1. 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

2. 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

3. 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?

4. 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

5. 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

6. 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

7. 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

8. Electron Transport Chain: A ‘waterfall’ of electron energy8

9. 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

10. 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

11. 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

12. 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?

13. 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

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

15. 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

16. 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

17. 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

18. 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.

19. 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

20. 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

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

22. 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

23. 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

24. 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?

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

26. 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?

27. ‘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?

28. 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?

29. 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.

30. 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.