1. BSC 2010 - Exam I Lectures and Text Pages I. Intro to Biology (2-29) II. Chemistry of Life – Chemistry review (30-46) – Water (47-57) – Carbon (58-67) – Macromolecules (68-91) III. Cells and Membranes – Cell structure (92-123) – Membranes (124-140) IV. Introductory Biochemistry – Energy and Metabolism (141-159) – Cellular Respiration (160-180) – Photosynthesis (181-200)

2. Citric Acid Cycle Citric acid cycle completes the energy-yielding oxidation of organic molecules The citric acid cycle – Takes place in the matrix of the mitochondrion

3. An overview of the citric acid cycle ATP 2 CO 2 3 NAD + 3 NADH + 3 H + ADP + P i FAD FADH 2 Citric acid cycle CoA Acetyle CoA NADH + H + CoA CO 2 Pyruvate (from glycolysis, 2 molecules per glucose) ATP Glycolysis Citric acid cycle Oxidative phosphorylatio n Figure 9.11

4. Figure 9.12 Acetyl CoA NADH Oxaloacetate Citrate Malate Fumarate Succinate Succinyl CoA  -Ketoglutarate Isocitrate Citric acid cycle SCoA SH NADH FADH 2 FAD GTP GDP NAD + ADP P i NAD + CO 2 CoA SH CoA SH CoA S H2OH2O + H + H2OH2O C CH 3 O OCCOO – CH 2 COO – CH 2 HO C COO – CH 2 COO – CH 2 HCCOO – HOCH COO – CH CH 2 COO – HO COO – CH HC COO – CH 2 COO – CH 2 CO COO – CH 2 CO COO – 1 2 3 4 5 6 7 8 Glycolysis Oxidative phosphorylation NAD + + H + ATP Citric acid cycle Figure 9.12 A closer look at the citric acid cycle

5. Pyruvate  AcetylCoA  Citric Acid Cycle Yield from each 2 pyruvate molecules (from 1 glucose) 6CO 2 (2 from Pyr.  AcetylCoA, 4 from CAC 8NADH (2 from Pyr.  AcetylCoA, 6 from CAC) 2FADH 2 (All from CAC) 2 ATP (All from CAC) Two pyruvates are produced from the glycolysis of each glucose molecule resulting in a total of 2 ATP from Citric Acid Cycle, and the NADH and FADH 2 go to power the Electron Transport Chain

6. Oxidative phosphorylation Chemiosmosis couples ETC to ATP synthesis ETC (fig 9.13) = collection of mostly proteins embedded in the inner mitochondrial membranes (cristae = foldings that increase SA) Each electron acceptor along the ETC is more electronegative than the previous  O 2 at the end, the final electron acceptor (most electronegative) NADH transfers e- to the 1st molecule of ETC (flavoprotein) in multiprotein complex I Ubiquinone (= small hydrophobic non-protein that’s mobile within the membrane system) transfers e- from multiprotein complex I  II FADH 2 transfers e- to the 2nd multiprotein complex (provides 1/3 less E than NADH) ATP is not directly made by the ETC  Chemiosmosis couples this E release with making ATP ETC – stores energy by pumping protons from the matrix across the inner mitochondrial membrane into the intermembrane space. (fig. 9.15) Chemiosmosis = E stored in H+ gradient across a membrane (proton-motive force) is used to drive ATP synthesis ATP synthase complexes in the membrane = only place H+ can freely move along concentration gradient and back into the matrix (fig. 9.14)

7. Oxidative Phosphorylation During oxidative phosphorylation, chemiosmosis couples electron transport to ATP synthesis NADH and FADH 2 – Donate electrons to the electron transport chain, which powers ATP synthesis via oxidative phosphorylation through chemiosmosis

8. The Pathway of Electron Transport In the electron transport chain – Electrons from NADH and FADH 2 lose energy in several steps H2OH2O O2O2 NADH FADH2 FMN FeS O FAD Cyt b Cyt c 1 Cyt c Cyt a Cyt a 3 2 H + + 1  2 I II III IV Multiprotein complexes 0 10 20 30 40 50 Free energy (G) relative to O 2 (kcl/mol) Figure 9.13 NADH passes electrons to multiprotein complex I. They are then passed to Ubiquinone which transfers them to multiprotein complex II. FADH 2 passes electrons directly to multiprotein complex II. Electrons are passed to more electron acceptors in the remaining multiprotein complexes. Finally they are passed to oxygen, the most electronegative acceptor, forming water.

9. ETC stores energy in an ion gradient At certain steps along the electron transport chain – Electron transfer causes protein complexes to pump H + from the mitochondrial matrix to the intermembrane space The resulting H + gradient – Stores energy – Drives chemiosmosis in ATP synthase – Is referred to as a proton-motive force

10. Chemiosmosis – Is an energy-coupling mechanism that uses energy in the form of a H + gradient across a membrane to drive cellular work

11. Chemiosmosis: The Energy-Coupling Mechanism ATP synthase – Is the enzyme that actually makes ATP INTERMEMBRANE SPACE H+H+ H+H+ H+H+ H+H+ H+H+ H+H+ H+H+ H+H+ P i + ADP ATP A rotor within the membrane spins clockwise when H + flows past it down the H + gradient. A stator anchored in the membrane holds the knob stationary. A rod (for “stalk”) extending into the knob also spins, activating catalytic sites in the knob. Three catalytic sites in the stationary knob join inorganic Phosphate to ADP to make ATP. MITOCHONDRIAL MATRIX Figure 9.14

12. Chemiosmosis and the electron transport chain Oxidative phosphorylation. electron transport and chemiosmosis Glycolysis ATP Inner Mitochondrial membrane H+H+ H+H+ H+H+ H+H+ H+H+ ATP P i Protein complex of electron carners Cyt c I II III IV (Carrying electrons from, food) NADH + FADH 2 NAD + FAD + 2 H + + 1 / 2 O 2 H2OH2O ADP + Electron transport chain Electron transport and pumping of protons (H + ), which create an H + gradient across the membrane Chemiosmosis ATP synthesis powered by the flow Of H + back across the membrane ATP synthase Q Oxidative phosphorylation Intermembrane space Inner mitochondrial membrane Mitochondrial matrix Figure 9.15

13. Energy Transfer Efficiency Complete oxidation of 1 mole of glucose releases 686 kcal of energy Phosphorylation of ADP  ATP stores 7.3 kcal/mol Respiration makes 38 ATP (x 7.3 kcal/mol) = 277.4 kcal (40% of 686 kcal) Only about 40% of E stored in glucose is used to make ATP (the rest is lost as HEAT)

14. An Accounting of ATP Production by Cellular Respiration During respiration, most energy flows in this sequence – Glucose to NADH to electron transport chain to proton-motive force to ATP

15. Three main processes in this metabolic enterprise Electron shuttles span membrane CYTOSOL 2 NADH 2 FADH 2 2 NADH 6 NADH 2 FADH 2 2 NADH Glycolysis Glucose 2 Pyruvate 2 Acetyl CoA Citric acid cycle Oxidative phosphorylation: electron transport and chemiosmosis MITOCHONDRION by substrate-level phosphorylation by substrate-level phosphorylation by oxidative phosphorylation, depending on which shuttle transports electrons from NADH in cytosol Maximum per glucose: About 36 or 38 ATP + 2 ATP + about 32 or 34 ATP or Figure 9.16 About 40% of the energy in a glucose molecule is transferred to ATP during cellular respiration, making approximately 38 ATP

16. Fermentation Fermentation = extension of glycolysis that can generate ATP solely by substrate- level phosphorylation (as long as there’s plenty of NAD+) by transferring e- from NADH to pyruvate (or its derivatives). Does not use oxygen. 2 common types of fermentation: 1. Alcohol fermentation (fig 9.17a) Pyruvate  ethanol (2 steps) – 1st step: releases CO 2 from pyruvate  acetaldehyde (2-C) – 2nd step: acetaldehyde reduced by NADH  ethanol – NAD+ continues glycolysis Used to make beer/wine and in baking 2. Lactic acid fermentation (fig 9.17b) Pyruvate  lactate Used to make cheese & yogurt (bacteria and fungi) Your muscles also make ATP this way when O 2 is scarce Facultative anaerobes = organisms that can either use pyruvate in fermentation OR in respiration (depending of O 2 availability) To make the same amt of ATP an organism w/o O 2 would have to consume sugar at a much faster rate

17. Fermentation enables some cells to produce ATP w/o oxygen: In aerobic respiration, O 2 pulls e- through the ETC – Yields up to 19 times more ATP w/o O 2, other e- acceptors can be used Glycolysis = exergonic process that uses NAD+ (not O 2 ) as an e- acceptor

18. Fermentation Fermentation enables some cells to produce ATP without the use of oxygen Cellular respiration – Relies on oxygen to produce ATP In the absence of oxygen – Cells can still produce ATP through fermentation

19. Glycolysis – Can produce ATP with or without oxygen, in aerobic or anaerobic conditions – Under anaerobic conditions, it couples with fermentation to produce ATP

20. Types of Fermentation Fermentation consists of – Glycolysis plus reactions that regenerate NAD +, which can be reused by glyocolysis

21. Alcohol Fermentation In alcohol fermentation – Pyruvate is converted to ethanol in two steps, one of which releases CO 2 2 ADP + 2 P1P1 2 ATP Glycolysis Glucose 2 NAD + 2 NADH 2 Pyruvate 2 Acetaldehyde 2 Ethanol (a) Alcohol fermentation 2 ADP + 2 P1P1 2 ATP Glycolysis Glucose 2 NAD + 2 NADH 2 Lactate (b) Lactic acid fermentation H H OH CH 3 C O – O C CO CH 3 H CO O–O– CO CO O CO C OHH CH 3 CO 2 2 Figure 9.17 2 pyruvate

22. Lactic Acid Fermentation During lactic acid fermentation – Pyruvate is reduced directly by NADH to form lactate as a waste product 2 ADP + 2 P1P1 2 ATP Glycolysis Glucose 2 NAD + 2 NADH 2 Pyruvate 2 Acetaldehyde 2 Ethanol (a) Alcohol fermentation 2 ADP + 2 P1P1 2 ATP Glycolysis Glucose 2 NAD + 2 NADH 2 Lactate (b) Lactic acid fermentation H H OH CH 3 C O – O C CO CH 3 H CO O–O– CO CO O CO C OHH CH 3 CO 2 2 Figure 9.17 2 pyruvate

23. Fermentation and Cellular Respiration Compared Both fermentation and cellular respiration – Use glycolysis to oxidize glucose and other organic fuels to pyruvate Fermentation and cellular respiration – Differ in their final electron acceptor Cellular respiration – Produces more ATP

24. Pyruvate Pyruvate is a key juncture in catabolism Glucose CYTOSOL Pyruvate No O 2 present Fermentation O 2 present Cellular respiration Ethanol or lactate Acetyl CoA MITOCHONDRION Citric acid cycle Figure 9.18

25. The Evolutionary Significance of Glycolysis Glycolysis – Occurs in nearly all organisms – Probably evolved in ancient prokaryotes (3.5 bya) before there was oxygen in the atmosphere – They did not have oxygen or mitochondria

26. Versatility in Catabolism Glycolysis and the citric acid cycle connect to many other metabolic pathways Our bodies generally use many sources of energy in respiration (fig 9.19)  regulated by feedback inhibition (fig 9.20) Carbohydrates  simple sugars, enter glycolysis Proteins  amino acids (used to build new proteins) – Excess amino acids are deaminated  intermediates of glycolysis or citric acid cycle, or form acetyl CoA Fats  gylcerol + fatty acids (where most E stored) – Gylcerol  intermediate of glycolysis – Beta oxidation breaks fatty acids down to 2-C fragments  citric acid cycle as acetyl CoA

27. The Versatility of Catabolism Catabolic pathways – Funnel electrons from many kinds of organic molecules into cellular respiration Glycolysis and the citric acid cycle connect to many other metabolic pathways

28. The catabolism of various molecules from food Amino acids Sugars Glycerol Fatty acids Glycolysis Glucose Glyceraldehyde-3- P Pyruvate Acetyl CoA NH 3 Citric acid cycle Oxidative phosphorylation Fats Proteins Carbohydrates Figure 9.19

29. Biosynthesis (Anabolic Pathways) The body – Uses small molecules to build other substances These small molecules – May come directly from food or through glycolysis or the citric acid cycle

30. Regulation of Cellular Respiration via Feedback Mechanisms Cellular respiration – Is controlled by allosteric enzymes at key points in glycolysis and the citric acid cycle – Releases energy, but does not produce it. Glucose Glycolysis Fructose-6-phosphate Phosphofructokinase Fructose-1,6-bisphosphate Inhibits Pyruvate ATP Acetyl CoA Citric acid cycle Citrate Oxidative phosphorylation Stimulates AMP + – – Figure 9.20