BCHM 2 exam 2 unfinished flashcards

Pentose Phosphate Pathway (PPP)

Functions:
- Maintains redox state.
- Interconnects metabolism of five-carbon and six-carbon sugars for interconversion.
- Provides pentose sugars for biosynthesis like DNA replication (ribose-5-phosphate).
Two Main Phases:
- Oxidative Pathway: Details are limited but crucial.
- Non-Oxidative Pathway:
- Key Enzymes: Transketolase and Transaldolase.
- Transketolase:
  - Transfers two-carbon units.
  - Similar reaction mechanism to pyruvate decarboxylase.
  - Utilizes thiamine pyrophosphate (TPP) as a cofactor.
  - Non-specific for substrates that are five carbons or shorter.
  - Example: Transfers two carbons between xylulose 5-phosphate (ketose) and erythrose 4-phosphate (aldose).
- Transaldolase:
  - Transfers three-carbon units.
  - Mechanism similar to Class 1 Aldolase with a lysine in the active site.
  - Forms a protonated Schiff base intermediate with a ketone substrate.
  - Mechanism involves a reverse (as opposed to hydrolysis) step.
- Function: Rearrangement of carbon skeletons; intermediates feed into glycolysis or biosynthetic pathways.
Stoichiometry and Pathway Connection:
- Starting from six five-carbon sugars generates five six-carbon sugars (gluconeogenesis related).
- Can feed five-carbon sugar metabolites into glycolysis.
- Glucose going through the PPP results in different ATP yield due to initial phosphorylation (glucose-6-phosphate).
Regulation:
- Involves allosteric mechanisms.
- NADPH is a key regulatory end product, likely through feedback inhibition.
Scenarios and Functions:
- During cell replication, PPP supplies nucleic acid precursors.
- Non-oxidative phase can generate energy by breaking down pentose sugars, followed by glycolysis.

Metabolic Regulation (General Principles)

Four General Regulation Methods:
1. Intrinsic reaction rates: Enzyme kinetics respond to substrate concentration changes.
2. Allosteric regulation: Metabolite binding at sites other than active site can inhibit or activate.
3. Protein concentration changes: Transcription, translation, and degradation alter enzyme levels.
4. Covalent modification: Enzyme activity altered by chemical modifications (e.g., phosphorylation).
Enzyme Kinetics:
- Michaelis-Menten Kinetics: Relates enzyme activity to substrate concentration.
- $V0 = \frac{V{max}[S]}{K_m + [S]}$
- $V_{max}$ : Maximum rate at saturation; depends on enzyme concentration.
- $Km$ : Substrate concentration at half of $V{max}$ .
- Large substrate concentration changes needed for significant reaction rate shifts.
Regulation Based on Factors:
- Intrinsic factors like metabolite concentrations and external signaling changes.
- Regulatory changes influenced by transcription, translation, and protein degradation rates.
Allosteric Regulation:
- Molecule binding affects active site catalytic activity.
- Often involves multimeric proteins; can affect both $Km$ and/or $V{max}$ .

Cooperativity

Occurs in enzymes with multiple active sites.
Substrate binding at one site impacts activity at others.
Results in sigmoidal kinetic plots; hemoglobin is a classic example.

Isozymes

Different enzymes from distinct genes catalyzing the same reaction.
Varied kinetic properties (e.g., differing $K_m$ values) and tissue-specific regulation.
- Example: Hexokinase: brain version (high affinity, low $Km$ ) for glucose, liver version (low affinity, high $Km$ ).

Glycogen Metabolism

Structure: Highly branched polymer of glucose with α(1→4) and α(1→6) bonds.
Glycogen Breakdown (Glycogenolysis):
- Glycogen Phosphorylase: Cleaves α(1→4) bonds to release glucose-1-phosphate using phosphate as a substrate.
- Glycogen Debranching Enzyme: Has transferase (transfers trisaccharides) and α(1→6) glucosidase activities.
- Phosphoglucomutase: Converts glucose-1-phosphate to glucose-6-phosphate.
Glycogen Synthesis (Glycogenesis):
- Phosphoglucomutase: Converts glucose-6-phosphate to glucose-1-phosphate.
- UDP-Glucose Pyrophosphorylase: Activates glucose-1-phosphate, forming UDP-glucose.
- Glycogen Synthase: Transfers glucose from UDP-glucose to glycogen, requiring a primer.
- Glycogen Branching Enzyme: Transfers blocks of glucose residues, creating α(1→6) branches.

Regulation of Glycogen Metabolism

Regulated by hormonal signaling (glucagon, epinephrine, insulin) activating intracellular cascades.
Glycogen Phosphorylase: Activated by phosphorylation, inhibited by ATP/glucose.
Glycogen Synthase: Inhibited by phosphorylation, activated by dephosphorylation/insulin and glucose-6-phosphate.
Coordination prevents futile cycles in glycogen breakdown and synthesis.

Oxidative Metabolism

Mitochondrial Processes:
- Requires oxygen for electron transport chain steps.
Pyruvate Dehydrogenase Complex (PDC):
- Links glycolysis to TCA cycle via oxidative decarboxylation of pyruvate to acetyl-CoA.
- Composed of three subunits (E1, E2, E3) and five cofactors (TPP, lipoic acid, FAD, NAD+, CoA).
- Overall reaction: $\text{Pyruvate} + \text{CoA} + \text{NAD}^+ \rightarrow \text{Acetyl-CoA} + \text{CO}_2 + \text{NADH}$ .
Citric Acid Cycle:
- Further oxidizes acetyl-CoA to CO2; generates NADH, FADH2, GTP.
- Multiple phases including citrate formation and oxidative decarboxylations.
Electron Transport Chain (ETC):
- Comprised of protein complexes and carriers, creating a proton gradient for ATP synthesis.
- Key molecules: NADH, FADH2, Coenzyme Q, cytochromes.
- Overall electron flow and pumping of protons result in ATP synthesis via ATP synthase.

Summary

Comprehensive understanding of metabolic pathways, regulation, and key enzymatic functions is crucial for exam preparation. Review molecular mechanisms, enzyme kinetics, and metabolic interconnections for a solid grasp. Good luck with your studies!