1. The Chemical Foundations of Life

2. The Chemical Foundations of Life What is Chemistry? Chemistry is the study of the properties of Matter—living and nonliving, and the transformation of all forms of matter Biochemistry is the study of chemical reactions that occur in organisms

3. The Chemical Foundations of Life What is Matter? Matter is the substantive portion of our Universe. Having material form, it occupies space and has a property we know as mass. Matter can exist in several physical states. What are these physical states? Solids Liquids Gases

4. Element vs. molecule Ionic bond vs. covalent bond Polar vs. nonpolar Hydrogen bond vs. van der Waals force Hydrophilic vs. hydrophobic vs. amphipathic Water – cohesion vs. adhesion solvent vs. solute acid vs. base vs. buffer

6. The Chemical Foundations of Life Here we can see the nucleus with protons and neutrons. 1/10000 質子中子 Electrons can be seen (much larger than they should be) orbiting around the nucleus. 電子

7. —18 electrons

8. The Chemical Foundations of Life The first three periods of the Periodic Table Figure 2-7

9. 同位素 ─ 中子數不同

10. Element vs. molecule Ionic bond vs. covalent bond Polar vs. nonpolar Hydrogen bond vs. van der Waals force Hydrophilic vs. hydrophobic vs. amphipathic Water – cohesion vs. adhesion solvent vs. solute acid vs. base vs. buffer

12. The Chemical Foundations of Life Salt crystal formation, the result of bonding. Ionic bond formation. Figure 2-9

14. Element vs. molecule Ionic bond vs. covalent bond Polar vs. nonpolar Hydrogen bond vs. van der Waals force Hydrophilic vs. hydrophobic vs. amphipathic Water – cohesion vs. adhesion solvent vs. solute acid vs. base vs. buffer

15. electronegativity

16. Element vs. molecule Ionic bond vs. covalent bond Polar vs. nonpolar Hydrogen bond vs. van der Waals force Hydrophilic vs. hydrophobic vs. amphipathic Water – cohesion vs. adhesion solvent vs. solute acid vs. base vs. buffer

18. Element vs. molecule Ionic bond vs. covalent bond Polar vs. nonpolar Hydrogen bond vs. van der Waals force Hydrophilic vs. hydrophobic vs. amphipathic Water – cohesion vs. adhesion solvent vs. solute acid vs. base vs. buffer

23. H 2 O + H 2 O  OH – + H 3 O + hydroxide ion H 2 O  H + + OH – hydrogen ion or proton Chemical Equilibrium pH ＝ – log [H + ] acidic pH < 7 basic pH > 7

24. The Chemical Foundations of Life The pH scale is the log 10 of the hydrogen ion concentration in a solution. Water is considered a reference or neutral point with a pH of 7.0. Figure 2-20

25. Buffer CO 2 + H 2 O  H 2 CO 3  H + + HCO 3  Carbon dioxide carbonic acid bicarbonate ion

26. Element vs. molecule Ionic bond vs. covalent bond Polar vs. nonpolar Hydrogen bond vs. van der Waals force Hydrophilic vs. hydrophobic vs. amphipathic Water – cohesion vs. adhesion solvent vs. solute acid vs. base vs. buffer

28. Functional Groups Hydroxyl group R-OH Carbonyl group R-C-H (or R) Carboxyl group R-C Amino group R-N Sulfhydryl group R-SH Phosphate group R-O-P-O – O O OH H H O O–O–

29. The hydrocarbon skeleton provides a basic framework: Biological Molecules Small and Large Figure 3-3 Saturated vs. unsaturated

30. Four Classes of Building Blocks Lipids Sugars – polysaccharides Nucleotides – nucleic acids Amino acids – proteins

31. Biological Molecules

33. The hydrocarbon skeleton provides a basic framework: Biological Molecules Small and Large Figure 3-3

34. One of the key concepts associated with the chemistry of carbon that will help us here is saturation. Carbon has an Atomic Number of 6. How many valence electrons does it have? 4 Biological Molecules Small and Large

35. That means that carbon can form up to 4 separate bonds The simplest organic molecule is methane, with a formula of CH 4. Biological Molecules Small and Large

36. The way a typical methane molecule would appear would be: HHCH H With 4 separate bonds to 4 separate atoms, carbon is said to be saturated. Biological Molecules Small and Large

37. If two methane molecules are joined together, they form a molecule known ethane. HHC HHCH H Biological Molecules Small and Large

38. HHC HHCH H How many carbons are present in ethane? 2 Is each of these carbons saturated? Yes. Biological Molecules Small and Large

39. Are these carbons saturated? HHC HHCH H Does this carbon have four bonds to four separate atoms? Yes Biological Molecules Small and Large

40. HHC HHCH H Does this carbon have four bonds to four separate atoms? Yes So both are saturated. Biological Molecules Small and Large

41. This molecule looks very similar to the previous molecule. Do the two carbons each have 4 bonds to 4 separate atoms? HHCHCH No, this a double bond and each of the carbons is unsaturated as a result. Biological Molecules Small and Large

42. So, if a molecule has a point of unsaturation, the carbons at that point have how many bonds? Three or fewer* single bonds to different or separate atoms (we don’t count the double bond as two separate bonds). (*Triple bonds are also possible.) Biological Molecules Small and Large

43. Therefore, if a carbon atom has less than four separate single bonds, we say it is unsaturated. Biological Molecules Small and Large

46. Functional Groups Hydroxyl group R-OH Carbonyl group R-C-H (or R) Carboxyl group R-C Amino group R-N Sulfhydryl group R-SH Phosphate group R-O-P-O – O O OH H H O O–O–

47. Four Classes of Building Blocks Lipids Sugars – polysaccharides Nucleotides – nucleic acids Amino acids – proteins

48. Condensation : monomer  oligomer  polymer

49. Four Classes of Building Blocks Lipids Sugars - polysaccharides Nucleotides – nucleic acids Amino acids – proteins

51. 三酸甘油酯

53. 膽固醇