MBIO 2710 / Topic 1: Glycolysis & Pyr Decarboxylation

> What’s the central/core metabolic pathway from which all other pathways branch?

> What are the two pathways that compose it?

> Glucose metabolism.

> (1) Glycolysis + (2) Tricarboxylic acid (TCA) / Krebs / Citric acid cycle

Can organisms convert glucose to pyruvate without oxygen? What happens after?

> Most can Glc → Pyr w/ or w/o O₂. Pw, Es, and rxns identical. Most of differences are in pw reg.

> What happens to Pyr depends on conditions.

> What is the goal of each phase of glycolysis? Mention what each costs or yields.

> What is the net yield of glycolysis?

> Phase 1 (first 5 steps ; preparatory): Glc phosphorylated into 2 × triose phosphates, costing 2 × ATP.

> Phase 2 (final 5 steps ; payoff): Oxidation and phosphorylation of triose phosphates yield 2 NADH + 4 ATP.

> Net yield = 2 × ATP + 2 × NADH + 2 × Pyr.

> Where does glycolysis occur?

> Where does pyr decarboxylation occur?

> Where does the TCA cycle occur?

> Where does the ETC occur?

> Cytoplasm.

> Mitochondrial matrix.

> Mitochondrial matrix.

> Inner mitochondrial membrane.

What happens to ATP + NADH post-glycolysis?

> ATP → cell energy.

> NADH if O₂ available → ETC to make ATP.

> NADH if O₂ unavailable → fermentation to regen NAD → glycolysis keeps running to make more ATP.

Explain the energy yield and efficiency of glycolysis vs complete glucose oxidation. No need to be too exact with numbers.

> Glycolysis: 146 kJ/mol released.

> Complete oxidation of glucose (Glycolysis + PD + TCA + ETC): 2840kJ/mol released.

> 146/2840 = 5.2% of free energy available from glycolysis.

> 61kJ/mol trapped as ATP.

> -146 + 61 = -85kJ/mol = 58% lost as heat.

> 61/146 = 42% conserved.

What’s the difference between the three kinds of phosphorylation rxns based on how they make ATP?

> Substrate-level → Direct transfer of Pi from S → ATP.

> Oxidative → ETC + proton gradient (needs O₂) → ATP.

> Photophosphorylation → Light-driven ETC + proton gradient → ATP.

How can an endergonic reaction with low Keq still proceed forward in metabolism? There are two reasons for this.

Rxn pulled forward b/c:

> Le Chatelier: Modification/removal of products in the following pathway steps.

> Gibbs: Overall free energy release by the entire pathway.

How is glycolysis regulated when ATP levels rise?

If ATP levels rise (glycolysis done) → PFK inhibition via negative feedback to not waste energy.

How is glycolysis regulated when ATP levels fall?

> Cells have adenylate kinase/myokinase to get more ATP outta ADP via 2ADP → ATP + AMP. AK can get 2ADP from steps 1 and 3 of glycolysis.

> As the rxn proceeds, adenine nts (ATP, ADP, AMP) “run down” to AMP w/o high-energy PO₄³⁻ bonds.

> If AMP levels rise → sign to make more ATP → activates PFK via positive feedback to make ATP.

What are the two rxns occurring in the step 6 of glycolysis?

> Oxidation.

> Phosphorylation.

In between: CHO oxidized to COOH and G released = energy to reduce NAD and to form COOP.

Why must NAD be regenerated for glycolysis to continue?

> NAD → NADH.

> No regeneration of NAD, e.g., via fermentation or ETC.

> Glycolysis would stop due to lack of oxidizing agent.

What is enzyme channeling in glycolysis, and which steps involve it?

> Steps G3PdeH₂ase + P-glycerate kinase → complex

> P of E passes directly to AS of next E w/o diffusing away.

> Why does P-glycerate mutase move the PO₄^3- from C3 to C2 in 3PGA → 2PGA of glycolysis?

> Why does enolase dehydrate the molecule at step 9 of glycolysis?

HINT: Both have the same goal.

→ Move PO₄^3- closer to the carboxyl oxyanion at C1 increases repulsion between (-) charges → Raises G.

→ Resonance structures of PEP → Raises G further.

> Higher-energy int = more energy release in the later step.

Why does PEP but not 2-PG have enough energy to make ATP?

> ∆G’º of hydrolysis of 2-PG (-17.6kJ/mol) = not enough to make ATP.

> ∆G of hydrolysis of PEP (-61.9kJ.mol) = enough to make ATP.

Why does muscle use NAD faster than the TCA cycle can regenerate it during intense exercise?

> Intense exercise = ↑ ATP demand.

> ATP needed to sustain muscle work.

> TCA + ETC (regen NAD) limited by O₂ delivery + mitochondrial capacity.

> Glycolysis faster than oxidative pathways → ↑ Glycolysis rate = ↑ ATP prod.

How do yeast and humans use OH deH₂ase differently?

> Yeast: Acetaldehyde → EtOH.

> Humans: EtOH → acetaldehyde → acetate.

Compare pyruvate decarboxylase (PdC) and pyruvate dehydrogenase (PdH). How are they similar & different?

Differences:

> PdC: Fermentation = Pyr (C₃) → Acetaldehyde (C₂) + CO₂

> PdH: Cell respiration = Pyr (C₃) → Acetyl-CoA (C₂) + CO₂

Similarities:

> Start w/ Pyr.

> Remove 1 C-atom / decarboxylation.

> Convert C₃ → C₂.

What are the roles of E1, E2, and E3 in the pyruvate dehydrogenase complex?

> E1 (pyruvate decrarboxylase): decarboxylates pyr + attaches it to TPP.

> E2 (dihydrolipoyl transacetylase): transfers acetyl group to CoA → acetyl-CoA.

> E3 (dihydrolipoyl dehydrogenase or NADH-FADH₂ oxidoreductase): regenerates oxidized lipoate + produces NADH.

How do energy signals regulate PDH via its kinase & phosphatase?

> Activators activate PdH kinase → phosphorylates & inhibits PdH → ↓ acetyl-CoA prod b/c cell has enough energy.

> Inhibitors inhibit PdH kinase → PdH stays active → ↑ acetyl-CoA prod b/c to produce more ATP in end.

What’s the incentive to get OAA back?

> OAA → TCA → ETC → ATP.

> ATP hydrolysis → release of energy.