2. AP Biology 2007-2008 The Chemistry of Life

3. AP Biology Life requires ~25 chemical elements  About 25 elements are essential for life  Four elements make up 96% of living matter: carbon (C) hydrogen (H) oxygen (O) nitrogen (N)  Four elements make up most of remaining 4%: phosphorus (P) calcium (Ca) sulfur (S) potassium (K)

4. AP Biology  Trace elements (< 0.01%) are required in only minute quantities  Fe (iron), I (iodine), Zn (zinc), etc… 3 (a) Nitrogen deficiency (b) Iodine deficiency (Goiter) Figure 2.3

5. AP Biology  Isotopes  Different forms of the same element  Have the same number of protons but different number of neutrons  May be radioactive giving off particles and energy  Uses: Date fossils and can be used in medicine to treat tumors 4 Cancero us throat tissue Figure 2.6

6. AP Biology 5 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 Figure 2.17 Determines how biological molecules recognize and respond to one another with specificity

7. AP Biology Bonding properties  Effect of electrons  electrons determine chemical behavior of atom  depends on number of electrons in atom’s outermost shell  valence shell How does this atom behave? Having a filled valence shell drives chemical reactions… and creates bonds

8. AP Biology Which of the following molecules is most likely to exist?

9. AP Biology 8

11. – – H 2 (hydrogen gas) Covalent bond Bonds in Biology  Weak bonds  hydrogen bonds  attraction between + and –  van derWaals forces  ionic  Strong bonds  covalent bonds Hydrogen bond H2OH2O H2OH2O

12. AP Biology Covalent bonds  Why are covalent bonds strong bonds?  two atoms share a pair of electrons  both atoms holding onto the electrons  very stable  Forms molecules – – H 2 (hydrogen gas) H — H H 2 O (water) H H Oxygen H H O

13. AP Biology Multiple covalent bonds  2 atoms can share >1 pair of electrons  double bonds  2 pairs of electrons  triple bonds  3 pairs of electrons  Very strong bonds

14. AP Biology H H Oxygen Polar covalent bonds  Pair of electrons shared unequally by 2 atoms  example: water = H 2 O  oxygen has stronger “attraction” for the electrons than hydrogen  oxygen has higher electronegativity  water is a polar molecule  + vs – poles  leads to many interesting properties of water… + + – – – – Ex: O-H N-H S-H O-C Ex: O-H N-H S-H O-C

15. AP Biology Electronegativity The more electronegative an atom, the more strongly it pulls electrons towards itself Remember affinity for electrons depends on how far the electrons are from the nucleus and the charge of the nucleus -Further the electrons = weaker force - Less protons = weaker force Remember affinity for electrons depends on how far the electrons are from the nucleus and the charge of the nucleus -Further the electrons = weaker force - Less protons = weaker force

16. AP Biology Nonpolar covalent bond  Pair of electrons shared equally by 2 atoms with similar electronegativities  Both ends are neutral  example: hydrocarbons or any covalent bond between two of the same elements  methane (CH 4 ), fatty acids, O 2, H 2 Oh, look hydrocarbons!

17. AP Biology Hydrogen bonding  Polar water creates molecular attractions  attraction between positive H in one H 2 O molecule to negative O in another H 2 O  Water can form up to 4 hydrogen bonds  Weak bond  An additive effect of many hydrogen bonds is strong

18. AP Biology The sodium and chloride ions are now attracted to each other and form an ionic bond. Ionic Bonds Ionic bond = bond between two oppositely charged ions cation anion

19. AP Biology Na + Cl - crystals are repeating arrays of Na + and Cl - held together by the electromagnetic force. General name given to ANY ionic compound (not just sodium chloride (Na + Cl - ) held together in a lattice structure. Na + Cl - K + Cl - Mg 2+ Cl 2 - Salt Crystals

20. AP Biology 1. Two non-polar molecules (say H 2 ) come into close proximity 2. By chance, the position of the electrons around one of the molecules (the one to the left) are more on one side of the molecule than the other causing one side to be slightly negative and the other side to be slightly positive. 3. This will then induce a dipole in the neighboring molecule as the neighboring molecule’s electrons will be attracted to the slightly positive region of the first molecule resulting again in an ever so slightly negative side and an ever so slightly positive side. Of course, the negative and positive will form a very weak interaction. Van der Waals Interactions  Even non-polar molecules can have some positively and negatively charged region briefly and can very weakly bond

21. AP Biology The additive affects of weak chemical bonds are important to biological systems ◦ Reinforce the shapes of large molecules ◦ Help molecules adhere to each other Plasma membrane are stabilized by the additive affect of Van der Waals interactions between non-polar fatty acid tails of phospholipids. H bonds The two strands of a DNA molecule are held together tightly by the additive affect of many, many weak Hydrogen Bonds Are weak bonds really weak?

22. AP Biology Chemistry of Life Properties of Water  All life occurs in water  Three-quarters of the Earth’s surface is submerged in water  Most cells are surrounded by water and cells are about 70-95% water  Allows earth to be habitable Intro to water video Intro to water video

23. AP Biology Chemistry of water  H 2 O molecules form H-bonds with each other  +H attracted to –O  creates a sticky molecule

24. AP Biology Elixir of Life  Special properties of water 1.cohesion & adhesion  surface tension, capillary action 2.good solvent  many molecules dissolve in H 2 O  hydrophilic vs. hydrophobic 3.lower density as a solid  ice floats! 4.high specific heat  water stores heat 5.high heat of vaporization  heats & cools slowly

25. AP Biology 1. Cohesion & Adhesion  Cohesion  H bonding between H 2 O molecules  water is “sticky”  surface tension  drinking straw  Adhesion  H bonding between H 2 O & other substances  capillary action  meniscus  water climbs up paper towel or cloth

26. AP Biology How does H 2 O get to top of trees? Transpiration is built on cohesion & adhesion

27. AP Biology 2. Water is the solvent of life  Polarity makes H 2 O a good solvent  polar H 2 O molecules surround + & – ions  solvents dissolve solutes creating solutions Lysozyme molecule (purple) in an aqueous environment such as tears or saliva Ionic and polar regions on the protein’s Surface attract water molecules. Hydration shell

28. AP Biology What dissolves in water?  Hydrophilic  substances have attraction to H 2 O  polar or non-polar?  Or ionic  Examples: Carbohydrates, salts “Like Dissolves Like”

29. AP Biology What doesn’t dissolve in water?  Hydrophobic  substances that don’t have an attraction to H 2 O  polar or non-polar? fat (triglycerol)

30. AP Biology The science behind soap Rule of thumb: LIKE DISSOLVES LIKE Soap is AMPHIPATHIC

31. AP Biology 3. The special case of ice  Most (all?) substances are more dense when they are solid, but not water…  Ice floats!  H bonds form a crystal

32. AP Biology Ice floats

33. AP Biology Why is “ice floats” important?  Oceans & lakes don’t freeze solid  surface ice insulates water below  allowing life to survive the winter  if ice sank…  ponds, lakes & even oceans would freeze solid  in summer, only upper few inches would thaw  seasonal turnover of lakes  sinking cold H 2 O cycles nutrients in autumn

34. AP Biology Heat and Temperature Kinetic energy Is the energy of motion Heat Is a measure of the total amount of kinetic energy due to molecular motion Temperature Measures the average kinetic energy of heat Which has a higher temperature? Which has more heat? The man swimming or the ocean

35. AP Biology 4. Specific heat  H 2 O resists changes in temperature  high specific heat  Is the amount of energy needed to be absorbed or lost for 1 gram of the substance to change its temperature by 1ºC  takes a lot to heat it up  takes a lot to cool it down Specific heat of iron: 0.1 cal/g/ o C Specific heat of water: 1 cal/g/ o C (1 calorie)

36. AP Biology Heat is absorbed in order to break hydrogen bonds (ex. Boiling water) Heat is released when hydrogen bonds form (ex. Freezing water) Specific Heat Water, because of it H-bonding (cohesive nature) has a very high specific heat relative to other molecules. It is difficult to get the water molecules to vibrate since they are all sticking to each other. The H-bonds need to be broken. Think about this analogy: is easy to push a single student and get them moving fast, but if you all hold hands, it becomes more difficult as I would need to break those bonds. Helps organisms resist change in temperature!!

37. AP Biology Specific heat & climate Water moderates air temperature due to its high specific heat By absorbing heat from warmer air in daytime and summer Releasing the stored heat to cooler air at night and during winter Temperature Moderation

38. AP Biology 5. Heat of vaporization Evaporative cooling Organisms rely on heat of vaporization to remove body heat  The amount of energy (heat) required to turn 1g of a substance from a liquid to a gas  Water has a high heat of vaporization  WHY?

39. AP Biology 5. Heat of vaporization Evaporative cooling 1.Molecules moving fast enough will overcome this attraction and depart from the liquid into the air, cooling the area around it 2.The molecules of water left behind will have a lower kinetic energy, and temperature decreases 3.Maintain homeostasis by panting or sweating (prevents overheating) 4.Stability of temperature in lakes and ponds

40. AP Biology Ionization of water & pH  Water ionizes  H + splits off from H 2 O, leaving OH –  if [H + ] = [ - OH], water is neutral  if [H + ] > [ - OH], water is acidic  if [H + ] < [ - OH], water is basic H Hydronium ion (H 3 O + ) H Hydroxide ion (OH – ) H H H H H H + – +

41. AP Biology pH Scale 10 –1 H + Ion Concentration Examples of Solutions Stomach acid, Lemon juice 1 pH 10 0 Hydrochloric acid0 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 hydroxide14 pH= -log [H + ] 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 +

42. AP Biology pH = -log [H + ] [H + ] = 10 -6 M pH = -log [H + ] x = -log [10 -6 M] pH = 6 pH = -log [10 -7 M] pH = 7 [H + ] = 10 -7 M 1. As [H + ] goes up, pH goes DOWN 3. A change in 1 pH corresponds to a 10 - fold change in [H + ] 2. As [H + ] goes down, pH goes UP What if the pH is 10X higher?

43. AP Biology How many times more acidic is lemon juice than urine? 10,000X more acidic

44. AP Biology How many times more basic is milk of magnesia (pH 11) compared to seawater (pH 8)? 1000X more basic

45. AP Biology Buffers & cellular regulation  pH of cells must be kept ~7  pH affects shape of molecules  shape of molecules affect function  pH affects cellular function  Control pH by buffers  reservoir of H +  donate H+ when [H + ] falls  absorb H+ when [H + ] rises

46. AP Biology The Threat of Acid Precipitation Acid precipitation Refers to rain, snow, or fog with a pH lower than pH 5.6 Is caused primarily by the mixing of different pollutants with water in the air Can damage life in Earth’s ecosystems Lakes, ponds, soil chemistry