1. UNIT 1: BIOCHEMISTRY AP Biology

2. AP Learning Objectives 2.8The student is able to justify the selection of data regarding the types of molecules that an animal, plant or bacterium will take up as necessary building blocks and excrete as waste products. [SP 4.1] 4.1The student is able to explain the connection between the sequence and the subcomponents of a biological polymer and its properties. [SP 7.1] 4.2The student is able to refine representations and models to explain how the subcomponents of a biological polymer and their sequence determine the properties of that polymer. [SP 1.3] 4.3The student is able to use models to predict and justify that changes in the subcomponents of a biological polymer affect the functionality of the molecule. [SP 6.1, 6.4] 4.17The student is able to analyze data to identify how molecular interactions affect structure and function. [SP 5.1] Text4.1-4.2, 5.1-5.5

3. Essential Questions  What types of molecules do organisms use for building blocks and excrete as wastes?  How do molecules and atoms from the environment build new molecules?  What interactions between molecules affect their structure and function?

4. Intro to Organic Chemistry 4.1-4.3

5. Carbon Properties  Forms four equivalent bonds  Hybrid orbitals are common (sp 3, sp 2, sp)  Forms long chains with other carbons  Forms single, double, and triple bonds  Forms complex and varied molecules

6.  Diamond: perfect sp 3  Graphite: sp 2

7. Carbon Skeletons are highly variable Length Branching Hybrid Orbitals

8. Which carbon are we looking at? 1 2 3 4 5 6 1 2 3 4 5 6

9. Naming Carbon Compounds  2-chlorohexane  2,3-dichlorohexane  1-fluoro 2,3-dichlorocyclohexane 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6

10. Isomers  Different configurations with the same formula  Commonly found in organic molecules

11. Structural Isomers  Differ in covalent partners propane2-methyl propane Molecular C 4 H 10 C 4 H 10 Structural CH 3 CH 2 CH 2 CH 3 CH 3 CH(CH 3 )CH 3 Alt Struc.CH 3 (CH 2 ) 2 CH 3

12. Cis- and Trans- Isomers  Differ in arrangement around a double bond  Due to the double bond, the atoms are not free to rotate Trans-1,2 dichloroetheneCis-1,2 dichloroethene

13. Enantiomers  Differ in spatial arrangement around asymmetric carbon  Mirror images  L and D (or S and R)  cannot be superimposed LD

14. Functional Groups HydroxylCarbonylCarboxylAminoSulfhydrylPhosphateMethyl Structure Properties — — OH Forms hydrogen bonds Polar O —— — C — Often aromatic — COOH Acid Loses H+ when ionized Ionized in cells — — NH2 Base- picks up H+ from surrounding — — SH Cross links in proteins — — OPO 3 2- Loses H to become ionized — — CH 3 Affects function of molecule Used in Alcohols Sugars Almost everything Ketones if R’ is C-based Aldehydes if R’ is H Weak acids (acetic acid) Amino acids Proteins Hair perms G3P, ATP, DNA Abbreviated as P Hormones DNA

15. Macromolecules  Carbohydrates  Lipids  Proteins  Nucleic acids

16. What can they do? Energy Storage Structure Carbohydrates Energy Storage Structure Regulation Lipids Structure Catalysts Energy Regulation Proteins Regulation Storage Nucleic Acids

17. Some Uses for Macromolecules Carbs Lipids Proteins Energy Carbs Lipids Nucleic acids Storage Carbs Lipids Proteins Structure Lipids Proteins Nucleic acids Regulation

18. Making and Breaking 5.1

19. Making & Breaking Macromolecules

21. 5.2 Carbohydrates

22. General information on carbohydrates  C n H 2n O n (for monomers)  n is usually between 3 and 8  -ose  Frequently form rings

23. Glucose Isomers

24. Carbohydrates α-D-Glucose 4 5 6 3 1

25.  Starch (Amylose)  α-1,4 linkage Carbohydrates as energy/storage plants 2 α-D-Glucose 4 5 6 3 1

27.  Glycogen  α-1,4 linkage & α-1, 6 linkage  Branched spirals due to H-bonds Carbohydrates as storage in animals α-D-Glucose 4 5 6 3 1

29.  Cellulose and H-bonds Carbohydrates as structure in plants  -D-Glucose 4 5 6 1 3 2

30. Hydrogen bonds

31. Carbohydrates as structure in animals  Chitin  α -glucosamine 1,4 linkage

32. Sequence these from highest to lowest energy

34. 5.3 Lipids

35.  Not water soluble  Polar carboxyl group  Non-polar hydrocarbon chain usual, but not steroids

36. Lipids

37.  Saturation determines room temperature state Lipids as Energy

39. Name that Molecule! Cis-9 octadecanoic acid aka oleic acid Octadecanoic acid aka stearic acid Cis-9, 12, 15 octadecanoic acid

40. Lipids as storage

41. Lipids as membranes

44. Lipids as protection

45. Lipids as hormones and vitamins

46. Steroids as regulators  4-ring structure

48. Proteins 5.4

49. Proteins

51. Proteins as structure Collagen Keratin Histones

52. Proteins for movement

53. Proteins as catalysts http://www.wiley.com/legacy/college/boyer/0 470003790/animations/catalysis_energy/cata lysis_energy.htm

54. Proteins as energy

55. Proteins for regulation

56. Proteins for just about everything!

57. Amino Acids  Different R groups give amino acids distinct properties

58. Protein Folding  Primary- amino acid sequence  Secondary- α -helix & β -pleated sheets  Tertiary- intra-molecular attraction/repulsion  Quaternary- 2 or more polypeptides join together and fold around one another  “Fold.it”

59. Primary

60. Primary continued

61. Secondary

62. Tertiary

64. Quaternary

65. When proteins break down  Δ pH  Δ temperature  Δ surroundings

66. Denaturing

67. Folding within a cell  Chaperonins (chaperone proteins)  Protect the new polypeptide from surroundings while it folds  Do not control folding pattern

68. Nucleic Acids 5.5

69. Nucleic acids

72. Note 5’ and 3’ ends

73. Fig. 3.16-1

74. Fig. 3.16-2

75.  http://www.yellowtang.org/animations/dna_subuni ts_adv.swf http://www.yellowtang.org/animations/dna_subuni ts_adv.swf Nucleic acids for data storage

76. Nucleic acids for regulation