Metabolism – Intro to Metabolism. CH339K. Going back to the early lectures. Why the big D G o ’ for Hydrolyzing Phosphoanhydrides ?. Electrostatic repulsion betwixt negative charges Resonance stabilization of products pH effects. pH Effects – D G o vs. D G o ’. (D G in kcal/mol).
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(DG in kcal/mol)
DGo’ for hydrolysis of ATP is about -31 kJ/mol
Cellular conditions are not standard, however:
In a human erythrocyte,
[ATP]≈2.25 mM, [ADP] ≈0.25 mM, [PO4] ≈1.65 mM
Excited state of oxyluciferin forms and decays
Excerpted from Baldwin, T. (1996) Structure4: 223 – 228,
Tobacco seedling w/ cloned luciferase
Southeast Asian firefly tree
Firefly squid (Watasenia scintillans) of Toyama Bay, Japan
New Zealand glowworm (Arachnocampa) cave
One beaker w/ ZnSO4 and a Zn electrode
One beaker w/ CuSO4 and a Cu electrode
Zinc gets oxidized and the electrode slowly vanishes
Copper gets reduced and the electrode gets fatter
Zinc gets oxidized
Copper gets reduced
What determines who gets oxidized?
For an actual half reaction aA + ne-⇌aA-
For an actual redox reaction:
A+n + ne- ⇌ A
B ⇌ B+n + ne-
A+n + B ⇌ A + B+n
(Analagous to the relation between DG and DGo’)
Atequilibrium, the two are equal:
Dr. Ready gets to the Point!
But we already know:
NAD+ is a common redox cofactor in biochemistry
Coenzyme Q is another electron carrier in the cell
What is DGo’ for the
Oxidation of NADH by Ubiquinone?
Vomiting and nausea, diarrhea, Headaches, Difficulty breathing, Pallor, Sweating, Palpitations, Lisps, Stomach pains/cramps, Seizures, Weakness, Drooling, and - of course - Death
C6H12O6 + 6O2 → 6CO2 + 6H2O
DGo’ = -2870 kJ/mol
It takes 31 kJ/mol to make an ATP. Enough energy is available for making ~90 (theoretically)
Glucose (a carb), mol. wt. = 180 g/mol
-2870 kJ/mol = -686 kcal/mol
-686 kcal/mol / 180 g/mol = 3.8 kcal/g
Palmitic Acid (a fatty acid) mol. wt. = 256 g/mol
-9959 kJ/mol = -2380 kcal/mol
-2380 kcal/mol / 256 g/mol = 9.3 kcal/g
Alanine (an amino acid) mol. wt. = 88 g/mol
-1297 kJ/mol = -310 kcal/mol
-310 kcal/mol / 88 g/mol = 3.5 kcal/g
Fat: 1 gram = 9 calories
Protein: 1 gram = 4 calories
Carbohydrates: 1 gram = 4 calories
The diet values come from the DGo’ for oxidizing the various biomolecules.
H8 in human erythrocyte PGM
The overall reaction of glycolysis is:
Glucose + 2 NAD+ + 2 ADP + 2 Pi
2 pyruvate + 2 NADH + 2 ATP + 2 H2O + 4 H+
• There is a net gain of 2 ATP per glucose molecule
• As glucose is oxidized, two NAD+ are reduced to 2 NADH
…there can be a problem.
Remember these guys?
Model of L. mexicana glyceraldehyde-3-phosphate dehydrogenase complexed with N6-(1-naphthylmethyl)-2¢-deoxy-2¢- (3-methoxybenzamido)-adenosine.
Binding mode of 2-amino-N6-(p-hydroxyphenethyl)adenosine to T. brucei phosphoglycerate kinase.
DGo values are scattered: + and -
DG in cells is revealing:
(Yeast, no O2)
(Critters, no O2)
In the absence of O2, no further oxidation occurs. NADH builds up, and NAD+ has to be regenerated to continue glycolysis
Pyruvate + NAD+ + HSCoA CO2 + Acetyl CoA + NADH
Hydrogen is Acidic
These highly toxic compounds react with “vicinal” dithiols such as the functional group of lipoamide.
Product inhibition byNADH&acetyl CoA:
Regulation by E1phosphorylation/dephosphorylation:
Specific regulatory Kinases & Phosphatases associated with Pyruvate Dehydrogenase in the mitochondrial matrix:
Pyruvate Dehydrogenase Kinases are activated by NADH & acetyl-CoA, providing another way the 2 major products of Pyruvate Dehydrogenase reaction inhibit the complex.
The resulting inhibition of Pyruvate Dehydrogenase prevents muscle and other tissues from catabolizing glucose & gluconeogenesis precursors.
Per glucose that entered glycolysis:
Thus, at the end of the cycle, we will have converted our glucose completely to CO2.
We still won’t have used any oxygen or made any water.
DGo’ = -20.9 kJ/mol
Oxidation: NAD+ oxidizes the hydroxyl carbon of isocitrate
Decarboxylation: A Mn+2 bound to the enzyme stabilizes the intermediate
Protonation: Reforms the carbonyl to generate product
General Principle: NAD+ is usually the electron recipient when oxidizing at a hydroxyl
CoA is displaced by an Orthophosphate
The phosphate group is transferred to a Histidine residue on the enzyme
Succinate leaves as a product
The enzyme is dephosphorylated, passing PO4-3 to a nucleotide diphosphate
General Principle: FAD is the preferred cofactor for oxidizing a carbon-carbon bond.
Succinate Dehydrogenase is an integral membrane protein
1. Substrate availability
2. Product inhibition
3. Competitive feedback inhibition.
The Krebs cycle is amphibolic – intermediates are also used to make stuff.