The Chemical Foundations of Life

1. The Chemical Foundations of Life

2. The Chemical Foundations of LifeWhat 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. Solids Liquids Gases The Chemical Foundations of LifeWhat 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?

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

7. —18 electrons

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

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. Ionic bond formation. The Chemical Foundations of Life Salt crystal formation, the result of bonding. 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. H2O + H2O  OH– + H3O+ • hydroxide • ion • H2O  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 log10 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 CO2 + H2O  H2CO3  H+ + HCO3 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 O H O–

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

34. Biological Molecules Small and Large 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

35. Biological Molecules Small and Large That means that carbon can form up to 4 separate bonds The simplest organic molecule is methane, with a formula of CH4.

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

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

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

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

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

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

42. Biological Molecules Small and Large 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.)

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

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 O H 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