Download Week 6 Pre-Lecture Slides

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
(a disaccharide of sucrose)
Peer Instruction
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?
Peer Instruction
Explain the enzymatic
here.
The FO unitreaction
is the base; occuring
the F1 unit is the
knob.
Intermembrane
space
+
+ H+ H+ H H
H+ + H+
H+
H+
+
H+ +H H+H +
H H H+
+
H
H+ H+
H+
FO unit
H
+
Mitochondrial
matrix
Stalk
H+
F1 unit
ADP + Pi
ATP
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”
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.
H
H
Peer Instruction
1) Describe the motion of the
protons. Where do they come
from, and where do they go?
e-
H
H
e-
2) Describe the motion of the
electrons. Where do they come
from, and where do they go?
3) Does the movement of protons require energy?
4) Describe the energy of the
electron throughout its path.
Electron Transport Chain:
A ‘waterfall’ of electron energy
Peer Instruction
What kind of molecule is NADH?
NADH or NAD+: Which has higher energy?
Where in the molecule is the electron carried?
NADH
(electron carrier)
NAD+
Nicotinamide
Reduction
Oxidation
Phosphate
Oxidized
Reduced
Ribose
Adenine
Phosphate
Ribose
Oxidized
Reduced
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
Peer Instruction
For these two reactions:
What is happening in each?
Is each a redox reaction? What kind?
R C C
O
O H
H H
O
R C C C
O H
H H
O
R C H
C
O
H H
O
R C C C
O H
Peer Instruction
Citrate
Isocitrate
α-Ketoglutarate
Succinyl CoA
Succinate
More
reduced
Fumarate
Malate
Oxaloacetate
More
oxidized
2*
Citrate
Incoming
Isocitrate
The Krebs cycle
Oxaloacetate
6-carbon molecule
α-Ketoglutarate
5-carbon molecule
Succinyl CoA
Malate
Fumarate
Succinate
4-carbon molecule
Explain these reactions.
What molecule changes are happening?
Krebs Cycle: Explain this to your neighbors
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
Peer Instruction
The two red carbons enter
the cycle via acetyl CoA
Linking Step:
Moving into the
Mitochondria
Coenzyme A
High energy sulfur
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
‘Trapping
Step’
Peer Instruction
‘Commitment
Step’
Where is energy invested into this process?
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?
Energy (Glycolysis --> Krebs)
GLYCOLYSIS
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
H+ H+
H+ H+ H+
Electrons
2 NADH
Oxidative
phosphorylation
ETC
6 NADH
2 FADH2
2 NADH
H+
H+ H+ +
H
H+H+
H+
+
H+ H
O2
H 2O
GLYCOLYSIS
Glucose
2 Pyruvate
2 ATP
Cytoplasm
2 Acetyl CoA
2 CO2
KREBS
CYCLE
2 ATP
4 CO2
25
ATP
26 ADP
25 ATP
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.
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
Peer Instruction
Where are these found in the
fake cells shown here?
•  Electron Transport Chain
•  Krebs Cycle
•  Linking Step
•  Glycolysis
Fake Animal Cell
Fake Plant Cell
Peer Instruction
Where are these found in the
cells shown here?
• 
• 
• 
• 
Electron Transport Chain
Krebs Cycle
Linking Step
Glycolysis
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?
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
Peer Instruction
This step
is regulated
by ATP
These steps are
also regulated via
feedback inhibition,
by ATP and NADH
Citrate
Acetyl CoA
Oxaloacetate
Does it make sense for the cell to use feedback inhibition here?
Peer Instruction
Why can a mutation that allows an additional input pathway
improve the relative fitness of an organism?
Peer Instruction
Pathway for synthesis
of RNA, DNA
Fats
Phospholipids
Fatty acids
Glycogen
or starch
Glucose
Pyruvate
Acetyl CoA
GLYCOLYSIS
KREBS
CYCLE
Lactate
(from fermentation)
How does diversification of metabolic output
improve fitness for an organism?
Several intermediates
used as substrates in
amino acid synthesis
Peer Instruction
‘Anaerobic’ means ‘without oxygen’.
What do anaerobic respirators do differently in metabolism?
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:
Fermentation
by-product
Peer Instruction
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?
Peer Instruction
Fermentation pathways:
Allowing cells to make ATP and regenerate NAD+ without oxygen
Fermentation
by-product
Intermediate accepts
electrons from NADH
Lactic acid fermentation occurs in humans.
No intermediate;
pyruvate accepts
electrons from NADH
2 Pyruvate
2 Lactate
Peer Instruction
Fermentation pathways:
Allowing cells to make ATP and regenerate NAD+ without oxygen
Fermentation
by-product
Intermediate accepts
electrons from NADH
Alcohol fermentation occurs in yeast.
2 Ethanol
2 Pyruvate