AP Biology: Chemistry B McGraw Hill AP Biology 2014-15 Contents 1 Carbohydrate 1 1.1 Structure .................................................. 1 1.2 Monosaccharides ............................................. 2 1.2.1 Classification of monosaccharides ................................ 2 1.2.2 Ring-straight chain isomerism .................................. 3 1.2.3 Use in living organisms ...................................... 3 1.3 Disaccharides ............................................... 3 1.4 Nutrition .................................................. 4 1.4.1 Classification ........................................... 5 1.5 Metabolism ................................................ 5 1.5.1 Catabolism ............................................ 5 1.6 Carbohydrate chemistry .......................................... 5 1.7 See also .................................................. 6 1.8 References ................................................. 6 1.9 External links ............................................... 7 2 Lipid 8 2.1 Categories of lipids ............................................ 8 2.1.1 Fatty acids ............................................. 8 2.1.2 Glycerolipids ........................................... 9 2.1.3 Glycerophospholipids ....................................... 9 2.1.4 Sphingolipids ........................................... 9 2.1.5 Sterol lipids ............................................ 10 2.1.6 Prenol lipids ............................................ 10 2.1.7 Saccharolipids ........................................... 10 2.1.8 Polyketides ............................................ 10 2.2 Biological functions ............................................ 11 2.2.1 Membranes ............................................ 11 2.2.2 Energy storage .......................................... 11 2.2.3 Signaling ............................................. 12 i ii CONTENTS 2.2.4 Other functions .......................................... 12 2.3 Metabolism ................................................ 12 2.3.1 Biosynthesis ............................................ 12 2.3.2 Degradation ............................................ 13 2.4 Nutrition and health ............................................ 13 2.5 See also .................................................. 13 2.6 References ................................................. 13 2.6.1 Bibliography ........................................... 17 2.7 External links ............................................... 17 3 Protein 19 3.1 Biochemistry ............................................... 20 3.2 Synthesis .................................................. 20 3.2.1 Biosynthesis ............................................ 20 3.2.2 Chemical synthesis ........................................ 21 3.3 Structure .................................................. 21 3.3.1 Structure determination ...................................... 22 3.4 Cellular functions ............................................. 23 3.4.1 Enzymes ............................................. 23 3.4.2 Cell signaling and ligand binding ................................. 24 3.4.3 Structural proteins ......................................... 24 3.5 Methods of study ............................................. 24 3.5.1 Protein purification ........................................ 25 3.5.2 Cellular localization ........................................ 25 3.5.3 Proteomics ............................................ 26 3.5.4 Bioinformatics .......................................... 26 3.6 Nutrition .................................................. 27 3.7 History and etymology ........................................... 27 3.8 See also .................................................. 28 3.9 Footnotes ................................................. 28 3.10 References ................................................. 31 3.11 External links ............................................... 31 3.11.1 Databases and projects ...................................... 31 3.11.2 Tutorials and educational websites ................................ 32 4 Enzyme 33 4.1 Etymology and history ........................................... 33 4.2 Structures and mechanisms ........................................ 34 4.2.1 Specificity ............................................. 35 CONTENTS iii 4.2.2 Mechanisms ............................................ 36 4.2.3 Allosteric modulation ....................................... 36 4.3 Cofactors and coenzymes ......................................... 37 4.3.1 Cofactors ............................................. 37 4.3.2 Coenzymes ............................................ 37 4.4 Thermodynamics ............................................. 37 4.5 Kinetics .................................................. 38 4.6 Inhibition ................................................. 39 4.7 Biological function ............................................. 41 4.8 Control of activity ............................................. 41 4.9 Involvement in disease ........................................... 42 4.10 Naming conventions ............................................ 42 4.11 Industrial applications ........................................... 43 4.12 See also .................................................. 43 4.13 References ................................................. 43 4.14 Further reading .............................................. 48 4.15 External links ............................................... 48 5 PH 49 5.1 History ................................................... 49 5.2 Definition and measurement ........................................ 49 5.2.1 pH ................................................. 49 5.2.2 p[H] ................................................ 50 5.2.3 pH indicators ........................................... 51 5.2.4 pOH ................................................ 51 5.2.5 Extremes of pH .......................................... 51 5.2.6 Non-aqueous solutions ...................................... 51 5.3 Applications ................................................ 52 5.3.1 pH in nature ............................................ 52 5.3.2 Seawater ............................................. 52 5.3.3 Living systems .......................................... 53 5.4 Calculations of pH ............................................. 53 5.4.1 Strong acids and bases ...................................... 54 5.4.2 Weak acids and bases ....................................... 54 5.4.3 General method .......................................... 55 5.5 References ................................................. 55 5.6 External links ............................................... 56 6 Chemical reaction 57 iv CONTENTS 6.1 History ................................................... 57 6.2 Equations ................................................. 58 6.3 Elementary reactions ........................................... 59 6.4 Chemical equilibrium ........................................... 59 6.5 Thermodynamics ............................................. 60 6.6 Kinetics .................................................. 60 6.7 Reaction types ............................................... 61 6.7.1 Four basic types .......................................... 61 6.7.2 Oxidation and reduction ..................................... 62 6.7.3 Complexation ........................................... 63 6.7.4 Acid-base reactions ........................................ 63 6.7.5 Precipitation ........................................... 63 6.7.6 Solid-state reactions ........................................ 64 6.7.7 Reactions at the solid|gas interface ................................ 64 6.7.8 Photochemical reactions ..................................... 64 6.8 Catalysis .................................................. 64 6.9 Reactions in organic chemistry ...................................... 65 6.9.1 Substitution ............................................ 65 6.9.2 Addition and elimination ..................................... 66 6.9.3 Other organic reaction mechanisms ................................ 67 6.10 Biochemical reactions ........................................... 68 6.11 Applications ................................................ 68 6.12 Monitoring ................................................. 68 6.13 See also .................................................. 68 6.14 References ................................................. 69 6.15 Bibliography ................................................ 70 6.16 Text and image sources, contributors, and licenses ............................ 71 6.16.1 Text ................................................ 71 6.16.2 Images .............................................. 76 6.16.3 Content license .......................................... 80 Chapter 1 Carbohydrate in plants and chitin in arthropods). The 5-carbon monosac- OH HO OH charide ribose is an important component of coenzymes (e.g., ATP, FAD, and NAD) and the backbone of the ge- O netic molecule known as RNA. The related deoxyribose O O HO OH is a component of DNA. Saccharides and their deriva- OH HO tives include many other important biomolecules that play OH key roles in the immune system, fertilization, preventing pathogenesis, blood clotting, and development.[7] Lactose is a disaccharide found in milk. It consists of a molecule In food science and in many informal contexts, the term of D-galactose and