AP Biology, Chapter 9
Cellular Respiration: Harvesting Chemical Energy

Summary
Introduction

PRINCIPLES OF ENERGY HARVEST
	Introduction
	Cellular respiration and fermentation are catabolic (energy-yielding) pathways
		1. Distinguish fermentation and cellular respiration.
			a. Fermentation
				i. Partial degradation of glucose
				ii. Uses no O2
				iii. Yields some ATP
			b. Cellular respiration
				i. Complete degradation to CO2 and H2O
				ii. Requires O2
				iii. Yields much more ATP
		2. Describe the summary equation for cellular respiration. Also note the specific chemical 
		equation for the degradation of glucose.
			a. Organic compounds + O2  CO2 + H2O + energy
			b. C6H12O6 + 6O2  6CO2 + 6H2O + energy (ΔG = -686 kcal/mol)
	Cells recycle the ATP they use for work
		3. Explain how ATP is recycled in cells.
			a. ADP + Pi + energy  ATP (ΔG = 7.3 kcal/mol)
			b. ATP  ADP + Pi + energy (ΔG = -7.3 kcal/mol)
	Redox reactions release energy when electrons move closer to electronegative atoms
		4. Define oxidation and reduction.
			a. Oxidation = loss of electrons; really the increase in oxidation number
			b. Reduction = gain of electrons; really the decrease in oxidation number
		5. Explain how redox reactions are involved in energy exchanges.
			a. When electrons are transferred, energy is released or stored
			b. Ex. electrons transferred to oxygen fall to lower energy states
	Electrons "fall" from organic molecules to oxygen during cellular respiration
		6. Explain why organic molecules that have an abundance of hydrogen are excellent 
		cellular fuels.
			a. Electrons are shared very equally between H and C
			b. Equal sharing means high energy
			c. Transfer to oxygen releases the energy
	The "fall" of electrons during respiration is stepwise, via NAD+ and an electron 
	transport chain
		7. Describe the role of NAD+ and the electron transport chain during respiration.
			a. NAD+ + 2H (with their high-energy electrons)  NADH + H+
			b. NADH passes high energy electrons to the top of the electron transport chain
			c. As electrons flow, H+ is pumped across the inner mitochondrial membrane
			d. O2 accepts the low-energy electrons at the end of the chain

THE PROCESS OF CELLULAR RESPIRATION
	Introduction
	Respiration involves glycolysis, the Krebs cycle, and electron transport: an overview
		8. Describe the cellular regions where glycolysis, the Krebs cycle, and the electron 
		transport chain occur.
			a. Glycolysis - cytoplasm
			b. Krebs cycle - mitochondrial matrix
			c. Electron transport - mitochondrial inner membrane, thylakoid membrane 
	Glycolysis harvests chemical energy by oxidizing glucose to pyruvate: a closer look
		9. Describe how the carbon skeleton of glucose changes as it proceeds through 
		glycolysis.
			a. Six-carbon  2 three-carbon
			b. Glucose  pyruvic acid + energy
		10. Explain why ATP is required for the preparatory steps of glycolysis.
			a. Adds energy to glucose molecule
				i. Hexokinase: glucose + ATP  glucose 6-phosphate + ADP + Pi
				ii. Phosphoglucoisomerase: G6P  fructose 6-phosphate
				iii. Phosphofructokinase: F6P + ATP  fructose 1,6-bisphosphate + ADP 
				+ Pi
			b. Breaks more easily
				i. Aldolase: F1,6P  dihydroxyacetone phosphate + glyceraldehyde 
				phosphate
				ii. Isomerase: dihydroxyacetone phosphate  glyceraldehyde phosphate 
		11. Identify where sugar oxidation, substrate-level phosphorylation, and the reduction of 
		NAD+ occur in glycolysis.
			a. Sugar oxidation/NAD+ reduction
				i. Performed by triose phosphate dehydrogenase
				ii. 2 glyceraldehyde phosphate + 2 NAD+ + 2 Pi  2 1,3-
				bisphosphoglycerate + 2 NADPH + 2 H+
			b. Substrate-level phosphorylation
				i. Phosphoglycerokinase: 2 1,3-bisphosphoglycerate + 2 ADP + 2 Pi 
				2 3-phosphoglycerate + 2 ATP
				ii. Phosphoglyceromutase: 2 3-phosphoglycerate  2 2- 
				phosphoglycerate
				iii. Enolase: 2 2-phosphoglycerate  2 phosphoenolpyruvate + 2 H2O
			c. Substrate-level phosphorylation (again)
				i. Performed by pyruvate kinase
				ii. 2 phosphoenolpyruvate + 2 ADP + 2 Pi  2 pyruvate + 2 ATP
			d. Energy yield
				i. Lose: 2 ATP getting the process started
				ii. Gain: 4 ATP and 2 NADH
				iii. Net: 2 ATP + 2 NADH
	The Krebs cycle completes the energy-yielding oxidation of organic molecules: a 
	closer look
		12. Describe where pyruvate is oxidized to acetyl CoA, what molecules are produced, and 
		how this process links glycolysis to the Krebs cycle.
			a. Pyruvate is actively transported into the mitochondrial matrix
			b. Performed by pyruvate dehydrogenase complex
			c. Pyruvate + Coenzyme A + NAD+  Acetyl CoA + CO2 + NADH
			d. The acetyl is the remaining high-energy piece of the glucose
			e. Acetyl CoA adds this piece into the Krebs (citric acid) cycle		
		13. Describe the form and fate of the carbons in the Krebs cycle. Note the role of 
		oxaloacetate in this cycle.
			a. Acetyl CoA + oxaloacetate  citrate + CoA
			b. Citrate  Isocitrate
			c. Isocitrate + NAD+  a-ketoglutarate + CO2 + NADH
			d. a-ketoglutarate + CoA + NAD+  Succinyl CoA + CO2 + NADH
			e. Succinyl CoA + ADP + Pi  succinate + CoA + ATP
			f. Succinate + FAD  fumarate + FADH2
			g. Fumarate + H2O  malate
			h. Malate + NAD+  oxaloacetate + NADH
		14. Describe the point at which glucose is completely oxidized during cellular respiration.
			a. The last step
			b. The carbon holding the hydroxyl of malate is from the original glucose
			c. In the last step it is oxidized to the carbonyl of oxaloacetate
	The inner mitochondrial membrane couples electron transport to ATP synthesis: a 
	closer look
		15. Describe how the exergonic "slide" of electrons down the electron transport chain is 
		coupled to the endergonic production of ATP by chemiosmosis.
			a. Electrons lose energy in electron transport = exergonic
				i. NADH donates high-energy electrons to a flavoprotein
				ii. FADH2 feeds in at a lower energy level
				ii. Also in the chain are FeS proteins, ubiquinone, and cytochromes
				iii. Oxygen accepts low-energy electrons from the last carrier
			b. The energy is used to transport H+ out of the matrix
		16. Describe the process of chemiosmosis.
			a. Electron transport establishes a proton gradient = proton-motive force
			b. ATP synthase: ADP + Pi + energy  ATP
			c. As ATP is made, H+ diffuses through a channel made by ATP synthase
			d. Oxygen ultimately accepts electrons, ATP is made = oxidative phosphorylation
		17. Explain how membrane structure is related to membrane function in chemiosmosis.
			a. ATP synthase is complex
				i. A cylindrical rotor and rod are embedded within the membrane
				ii. Attached to the rod on the matrix-side of the membrane is catalytic 
				knob
			b. The rotor is the channel
				i. As H+ flows the rotor spins
				ii. The rod rotates within the catalytic knob
				iii. The rods changes the conformation of the catalytic sites
				iv. ATP is ejected from the catalytic sites as the rod rotates
			c. ATP synthase not energized by PMF?
				i. Read Section 18.4.2 at: 					
				http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=stryer.section.2528
				ii. You responsible for the experiment using H218O
	Cellular respiration generates many ATP molecules for each sugar molecule it 
	oxidizes: a review
		18. Summarize the net ATP yield from the oxidation of a glucose molecule by 
		constructing an ATP ledger that includes coenzyme production during the different stages 
		of glycolysis and cellular respiration.
			a. Glycolysis	2 ATP	0-2 NADH
			b. Pyruvate dehydrogenase		2 NADH
			c. Krebs cycle	2 ATP	6 NADH		2 FADH2

			d. Oxidative phosphorylation	32-34 ATP
			e. Total				36-38 ATP

RELATED METABOLIC PROCESSES
	Introduction
	Fermentation enables some cells to produce ATP without the help of oxygen
		19. Explain why fermentation is necessary.
			a. Fermentation is anaerobic
			b. Oxygen is not present to accept drained electrons
			c. NAD+ needed in glycolysis must be regenerated from NADH
		20. Compare the fate of pyruvate in alcohol fermentation and lactic acid fermentation.
			a. Alcohol fermentation
				i. 2 pyruvate  2 CO2 + 2 acetaldehyde
				ii. 2 acetaldehyde + 2 NADH  2 ethanol + 2 NAD+
			b. Lactic acid fermentation
				i. 2 pyruvate + 2 NADH  2 lactate + 2 NAD+
				ii. Also performed in muscle under anaerobic, strenuous conditions
		21. Compare the processes of fermentation and cellular respiration.
			a. Fermentation
				i. Anaerobic
				ii. = glycolysis + regeneration of NAD+
				iii. Takes place in the cytoplasm
				iv. Yields 2 ATP
			b. Cellular respiration
				i. Aerobic
				ii. = glycolysis + Krebs cycle + electron transport + chemiosmosis
				iii. Takes place in the cytoplasm, then mitochondrion
				iv. Yields 36-38 ATP
			c. Facultative anaerobes include some fungi and bacteria
				i. Perform cellular respiration when O2 is present
				ii. Perform fermentation when its not
		22. Describe evidence that the first prokaryotes produced ATP by glycolysis.
			a. 3.5-2.5 bya: very little oxygen in the atmosphere
			b. Highly conserved in evolution
			c. Takes place in cytoplasm; no organelle required
	Glycolysis and the Krebs cycle connect to many other metabolic pathways
		23. Describe how food molecules other than glucose can be oxidized to make ATP.
			a. Proteins  amino acids  pyruvate + acetyl CoA
			b. Fats  glycerol + fatty acids  glyceraldehyde phosphate + acetyl CoA
		24. Explain how glycolysis and the Krebs cycle can contribute to anabolic pathways.
			a. Intermediates are starting points for making amino acids and fats
			b. Amino acids and fats can be interconverted in glycolysis and the Krebs cycle
			c. Gluconeogenesis runs glycolysis in reverse when blood sugar is low
	Feedback mechanisms control cellular respiration
		25. Explain how ATP production is controlled by the cell and what role the allosteric 
		enzyme phosphofructokinase plays in the process.
			a. Feedback inhibition shuts off a pathway when enough product is present
			b. Phosphofructokinase
				i. Catalyzes last step before commitment to glycolysis
				ii. Inhibited by ATP and citrate
				iii. Stimulated by AMP