1. Chemistry for Bio 11

2. Chemistry is relevant to Biological Concepts All Living things are made of matter The interactions of matter are described by chemical principles Biolgists are interested in: – Biochemical reactions – Complex biological molecules – Chemical energy – The chemical environment

3. Biochemical reactions All living things are collections of a vast number of chemical reactions Even the simplest living things contain impossibly complex pathways

5. Complex biological molecules All living things are made of complex macromolecules Chemical principles rule their assembly

6. Chemical energy Photosynthesis creates molecules rich in energy: 6CO 2(g) + 6H 2 O (l) + hν  C 6 H 12 O 6(s) + 6O 2(g)

7. The Chemical Environment The physical properties of water determine the fate of life on earth pH, salinity and other chemical factors influence

8. Basic principles of chemistry

9. Atoms

10. Atoms are the smallest individual unit of matter Atoms are comprised of protons, neutrons and electrons Proton: Charge= +1, Mass= 1 Neutron: Chg= 0, mass= 1 Electron: Chg = -1, mass= ~0 Mass= p + n Charge = p - e

11. LE 2-4a 2 2 2 Protons Neutrons Electrons Helium atom Mass number = 4 6 6 6 Protons Neutrons Electrons Carbon atom Mass number = 12 Electron cloud Nucleus 2e – 6e –

13. Elements are defined by the number of their protons There are 92 naturally occurring elements Many others have been synthesized Atomic number: # protons Atomic mass: protons Isotopes- different atoms of same element, with different # neutrons Atomic weight: Naturally occurring average of isotopes of a substance

14. 96% of human tissue is comprised of 6 elements Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorous, Sulfur (CHNOPS) 25 elements serve known functions in the body, incl. Ca, K, Na, Cl, Mg, Fe

15. Atomic structure Protons and electrons in the nucleus Electrons orbit around Bohr atom- classic model featuring electrons in “planetary” orbitals Each orbit holds a determined number of electrons (first holds two, 2 nd and 3 rd hold eight

16. The number of neutrons in atoms is variable Isotopes Some isotopes are stable, others are radioactive

17. Isotopes of carbon have important applications in biology and archaeology

18. Other radioactive isotopes are also important

19. Electron cloud model Currently accepted model of atomic structure 90% probability cloud Mostly empty space Unfilled orbitals found in unstable, reactive elements Therefore, orbitals influence bonding

20. Molecules, compounds, chemical reactions, and bonding

21. Elements combine in chemical reactions to form compounds Molecules- 2 or more atoms combined in a specific way Compounds- different elements in a molecule, in exact, whole-number ratios, joined by a chemical bond 2 major means of intramolecular chemical bonding: Covalent (incl. polar and nonpolar) and Ionic

22. Atoms are stable when their outer shells are filled with electrons Shell 1: Holds 2 electrons Shell 2: Holds 8 Shell 3: Holds 8 Hydrogen- 1p, 1e, seeks a second electron in its outermost shell Carbon seeks 4 The electrons in the outermost shell are called valence electrons

23. Noble gases have a stable electron structure Their outer orbitals have a full complement of electrons Noble gases are very unreactive

24. In ionic bonding, an atom takes an electron from another atom, forming 2 ions LE 2-7 Transfer of electron Na Sodium atom Cl Chlorine atom Na  Sodium ion Cl  Chloride ion Sodium chloride (NaCl)

25. Ions Ions- Charged atoms or molecules Anion- negative ion Cation- positive ion Ionization- reaction producing ions Salt- a neutral compound comprised of ions

26. LE 2-7a-2 Na  Sodium ion Cl  Chloride ion Sodium chloride (NaCl)

27. LE 2-7b Na  Cl 

28. In covalent bonding, pairs of valence electrons are shared, and molecules are formed

29. LE 2-17a  2 H 2 O2O2 2 H 2 O 

30. LE 2-6b Nitrogen (N) Atomic number = 7 Oxygen (O) Atomic number = 8

31. In neutral molecules, carbon always forms 4 bonds Structural formula Ball-and-stick model Space-filling model Methane The 4 single bonds of carbon point to the corners of a tetrahedron.

32. LE 3-1b EthanePropane Carbon skeletons vary in length.

33. LE 3-1c ButaneIsobutane Skeletons may be unbranched or branched.

34. LE 3-1d 1-Butene2-Butene Skeletons may have double bonds, which can vary in location.

35. LE 3-1e Skeletons may be arranged in rings. CyclohexaneBenzene

36. Organic Chemistry The chemistry of carbon Hydrocarbons are the most basic example – Combustible – Can form rings

37. The variety of carbon compounds is limitless All terrestrial life is based on carbon

38. Covalent bonds hold together the macromolecules of life Living things create macromolecular products for structure: 6CO 2(g) + 6H 2 O (l) + hν  C 6 H 12 O 6(s) + 6O 2(g) Macromolecules as reactants are broken down for energy: C 6 H 12 O 6(s) + 6O 2(g)  6CO 2(g) + 6H 2 O (l) All the reactions of a living thing are called its metabolism

39. Electronegativity determines properties of covalently bonded molecules

40. Electronegativity = “electron greediness” Atoms in covalently bonded molecules do not always share electrons equally This creates polar molecules Polar regions of water molecules interact to form hydrogen bonds Hydrogen bonds: weak/temporary intermolecular forces

41. Hydrogen bonding in water determine many of water’s unique properties H-bonds can form a lattice (ice) H-bonds require much energy to break H-bonds give water surface tension Hydrogen bond

42. Water dissolves many ionic compounds (“like dissolves like”)

43. Figure 2.11

44. Figure 2.12

45. LE 2-13 Hydrogen bond Ice Hydrogen bonds are stable Liquid water Hydrogen bonds constantly break and re-form

46. pH is a measure of acidity/basicity pH = -log [H + ] (logarithmic scale) pH 1  6.9: acid pH 7.1  14: base pH 7  neutral Acids donate [H + ] to water Bases remove [H + ] from water (or donate [OH - ] to water) Proteins are very sensitive to small changes in pH

47. LE 2-15 Acidic solution OH  HH HH HH HH HH HH HH HH HH HH HH HH HH Increasingly ACIDIC (Higher concentration of H  ) Neutral solution OH  HH HH Basic solution NEUTRAL  H        pH scale Lemon juice, gastric juice Grapefruit juice, soft drink Tomato juice Human urine Pure water Human blood Seawater Milk of magnesia Household ammonia Household bleach Oven cleaner Increasingly BASIC (Lower concentration of H  )

48. Figure 2.16a

49. Figure 2.16b