Biochemistry Study Guide: Glycolysis, Citric Acid Cycle, Electron Transport Chain, Oxidative Phosphorylation, Pentose Phosphate Pathway, and Gluconeogenesis

Glycolysis

Overview and Net Equation

Glycolysis is the metabolic pathway that converts glucose into pyruvate, generating ATP and NADH in the process. It consists of 10 enzymatic steps.

• Net equation: $\text{Glucose} + 2\,\text{NAD}^+ + 2\,\text{ADP} + 2\,\text{P}_i \rightarrow 2\,\text{Pyruvate} + 2\,\text{NADH} + 2\,\text{ATP} + 2\,\text{H}_2\text{O}$

• Substrate, product, and enzyme for each step: Know the reactants and products for all 10 steps, and the enzyme that catalyzes each.

• Irreversible and reversible steps: Identify which steps are irreversible (e.g., hexokinase, phosphofructokinase-1, pyruvate kinase) and which are reversible.

• Energy production: ATP is produced in substrate-level phosphorylation steps.

• Reaction coupling: Some steps are coupled to ATP hydrolysis or formation to drive the reaction forward.

• Phosphorylation: Phosphorylation of glucose and intermediates is key for trapping glucose in the cell and for energy transfer.

• Fermentation: Pyruvate can be converted to lactate or ethanol under anaerobic conditions to regenerate NAD+.

• NAD+ regeneration: Essential for glycolysis to continue under anaerobic conditions.

• Substrate-level phosphorylation: Direct synthesis of ATP from ADP and a phosphorylated intermediate.

• Glycogen conversion: Glucose-1-phosphate from glycogen can enter glycolysis.

• Fructose entry: Fructose can enter glycolysis via two pathways, depending on tissue type.

• UDP-glucose: Role in glycogen synthesis and galactose entry into glycolysis.

Citric Acid Cycle (CAC)

Key Concepts and Enzymes

The citric acid cycle (Krebs cycle) is a series of reactions that oxidize acetyl-CoA to CO2, generating NADH, FADH2, and GTP/ATP.

• Coenzyme, cofactor, prosthetic group: Definitions and roles in enzyme function.

• TPP (Thiamine pyrophosphate): Structure and function in decarboxylation reactions.

• Vitamins and disease: Relationship between vitamin deficiencies and enzyme function.

• PDH (Pyruvate dehydrogenase): Structure, activity, and regulation; links glycolysis to CAC.

• Regulation: PDH is regulated by phosphorylation and allosteric effectors.

• CAC steps: Know the substrate and product for each step, and the enzyme involved.

• GTP/ATP production: Substrate-level phosphorylation occurs at the succinyl-CoA synthetase step.

• Carbon tracking: Follow carbon atoms through the cycle to understand their fate.

• Pyruvate carboxylase: Converts pyruvate to oxaloacetate, replenishing CAC intermediates.

• Regulation: CAC is regulated by substrate availability, product inhibition, and allosteric effectors.

• ATP yield: Calculate total ATP produced from complete oxidation of glucose.

Electron Transport Chain (ETC)

Complexes and Mechanisms

The electron transport chain consists of four complexes that transfer electrons from NADH and FADH2 to oxygen, generating a proton gradient across the inner mitochondrial membrane.

• Complexes I-IV: Know the electron flow and what drives the transfer.

• Proton pumping: Each complex pumps protons to create an electrochemical gradient.

• Q cycle: Mechanism for electron transfer in complex III.

• Chemiosmotic theory: Explains how the proton gradient drives ATP synthesis.

• Coenzyme Q and cytochrome c: Mobile electron carriers in the ETC.

• Equation for electron transport: $\text{NADH} + \text{H}^+ + 1/2\,\text{O}_2 \rightarrow \text{NAD}^+ + \text{H}_2\text{O}$

• Calculating E0 and ΔG0: Use standard reduction potentials to calculate free energy changes.

Oxidative Phosphorylation

ATP Synthesis and Regulation

Oxidative phosphorylation couples the electron transport chain to ATP synthesis via the proton motive force.

• Proton motive force: The electrochemical gradient that drives ATP synthesis.

• ATP synthase: Structure and function; F1 and F0 components.

• Uncouplers: Compounds that dissipate the proton gradient, preventing ATP synthesis.

• Regulation: ADP levels regulate the rate of ATP synthesis.

• ATP yield: Calculate how many ATPs are produced per glucose molecule.

• Transporters: Import of cytosolic NADH into mitochondria via shuttle mechanisms.

Pentose Phosphate Pathway (PPP) and Glycogenesis

PPP and Glycogen Metabolism

The pentose phosphate pathway generates NADPH and ribose-5-phosphate for biosynthetic reactions. Glycogenesis is the synthesis of glycogen from glucose.

• PPP: Know why it stops at glucose-6-phosphate in most tissues except liver.

• Futile cycle: Definition and examples in metabolism.

• Regulation: Describe how each bypass is regulated.

• Fructose-1,6-bisphosphate vs. fructose-2,6-bisphosphate: Contrast their roles in regulation.

• Glycogen synthesis: Steps and regulation; role of sugar nucleotides.

• Interconnection: PPP, glycolysis, and gluconeogenesis are interconnected to meet metabolic needs.

• NADH vs. NADPH: Differentiate their roles in metabolism.

• Anabolic and catabolic reactions: How cells separate these processes.

Gluconeogenesis

Pathway and Regulation

Gluconeogenesis is the synthesis of glucose from non-carbohydrate precursors, primarily in the liver.

• Reactants, products, enzymes: Know each step and the enzyme involved.

• Tissue specificity: Know which tissues perform gluconeogenesis.

• Three bypass steps: Steps that circumvent the irreversible reactions of glycolysis.

• Lactate and pyruvate: Differences in using these as starting sources.

• Malate-aspartate shuttle: Role in transferring reducing equivalents.

• Carboxylation of pyruvate: Mechanism and importance.

• Regulation: Why gluconeogenesis stops at glucose-6-phosphate in most tissues.

• Futile cycle: Definition and metabolic significance.

• Fructose-1,6-bisphosphate vs. fructose-2,6-bisphosphate: Regulatory roles.

• Glucokinase: Why its unique properties are beneficial.

HTML Table: Comparison of NADH and NADPH

Property	NADH	NADPH
Role	Catabolic reactions (energy production)	Anabolic reactions (biosynthesis)
Pathways	Glycolysis, CAC, ETC	Pentose phosphate pathway, fatty acid synthesis
Cellular location	Mitochondria, cytosol	Cytosol
Electron acceptor/donor	Donates electrons to ETC	Donates electrons for reductive biosynthesis

Additional info:

• Some details were inferred from standard biochemistry curricula to ensure completeness and clarity.

• Equations and regulatory mechanisms were expanded for academic context.