1. Lecture 2 Chemistry Comes Alive THE CHEMICAL LEVEL

5. Figure 2.1 : The structure of an atom, p. 27. Nucleus Helium atom 2 protons (p + ) 2 neutrons (n 0 ) 2 electrons (e – ) (a) Planetary model Key: Helium atom 2 protons (p + ) 2 neutrons (n 0 ) 2 electrons (e – ) (b) Orbital model = Electron = Electron cloud = Proton = Neutron Nucleus

6. Figure 2.4: Chemically inert and reactive elements, p. 32. Helium (He) (2p + ; 2n 0 ; 2e – ) Neon (Ne) (10p + ; 10n 0 ; 10e – ) He Ne 2e 2e 8e Hydrogen (H) (1p + ; 0n 0 ; 1e – ) Carbon (C) (6p + ; 6n 0 ; 6e – ) Oxygen (O) (8p + ; 8n 0 ; 8e – ) Sodium (Na) (11p + ; 12n 0 ; 11e – ) H C Na O 2e 1e 4e 2e 8e 1e 6e 2e (a ) Chemically inert elements (valence shell complete ) (b ) Chemically active elements (valence shell incomplete )

10. Figure 2.7b-c: Formation of covalent bonds, p. 35. + or Oxygen atom Oxygen atom Molecule of oxygen gas (O 2 ) or Nitrogen atom Nitrogen atom Molecule of nitrogen gas (N 2 ) + (b) Formation of a double covalent bond (c) Formation of a triple covalent bond O O O O O O N N N N N N

11. Figure 2.7a: Formation of covalent bonds, p. 35. Hydrogen atoms Carbon atom Molecule of methane gas (CH 4 ) or + (a) Formation of four single covalent bonds H H H H H H H H C C C H H H H

12. Figure 2.5: Formation of an ionic bond, p. 33. + Sodium atom (Na) (11p + ; 12n 0 ; 11e – ) Chlorine atom (Cl) (17p + ; 18n 0 ; 17e – ) Sodium ion (Na + ) Chloride ion (Cl – ) Sodium chloride (NaCl) CI – Na + (a) (b) Cl Na Cl Na –

13. Figure 2.10a: Hydrogen bonding between polar water molecules, p. 37. (a)  –  –  –  –  –  +  +  +  +  +  + H H H H H O O O O O H H H H H Hydrogen bonds

14. Figure 2.9: Comparison of ionic, polar covalent, and nonpolar covalent bonds , p. 36. Ionic bond Complete transfer of electrons Separate ions (charged particles) form Na + Cl – Sodium chloride Water Carbon dioxide Polar covalent bond Unequal sharing of electrons Nonpolar covalent bond Equal sharing of electrons Charge balanced among atoms H H O O O C Slight negative charge (  – ) at one end of molecule, slight positive charge (  + ) at other end  +  +  – Hydrogen bond weakest strongest

18. Figure 2.13: The pH scale and pH values of representative substances , p. 42. Concentration in moles/liter [OH – ] 10 –14 10 –13 10 –12 10 –11 10 –10 10 –9 10 –8 10 –7 10 –6 10 –5 10 –4 10 –3 10 –2 10 –1 10 0 10 –5 10 –6 10 –7 10 –8 10 –9 10 –10 10 –11 10 –12 10 –13 10 –14 10 –4 10 –3 10 –2 10 –1 10 0 5 6 7 8 9 10 11 12 13 14 4 3 2 1 0 [H + ] pH Examples Lemon juice; gastric juice (pH 2) Grapefruit juice (pH 3) Sauerkraut (pH 3.5) Tomato juice (pH 4.2) Coffee (pH 5.0) Urine (pH 5–8) Saliva; milk (pH 6.5) Distilled water (pH 7) Human blood; semen (pH 7.4) Egg white (pH 8) Seawater (pH 8.4) Milk of magnesia (pH 10.5) Household ammonia (pH 11.5–11.9) Household bleach (pH 12) Oven cleaner (pH 13.5) Increasing alkalinity (basicity) Increasing acidity Neutral [H + ] = [OH – ]

19. Figure 2.12: Dissociation of a salt in water , p. 40. olecule Salt crystal Ions in solution H H O Na + Cl – Na + Cl –  –  +  + Salts are ionic compounds that dissociate completely in water to give CATIONS and ANIONS Ex. NaCl, KCl

22. Figure 2.14a-b: Carbohydrate molecules , p. 45. Glucose Fructose Galactose Deoxyribose Ribose Glucose Fructose Dehydration synthesis Hydrolysis Glucose Glucose Maltose Sucrose Galactose Glucose Lactose (a) Monosaccharides- monomers or building blocks of Carbohydrates CH 2 OH H OH H CH 2 OH H OH H OH OH OH OH O H OH OH H HO H H O HO H CH 2 OH H HO HOCH 2 O H OH H OH H HO H O HOCH 2 H H H OH H O HOCH 2 H H H OH H + O CH 2 OH H H OH OH H HO H H OH O OH HO H H CH 2 OH H HO H 2 O H 2 O HOCH 2 O HOCH 2 H H OH OH H HO H H O HOCH 2 H H H OH OH OH H H (b) Disaccharides – composed of 2 monosaccharides – hexose sugars CH 2 OH H O O HOCH 2 HOCH 2 H OH HOCH 2 H OH O H OH H H HO H O H H OH OH H H O O H H OH OH HO H H O OH HO H H CH 2 OH H

23. Figure 2.14c: Carbohydrate molecules, p. 45. Glycogen (c) Portion of a polysaccharide molecule (glycogen ) O O O O O O O O O CH 2 O O O O O O O

25. Figure 2.15a: Lipids, p. 47. Glycerol 3 fatty acid chains Triglyceride, or neutral fat 3 water molecules (a) Formation of a triglyceride H H H C C C O O O H H H C O CH 2 CH 2 CH 2 CH 2 CH 3 C O CH 2 CH 2 CH 2 CH 2 CH 3 CH 2 CH 2 CH 2 CH 2 CH 3 HO HO HO H H H H H C C C O O O H H CH 2 CH 2 CH 2 CH 2 CH 3 CH 2 CH 2 CH 2 CH 2 CH 3 CH 2 CH 2 CH 2 CH 2 CH 3 3H 2 O C O C O C O C O + +

27. Figure 2.15b-c: Lipids, p. 47. Glycerol backbone Phosphorus-containing group (polar end) 2 fatty acid chains (nonpolar end) Polar “head” Nonpolar “tail” (b) Phospholipid molecule (phosphatidylcholine) (c) Cholesterol C O O C O P O N + CH 2 CH 2 O O CH 3 CH 3 O O CH 3 CH 2 CH 2 CH O CH 2 CH 2 CH 2 C H CH 2 CH 2 CH 2 CH 2 CH 2 CH 2 CH 2 CH 3 CH 2 CH 3 CH 3 CH 3 CH 3 H 3 C HO H C CH 2 CH 3

30. Figure 2.16: Amino acid structures, p. 49. Amine group Acid group (a) Generalized structure of all amino acids (b) Glycine (the simplest amino acid) (d) Lysine (a basic amino acid) (e) Cysteine (a sulfur-containing amino acid) (c) Aspartic acid (an acidic amino acid) R H C OH H 2 N H CH 2 COOH CH 2 SH C OH H 2 N CH 2 NH 2 H H CH 2 CH 2 C C OH H 2 N H H OH H 2 N H C C OH H 2 N H O C O C O C O C O C

31. Figure 2.17: Amino acids are linked together by dehydration synthesis, p. 49. Amino acid Amino acid Dehydration synthesis Hydrolysis Dipeptide Peptide bond + N H H C R H O N H H C R C C H O H 2 O H 2 O N H H C R C H O N H C R C H O OH OH OH

33. Figure 2.18a,c: Levels of protein structure, p. 51. O O (c) Secondary structure (  -pleated sheet) (a) Primary structure (polypeptide strand) C C R H N N C H C R H H C R H O O

34. Figure 2.18b,d,e: Levels of protein structure, p. 51. Heme group (b) Secondary structure (  -helix) (d) Tertiary structure (e) Quaternary structure (hemoglobin molecule)  -helix

36. Figure 2.19: Denaturation of a globular protein such as an enzyme , p. 53. Substrate “fits” with active site Active site Functional enzyme Substrate unable to bind Denatured enzyme (a) (b)

37. 4 th type of Organic compounds in the body: NUCLEIC ACIDS - Structure of DNA, p. 56. (b) A A G A T T T C G C G C A A G G A (c) Thymine (T) Adenine (A) Cytosine (C) Guanine (G) Deoxyribose sugar Phosphate Hydrogen bond Key: Sugar-phosphate backbone