Atoms and Bonds in Molecules: Understanding Matter in Cells

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 (12C) and Carbon 14 (14C) both are carbon, must have 6 protons 12C has 6 protons and 6 neutrons 14C 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. 14C  14N + 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 H2O glucose C6H12O6 oxygen gas O2

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 bondChlorine atoms share 1 pair of electrons similar to Fig. 2.8

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

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

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. glucoseO-H bond is polar covalent

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

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 moleculeUsually 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. NADox + e- + H+ NADHrelower energy higher 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. HCO3- + H+  H2CO3NaOH  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 concentrationBased on logarithms, each whole number change represents a 10-fold change in H+.pH 6 is ______ more acidic than pH 7Negative log is why larger pH numbers represent lower acidity.100 = 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.H2O + CO2 H2CO3  HCO3- + 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 compoundsOrganic molecule- a molecule synthesized by living organisms(no longer useful)- a molecule containing 2 or more carbon atoms(What about methane, CH4?)- a molecule containing at least the elements ________ and __________

34. Functional Groups - parts of organic molecules • Hydroxyl group -OH • Methyl group -CH3 • Carboxyl (acidic) group -COOH • Amino group -NH2 • Phosphate group -PO3

35. Can you identify the functional groups?

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

37. Can you identify the functional groups?__________, -CH3

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

39. Can you identify the functional groups?______________, -PO3

40. Can you identify the functional groups?__________, -NH2

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, C6H12O6 ribose, C5H10O5

45. _________________ • Composed of 2 simple sugars bonded together • C:H:O ratio not quite 1:2:1 e.g. sucrose, C12H22O11, made from joining glucose and fructose, both C6H12O6 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 Acids Glycerides Phospholipids Steroids