BIO 3A Fall 2015 Chapters 2,3 And 4

1. BIO 3A Fall 2015Chapters 2,3 And 4

2. Chapter 2 Chemical Context

3. Figure 2.1

4. EXPERIMENT Cedrela sapling Insect barrier Duroia tree Outside, protected Inside, unprotected Inside, protected Figure 2.2 Devil’s garden Outside, unprotected RESULTS 16 12 Dead leaf tissue (cm2) after one day 8 4 0 Outside, protected Inside, protected Inside, unprotected Outside, unprotected Cedrela saplings, inside and outside devil’s gardens

5. EXPERIMENT Insect barrier Cedrela sapling Figure 2.2a Duroia tree Outside, protected Inside, unprotected Inside, protected Devil’s garden Outside, unprotected

6. RESULTS 16 Figure 2.2b 12 Dead leaf tissue (cm2) after one day 8 4 0 Inside, protected Outside, protected Outside, unprotected Inside, unprotected Cedrela saplings, inside and outside devil’s gardens

7. Figure 2.3 Chlorine Sodium Sodium chloride

8. Table 2.1

9. Cloud of negative charge (2 electrons) Electrons Nucleus Figure 2.5 (a) (b)

10. (a) A ball bouncing down a flight of stairs provides an analogy for energy levels of electrons. Figure 2.8 Third shell (highest energy level in this model) Energy absorbed Second shell (higher energy level) First shell (lowest energy level) Energy lost Atomic nucleus (b)

11. Helium 2He Atomic number Hydrogen 1H 2 He 4.00 Mass number Element symbol First shell Electron distribution diagram Figure 2.9 Lithium 3Li Beryllium 4Be Boron 5B Nitrogen 7N Fluorine 9F Oxygen 8O Carbon 6C Neon 10Ne Second shell Sodium 11Na Magnesium 12Mg Aluminum 13Al Sulfur 16S Argon 18Ar Silicon 14Si Chlorine 17Cl Phosphorus 15P Third shell

12. First shell Neon, with two filled Shells (10 electrons) Second shell (a) Electron distribution diagram First shell Second shell Figure 2.10 y x z 1s orbital 2s orbital Three 2p orbitals (b) Separate electron orbitals 1s, 2s, and 2p orbitals (c) Superimposed electron orbitals

13. Hydrogen atoms (2 H) Figure 2.11-3 Hydrogen molecule (H2)

14. Lewis Dot Structure and Structural Formula Space- Filling Model Electron Distribution Diagram Name and Molecular Formula (a) Hydrogen (H2) Figure 2.12 (b) Oxygen (O2) (c) Water (H2O) (d) Methane (CH4)

15. – Figure 2.13 O H H + + H2O

16. – + Figure 2.14-2 Na+ Sodium ion (a cation) Cl– Chloride ion (an anion) Na Sodium atom Cl Chlorine atom Sodium chloride (NaCl)

17. Figure 2.15 Na+ Cl–

18. + – Water (H2O) Figure 2.16 + Hydrogen bond – Ammonia (NH3) + + +

19. Figure 2.UN01

20. Nitrogen Carbon Sulfur Hydrogen Natural endorphin Oxygen Morphine Figure 2.18 (a) Structures of endorphin and morphine Natural endorphin Morphine Endorphin receptors Brain cell (b) Binding to endorphin receptors

21. Chapter 3 starts about hereWater and Life

22. Figure 3.1

23.   Figure 3.2 Hydrogen bond +  Polar covalent bonds   +  +      + 

24. Adhesion Two types of water-conducting cells Figure 3.3 Cohesion Direction of water movement 300 m

25. Figure 3.4

26. Figure 3.5 San Bernardino 100° Burbank 90° Santa Barbara 73° Riverside 96° Los Angeles (Airport) 75° Santa Ana 84° Palm Springs 106° 70s (°F) 80s Pacific Ocean 68° 90s 100s 40 miles San Diego 72°

27. Figure 3.6 Hydrogen bond Liquid water: Hydrogen bonds break and re-form Ice: Hydrogen bonds are stable

28. Figure 3.7  Na        Na    Cl Cl        

29. Figure 3.8 +      + 

30. Figure 3.9

31. Figure 3.UN02 +  2 H2O Hydronium ion (H3O+) Hydroxide ion (OH)

32. Figure 3.10 pH Scale 0 1 Battery acid 2 Gastric juice, lemon juice H+ H+ H+ Vinegar, wine, cola OH 3 H+ Increasingly Acidic [H+] > [OH] H+ OH H+ H+ H+ 4 Tomato juice Acidic solution Beer Black coffee 5 Rainwater 6 Urine OH Saliva Neutral [H+] = [OH] OH 7 Pure water OH H+ H+ OH OH Human blood, tears H+ H+ H+ 8 Seawater Neutral solution Inside of small intestine 9 10 Increasingly Basic [H+] < [OH] Milk of magnesia OH OH 11 OH H+ OH Household ammonia OH OH OH H+ 12 Basic solution Household bleach 13 Oven cleaner 14

33. Figure 3.11 CO2 CO2 +H2O H2CO3 H2CO3 H+ +HCO3 HCO3 H+ +CO32 CO32 + Ca2+ CaCO3

34. Chapter 4 Starts about here Carbon Chemistry

35. Figure 4.1

36. EXPERIMENT “Atmosphere” CH4 Water vapor Electrode NH3 H2 Figure 4.2 Condenser Cooled “rain”containingorganicmolecules Cold water H2O “sea” Sample for chemical analysis

37. Name andComment Structural Formula Space-Filling Model Molecular Formula Ball-and- Stick Model (a) Methane CH4 Figure 4.3 (b) Ethane C2H6 (c) Ethene (ethylene) C2H4

38. Oxygen (valence  2) Hydrogen (valence  1) Nitrogen (valence  3) Carbon (valence  4) Figure 4.4

39. Figure 4.UN01 Urea

40. (c) Double bond position (a) Length Figure 4.5 Ethane Propane 2-Butene 1-Butene (b) Branching (d) Presence of rings Benzene 2-Methylpropane (isobutane) Butane Cyclohexane

41. Nucleus Figure 4.6 Fat droplets 10 m (a) Part of a human adipose cell (b) A fat molecule

42. (a) Structural isomers Figure 4.7 (b) Cis-trans isomers cis isomer: The two Xsare on the same side. trans isomer: The two Xsare on opposite sides. (c) Enantiomers CO2H CO2H H NH2 H NH2 CH3 CH3 L isomer D isomer

43. Ineffective Enantiomer Effective Enantiomer Drug Condition Figure 4.8 Pain;inflammation Ibuprofen S-Ibuprofen R-Ibuprofen Albuterol Asthma R-Albuterol S-Albuterol

44. Estradiol Figure 4.UN02 Testosterone

45. CHEMICAL GROUP Hydroxyl Carbonyl Carboxyl STRUCTURE (may be written HO—) Alcohols (Their specific namesusually end in -ol.) NAME OF COMPOUND Ketones if the carbonyl group iswithin a carbon skeleton Carboxylic acids, or organic acids Aldehydes if the carbonyl groupis at the end of the carbon skeleton Figure 4.9_a EXAMPLE Acetic acid Ethanol Acetone Propanal FUNCTIONAL PROPERTIES • Acts as an acid; can donate an H+ because the covalent bond between oxygen and hydrogen is so polar: • A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal. • Is polar as a result of the electrons spending more time near the electronegative oxygen atom. • Can form hydrogen bonds with water molecules, helping dissolve organic compounds such as sugars. • Ketone and aldehyde groups are also found in sugars, giving rise to two major groups of sugars: ketoses (containing ketone groups) and aldoses (containing aldehyde groups). Nonionized Ionized • Found in cells in the ionized form with a charge of 1 and called a carboxylate ion.

46. Amino Sulfhydryl Phosphate Methyl (may bewritten HS—) Organic phosphates Amines Thiols Methylated compounds Figure 4.9_b Glycerol phosphate Cysteine Glycine 5-Methyl cytidine • Contributes negative charge to the molecule of which it is a part (2– when at the end of a molecule, as above; 1– when located internally in a chain of phosphates). • Acts as a base; can pick up an H+ from the surrounding solution (water, in living organisms): • Two sulfhydryl groups can react, forming a covalent bond. This “cross-linking” helps stabilize protein structure. • Addition of a methyl group to DNA, or to molecules bound to DNA, affects the expression of genes. • Arrangement of methyl groups in male and female sex hormones affects their shape and function. • Cross-linking of cysteines in hair proteins maintains the curliness or straightness of hair. Straight hair can be “permanently” curled by shaping it around curlers and then breaking and re-forming the cross-linking bonds. • Molecules containing phosphate groups have the potential to react with water, releasing energy. Nonionized Ionized • Found in cells in the ionized form with a charge of 1+.