1. AP Biology AP Biology John D. O’Bryant School of Mathematics and Science February 5, 2013

2. AP Biology Do Now  What is a virus?  What makes a virus function?

3. AP Biology Agenda  Do Now (Quiz)  Review: Biochemistry, Cellular Respiration, Photosynthesis  Genetics of Viruses

4. Table of Contents (Notes/Classwork) DateTopicPage number 1/29/13What Darwin Never Knew 2/4/13Review: Biochemistry, Cellular Respiration, Photosynthesis; Animal Behavior 2/5/13Review: Biochemistry, Cellular Respiration, Photosynthesis; Animal Behavior; Genetics of Viruses

5. AP Bio Exam Review: Biochemistry & Cells

6. Elements of Life 25 elements 96% : C, O, H, N ~ 4% : P, S, Ca, K & trace elements (ex: Fe, I) Hint: Remember CHNOPS

7. II. Atomic Structure Atom = smallest unit of matter that retains properties of an element Subatomic particles: Mass (dalton or AMU) LocationCharge neutron1nucleus0 proton1nucleus+1 electronnegligibleshell

8. Bonds CovalentIonicHydrogen All important to life Form cell’s molecules Quick reactions/ responses H bonds to other electronegative atoms Strong bond Weaker bond (esp. in H 2 O) Even weaker Made and broken by chemical reactions

9. Weaker Bonds: Van der Waals Interactions: slight, fleeting attractions between atoms and molecules close together – Weakest bond – Eg. gecko toe hairs + wall surface

10. 1. Polarity of H 2 O O - will bond with H + on a different molecule of H 2 O = hydrogen bond H 2 O can form up to 4 bonds

11. H 2 O Property Chemical Explanation Examples of Benefits to Life Cohesion polar H-bond like-like ↑gravity plants, trees transpiration Adhesion H-bond unlike-unlike plants  xylem blood  veins Surface Tension diff. in stretch break surface H-bond bugs  water Specific Heat Absorbs & retains E H-bond ocean  moderates temps  protect marine life (under ice) Evaporation liquid  gas KE Cooling Homeostasis Universal Substance Polarity  ionic H-bond Good dissolver solvent

12. 4. Solvent of life “like dissolves like” HydrophilicHydrophobic Affinity for H 2 OAppears to repel Polar, ionsNonpolar Cellulose, sugar, saltOils, lipids BloodCell membrane

13. Acids and Bases Acid: adds H + (protons); pH<7 Bases: removes protons, adds OH - ; pH>7 Buffers = substances which minimize changes in concentration of H + and OH - in a solution (weak acids and bases) Buffers keep blood at pH ~7.4 Good buffer = bicarbonate

14. Figure 3.9 The pH of some aqueous solutions

16. Functional Groups Functional GroupMolecular FormulaNames & CharacteristicsDraw an Example Hydroxyl-OHAlcoholsEthanol Carbonyl>CO Ketones (inside skeleton) Aldehydes (at end) Acetone Propanol Carboxyl-COOH Carboxylic acids (organic acids) Acetic acid Amino-NH 2 AminesGlycine Sulfhydryl-SHThiolsEthanethiol Phosphate-OPO 3 2- / -OPO 3 H 2 Organic phosphatesGlycerol phosphate

17. MonomersPolymersMacromolecules Small organic Used for building blocks of polymers Connects with condensation reaction (dehydration synthesis) Long molecules of monomers With many identical or similar blocks linked by covalent bonds Giant molecules 2 or more polymers bonded together ie. amino acid  peptide  polypeptide  protein smaller larger

18. Dehydration Synthesis (Condensation Reaction) Hydrolysis Make polymersBreakdown polymers Monomers  PolymersPolymers  Monomers A + B  ABAB  A + B + H 2 O + +

19. I. Carbohydrates Fuel and building Sugars are the smallest carbs  Provide fuel and carbon monosaccharide  disaccharide  polysaccharide Monosaccharides: simple sugars (ie. glucose) Polysaccharides:  Storage (plants-starch, animals-glycogen)  Structure (plant-cellulose, arthropod-chitin) Differ in position & orientation of glycosidic linkage

20. II. Lipids A.Fats: store large amounts of energy – saturated, unsaturated, polyunsaturated B.Steroids: cholesterol and hormones C.Phospholipids: cell membrane – hydrophilic head, hydrophobic tail – creates bilayer between cell and external environment Hydrophilic head Hydrophobic tail

21. Four Levels of Protein Structure: 1.Primary – Amino acid sequence – 20 different amino acids – peptide bonds 2.Secondary – Gains 3-D shape (folds, coils) by H-bonding – α helix, β pleated sheet 3.Tertiary – Bonding between side chains (R groups) of amino acids – H & ionic bonds, disulfide bridges 4.Quaternary – 2+ polypeptides bond together

22. amino acids  polypeptides  protein

23. Protein structure and function are sensitive to chemical and physical conditions Unfolds or denatures if pH and temperature are not optimal

24. IV. Nucleic Acids Nucleic Acids = Information Monomer: nucleotide DNARNA Double helix Thymine Carries genetic code Longer/larger Sugar = deoxyribose Single strand Uracil Messenger (copies), translator tRNA, rRNA, mRNA, RNAi Work to make protein Sugar = ribose

25. Comparisons of Scopes Light Visible light passes through specimen Light refracts light so specimen is magnified Magnify up to 1000X Specimen can be alive/moving color Electron Focuses a beam of electrons through specimen Magnify up to 1,000,000 times Specimen non-living and in vacuum Black and white

26. Prokaryote Vs. Eukaryote “before” “kernel” No nucleus DNA in a nucleoid Cytosol No organelles other than ribosomes Small size Primitive i.e. bacteria “true” “kernel” Has nucleus and nuclear membrane Cytosol Has organelles with specialized structure and function Much larger in size More complex i.e. plant/animal cell

27. Parts of plant & animal cell p 108-109

29. Cells must remain small to maintain a large surface area to volume ratio Large S.A. allows increased rates of chemical exchange between cell and environment

36. Animal cells have intercellular junctions: Tight junction = prevent leakage Desomosome = anchor cells together Gap junction = allow passage of material

37. Cell Membrane

38. 6 types of membrane proteins

39. Passive vs. Active Transport Little or no Energy Moves from high to low concentrations Moves down the concentration gradient i.e. diffusion, osmosis, facilitated diffusion (with a transport protein) Requires Energy (ATP) Moves from a low concentration to high Moves against the concentration gradient i.e. pumps, exo/endocytosis

40. hypotonic / isotonic / hypertonic

42. Exocytosis and Endocytosis transport large molecules 3 Types of Endocytosis: Phagocytosis (“cell eating” - solids) Pinocytosis (“cell drinking” - fluids) Receptor-mediated endocytosis Very specific Substances bind to receptors on cell surface

43. End 2/4/13

44. Concept 1: Analyzing the Processes of Cellular Respiration. Refer to pg 75-80 in Holtzclaw, Ch 9 in Campbell and media resources Refer to pg 326-328 in Holtzclaw, Lab 5 in LabBench

45.  Are these statements true or false? 1. Photosynthesis is the plant’s form of cellular respiration. 2. Plants respire only when they don’t photosynthesize. 3. Cellular respiration takes place only in plant roots, not throughout the plant.

46.  ALL OF THESE ARE FALSE! 1. Photosynthesis is the plant’s form of cellular respiration. FALSE 2. Plants respire only when they don’t photosynthesize. FALSE 3. Cellular respiration takes place only in plant roots, not throughout the plant. FALSE

47.  How is cellular metabolism relevant to higher levels of biological organization: physiology (breathing, digestion), ecology (communities)?

49.  Cellular Respiration  Catabolic ▪ Breaks down complex molecules into smaller ones  Exergonic ▪ Releases energy that can be used to do work (such as build ATP from ADP and Pi)

50.  Cellular Respiration  If you released all of the energy in sugar at once, what would happen? ▪ Quick combustion! FIRE ▪ Example: Marshmellows on Fire

51.  Cellular Respiration  Instead, your mitochondria use a series of controlled steps, releasing energy in small amounts at a time ▪ Some energy still lost as heat ▪ The rest is converted to chemical energy in ATP for use in the cell! ▪ HOW?????

52.  Redox Reactions!  Follows the movement of ELECTRONS from one chemical to another  “X” is losing electrons  “Y” is gaining electrons

53.  Redox Reactions!  Lose Electrons, Oxidize  Gain Electrons, Reduce

54.  Redox Reactions!  Classic Chemistry Example…

55.  Redox Reactions!  Cellular Respiration…  Do you have any ideas as to how you can harness the movement of electrons to split up cellular respiration into steps??

56.  Introducing…NAD +, a coenzyme electron carrier  NAD + + 2e - + H + produces NADH  Is NAD + reduced or oxidized?

57.  Introducing…NAD +, a coenzyme electron carrier  NAD + + 2e - + H + produces NADH  Gain Electrons Reduce

58.  Also…FAD, a coenzyme electron carrier  FAD + 2e - + 2H + produces FADH 2  Gain Electrons Reduce

59.  Cellular respiration has three stages: 1. Glycolysis (breaks down glucose into two molecules of pyruvate) 2. The citric acid cycle (completes the breakdown of glucose) 3. Oxidative phosphorylation (accounts for most of the ATP synthesis)

65. C 6 H 12 O 6 + 6 O 2  6 CO 2 + 6 H 2 O + Energy (ATP + heat) Where can you find all of these reactants/products?  To Prepare…  Finish Comparison Chart  Try Animations and Bioflix!Bioflix  Think of Project Ideas…

66.  The role of glycolysis in oxidizing glucose to two molecules of pyruvate  The process that brings pyruvate from the cytosol into the mitochondria and introduces it into the citric acid cycle  How the process of chemiosmosis utilizes the electrons from NADH and FADH2 to produce ATP  The difference between fermentation and cellular respiration

67. Concept 2: Analyzing the Processes of Photosynthesis  Refer to pg 81-90 in Holtzclaw, Ch 10 in Campbell and media resources  Refer to pg 321-323 in Holtzclaw, Lab 4 in LabBench

68. Try This!  Where does the biomass of a tree primarily come from? A.Oxygen B.Water C.Carbon dioxide D.Light E.Fertilizer

69. Try This!  Where does the biomass of a tree primarily come from? A.Oxygen B.Water C.Carbon dioxide D.Light E.Fertilizer

70. Try This! An acorn grows into an oak tree. The main source of the additional mass present in the oak tree is: a. Water from the soil b. Minerals from the soil c. CO 2 from the air

71. Try This! An acorn grows into an oak tree. The main source of the additional mass present in the oak tree is: a. Water from the soil b. Minerals from the soil c. CO 2 from the air

76. Chapter 10 You must know:  How photosystems convert solar energy to chemical energy  How linear electron flow in the light reactions results in the formation of ATP, NADPH, and O 2  How chemiosmosis generates ATP in the light reactions  How the Calvin cycle uses the energy molecules of the light reactions to produce G3P  The metabolic adaptations of C 4 and CAM plants to arid, dry regions

77. AP Lab 4 You must know:  The equation for photosynthesis and understand the process of photosynthesis  The principles of chromatography and how to calculate Rf values  The relationship between light wavelength or intensity and photosynthetic rate  How to determine the rate of photosynthesis and then be able to design a controlled experiment to test the effect of some variable factor on photosynthesis

80. Photosynthesis – The Basics CO 2 + H 2 O → C 6 H 12 O 6 + O 2 1)Light Reactions “photo” 2)Calvin Cycle “synthesis”

87. The Light Reactions  Light energy excites electrons in chlorophyll  Removal of electrons from H 2 O  Formation of O 2  Electron Transport Chain  Reduction of NADP + to NADPH  Proton Motive Force  ATP Synthase to produce ATP

98. Try This  Unlike in cellular respiration, the proton motive force generated by the light reactions in photosynthesis happens in three ways… Can you remember the three ways? 1. Electron transport chain powering the active transport of H + into the thylakoid space 2.H + produced in the thylakoid space from the splitting and oxidation of water 3. Removal of H + from stroma during the reduction of NADP + to NADPH

99. The Light Reactions  Light energy excites electrons in chlorophyll  Removal of electrons from H 2 O  Formation of O 2 (leaves stomata as a gas)  Electron Transport Chain  Reduction of NADP + to NADPH  Proton Motive Force  ATP Synthase to produce ATP

100. The Light Reactions  The whole point was to transfer light energy to chemical energy in the form of:  electrons in NADPH  ATP  Why?  To power carbon fixation in the Calvin Cycle…

102. The Calvin Cycle  CO 2 enters as a gas through the stomata (openings) of the leaves  Through the power of NADPH and ATP, CO 2 gets converted into an organic compound: a 3-carbon sugar called glyceraldehyde-3-phosphate (G3P)  Can be converted to glucose, sucrose, starch, etc…

108. Try This!  Which experiment will produce 18 O 2 ? A.Exp 1 B.Exp 2 C.Both! D.Neither!

109. Try This!  Which experiment will produce 18 O 2 ? A.Exp 1 B.Exp 2 C.Both! D.Neither!

110. Watch BioflixWatch Bioflix!

111. Chapter 10 You must know:  How photosystems convert solar energy to chemical energy  How linear electron flow in the light reactions results in the formation of ATP, NADPH, and O 2  How chemiosmosis generates ATP in the light reactions  How the Calvin cycle uses the energy molecules of the light reactions to produce G3P  The metabolic adaptations of C 4 and CAM plants to arid, dry regions

112. Next Class…  Adaptations to hot, arid climates …  CAM plants and C 4 plants

113. Now…  Practice  Try #12 – 15, 17-19, 21-22 p. 91-92  Go over Comparison Charts  Try animation activities (Campbell Online)  Read about CAM plants and C 4 plants  P. 88-89 Holtzclaw  P. 200-202 Campbell  Activity: Photosynthesis in Dry Climates (Campbell Online)

114. Concept 2: Analyzing the Processes of Photosynthesis PART 2 – Adaptations to Dry Climates  Refer to pg 81-90 in Holtzclaw, Ch 10 in Campbell and media resources  Refer to pg 321-323 in Holtzclaw, Lab 4 in LabBench

116. Try This!  Where does the organic biomass of a tree primarily come from? A.Oxygen B.Water C.Carbon dioxide D.Light E.Fertilizer

117. Try This!  Where does the organic biomass of a tree primarily come from? A.Oxygen B.Water C.Carbon dioxide D.Light E.Fertilizer

118. Chapter 10 You must know:  How photosystems convert solar energy to chemical energy  How linear electron flow in the light reactions results in the formation of ATP, NADPH, and O 2  How chemiosmosis generates ATP in the light reactions  How the Calvin cycle uses the energy molecules of the light reactions to produce G3P  The metabolic adaptations of C 4 and CAM plants to arid, dry regions

119. AP Lab 4 You must know:  The equation for photosynthesis and understand the process of photosynthesis  The principles of chromatography and how to calculate Rf values  The relationship between light wavelength or intensity and photosynthetic rate  How to determine the rate of photosynthesis and then be able to design a controlled experiment to test the effect of some variable factor on photosynthesis

122. Photosynthesis – The Basics CO 2 + H 2 O → C 6 H 12 O 6 + O 2 1)Light Reactions “photo” 2)Calvin Cycle “synthesis”

127. The Light Reactions

128.  Light energy excites electrons in chlorophyll  Removal of electrons from H 2 O  Formation of O 2  Electron Transport Chain  Reduction of NADP + to NADPH  Proton Motive Force  ATP Synthase to produce ATP

131. Try This  Unlike in cellular respiration, the proton motive force generated by the light reactions in photosynthesis happens in three ways… Can you remember the three ways? 1. Electron transport chain powering the active transport of H + into the thylakoid space 2.H + produced in the thylakoid space from the splitting and oxidation of water 3. Removal of H + from stroma during the reduction of NADP + to NADPH

132. The Light Reactions  The whole point was to transfer light energy to chemical energy in the form of:  electrons in NADPH  ATP  Why?  To power carbon fixation in the Calvin Cycle…

134. The Calvin Cycle  CO 2 enters as a gas through the stomata (openings) of the leaves  Through the power of NADPH and ATP, CO 2 gets converted into an organic compound: a 3-carbon sugar called glyceraldehyde-3-phosphate (G3P)  Can be converted to glucose, sucrose, starch, etc…

140. Chapter 10 You must know:  How photosystems convert solar energy to chemical energy  How linear electron flow in the light reactions results in the formation of ATP, NADPH, and O 2  How chemiosmosis generates ATP in the light reactions  How the Calvin cycle uses the energy molecules of the light reactions to produce G3P  The metabolic adaptations of C 4 and CAM plants to arid, dry regions

141. NOW…  Adaptations to hot, arid climates …  CAM plants and C 4 plants Sugarcane – C 4 plant Pineapple – CAM plant

142. Hot, Dry Climates  What’s the big deal?  Stomata – water loss  Rubisco – photorespiration

143. Stomata…

144.  Water exits via stomata during transpiration (evaporation of water through the stomata - which pulls water up the plant from the roots)  If it’s a hot, dry day, plants need to minimize water loss!  Solution?  Close/minimize stomata  BUT? Lowers CO 2 intake…

145. Rubisco…  Remember rubisco?  It’s the enzyme that fixes CO 2 in the Calvin cycle of C 3 plants  The thing is… rubisco will also bind O 2 in absence of CO 2  Causes breakdown of Calvin Cycle products… Photorespiration  Solution?  Adapt!

149. Try This!  The presence of only Photosystem I, not Photosystem II, in the bundle sheath cells of C 4 plants has an effect on O 2 concentration. What is that effect, and how might that benefit the plant?

150. Try This!  The presence of only Photosystem I, not Photosystem II, in the bundle sheath cells of C 4 plants has an effect on O 2 concentration. What is that effect, and how might that benefit the plant?  Without PS II, no O 2 is generated in the bundle-sheath cells!  This avoids the problem of O 2 competing with CO 2 for binding to rubisco  No photorespiration

151. Now…  Practice  Try #12 – 15, 17-19, 21-22 p. 91-92  Go over Comparison Charts  Try animation activities (Campbell Online)  Re-Read about CAM plants and C 4 plants and do worksheet  P. 88-89 Holtzclaw  P. 200-202 Campbell  Activity: Photosynthesis in Dry Climates (Campbell Online)  Get Ready for Lab 4  Go through Lab 4 LabBench  Checkpoint Next Class on Photosynthesis (Concept 2)