1. Chapter 2 The Molecules of Cells Pages 19-44

2. Matter - a substance that occupies space and has ________; - a substance composed of _________

3. Atom - the smallest unit of an _________ that possesses all the characteristics of that element - unit of an element that is not easily divisible by ordinary chemical means

4. Atom Composed of : 1 or more _________ (positive charge), usually 1 or more neutrons (no charge), and 1 or more __________ (negative charge) Often the number of protons and electrons are equal. The resulting atom has no net charge.

5. similar to Fig. 2.2

6. ____________ a pure substance composed of only one kind of atom e.g. hydrogen (H), carbon (C), oxygen (O) (See Blackboard for a list of chemical symbols you should know.) Different elements MUST have a different number of protons in the nucleus

7. Isotope an atom of an element that differs in the number of ____________ in the nucleus e.g. Carbon 12 ( 12 C) and Carbon 14 ( 14 C) both are carbon, must have 6 protons 12 C has 6 protons and 6 neutrons 14 C has 6 protons and 8 neutrons

8. ____________ Isotope an unstable isotope; an atom that will decay (change) into a different element as subatomic particles are lost from the nucleus e.g. 14 C  14 N + 1e - 6p + 8n 7p + 7n

9. Ion an atom of an element that has gained or lost one or more ___________ e.g. H +, Na + - both have lost one electron Cl - - has gained one electron

10. outer electron is lost

11. _____________ a substance composed of two or more atoms; the atoms may be identical or may be different elements (compound). e.g. water H 2 O glucose C 6 H 12 O 6 oxygen gas O 2

12. Chemical Bond an attractive force between two atoms Three different types: __________ ______________ _____________

13. Ionic Bond the chemical bond that results from the attractive force between two oppositely charged _________ e.g. table salt Na + - Cl - Ionic bonds are not extremely strong.

14. Fig. 2.7

15. Covalent Bonds chemical bonds that result from two atoms sharing one or more pairs of ____________; produces a relatively strong bond Two types of covalent bonds: Nonpolar covalent bond – the pair(s) of electrons are shared equally Polar covalent bond – the pair(s) of electrons are not shared equally

16. Nonpolar covalent bond Chlorine atoms share 1 pair of electrons similar to Fig. 2.8

17. Polar covalent bonds O and H do not share electrons equally similar to Fig. 2.9

18. O and H have partial charges due to polar covalent bonds Pg. 26 O HH

19. _____________ Bond an attractive force between two atoms with opposite partial charges The atoms are not ions, the partial charges result from the atoms being polar covalently bonded to some other atom. weak bonds, but very important in living systems

20. O forms hydrogen bonds with H BETWEEN water molecules Fig. 2.9

21. Properties of water very good __________ for polar substances water molecules are adhesive and cohesive takes a lot of energy to warm (high heat capacity) or vaporize (high heat of vaporization) water ice (solid water) is ________ dense than liquid water

22. ________________ - the substance is attracted to water; will form H bonds with water; contains some polar covalent bonds ________________ - the substance is repelled by water; will not form H bonds with water; contains mostly nonpolar covalent bonds

23. Hydrophilic – e.g. glucose O-H bond is polar covalent

24. A fatty acid – all the C-C and C-H bonds are nonpolar covalent Will this molecule form any H bonds with water? see also Fig. 2.20

25. See page 110 in Chapt. 6 ____________ – the loss of one or more electrons from an atom or molecule _____________ – the gaining of one or more electrons from an atom or molecule Usually linked; referred to as oxidation/reduction (redox) reactions

26. Oxidation/reduction is important in living systems because energy is transferred from molecule to molecule with the electrons. Oxidation – loss of e - and _______ Reduction – gaining of e - and energy

27. NAD ox + e - + H +  NADH re lower energyhigher energy

28. Acid - a substance that releases _________ ions when placed in solution e.g. HCl  H + + Cl - ________ - a substance that combines with H + or releases OH - when placed in solution e.g. HCO 3 - + H +  H 2 CO 3 NaOH  Na + + OH -

29. _____ - a measure of the hydrogen ion concentration of a solution - ranges from 0 to 14 0 – the most acidic, lots of H + 14 – the least acidic, very few H + (most alkaline or basic) 7 – neutral, neither acidic or basic

30. pH is the negative logarithm of the hydrogen ion concentration Based on logarithms, each whole number change represents a 10-fold change in H +. pH 6 is ______ more acidic than pH 7 Negative log is why larger pH numbers represent lower acidity. 10 0 = 1 10 -1 = 0.1 10 -2 = 0.01 10 -14 = 0.000,000,000,000,01

31. __________ - a substance, that within a certain range, maintains a constant pH by combining with H + when mixed with an acid, or releasing H + when mixed with a base - Buffers do not necessarily maintain a pH of 7. H 2 O + CO 2  H 2 CO 3  HCO 3 - + H +  

32. Organic Chemistry “Organic chemistry nowadays almost drives me mad. To me it appears like a primeval tropical forest full of the most remarkable things, a dreadful endless jungle into which one does not dare enter for there seems to be no way out.” Fredrich Wohler 1835

33. Organic Chemistry - the study of ___________ containing compounds Organic molecule - a molecule synthesized by living organisms (no longer useful) - a molecule containing 2 or more carbon atoms (What about methane, CH 4 ?) - a molecule containing at least the elements ________ and __________

34. Functional Groups - parts of organic molecules Hydroxyl group -OH Methyl group -CH 3 Carboxyl (acidic) group-COOH Amino group-NH 2 Phosphate group-PO 3

35. Can you identify the functional groups?

36. Can you identify the functional groups? _____________, -COOH

37. Can you identify the functional groups? __________, -CH 3

38. Can you identify the functional groups? _____________, -OH

39. Can you identify the functional groups? ______________, -PO 3

40. Can you identify the functional groups? __________, -NH 2

41. Families of Organic Molecules Carbohydrates Lipids Proteins Nucleic Acids Note – this list does not contain all the different kinds of organic molecules

42. ____________________ Contain only C, H and O Lots of hydroxyl groups Three groups we’ll look at Monosaccharides – simple sugars Disaccharides – made from 2 simple sugars Polysaccharides – polymers of simple sugars

43. _____________ - a large molecule composed of repeating subunits, monomers e.g. polysaccharides, proteins, DNA, plastics, etc.

44. Monosaccharides – simple sugars Contain only C, H, and O Ratio of these three elements is: ___C : ___H : ___O Lots of hydroxyl groups, -O-H Dissolve easily in water. Why? e.g. glucose or fructose, C 6 H 12 O 6 ribose, C 5 H 10 O 5

45. _________________ Composed of 2 simple sugars bonded together C:H:O ratio not quite 1:2:1 e.g. sucrose, C 12 H 22 O 11, made from joining glucose and fructose, both C 6 H 12 O 6 Easily digested to simple sugars

46. Fig. 2.16 Dehydration aka

47. ______________________ Contain only C, H and O Ratio not 1C:2H:1O, but still contains lots of O Size limits solubility in water e.g. starch and cellulose are both polysaccharides made from only glucose starch – easily digested cellulose – undigestible by most organisms

48. similar to Fig. 2.17

49. similar to Fig. 2.19

50. __________ Usually contain only C, H and O Ratio of C:H:O nowhere near 1:2:1 lots of C and H, relatively little O 4 types we’ll look at: Fatty AcidsGlycerides PhospholipidsSteroids

51. Fatty Acids Consist of a carboxyl group and a ____________________ chain similar to Fig. 2.20

52. ________________ Fatty Acids at least 2 H atoms bonded to each of the C in the hydrocarbon chain Common in animal fats; solid at room temperature from Fig. 2.20

53. _________________ Fatty Acids One or more C atoms in the hydrocarbon chain have less than 2 H atoms bonded to them. Common in vegetable oils; liquid at room temp. Trans fats - partially hydrogenated vegetable oils, not typically made by living organisms from Fig. 2.20

54. Glycerides Glycerol and 1, 2 or 3 ________ _____ (mono-, di-, or triglycerides) How are they synthesized? How do you digest them?

55. When did your great grandmother use hydrolysis of triglycerides? similar to Fig. 2.20 Dehydration

56. Will this molecule form any H bonds with water? Is it hydrophilic or hydrophobic? Fig. 2.20

57. ________________ A diglyceride + phosphate group + R group Lipid end is hydrophobic Phosphate and R group end is hydrophilic Form the basic structure of all cell membranes

58. similar to Fig. 2.21

59. Steroids Non-fatty acid lipids Contain only lots of C, H and little O Behaves like other lipids e.g. _________________ Absolutely necessary – e.g. cell membranes, sex hormones

60. similar to Fig. 2.22

61. Proteins Contain __________, in amino groups Made from long chains of amino acids Very diverse group of molecules; very diverse functions Shape is extremely important

62. Amino Acids An _________ group and a ____________ group bonded to the same carbon atom Differ in the R group attached to the central carbon atom

63. Amino Acids All proteins made from different combinations of the same 20 amino acids Humans have 8 (children 9) _____________ amino acids – must be present in diet

64. similar to Fig. 2.23

65. Polypeptide A small polymer of ______ _____; part of a protein molecule. Peptide bonds – a covalent bond between the carboxyl group of one amino acid and the amino group of the following amino acid. Synthesis? Digestion?

66. similar to Fig. 2.24 Dehydration

67. _______________ A change in the shape of a molecule. Shape is very important in organic molecules, especially proteins. e.g. frying an egg; sickle-cell anemia

68. _____________ _______ An organic molecule composed of long chains of nucleotides. e.g. DNA, RNA

69. Nucleotides An organic molecule composed of: 1 or more phosphate groups, a 5-carbon sugar, and a _______________ base

71. similar to Fig. 2.26

72. Adenosine Triphosphate - ______ A nucleotide involved in most of the reactions in which energy is transferred in living organisms Composed of Adenine (N-base), 5-C sugar and three phosphate groups

73. similar to Fig. 2.27