1. Biol 210 General Biology 1 Lecture 2 Review Chemical Bonds

2. Atomic Structure Nucleus –Protons, mass = 1, charge = +1 –Neutrons, mass = 1, charge = 0 Electrons –Mass = negligible –Charge = -1 –# e – = # protons –Outer shell (most energenic) e – ’s form chemical bonds

3. Isotopes Some isotopes are stable, such as 1 H 2 Other isotopes are unstable, such as 1 H 3. When tritium decays, it gives off  particle. Because the mass of an element includes the average isotope abundance, the mass and the atomic weight differ slightly Helium, He, atomic number 4, mass 4.003

4. Important Elements C HOPKINS CaFe Mg –C = carbon –H = hydrogen –O = oxygen –P = phosphorous –K = potassium –I = iodine –N = nitrogen –S = sulfur –Ca = calcium –Fe = iron –Mg = magnesium Na = sodium Cl = chloride

5. Every atom has a characteristic total number of covalent bonds that it can form = an atom’s valence. The valence of hydrogen is 1. Oxygen is 2. Nitrogen is 3. Carbon is 4. Phosphorus should have a valence of 3, based on its three unpaired electrons, but in biological molecules it generally has a valence of 5, forming three single covalent bonds and one double bond.

6. Chemical Bonds Two atoms share one or more pairs of valence electrons Four kinds of chemical bonds –Covalent –Hydrogen –Ionic –Van der Waals You must know the first 3 kinds

7. Covalent Bonds Two atoms share one or more pairs of electrons

8. Covalent Bonds Two atoms share one or more pairs of electrons Strongest chemical bond

9. Covalent Bonds Two atoms share one or more pairs of electrons Strongest chemical bond 50-110 kcal/mol

10. Hydrogen molecule Hydrogen atoms have one valence electron each Innermost shell can accommodate two electrons Each atom contributes an electron Electrons effectively fill valence shell for both atoms

11. Oxygen Oxygen has 2 valence electrons Can share two pairs of electrons Two O atoms can form 2 covalent bonds

12. Oxygen + Hydrogen Oxygen can form bonds with hydrogen atoms

13. Oxygen + Hydrogen Oxygen can form bonds with hydrogen atoms Since H can only form one covalent bond

14. Oxygen + Hydrogen Oxygen can form bonds with hydrogen atoms Since H can only form one covalent bond O must bond two H atoms

15. Oxygen + Hydrogen Oxygen can form bonds with hydrogen atoms Since H can only form one covalent bond O must bond two H atoms H 2 O = water

16. Carbon Carbon has a valence of 4 electrons

17. Carbon Carbon has a valence of 4 electrons Can form 4 covalent bonds

18. Carbon Carbon has a valence of 4 electrons Can form 4 covalent bonds Biological molecules are largely carbon- containing molecules

19. Carbon Carbon has 4 valence electrons Can form 4 covalent bonds Biological molecules are largely carbon- containing molecules Organic = derived from organisms

20. s orbital Z Three p orbitals X Y Four hybrid orbitals (a) Hybridization of orbitals. The single s and three p orbitals of a valence shell involved in covalent bonding combine to form four teardrop-shaped hybrid orbitals. These orbitals extend to the four corners of an imaginary tetrahedron (outlined in pink). Tetrahedron Figure 2.16 (a)

21. H—H O=O H—O—H CH 4

22. 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

23. Ionic Bond Covalent bonds result from two atoms sharing electrons

24. Ionic Bond Covalent bonds result from two atoms sharing electrons Sometimes one atom “takes” the electron from another atom.

25. Ionic Bond One atom has more protons than electrons = +1

26. Ionic Bond One atom has more protons than electrons = +1 Other atom has one more electron than protons = - 1

27. Ionic Bond One atom has more protons than electrons = +1 Other atom has one more electron than protons = - 1 Opposite charges attract weakly (3-7 kcal/mol)

28. Hydrogen Bond We have studied two bonding extremes

29. Hydrogen Bond We have studied two bonding extremes Covalent bond = atoms share electrons

30. Hydrogen Bond We have studied two bonding extremes Covalent bond = atoms share electrons Ionic bond = one atom “take”s electrons

31. Hydrogen Bond Unequal e - sharing = partial charges on molecule

32. Hydrogen Bond Unequal e - sharing = partial charges on molecule Oxygen nucleus more attractive to electrons

33. Hydrogen Bond Unequal e - sharing = partial charges on molecule Oxygen nucleus more attractive to electrons Hydrogen nucleus less attractive

34. Hydrogen Bond Unequal e - sharing = partial charges on molecule Oxygen nucleus more attractive to electrons Hydrogen nucleus less attractive Partial charges, O more neg, H more pos

35. Hydrogen Bond Water = polar molecule

36. Hydrogen Bond Water = polar molecule Can interact weakly with other polar molecules

37. Hydrogen Bond Water = polar molecule Can interact weakly with other polar molecules H-bond 3-7 kcal/mol

38. Comparative Bond Strength Covalent bond = 50-110 kcal/mol Ionic bond = 3-7 kcal/mol H-bond = 3-7 kcal/mol van der Waals bond = ~1 kcal/mol

39. Predicted BP for water = -76°C

40. Predicted MP for water = -87°C

41. Predicted BP for water = -76°C Predicted MP for water = -87°C Temp. range for liquid water = 11°

42. Predicted BP for water = -76°C Predicted MP for water = -87°C Predicted temp. range for liquid water = 11° Actual: 0–100°C

43. Predicted BP for water = -76°C Predicted MP for water = -87°C Predicted temp. range for liquid water = 11° Actual: 0–100°C Rationale: H-bonds

44. Hydrogen bonds + + H H + +  – –  – –  – –  – – Figure 3.2 The polarity of water molecules

45. Hydrogen bonds + + H H + +  – –  – –  – –  – – Figure 3.2 The polarity of water molecules – Allows them to form hydrogen bonds with each other

46. Hydrogen bonds + + H H + +  – –  – –  – –  – – Figure 3.2 The polarity of water molecules – Allows them to form hydrogen bonds with each other – Contributes to the various properties water exhibits

47. The different regions of the polar water molecule can interact with ionic compounds called solutes and dissolve them + + + + Cl – – – – – Na + + + + + – – – – – – Cl – Figure 3.6

48. The different regions of the polar water molecule can interact with ionic compounds called solutes and dissolve them Negative oxygen regions of polar water molecules are attracted to sodium cations (Na + ). + + + + Cl – – – – – Na + + + + + – – – – – – Cl – Figure 3.6

49. The different regions of the polar water molecule can interact with ionic compounds called solutes and dissolve them Negative oxygen regions of polar water molecules are attracted to sodium cations (Na + ). + + + + Cl – – – – – Na + Positive hydrogen regions of water molecules cling to chloride anions (Cl – ). + + + + – – – – – – Na + Cl – Figure 3.6

50. Water can also interact with polar molecules such as proteins This oxygen is attracted to a slight positive charge on the lysozyme molecule. This oxygen is attracted to a slight negative charge on the lysozyme molecule. (a) Lysozyme molecule in a nonaqueous environment (b) Lysozyme molecule (purple) in an aqueous environment such as tears or saliva (c) Ionic and polar regions on the protein’s Surface attract water molecules. ++ –– Figure 3.7

51. pH Water can dissociate H Hydronium ion (H 3 O + ) H Hydroxide ion (OH – ) H H H H H H + – + Figure on p. 53 of water dissociating

52. pH Water can dissociate –Into hydronium ions and hydroxide ions H Hydronium ion (H 3 O + ) H Hydroxide ion (OH – ) H H H H H H + – + Figure on p. 53 of water dissociating

53. pH Water can dissociate –Into hydronium ions and hydroxide ions Changes in the concentration of these ions H Hydronium ion (H 3 O + ) H Hydroxide ion (OH – ) H H H H H H + – + Figure on p. 53 of water dissociating

54. pH Water can dissociate –Into hydronium ions and hydroxide ions Changes in the concentration of these ions –Can have a great affect on living organisms H Hydronium ion (H 3 O + ) H Hydroxide ion (OH – ) H H H H H H + – + Figure on p. 53 of water dissociating

55. The pH scale and pH values of various aqueous solutions Increasingly Acidic [H + ] > [OH – ] Increasingly Basic [H + ] < [OH – ] Neutral [H + ] = [OH – ] Oven cleaner 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 pH Scale Battery acid Digestive (stomach) juice, lemon juice Vinegar, beer, wine, cola Tomato juice Black coffee Rainwater Urine Pure water Human blood Seawater Milk of magnesia Household ammonia Household bleach Figure 3.8

56. The pH scale and pH values of various aqueous solutions Increasingly Acidic [H + ] > [OH – ] Increasingly Basic [H + ] < [OH – ] Neutral [H + ] = [OH – ] Oven cleaner 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 pH Scale Battery acid Digestive (stomach) juice, lemon juice Vinegar, beer, wine, cola Tomato juice Black coffee Rainwater Urine Pure water Human blood Seawater Milk of magnesia Household ammonia Household bleach Figure 3.8 —pH 7.4