><ul><li>hydrophobic & hydrophilic interactions </li></ul></ul><ul><ul><ul><li>interaction with H 2 O </li></ul></ul></ul><ul><ul><li>van derWaals forces </li></ul></ul><ul><ul><li>(ionic) </li></ul></ul><ul><li>Strong bonds </li></ul><ul><ul><li>covalent bonds </li></ul></ul>Covalent bond Hydrogen bond H 2 O H 2 O – – H 2 (hydrogen gas)
    12. 12. Covalent bonds <ul><li>Why are covalent bonds strong bonds? </li></ul><ul><ul><li>two atoms share a pair of electrons </li></ul></ul><ul><ul><li>both atoms holding onto the electrons </li></ul></ul><ul><ul><li>very stable </li></ul></ul><ul><li>Forms molecules </li></ul>H 2 (hydrogen gas) H — H H 2 O (water) – – H H Oxygen H H O
    13. 13. Multiple covalent bonds <ul><li>2 atoms can share >1 pair of electrons </li></ul><ul><ul><li>double bonds </li></ul></ul><ul><ul><ul><li>2 pairs of electrons </li></ul></ul></ul><ul><ul><li>triple bonds </li></ul></ul><ul><ul><ul><li>3 pairs of electrons </li></ul></ul></ul><ul><li>Very strong bonds </li></ul>More is better ! H H–C–H H – –
    14. 14. Nonpolar covalent bond <ul><li>Pair of electrons shared equally by 2 atoms </li></ul><ul><ul><li>example : hydrocarbons = C x H x </li></ul></ul><ul><ul><ul><li>methane (CH 4 ) </li></ul></ul></ul>balanced, stable, good building block
    15. 15. Polar covalent bonds <ul><li>Pair of electrons shared unequally by 2 atoms </li></ul><ul><ul><li>example : water = H 2 O </li></ul></ul><ul><ul><ul><li>oxygen has stronger “ attraction ” for the electrons than hydrogen </li></ul></ul></ul><ul><ul><ul><li>oxygen has higher electronegativity </li></ul></ul></ul><ul><ul><ul><li>water is a polar molecule </li></ul></ul></ul><ul><ul><ul><ul><li>+ vs – poles </li></ul></ul></ul></ul><ul><ul><ul><ul><li>leads to many interesting properties of water… </li></ul></ul></ul></ul>+ + – – – – H H Oxygen
    16. 16. Hydrogen bonding <ul><li>Polar water creates molecular attractions </li></ul><ul><ul><li>attraction between positive H in one H 2 O molecule to negative O in another H 2 O </li></ul></ul><ul><ul><li>also can occur wherever an - OH exists in a larger molecule </li></ul></ul><ul><li>Weak bond </li></ul>Let’s go to the videotape ! H O H
    17. 17. Chemistry of Life Properties of Water
    18. 18. More about Water Why are we studying water? <ul><li>All life occurs in water </li></ul><ul><ul><li>inside & outside the cell </li></ul></ul>
    19. 19. Chemistry of water <ul><li>H 2 O molecules form H-bonds with each other </li></ul><ul><ul><li>+H attracted to –O </li></ul></ul><ul><ul><li>creates a sticky molecule </li></ul></ul>
    20. 20. Elixir of Life <ul><li>Special properties of water </li></ul><ul><ul><li>1. cohesion & adhesion </li></ul></ul><ul><ul><ul><li>surface tension, capillary action </li></ul></ul></ul><ul><ul><li>2. good solvent </li></ul></ul><ul><ul><ul><li>many molecules dissolve in H 2 O </li></ul></ul></ul><ul><ul><ul><li>hydrophilic vs. hydrophobic </li></ul></ul></ul><ul><ul><li>3. lower density as a solid </li></ul></ul><ul><ul><ul><li>ice floats! </li></ul></ul></ul><ul><ul><li>4. high specific heat </li></ul></ul><ul><ul><ul><li>water stores heat </li></ul></ul></ul><ul><ul><li>5. high heat of vaporization </li></ul></ul><ul><ul><ul><li>heats & cools slowly </li></ul></ul></ul>Ice ! I could use more ice !
    21. 21. 1. Cohesion & Adhesion <ul><li>Cohesion </li></ul><ul><ul><li>H bonding between H 2 O molecules </li></ul></ul><ul><ul><li>water is “sticky” </li></ul></ul><ul><ul><ul><li>surface tension </li></ul></ul></ul><ul><ul><ul><li>drinking straw </li></ul></ul></ul><ul><li>Adhesion </li></ul><ul><ul><li>H bonding between H 2 O & other substances </li></ul></ul><ul><ul><ul><li>capillary action </li></ul></ul></ul><ul><ul><ul><li>meniscus </li></ul></ul></ul><ul><ul><ul><li>water climbs up paper towel or cloth </li></ul></ul></ul>Try that with flour… or sugar…
    22. 22. How does H 2 O get to top of trees? <ul><li>Transpiration is built on cohesion & adhesion </li></ul>Let’s go to the videotape !
    23. 23. 2. Water is the solvent of life <ul><li>Polarity makes H 2 O a good solvent </li></ul><ul><ul><li>polar H 2 O molecules surround + & – ions </li></ul></ul><ul><ul><li>solvents dissolve solutes creating solutions </li></ul></ul>
    24. 24. What dissolves in water? <ul><li>Hydrophilic </li></ul><ul><ul><li>substances have attraction to H 2 O </li></ul></ul><ul><ul><li>polar or non-polar ? </li></ul></ul>
    25. 25. What doesn’t dissolve in water? <ul><li>Hydrophobic </li></ul><ul><ul><li>substances that don’t have an attraction to H 2 O </li></ul></ul><ul><ul><li>polar or non-polar ? </li></ul></ul>fat (triglycerol) Oh, look hydrocarbons !
    26. 26. 3. The special case of ice <ul><li>Most (all?) substances are more dense when they are solid, but </li></ul><ul><li>not water… </li></ul><ul><li>Ice floats ! </li></ul><ul><ul><li>H bonds form a crystal </li></ul></ul>And this has made all the difference !
    27. 27. Ice floats
    28. 28. Why is “ice floats” important? <ul><li>Oceans & lakes don’t freeze solid </li></ul><ul><ul><li>surface ice insulates water below </li></ul></ul><ul><ul><ul><li>allowing life to survive the winter </li></ul></ul></ul><ul><ul><li>if ice sank… </li></ul></ul><ul><ul><ul><li>ponds, lakes & even oceans would freeze solid </li></ul></ul></ul><ul><ul><ul><li>in summer, only upper few inches would thaw </li></ul></ul></ul><ul><ul><li>seasonal turnover of lakes </li></ul></ul><ul><ul><ul><li>sinking cold H 2 O cycles nutrients in autumn </li></ul></ul></ul>
    29. 29. 4. Specific heat <ul><li>H 2 O resists changes in temperature </li></ul><ul><ul><li>high specific heat </li></ul></ul><ul><ul><li>takes a lot to heat it up </li></ul></ul><ul><ul><li>takes a lot to cool it down </li></ul></ul><ul><li>H 2 O moderates temperatures on Earth </li></ul>
    30. 30. Specific heat & climate
    31. 31. 5. Heat of vaporization <ul><li>Organisms rely on heat of vaporization to remove body heat </li></ul>Evaporative cooling
    32. 32. Ionization of water & pH <ul><li>Water ionizes </li></ul><ul><ul><li>H + splits off from H 2 O, leaving OH – </li></ul></ul><ul><ul><ul><li>if [ H + ] = [ - OH ], water is neutral </li></ul></ul></ul><ul><ul><ul><li>if [ H + ] > [ - OH ], water is acidic </li></ul></ul></ul><ul><ul><ul><li>if [ H + ] < [ - OH ], water is basic </li></ul></ul></ul><ul><li>pH scale </li></ul><ul><ul><li>how acid or basic solution is </li></ul></ul><ul><ul><li>1  7  14 </li></ul></ul>H 2 O  H + + OH –
    33. 33. pH Scale tenfold change in H+ ions pH1  pH2 10 -1  10 -2 10 times less H + pH8  pH7 10 -8  10 -7 10 times more H + pH10  pH8 10 -10  10 -8 100 times more H + 10 –1 H + Ion Concentration Examples of Solutions Stomach acid, Lemon juice 1 pH 10 0 Hydrochloric acid 0 10 –2 2 10 –3 Vinegar, cola, beer 3 10 –4 Tomatoes 4 10 –5 Black coffee, Rainwater 5 10 –6 Urine, Saliva 6 10 –7 Pure water, Blood 7 10 –8 Seawater 8 10 –9 Baking soda 9 10 –10 Great Salt Lake 10 10 –11 Household ammonia 11 10 –12 Household bleach 12 10 –13 Oven cleaner 13 10 –14 Sodium hydroxide 14
    34. 34. Buffers & cellular regulation <ul><li>pH of cells must be kept ~7 </li></ul><ul><ul><li>pH affects shape of molecules </li></ul></ul><ul><ul><li>shape of molecules affect function </li></ul></ul><ul><ul><li>pH affects cellular function </li></ul></ul><ul><li>Control pH by buffers </li></ul><ul><ul><li>reservoir of H + </li></ul></ul><ul><ul><ul><li>donate H+ when [H + ] falls </li></ul></ul></ul><ul><ul><ul><li>absorb H+ when [H + ] rises </li></ul></ul></ul>1 0 0 1 2 3 4 5 6 7 8 9 3 Amount of base added Buffering range 4 5 2 pH
    35. 35. He’s gonna earn a Darwin Award ! Do one brave thing today…then run like hell! Any Questions?
    36. 36. Ice Fishing in Barrow, Alaska

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