Major concepts:

1. What is gluconeogenesis, and why is it needed? As a pathway, does gluconeogenesis require energy or produce energy?
2. What type of enzyme is pyruvate carboxylase, and how does it catalyze carboxylation?
3. Where in the cell is pyruvate carboxylase, and why does that matter?
4. What are the functions of the pentose phosphate pathway? How are the two phases of the pathway related to its functions?

Core knowledge:

1. Which glycolysis enzymes catalyze irreversible reactions? What gluconeogenesis enzymes are required to reverse the glycolysis reactions?
2. What is the energy cost or gain for each of the following reactions?
(a) pyruvate carboxylase; (b) PEP carboxykinase; (c) malate dehydrogenase (matrix);
(d) malate dehydrogenase (cytosol); (e) GAPDH in gluconeogenesis; (f) FBPase-1;
(g) glucose-6-phosphatase.
3. What molecules can be used for gluconeogenesis? Which molecules can not be used?
4. What happens to glucose during the oxidative phase of the pentose phosphate pathway?
What is the energy yield per glucose? How is NADPH different from NADH?
5. What reaction does an epimerase catalyze? What reaction does a transketolase catalyze?
How is each related to the functions of the pentose phosphate pathway?

Definition and why this pathway is important:
Gluconeogenesis = synthesis of glucose from smaller organic molecules
     (not photosynthesis, which is synthesis of glucose from CO₂ )
     Occurs almost exclusively in liver cells
Helps to maintain appropriate blood glucose level so cells have an energy supply.
     Not all cells store energy; some require a constant blood supply.

Many enzymes for gluconeogenesis are the same as for glycolysis.
Exceptions: irreversible reactions in glycolysis = hexokinase, PFK-1, pyruvate kinase
Complication: Transport across the mitochondrial membrane is required.

Reversing pyruvate kinase:
1. pyruvate carboxylase catalyzes a three-step reaction:
     a. ATP + HCO₃⁻ → carboxy-phosphate + ADP
     b. carboxy-phosphate + biotin → carboxybiotin + P_i
     c. carboxybiotin + pyruvate → oxaloacetate
2. PEP carboxykinase catalyzes a coordinated reaction:
      a. removal of oxaloacetate carboxyl group (no TPP involved) → enolate anion
      b. anion attacks terminal phosphate on GTP → PEP
3. Oxaloacetate is synthesized in the mitochondrial matrix but needed in the cytosol.
     There is no oxaloacetate carrier, so oxaloacetate is reduced to malate (NADH is used)
         in the matrix by malate dehydrogenase (reversible reaction).
      Malate is transported by a malate carrier (uniport).
     Malate is oxidized to oxaloacetate in the cytosol, producing NADH.
4. Summary of reactions that reverse pyruvate kinase:
     HCO₃⁻ + ATP + pyruvate + NADH_matrix + GTP
         → CO₂ + ADP + GDP + PEP + 2 P_i + NADH_cytosol
     Requires 3 enzymes + carrier + 2 high energy bonds

Going from PEP to fructose-1,6-bis-phosphate:
Requires using 2 ATP to make 2 1,3-bis-phosphateglycerate molecules.
Requires using 2 NADH to reduce both phosphoglycerates to glyceraldehyde-phosphates.

Reversing PFK-1:
Fructose 1,6-bis-phosphatase (FBPase-1) catalyzes a hydrolysis reaction:
fructose 1,6-bis-phosphate + H₂O → fructose-6-phosphate + P_i                 ΔG°′ = - 16.3 kJ/mol
No ATP is generated, although ATP was used for synthesizing fructose-1,6-bis-phosphate.

Reversing hexokinase:
Glucose-6-phosphatase catalyzes a hydrolysis reaction:
glucose-6-phosphate + H₂O → glucose + P_i                         ΔG°′ = − 13.8 kJ/mol

Gluconeogenesis is energetically favorable.
Glycolysis and gluconeogenesis are reciprocally regulated.

Additional molecules that can be used for gluconeogenesis:
glucogenic amino acids, citric acid cycle intermediates, glycerol
NOT fatty acids or AcCoA

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