Respiration: Big Picture and the Electron Transport Chain Monday February 6th, 2017 Class 20 Learning Goals Respiration: Big Picture and the Electron Transport Chain After this class, you should be able to: Identify parts of molecules that contain most of the redox energy Justify the use of ATP or NADH2 as an energy currency molecule Predict the effects of specific mutations in ATP synthase on the energy harvesting of the proton gradient Describe three different kinds of energy within respiration and explain the transitions between them

Metabolism: The Big Picture Peer Instruction What is the energy currency of the cell? Why is it useful to have a main energy currency? We don’t directly eat ATP, though? Define Metabolism in terms of these molecules Glucose ATP 2

Peer Instruction (a disaccharide of sucrose) Where is the chemical energy in this molecule? Which contains more redox energy? A highly reduced molecule or a highly oxidized molecule The reaction X  Y results in the production of the oxidized molecule Y. What else must have happened?

Explain the enzymatic reaction occuring here. Peer Instruction Explain the enzymatic reaction occuring here. The FO unit is the base; the F1 unit is the knob. H+ Intermembrane space H+ H+ H+ FO unit Mitochondrial matrix Stalk H+ F1 unit ADP + Pi ATP 4

Why is this called the‘proton motive force’? Peer Instruction Does ATP synthase works best with more protons inside or outside of the membrane? Why is this called the‘proton motive force’? Where does this occur in prokaryotes and eukaryotes? This indirect pathway is an evolutionary trick that has raised the energy levels available to life on Earth: ‘The Chemiosmotic Hypothesis” 5

Explain what is happening in this diagram of the ETC. Peer Instruction Occurs in the inner membrane of the mitochondrion High-energy molecule carrying 2 electrons (and a proton) Explain what is happening in this diagram of the ETC. 6

3) Does the movement of protons require energy? Peer Instruction H H 1) Describe the motion of the protons. Where do they come from, and where do they go? e- 2) Describe the motion of the electrons. Where do they come from, and where do they go? H e- H 3) Does the movement of protons require energy? 4) Describe the energy of the electron throughout its path. 7

Electron Transport Chain: A ‘waterfall’ of electron energy 8

Peer Instruction What kind of molecule is NADH? NADH or NAD+: Which has higher energy? Where in the molecule is the electron carried? NADH NAD+ (electron carrier) Nicotinamide Phosphate Ribose Adenine Reduction Oxidation Oxidized Reduced 9

Respiration: The Krebs Cycle and Glycolysis Tuesday February 7th, 2017 Class 21 Learning Goals Respiration: The Krebs Cycle and Glycolysis After this class, you should be able to: Describe the logic of the Krebs cycle and identify a working analogous cycle from the hypothetical species Describe the mechanism of the Linking step from three perspectives: chemical, energetic and spatial Critically examine the costs and gains of glycolysis and suggest improvements to the enzymes used

C O H R R C O H C O H R For these two reactions: What is happening in each? Is each a redox reaction? What kind? Peer Instruction C O H R R C O H C O H R 11

2* 6-carbon molecule 5-carbon molecule 4-carbon molecule Peer Instruction Citrate Isocitrate -Ketoglutarate Succinyl CoA Succinate Fumarate Malate Oxaloacetate More reduced More oxidized 2* 6-carbon molecule ‘Incoming’ Citrate Isocitrate The Krebs cycle Oxaloacetate -Ketoglutarate 5-carbon molecule Malate Succinyl CoA 4-carbon molecule Fumarate Succinate Explain these reactions. What molecule changes are happening?

Krebs Cycle: Explain this to your neighbors Peer Instruction The two red carbons enter the cycle via acetyl CoA THE KREBS CYCLE 5 different redox reactions within the Krebs cycle fuel the mitochondria with reducing equivalents All 8 reactions of the Krebs cycle occur in the mitochondrial matrix

Linking Step: Moving into the Mitochondria Coenzyme A High energy sulfur

Why is it a good idea to add a phosphate to Peer Instruction Why is it a good idea to add a phosphate to a valuable molecule in the cytoplasm? All 10 reactions of glycolysis occur in cytosol How does this process use both 3-C molecules? Glucose ‘Commitment Step’ ‘Trapping Step’ Where is energy invested into this process? 15

Follow the carbons and phosphates! Water will drive you crazy… Peer Instruction Follow the carbons and phosphates! Water will drive you crazy… Why do these molecules have ‘2’? Pyruvate Overall, do these steps spend ATP or gain ATP? Overall, does glycolysis spend ATP or gain ATP? 16

Energy (Glycolysis --> Krebs) PYRUVATE PROCESSING AND KREBS CYCLE Glucose Pyruvate Acetyl CoA In each of these drops, energy is transferred to energy-storing molecules ATP, NADH, and FADH2 Oxaloacetate

Metabolism: Final Results for aerobic eukaryotes SUMMARY OF CELLULAR RESPIRATION Oxidative phosphorylation ETC H+ H+ H+ H+ H+ Electrons H+ H+ H+ H+ H+ H+ H+ H+ 6 NADH H+ 2 NADH 2 NADH 2 FADH2 O2 H2O 25 ATP GLYCOLYSIS 26 ADP Glucose 2 Pyruvate 2 Acetyl CoA KREBS CYCLE 4 CO2 2 CO2 2 ATP 2 ATP 25 ATP Cytoplasm Mitochondrion Maximum yield of ATP per molecule of glucose: 29 ATP/ glucose One of the most argued-about numbers in biology… …what matters is that it is big.

Respiration: Regulation and Fermentation Wednesday February 8th, 2017 Class 22 Learning Goals Respiration: Regulation and Fermentation After this class, you should be able to: Classify a microorganism as eukaryotic or prokaryotic based on respiration details Critically assess the usefulness of a particular regulation mechanism or feedback loop for a respiring organism or cell Describe several different respiration schemes that are not aerobic respiration (and note environments in which these schemes might be most favored) Identify a fermentation reaction and compare the energetic output with a similar aerobic reaction

Where are these found in the fake cells shown here? Peer Instruction Electron Transport Chain Krebs Cycle Linking Step Glycolysis Fake Animal Cell Fake Plant Cell 20

Where are these found in the cells shown here? Peer Instruction Electron Transport Chain Krebs Cycle Linking Step Glycolysis 21

Why is this negative feedback loop a good idea for the cell? Peer Instruction Why is this negative feedback loop a good idea for the cell? How can the product molecule regulate an enzyme? Why are positive feedback loops rare in biology? 22

Explain how “feedback inhibition” works with this enzyme. Peer Instruction When ATP binds here, the reaction rate slows dramatically Fructose-1,6- bisphosphate at active site (as the reaction is completed) ADP at active site 23

Does it make sense for the cell to use feedback inhibition here? Peer Instruction These steps are also regulated via feedback inhibition, by ATP and NADH This step is regulated by ATP Citrate Acetyl CoA Oxaloacetate Does it make sense for the cell to use feedback inhibition here?

Why can a mutation that allows an additional input pathway improve the relative fitness of an organism? Peer Instruction

Peer Instruction Pathway for synthesis of RNA, DNA Fats Phospholipids Fatty acids Several intermediates used as substrates in amino acid synthesis Glycogen or starch Glucose Pyruvate Acetyl CoA KREBS CYCLE GLYCOLYSIS Lactate (from fermentation) How does diversification of metabolic output improve fitness for an organism?

‘Anaerobic’ means ‘without oxygen’. What do anaerobic respirators do differently in metabolism? Peer Instruction Are C-C and C-H the only bonds that contain energy? What molecules are broken down by chemolithotrophs? Is ATP synthase the only ATP source in human respiration?

Fermentation pathway: Peer Instruction Fermentation by-product Intermediate accepts electrons from NADH Explain how fermentation works. How does the ATP yield of fermentation compared to that of aerobic respiration? In what conditions would the evolution of enzymes and regulation to allow fermentation be advantageous?

Lactic acid fermentation occurs in humans. Fermentation pathways: Allowing cells to make ATP and regenerate NAD+ without oxygen Peer Instruction Fermentation by-product Intermediate accepts electrons from NADH 2 Pyruvate 2 Lactate No intermediate; pyruvate accepts electrons from NADH Lactic acid fermentation occurs in humans.

Alcohol fermentation occurs in yeast. Fermentation pathways: Allowing cells to make ATP and regenerate NAD+ without oxygen Peer Instruction Fermentation by-product Intermediate accepts electrons from NADH 2 Pyruvate 2 Ethanol Alcohol fermentation occurs in yeast.