Atoms, Bonds, and Molecules What is “stuff” made of?

1. Atoms, Bonds, and Molecules What is “stuff” made of?

2. Atoms and Bonds I. Atoms A. Matter     1. ‘Elemental’ forms of matter, or ‘the elements’, are different forms of matter which have different chemical and physical properties, and can not be broken down further by chemical reactions.

3. Atoms and Bonds I. Atoms A. Matter     1. ‘Elemental’ forms of matter, or ‘the elements’, are different forms of matter which have different chemical and physical properties, and can not be broken down further by chemical reactions. There are 92 naturally occurring elements…

4. Atoms and Bonds I. Atoms A. Matter     1. Elements are different forms of matter which have different chemical and physical properties, and can not be broken down further by chemical reactions. 2. The smallest unit of an element that retains the properties of that element is an atom.

5. Atoms and Bonds I. Atoms A. Matter     1. Elements are different forms of matter which have different chemical and physical properties, and can not be broken down further by chemical reactions. 2. The smallest unit of an element that retains the properties of that element is an atom. 3. Atoms are WICKED SMALL and are mostly SPACE. The material ‘things’ in atoms are protons and neutrons in the nucleus, orbited by electrons: Proton: in nucleus; mass = 1, charge = +1 - Defines Element Neutron: in nucleus; mass = 1, charge = 0 Electron: orbits nucleus; mass ~ 0, charge = -1 NOT TO SCALE

6. Atoms and Bonds I. Atoms A. Matter B. Properties of Atoms 1. Subatomic Particles Proton: in nucleus; mass = 1, charge = +1 - Defines Element Neutron: in nucleus; mass = 1, charge = 0 Electron: orbits nucleus; mass ~ 0, charge = -1 Orbit at quantum distances (shells) Shells 1, 2, and 3 have 1, 4, and 4 orbits (2 electrons each) Shells hold 2, 8, 8 electrons = distance related to energy

7. Neon (Bohr model)

8. Atoms and Bonds I. Atoms A. Matter B. Properties of Atoms 1. Subatomic Particles 2. Mass = protons + neutrons 8 O 15.99

9. Atoms and Bonds I. Atoms A. Matter B. Properties of Atoms 1. Subatomic Particles 2. Mass = protons + neutrons 3. Charge = (# protons) - (# electrons)... If charge = 0, then you have an ...ION

10. Atoms and Bonds I. Atoms A. Matter B. Properties of Atoms 4. Isotopes -

11. Atoms and Bonds I. Atoms A. Matter B. Properties of Atoms 4. Isotopes - 'extra' neutrons... heavier Some are stable Some are not... they 'decay' - lose the neutron These 'radioisotopes' emit energy (radiation)

12. Atoms and Bonds I. Atoms A. Matter B. Properties of Atoms 4. Isotopes - 'extra' neutrons... heavier Some are stable Some are not... they 'decay' - lose protrons/neutrons These 'radioisotopes' emit energy (radiation) So, K40, with 19 protons and 21 neutrons, decays to Ar40 (18 protons, 22 neutrons) with the conversion of a proton into a neutron. As neutrons weigh slightly less than protons, the mass that is lost in this conversion is lost as energy (E = mc2)

13. Atoms and Bonds I. Atoms A. Matter B. Properties of Atoms 4. Isotopes - 'extra' neutrons... heavier Some are stable Some are not... they 'decay' - lose the neutron These 'radioisotopes' emit energy (radiation) This process is not affected by environmental conditions and is constant; so if we know the amount of parent and daughter isotope, and we know the decay rate, we can calculate the time it has taken for this much daughter isotope to be produced.

14. Atoms and Bonds I. Atoms II. Bonds A. Molecules

15. Atoms and Bonds I. Atoms II. Bonds A. Molecules   1. atoms chemically react with one another and form molecules - the atoms are "bound" to one another by chemical bonds - interactions among electrons or charged particles.

16. Atoms and Bonds I. Atoms II. Bonds A. Molecules     1. atoms chemically react with one another and form molecules - the atoms are "bound" to one another by chemical bonds - interactions among electrons or charged particles.    2. Bonds form because atoms attain a more stable energy state if their outermost shell is full. It can do this by loosing, gaining, or sharing electrons.  This is often called the 'octet rule' because the 2nd and 3rd shells can contain 8 electrons.

17. Atoms and Bonds I. Atoms II. Bonds A. Molecules B. Covalent Bonds - atoms are shared

18. Atoms and Bonds I. Atoms II. Bonds A. Molecules B. Covalent Bonds - atoms are shared C. Ionic Bond - transfer of electron and attraction between ions Na Cl

19. Atoms and Bonds I. Atoms II. Bonds A. Molecules B. Covalent Bonds - atoms are shared C. Ionic Bond - transfer of electron and attraction between ions D. Hydrogen Bonds - weak attraction between partially charged hydrogen atom in one molecule and a negative region of another molecule

20. D. Hydrogen Bonds - weak attraction between partially charged hydrogen atom in one molecule and a negative region of another molecule

21. D. Hydrogen Bonds - weak attraction between partially charged hydrogen atom in one molecule and a negative region of another molecule

22. D. Hydrogen Bonds - weak attraction between partially charged hydrogen atom in one molecule and a negative region of another molecule

23. Biologically Important Molecules

24. Biologically Important Molecules • Water

25. Biologically Important Molecules • Water • A. Structure • - polar covalent bonds

26. Biologically Important Molecules • Water • A. Structure • - polar covalent bonds

27. Biologically Important Molecules • Water • A. Structure • - polar covalent bonds • - partial charges

28. Biologically Important Molecules • Water • A. Structure • - polar covalent bonds • - partial charges • - hydrogen bonds

29. Water • A. Structure • B. Properties • - 1. cohesion • “water sticks to itself through H-bonds”

30. I. Water B. Properties - 2. adhesion “water sticks to other charged surfaces”

31. I. Water B. Properties - consequences of cohesion/adhesion Capillary action – rotating water water molecules stick to the inner surface of thin tubes, and act as a fulcrum for other water molecules that can spin and contact the surface above them… through cohesion, those in contact with the new surface are themselves a surface for now water molecules to attach. - important in the mvmt of soil water up from the water table to the root zone, and up vascular plants in xylem tissue.

32. I. Water B. Properties - 3. High specific heat ‘specific heat’ is the amount of energy change required to change the temperature of 1 g of that substance 1oC. By definition, a calorie is a change in heat energy needed to change 1ml (or g) of water 1oC. (Dietary “calories” are usually kilocalories).

33. I. Water B. Properties - 3. High specific heat ‘specific heat’ is the amount of energy change required to change the temperature of 1 g of that substance 1oC. By definition, a calorie is a change in heat energy needed to change 1ml (or g) of water 1oC. (Dietary “calories” are usually kilocalories). Water has a high specific heat because of the hydrogen bonds, which must be broken before the molecules can move faster (increase temperature).

34. I. Water B. Properties - consequences of water’s high specific heat Water is an excellent thermal buffer - aqueous solutions change temperature more slowly than air (less dense aqueous solution).

35. I. Water B. Properties - consequences of water’s high specific heat Water is an excellent thermal buffer - aqueous solutions change temperature more slowly than air (less dense aqueous solution). So, aqueous environments are more thermally stable (air temps vary more dramatically than water temps…)

36. I. Water B. Properties - consequences of water’s high specific heat Water is an excellent thermal buffer - aqueous solutions change temperature more slowly than air (less dense aqueous solution). So, aqueous environments are more thermally stable (air temps vary more dramatically than water temps…) So, terrestrial organisms change temperature more slowly than the environment, giving them time to adjust behaviorally (like leaving!)

37. I. Water B. Properties - 4. High heat of vaporization Quantity of heat a liquid must absorb for 1 g of it to change to a gas. Water’s high heat of vaporization means that: - water doesn’t change state quickly; it can absorb a lot of energy without changing state.

38. I. Water B. Properties - 4. High heat of vaporization Quantity of heat a liquid must absorb for 1 g of it to change to a gas. Water’s high heat of vaporization means that: - water doesn’t change state quickly; it can absorb a lot of energy without changing state. - when it does change state, the most energetic molecules evaporate and leave the liquid (or surface); so the average kinetic energy (temperature) of the liquid or surface drops dramatically – this is evaporative cooling.

39. I. Water B. Properties - 4. High heat of vaporization Quantity of heat a liquid must absorb for 1 g of it to change to a gas. Water’s high heat of vaporization means that: - water doesn’t change state quickly; it can absorb a lot of energy without changing state. - when it does change state, the most energetic molecules evaporate and leave the liquid (or surface); so the average kinetic energy (temperature) of the liquid or surface drops dramatically – this is evaporative cooling. - evaporative cooling keeps water bodies cooler than air, and cools living organisms (evapotranspiration, perspiration).

40. I. Water B. Properties - 6. solvent Ionic and polar compounds dissolve in water Salts dissolve in water when their constituent ions separate and bond to water molecules instead of each other.

41. I. Water B. Properties - 7. Water dissociates Although the H+ is always bound to another water molecule (as a hydronium ion), we represent it (H+) and it’s concentration as if it is ‘free’. In pure water, the concentration is 1 x 10-7.

42. I. Water B. Properties - 7. Water dissociates In all aqueous solutions at 25oC, The product of [H+][OH-] = 1 x 10-14 So, if the pH is 6.0, the concentration of OH- ions is 1 x 10-8

43. I. Water • C. Water and Life • Why Life on Earth in Water?

44. I. Water • C. Water and Life • Life on Earth is inconceivable without water. • Life requires rapid and continuous chemical reactions facilitated by a dissolution of reactants in a liquid solvent. • Water’s solvent properties are ideal. • Water is a liquid over a wide temperature range that is very common on Earth. (High specific heat, vaporization). • Water is abundant on Earth, covering over 70% of the surface. • Water is a thermally stable internal/external environment. • No surprize that life probably originated in water, and did not adapt to exploit the desiccating terrestrial environments until the last 10% of Earth history.

45. Biologically Important Molecules • Water • Carbohydrates

46. Carbohydrates • A. Structure • 1. monomer = monosaccharide • typically 3-6 carbons, and CnH2nOn formula

47. Carbohydrates • A. Structure • 1. monomer = monosaccharide • typically 3-6 carbons, and CnH2nOn formula • have carbonyl and hydroxyl groups

48. Carbohydrates • A. Structure • 1. monomer = monosaccharide • typically 3-6 carbons, and CnH2nOn formula • have carbonyl and hydroxyl groups • carbonyl is either ketone or aldehyde • in aqueous solutions, they form rings

49. Carbohydrates • A. Structure • 1. monomer = monosaccharide • 2. polymerization: • dehydration synthesis reaction

50. Carbohydrates • A. Structure • 1. monomer = monosaccharide • 2. polymerization • 3. Polymers = polysaccharides