BICH Exam 1 Study Guide

1. Reactions in Glycolysis:

  • Reactions that consume ATP:

    1. Hexokinase: Glucose → Glucose-6-phosphate (Consumes 1 ATP)

    2. Phosphofructokinase-1 (PFK-1): Fructose-6-phosphate → Fructose-1,6-bisphosphate (Consumes 1 ATP)

  • Reactions that yield ATP:

    1. Phosphoglycerate kinase (PGK): 1,3-Bisphosphoglycerate → 3-Phosphoglycerate (Yields 1 ATP)

    2. Pyruvate kinase (PK): Phosphoenolpyruvate (PEP) → Pyruvate (Yields 1 ATP)

  • Reactions that yield non-ATP energy products (NADH, NADPH):

    1. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH): Glyceraldehyde-3-phosphate → 1,3-bisphosphoglycerate (Generates NADH)

  • Reactions that operate near equilibrium:

    1. Hexokinase

    2. Phosphofructokinase

    3. Glyceraldehyde-3-phosphate dehydrogenase

    4. Phosphoglycerate kinase

  • Reactions that operate far from equilibrium:

    1. Phosphofructokinase-1 (PFK-1)

    2. Pyruvate kinase

    3. Hexokinase



2. Required Cofactors and Active Site Residues for Enzymes:

  • Phosphoglucoisomerase: Requires Mg²⁺ as a cofactor. The active site contains generic acid/base residues for isomerization.

  • Triose phosphate isomerase (TIM): Active site contains histidine for proton transfer in isomerization.

  • Aldolase: Active site contains lysine for Schiff base formation in cleavage.

  • Transketolase: Requires thiamine pyrophosphate (TPP) as a cofactor.

  • GAPDH: Requires NAD⁺ as a cofactor and a cysteine residue in the active site.

  • Transaldolase: Requires a lysine residue in the active site for aldol condensation.

  • Pyruvate decarboxylase: Requires thiamine pyrophosphate (TPP) as a cofactor.

  • Phosphoglycerate mutase: Requires 2,3-bisphosphoglycerate (2,3-BPG) as a cofactor.

  • Pyruvate carboxylase: Requires biotin as a cofactor.

  • Lactate dehydrogenase: Requires NAD⁺ as a cofactor.

  • Phosphoglucomutase: Requires a phosphorylated serine residue in the active site.



3. Chemical Logic Behind Enzyme Reactions:

  • Hexokinase: The phosphorylation of glucose traps glucose in the cell and prepares it for further metabolism.

  • Glycogen phosphorylase: Breaks down glycogen by cleaving α(1→4) bonds, releasing glucose-1-phosphate.

  • Aldolase: Catalyzes the reversible cleavage of fructose-1,6-bisphosphate into two triose sugars.

  • Enolase: Catalyzes the dehydration of 2-phosphoglycerate to phosphoenolpyruvate (PEP).

  • GAPDH: Catalyzes the oxidation and phosphorylation of glyceraldehyde-3-phosphate to form 1,3-bisphosphoglycerate and NADH.

  • UDP-glucose pyrophosphorylase: Converts glucose-1-phosphate into UDP-glucose, an active donor for glycogen synthesis.



4. Net Energy Yield for Sugars Entering Glycolysis:

  • A. Galactose:

    • Galactose is converted to glucose-6-phosphate via the Leloir pathway, consuming 1 ATP in the process. The rest of the glycolytic pathway is similar to glucose.

  • B. Fructose (in muscle):

    • Fructose is phosphorylated by hexokinase to fructose-6-phosphate, entering glycolysis without ATP consumption.

  • C. Mannose:

    • Mannose is converted to mannose-6-phosphate, which is isomerized to fructose-6-phosphate, entering glycolysis without ATP consumption.

  • D. Fructose (in liver, shortest pathway):

    • Fructose is converted to fructose-1-phosphate by fructokinase, yielding DHAP and G3P, both of which enter glycolysis.

  • E. Fructose (in liver, glycerol pathway):

    • Fructose is converted to glycerol-3-phosphate, which is eventually converted to DHAP and enters glycolysis.

  • F. Glycerol:

    • Glycerol is converted to glycerol-3-phosphate, which enters glycolysis.

  • G. Ribulose-5-phosphate:

    • Ribulose-5-phosphate is converted into intermediates like fructose-6-phosphate through the pentose phosphate pathway (PPP), entering glycolysis indirectly.



5. Pathways for G6P Utilization Based on Cell Needs:

  • Needs both R5P and NADPH: Pentose phosphate pathway (PPP).

  • Needs R5P but not NADPH: The non-oxidative phase of the PPP.

  • Needs NADPH, ATP but not R5P: The oxidative phase of the PPP.

  • Needs NADPH, but neither ATP nor R5P: Reduction of oxidative stress, such as in red blood cells.



6. Effect on ATP Yield from Glycolysis when G6P Enters PPP:

If glucose-6-phosphate (G6P) enters the pentose phosphate pathway (PPP), it is converted to ribulose-5-phosphate, NADPH, and CO₂. If intermediates like fructose-6-phosphate and GAP re-enter glycolysis, ATP generation will be reduced because the PPP bypasses direct ATP production.



7. Allosteric Effectors for Enzymes:

  • PFK (Phosphofructokinase-1):

    • Activators: AMP, fructose-2,6-bisphosphate.

    • Inhibitors: ATP, citrate.

  • FBPase (Fructose-1,6-bisphosphatase):

    • Activators: Citrate.

    • Inhibitors: AMP, fructose-2,6-bisphosphate.

  • Glycogen synthase:

    • Activators: Glucose-6-phosphate.

    • Inhibitors: AMP.

  • Glycogen phosphorylase B:

    • Activators: AMP.

    • Inhibitors: ATP, glucose-6-phosphate.

  • Glycogen phosphorylase A:

    • Activators: AMP.

    • Inhibitors: ATP, glucose-6-phosphate.



8. Key Regulatory Steps:

  • A. Glycolysis: PFK-1, pyruvate kinase.

  • B. Gluconeogenesis: FBPase-1, PEP carboxykinase.

  • C. Glycogen Synthesis: Glycogen synthase.

  • D. Glycogen Degradation: Glycogen phosphorylase.

  • E. PPP: Glucose-6-phosphate dehydrogenase.



9. Phosphorylation Cascade (Epinephrine/Glucagon Stimulation):

Epinephrine and glucagon trigger a phosphorylation cascade that activates protein kinase A (PKA), which then phosphorylates and activates glycogen phosphorylase kinase, leading to the activation of glycogen phosphorylase and inhibition of glycogen synthase.



10. Dephosphorylation Cascade (Insulin Stimulation):

Insulin activates protein phosphatase-1 (PP1), which dephosphorylates and activates glycogen synthase, while inhibiting glycogen phosphorylase by dephosphorylation.



11. Glycogen Regulation in Liver vs. Muscle:

  • Liver: Glycogen phosphorylase is regulated by blood glucose levels; insulin and glucagon balance glycogen synthesis and degradation.

  • Muscle: Glycogen breakdown is regulated by energy demand, with epinephrine and AMP promoting glycogen breakdown during exercise.



12. Mechanisms of Kinases, Isomerases, Mutases, Decarboxylases, etc.:

  • Kinases: Transfer phosphate groups, typically from ATP to a substrate.

  • Isomerases: Rearrange atoms within a molecule.

  • Mutases: Transfer functional groups, like phosphate groups, to different positions on a molecule.

  • Decarboxylases: Remove a carboxyl group, typically releasing CO₂.

  • Aldolases/Transaldolases: Break or form carbon-carbon bonds by splitting or combining sugars.



13. Reactions of Gluconeogenesis:

A. Reactions that Consume ATP:

  • Pyruvate Carboxylase: Pyruvate → Oxaloacetate (Consumes 1 ATP).

  • Phosphoenolpyruvate Carboxykinase (PEPCK): Oxaloacetate → Phosphoenolpyruvate (Consumes 1 GTP, not ATP directly, but can be considered an energy-consuming reaction).

  • Phosphofructokinase-1 (PFK-1) reversal: Fructose-1,6-bisphosphate → Fructose-6-phosphate (Consumes 1 ATP).

B. Reactions that Consume Non-ATP Energy Products:

  • GTP: PEP carboxykinase uses GTP to form PEP from oxaloacetate.

D. Reactions that Operate Near Equilibrium:

  • Glycolysis Reactions that also appear in gluconeogenesis:

    • Glyceraldehyde-3-phosphate dehydrogenase (GAPDH): Glyceraldehyde-3-phosphate → 1,3-bisphosphoglycerate.

    • Phosphoglycerate kinase (PGK): 1,3-bisphosphoglycerate → 3-phosphoglycerate.

    • Phosphoglycerate mutase (PGM): 3-phosphoglycerate → 2-phosphoglycerate.

E. Reactions that Operate Far from Equilibrium:

  • Pyruvate Carboxylase: Pyruvate → Oxaloacetate (This reaction is highly regulated and operates far from equilibrium).

  • Phosphoenolpyruvate Carboxykinase (PEPCK): Oxaloacetate → Phosphoenolpyruvate.

  • Fructose-1,6-bisphosphatase (FBPase-1): Fructose-1,6-bisphosphate → Fructose-6-phosphate (This step is a major regulatory point in gluconeogenesis).



14. Activity of PFK-2 and FBPase-2 with Glucagon or Insulin Stimulation:

  • PFK-2 (Phosphofructokinase-2) and FBPase-2 (Fructose-2,6-bisphosphatase) are part of the same bifunctional enzyme.

    • Glucagon and epinephrine lead to phosphorylation of the enzyme by protein kinase A (PKA), which activates FBPase-2 (decreasing Fructose-2,6-bisphosphate) and inactivates PFK-2 (inhibiting the synthesis of Fructose-2,6-bisphosphate).

      • Result: Lower levels of Fructose-2,6-bisphosphate, leading to inhibition of glycolysis and stimulation of gluconeogenesis (more FBPase-1 activity).

    • Insulin activates phosphoprotein phosphatase-1 (PP1), which dephosphorylates the bifunctional enzyme, activating PFK-2 and inhibiting FBPase-2.

      • Result: Higher levels of Fructose-2,6-bisphosphate, promoting glycolysis and inhibiting gluconeogenesis.



15. Function of the Cori Cycle:

The Cori cycle is the process by which lactate produced by anaerobic glycolysis in muscles is transported to the liver, where it is converted back into glucose via gluconeogenesis. The newly formed glucose is then returned to the muscles to be used again in glycolysis. This cycle helps to prevent lactate accumulation in the muscles and allows for the continued production of ATP in the absence of oxygen.



16. Significance of Tissue Location of Glucose-6-Phosphatase:

  • Glucose-6-phosphatase is present in the liver and kidneys but not in muscle cells. Its location in the liver is crucial because it allows the liver to dephosphorylate glucose-6-phosphate (G6P) to free glucose, which can then be released into the bloodstream to maintain blood glucose levels. This is an essential step in gluconeogenesis and glycogenolysis. Muscle cells, lacking glucose-6-phosphatase, cannot release free glucose into the bloodstream and instead use it locally.



17. Roles of Various Tissues in Carbohydrate Metabolism:

A. Role of Muscle Tissue in Carbohydrate Metabolism:

  • Muscle primarily uses glucose for energy production via glycolysis during exercise. Muscles store glycogen as a quick energy source, which is broken down via glycogenolysis to provide glucose-6-phosphate (G6P) for glycolysis.

B. Role of Liver Tissue in Carbohydrate Metabolism:

  • Liver maintains blood glucose levels by performing gluconeogenesis (producing glucose from non-carbohydrate precursors) and glycogenolysis (breaking down glycogen into glucose). The liver also stores glucose as glycogen and releases it into the bloodstream when blood glucose levels are low.

C. Purpose of Glycolysis:

  • Glycolysis is the breakdown of glucose into pyruvate, producing ATP and NADH. It occurs in cytosol of all cells and provides energy, especially under anaerobic conditions.

D. Purpose of Gluconeogenesis:

  • Gluconeogenesis is the synthesis of glucose from non-carbohydrate precursors, such as lactate, pyruvate, glycerol, and certain amino acids. It occurs primarily in the liver and to a lesser extent in the kidneys. It is activated when blood glucose levels are low (e.g., during fasting).

E. Purpose of Glycogen Synthesis:

  • Glycogen synthesis (glycogenesis) is the process of storing glucose as glycogen, mainly in the liver and muscles. It is triggered by high blood glucose levels and insulin.

F. Purpose of Glycogen Degradation:

  • Glycogen degradation (glycogenolysis) is the breakdown of glycogen to release glucose. In the liver, this glucose can be released into the bloodstream. In muscle, glucose is used locally for energy production.



Hormonal Regulation of Pathways in Liver and Muscle Tissue:

Insulin:

  • Released when blood glucose is high (after meals).

  • Stimulates glycolysis and glycogen synthesis in both liver and muscles.

  • Inhibits gluconeogenesis and glycogen degradation.

Glucagon:

  • Released when blood glucose is low (during fasting).

  • Stimulates gluconeogenesis and glycogen degradation in the liver.

  • Inhibits glycolysis and glycogen synthesis in the liver.

Epinephrine:

  • Released during stress or exercise.

  • Stimulates glycogen degradation in both liver and muscle.

  • Inhibits glycogen synthesis in both liver and muscle.



J. Effects of Insulin on Enzyme Activity:

Since insulin stimulates dephosphorylation via protein phosphatase-1 (PP1):

  • Glycogen synthase is activated (by dephosphorylation).

  • Glycogen phosphorylase is inhibited (by dephosphorylation).

  • PFK-1 is stimulated, promoting glycolysis.

  • FBPase-1 is inhibited, preventing gluconeogenesis.



K. Effects of Epinephrine/Glucagon on Enzyme Activity:

Since epinephrine and glucagon stimulate a phosphorylation cascade via protein kinase A (PKA):

  • Glycogen synthase is inhibited (by phosphorylation).

  • Glycogen phosphorylase is activated (by phosphorylation).

  • PFK-1 is inhibited, reducing glycolysis.

  • FBPase-1 is stimulated, promoting gluconeogenesis.