Comprehensive Biochemistry and Metabolic Pathways Study Guide

Lipoprotein Transport and Lipid Metabolism

• VLDL (Very-Low-Density Lipoprotein): Functionally carries triacylglycerols from the liver to adipose cells for storage.

• ATGL (Adipose Triglyceride Lipase): Converts TAG (triacylglycerol) to DAG (diacylglycerol) and free fatty acids.

• Epinephrine and Lipid Regulation:     

  • The \beta-adrenergic receptor acts as a GEF (Guanine Nucleotide Exchange Factor) on $\alpha \text{-GDP}$ in response to epinephrine.     

  • Adenylate cyclase is activated by $G_{\alpha} \text{-GTP}$ to produce cAMP.    

  • cAMP binds to a subunit to remove "fake substrate" from the active site of PKA (Protein Kinase A).    

  • PKA activates removal of perilipin.    

  • PKA activates Hormone-Sensitive Lipase (HSL) to convert DAG to MAG (monoacylglycerol) and free fatty acid in adipose cells.

• Acetyl-CoA Carboxylase (ACC):     

  • ACC produces malonyl CoA.     

  • Inactivated by AMPK when glucose levels are low.    

  • Activated by PP1 when glucose levels are high.

• Fatty Acid Synthesis and Entry:    

  • Malonyl CoA inhibits the entry of acylCoAs into the mitochondrial matrix while FAS (Fatty Acid Synthase) is occurring.    

  • FAS CoAs include many acetyl CoAs and NADPH for palmitate synthesis.     

  • Desaturate: Converts stearoyl CoA to "deoxicoa CoA."     

  • Acyl CoA Synthetase: Modifies fatty acids entering the cytoplasm so they can be used in beta oxidation.

• Beta Oxidation:    

  • Involves the oxidation of 3-hydroxyacylCoAs and the reduction of NAD+ simultaneously.    

  • FAD is reduced first in the two-step oxidation and costs by "acylCoAdehydrogenase."

• HMG-CoA Reductase:     

  • Termed a regulated gateway enzyme that produces mevalonate.    

  • Inactivated by AMPK when glucose levels are low.     

  • Activated by PP1 when glucose levels are high.     

  • Inhibited pharmaceutically by statins.

• Ketogenesis:     

  • Acetone is a waste product of "ketogenesis."     

  • Thiolase converts acetyl CoAs to acetoacyl CoA to enter ketogenesis.

Carbohydrate Metabolism and Glycolysis

• GAPDH (Glyceraldehyde 3-phosphate Dehydrogenase):     

  • Known as the redox enzyme of glycolysis.     

  • Requires $NAD^+$ as an essential substrate to remove a hydride from the $c_1$ of glyceraldehyde 3-phosphate.    

  • Releases $P_i$.     

  • Histidine withdraws a proton within the GAPDH active site.

• Pyruvate Metabolism:     

  • Pyruvate is reduced to provide NAD+ to GAPDH.     

  • PDH (Pyruvate Dehydrogenase) Complex: "Does the math" $3-1=2$ . Decarboxylates pyruvate, donates one "H-" to NAD+, and forms acetyl-CoA. Lipoamide is an elongated cofactor attached to the subunits of the PDH complex.   

  • Pyruvate Carboxylase: Produces substrate for the CAC (Citric Acid Cycle) and gluconeogenesis. Biotin is the cofactor for carboxylation within this enzyme. Acetyl-CoA is essential to its tetrameric state.

• Phosphofructokinase Regulation:     

  • Fructose-2,6-bisphosphate is the most allosteric effector for PFK1.     

  • PFK2: Either produces fructose-2,6-bisphosphate or removes a phosphate depending on its phosphorylation state

  • Regulation: PKA phosphorylates PFK2 at position $S32$ in response to glucose levels. PP1 removes a phosphate from $S32$ of PFK2 in response to insulin. PP2A removes a phosphate from $S32$ of PFK in response to low glucose.

• Glucose Retention and Transport:     

  • Insulin promotes glucose retention through activation of PP1 action on the liver.     

  • Glucagon blocks glucose retention by activating PKA action on liver PFK2.     

  • GKRP (Glucokinase Regulatory Protein): Restricts glucokinase in the liver under low glucose conditions. Fructose-1-phosphate activates GKRP separation from glucokinase.

• Pentose Phosphate Pathway:     

  • Glucose-6-phosphate is the first substrate oxidized in the pathway.     

  • Produces NADPH and pentose phosphates.

• Additional Compounds:     

  • 3-phosphoglycerate: A low-energy compound produced by phosphoglycerate kinase.    

  • MCT4: Transports lactic acid out of muscle cells; functions to partly deacidify the cytoplasm.

Cellular Respiration and The Citric Acid Cycle (CAC)

• Citric Acid Cycle Enzymes and Kinetics:     

  • Citrate Synthase: "Does the math" $4+2=6$ . Produces OAA and acetyl-CoA in the "citrate shuttle."    

  • Dehydrogenase: Mathematical value of $6-1=5$ .     

  • $\alpha \text{-ketoglutarate Dehydrogenase}$ : "Does the math" $5-1=4$ .

  • $NH_4$ binds to this enzyme in competition with glutamate.    

  • Succinate Dehydrogenase: An enzyme integral to the inner membrane. Histidine is bound to the FAD cofactor. FAD is reduced by a hydride from succinate.     

  • Malate Dehydrogenase: Catalyzes the most positive $\Delta G^\circ$ in the CAC.     

  • Succinyl-CoA Synthetase: Utilizes an acyl phosphate intermediate to produce ATP or GTP.

• Electron Transport System (ETS) and Oxidative Phosphorylation:     

  • Complex IV (Cytochrome C Oxidase): Reduces molecular $O_2$ by using electrons in the intermembrane space.

  • Cytochrome C: Delivers $1 e^-$ ("Theta") to Complex IV from Complex III.     

  • Ubiquinone: Produced by Complex III.     

  • Chemiosmosis: Molecular $O_2$ consumption rate is affected by the delivery of $H^+$.     

  • $H_2O$ : Completes the flow of electrons through the ETS.

• ATP Synthase (Complex V):    

  • C-subunit: $10$ proteins form a "merry-go-round." The C-subunit is attracted forward to spin assembly via an "I-click."    

  • Aspartic acid is found on the "9, 10" subunits of the merry-go-round.    

  • Conformational States:        

    • T-state (Trapped State): Bonds to the "poor H of OH2." Also described as the state of "climenthats bound to OHAPT2."        

    • O-state: State after the dimer has emptied its products.         

    • L-state: "His diner" when bound to ADP + $P_i$.     

      • Phase Transition: ADP and $P_i$ ligands are required to allow the transition from the O-state to the L-state.     

      • The $parallel\beta\text{-sheet}$ is disrupted by an asymmetric cam shift to eject products.

Nitrogen Metabolism and Inter-Organ Shuttles

• Urea Cycle and Amino Acids:     -

  • $NH_4$ is converted to carbamoyl phosphate in the urea cycle.     -

  • Arginine: A cationic monomer; products of its hydrolysis include urea and ornithine.     -

  • Ornithine and Citrulline: Intermediates in the cycle.     -

  • Citrate Shuttle: Inlinked with malic enzyme which reduces "NDAP"; its substrate is decarboxylated.     -

  • ASPT: Converts OAA to a molecule that can exit the matrix.     -

  • ALAT: Amino acid product is glutamate.

• Protein Turnover and Muscle Metabolism:     -

  • Cortisol: Activates protein breakdown in muscles.     -

  • Ubiquitin: Attaches to target myosin in muscle to move them into the proteasome.     -

  • Alanine: Sent from muscle to liver to feed gluconeogenesis.

• Lipoprotein Receptors:     -

  • Apob100 binds to LDL receptors.