Biochemistry Exam 4 Review Notes

Pentose-Phosphate Pathway (PPP)

• Uses of Glucose 6-Phosphate:

  • Makes ribose 5-phosphate for nucleic acid synthesis.

  • Generates NADPH for synthetic reactions (biosynthesis).

  • Converts 5C and 3C sugars, operates in the cytoplasm of all organisms.

Phases of the Pentose-Phosphate Pathway

• Phase 1: Oxidative

  • Enzymatic Reactions:

    • Glucose 6-phosphate dehydrogenase (G6PDH): oxidizes glucose 6-phosphate, reduces NADP+ to NADPH.

    • Lactonase: catalyzes the hydrolysis of lactones.

    • 6-phosphogluconate dehydrogenase: catalyzes decarboxylation to form ribulose 5-phosphate, producing another NADPH.

• Phase 2: Non-Oxidative

  • Enzymatic Reactions:

    • Phosphopentose isomerase: converts ribulose 5-phosphate to ribose 5-phosphate.

    • Transketolase: transfers 2C units between sugar molecules.

    • Transaldolase: transfers 3C units between sugar molecules.

    • Phosphopentose epimerase: interconverts ribulose 5P and xylulose 5P.

Comparison: Nonoxidative Phase vs. Calvin Cycle

• ATP Hydrolysis:

  • PPP does not require ATP; Calvin Cycle is ATP dependent.

• Reversibility:

  • PPP is more reversible, allowing for flexibility in the reaction direction, while the Calvin Cycle is directional.

• Similar Enzymes:

  • Some enzymes are shared between the two pathways.

Regulation of PPP

• Committed Step:

  • G6PDH is the main regulatory enzyme, inhibited by NADPH binding.

• Inhibition Mechanism:

  • High ratio of NADPH:NADP+ indicates a low need for further NADPH production.

Flux through the Pentose-Phosphate Pathway

1. Rapid Cell Division (Need for ribose): High ribose demand with minimal NADPH production.

   • Reaction: 5 ext{G6P} + ext{ATP}
     ightarrow 6 ext{ribose 5P} + ext{ADP}

2. Need for Both Ribose and NADPH: Produces both through the oxidative phase.

3. Need for NADPH (Biosynthesis): Oxidative phase primarily provides NADPH.

4. Need for Both ATP and NADPH: Final stage generates products (F6P and G3P) that pass through glycolysis.

Oxidative Stress and Glutathione Pathway

• Glutathione Mechanism:

  • Glutathione reduces reactive oxygen species (ROS) by converting them into less harmful alcohols (ROOH to ROH).

  • Glutathione Reductase: regenerates reduced glutathione, requiring NADPH to maintain a protective state against ROS.

Fatty Acid Metabolism

• Mobilization of Fatty Acids:

  • Stored in adipose tissues as triglycerides.

  • Hormonal signals (glucagon, epinephrine) trigger mobilization via lipases (e.g., adipose triglyceride lipase).

• Key Lipases Function:

  • Perilipin: allows lipases access to lipid droplets.

  • Hormone-sensitive lipase: cleaves DAG.

Fatty Acid Oxidation Process

• Preparation for Oxidation:

  • Fatty acids are activated to acyl-CoA before transport into mitochondria (uses carnitine).

• Beta-Oxidation Pattern (OHOT):

  • Steps:

  1. Oxidation (generates FADH2)

  2. Hydration (adds OH)

  3. Oxidation (produces NADH)

  4. Thiolysis (shortening the acyl-CoA by 2C).

• Products per cycle:

  • Acyl CoA, FADH2, NADH, Acetyl CoA, H+.

Synthesis of Fatty Acids

• Fundamentals: Key precursor is Acetyl CoA.

  • Three Stages:

  1. Transfer acetyl-CoA to cytoplasm.

  2. Activation to malonyl CoA via carboxylation.

  3. Formation via condensation, reduction, dehydration, and reduction steps.

Amino Acid Metabolism

• Key Enzymes in Amino Acid Degradation:

  • Aminotransferases: transfer amine groups to form glutamate.

  • Dehydrogenases: remove the amine groups and release NH4+.

• Urea Cycle Overview:

  • Involves ammonia conversion; regulated by specific enzymes like CPS1 and Arginosuccinate Synthetase.

Regulation of Amino Acid Synthesis

• Involves feedback inhibition mechanisms where specific end-products inhibit their own synthesis pathways.

Nucleotide Metabolism**

• De Novo Synthesis of Pyrimidines and Purines:

  • Pyrimidine pathway uses CPSII and transcarbamoylase enzymes.

  • Purine pathway involves assembling the ring on ribose phosphate using glycine, glutamine, and aspartate as precursors.

Important Nucleotide Structures**

• Nucleotides consist of bases, sugars and phosphates, with crucial biological significance in energy transfer and genetic code maintenance.

DNA/RNA Structure**

• DNA vs. RNA:

  • DNA has deoxyribose and uses thymine; RNA has ribose and uses uracil.

  • Structure: DNA forms a double helix with base pairing and grooves for protein interactions.

  • DNA Supercoiling: Adjusts topology through twisting or writhing that affects packaging in the cell.